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Merge the Bioconductor devel history: the package source keeps no pkgdown content The two histories hold the same work in a different shape. This merge keeps the tree of the GitHub main branch, which is the one without the pkgdown site, and records the devel history as merged so the next push stays a fast-forward.
chore: keep the pkgdown site out of the package source (#49) Bioconductor requires the pkgdown content to be kept off the devel branch and held on a branch of its own. It now lives on `docs-site`, which is where the published site is built from: the site configuration, its assets, the article written only for the website, and the workflow that builds and deploys it. None of it was ever needed to build, check or install the package. All of it was already listed in .Rbuildignore, so the source tarball never carried any of it. What the repository did carry was 3.3 MB of generated HTML under docs/, left from when GitHub Pages was served out of that directory; Pages has been publishing the workflow artifact for some time, so the directory had no reader left. docs/ is now ignored, so a local site build cannot put it back. The site itself does not move and stays at https://drake69.github.io/ctdR/. Version 0.99.10.
fix(readme): the first example on the landing page did not run It built its gene list with a column named `entrez_ids`. The package needs `EntrezID`, so anyone copying the first block from the README got: mapIds must have at least one key to match against an error from AnnotationDbi, naming neither the column at fault nor the function that wanted it. The input schema table below the example carried the same wrong name, so the README was internally consistent and consistently wrong. Both are fixed, and enrichment_CTD() now checks for the column before the data reaches AnnotationDbi, reporting which columns it did find. The README also now covers what this release changed: the size thresholds, the provenance record, and the `alpha` form of ORA, which is the one to reach for when the whole differential expression table is at hand. Its list of Bioconductor dependencies was missing BiocIO, BiocFileCache, S4Vectors and SummarizedExperiment, which matters for the install_github path the README documents while the package is under review. Found by checking the README against the codebase rather than by anyone running it, which is how it survived this long: it is the one file in the package that nothing executes.
Merge pull request #74 from rcavalcante/seqinfo Check genomes in annotate_regions(), and fix seqinfo of annotations
Check genomes in annotate_regions(), and fix seqinfo of annotations - annotate_regions() checks the regions and annotations before overlapping them: a clear error for different genomes (instead of findOverlaps()'s "incompatible genomes" listing every chromosome) or no chromosome names in common (instead of a warning and "No annotations intersect"), and a once-per-session message suggesting read_regions(genome = ...) for regions without a genome. - Lifted-over hg38 and mm10 enhancers get the seqinfo of their genome, which liftOver() dropped. - Compute intergenic and interCGI gaps only on chromosomes with genes or CpG islands, so contigs without any aren't entirely intergenic or interCGI (272 whole-contig intergenic ranges for hg19). - Add a "Genome Information" vignette section, and the missing coannotation_pairs() man page. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
update
fixed r check
rm other tools vignette
fix: evaluate compareCluster categorySizeBy formulas in their own environment The legacy-argument shim added in 9c33a73 reassigns `categorySizeBy` before cnetplot.compareClusterResult captures it with enquo(). A forced argument yields a value-quosure with an empty environment, so the captured formula's expression was evaluated with a data mask whose parent had no base functions: every call using a formula failed at draw time with e.g. Error in `-log10(p.adjust)`: could not find function "-" A formula carries the environment it was written in, and that is the environment the expression must be evaluated in, so prefer it when it is available. Promises that have not been forced are unaffected: a formula captured as an unevaluated call has no environment of its own and keeps using the quosure's. Adds a regression test covering an inline formula, a formula built in another frame (closure variables must still resolve) and the legacy `categorySize` alias. Full suite: FAIL 0 | PASS 449 (the 2 warnings are the pre-existing qvalue ones in test-converters.R).
fix: explain a missing similarity matrix instead of crashing treeplot()/emapplot()/ssplot() died with "no 'dimnames' attribute for array" when the result had not been through pairwise_termsim(): the unpopulated termsim was subsetted in fill_termsim() and handed straight to the graph builder from graph_from_compareClusterResult(). The message now says what is missing and shows the call to make. has_pairsim() already existed for this purpose but was never called; it is now wired into fill_termsim(), graph_from_compareClusterResult() and prepare_emapplot_data(), and its message mentions the affected functions.
fix: warn when foldChange names match nothing, #177 cnetplot()/heatplot() drew every item node grey when none of the names in foldChange matched the genes of the result, which reads as "foldChange was ignored" and gave the reporter nothing to act on. fc_readable() now reports the mismatch and names the expected ID style. The plotting behaviour is unchanged: the plot still builds with a mismatched vector.
cnetplot() supports node_label_size, #41 Expose the font size of category/item node labels, backed by the same parameter in ggtangle; defaults to the built-in size when NULL.
improve: default gseaplot2 pvalue_table to NES and p.adjust Users kept requesting NES in the p-value table instead of two redundant p-value columns (#134, #203), and separately asked how to hide the row-names overlay (#238). The table is already fully configurable via pvalue_table_columns and pvalue_table_rownames; this only fixes the default columns to the more useful NES + p.adjust pair.
fix: keep small mnsea ridgeplot groups instead of dropping them The undersized-gene-set guard (min_size = 3, added for gseaResult density estimation) was being applied unconditionally to the mnsea mechanism path. mnsea ridgeplots are built from per-feature layer contributions that are typically only 2 points per pathway, so every group was dropped and the call aborted. Scope the guard to gseaResult and only drop empty mnsea groups, which restores layered mnsea ridgeplots.
fix: format small p-values readably in dotplot color legends (#277) Add a scientific-notation label formatter for p-value / p-adjust / q-value color scales in dotplot so very small adjusted p-values no longer render as long unreadable decimals. Document the default geneRatio size behavior for gseaResult (#206).
docs: document emapplot group/group_legend and plotting.clusterProfile width
docs: add interface rules for rebuilt features
test: clean stability fixes regression file Remove leftover cherry-pick conflict markers and align the dotplot ordering regression with the explicit Count-based path it is meant to cover.
fix: restore legacy cnetplot compatibility args Accept legacy circular, colorEdge, and categorySize arguments in cnetplot so older calls keep building on the current ggtangle-backed implementation.
fix: stabilize heatplot dot-mode pvalue scaling Clamp zero and non-positive gene p-values before the reversed log-size transform so dot-mode heatplots build cleanly without infinite-value warnings, and cover the edge case with a regression test.
fix: drop undersized ridgeplot gene sets `ridgeplot()` kept pathways with fewer than three ranked values in its y-axis levels, which left blank rows when tiny core gene sets could not produce a density. Filter undersized pathways before building the plot, fail clearly when nothing remains, and add regression coverage for #288.
fix: keep compareCluster cnetplot terms distinct Use stable ID-backed labels in compareCluster cnetplots so terms that share a Description are not merged into one node. This closes the remaining duplicate-description gap in the compareCluster plotting path and records the 1.99.4 regression fix.
test: guard compareCluster cnetplot category growth Record that compareCluster cnetplot pies remain stable as showCategory increases so term-node growth does not regress across count-based pie plots.
test: guard treeplot tidytree compatibility Record the current treeplot compatibility with tidytree's private offspring helper so helper renames do not silently break treeplot again.
test: guard compareCluster dotplot cluster labels Record the current fix for compareCluster dotplots by asserting that geneRatio and count sizing both preserve non-missing cluster labels.
fix: keep treeplot split metadata for faceting Teach treeplot to carry split variables into tree, tip, and clade metadata so GSEA split facets build correctly instead of dropping the faceting column from every layer.
fix: order treeplot clusters numerically Keep treeplot cluster palettes and clade labels aligned by numeric cluster id so two-digit clusters no longer inherit colors or labels from lexical ordering.
Merge branch 'feature/converters' into devel
feat: import enrichment results from external tools Add import_enrichr(), import_gprofiler2(), import_webgestalt() and import_fgsea() mapping the output tables of these tools to enrichResult / gseaResult objects, and re-export the enrichit constructors as_enrichResult() / as_gseaResult() for arbitrary result tables. Includes roxygen docs, tests and the other-tools vignette.
fix: keep emapplot compareCluster pies ontology-aware Align compareCluster emapplot pie layers with the union term labels used for termsim so ontology-specific terms that share descriptions stay distinct, and cover the ALL-ontology case with a regression test.
fix: tolerate top-level GO terms in goplot Drop synthetic GO root edges before building the goplot DAG so results that include top-level terms no longer fail when igraph validates the vertex set.
fix: restore compareCluster treeplot dotplot panels Pass the plain term columns through to ggtreeExtra::geom_fruit() so compareCluster treeplot dotplot panels render correctly again. Add a regression test to cover the restored panel behavior.
fix: restore compareCluster treeplot heatmap panels Pass the active tree plot object to ggtree::gheatmap() so compareCluster treeplot heatmap panels render correctly again. Add a regression test to cover the restored behavior.
chore: relax aplot requirement for cowplot support Keep enrichplot compatible with older aplot releases by treating cowplot composition support as an optional upstream enhancement, and update NEWS to describe the behavior accurately.
chore: require aplot cowplot compatibility release Depend on aplot 0.3.2 so gglist cowplot compatibility comes from the upstream package, and add cowplot to Suggests for the related regression path.
fix: harden dotplot ordering and legends Apply numeric `showCategory` after `orderBy` sorting and keep hollow size-legend keys when dotplots are composed with cowplot. Add focused regression coverage and group the barplot/dotplot fixes under the 1.99.2 NEWS section.
fix: support Percentage sizing in dotplot Derive a Percentage measure from GeneRatio for enrichResult and gseaResult dotplots so `size = "Percentage"` no longer fails at draw time. Add a stability regression test and a NEWS entry for issue #118.
fix: honor barplot width parameter Forward `width` through the enrichplot barplot helpers so users can change bar thickness directly for enrichResult and compareClusterResult plots. Add regression coverage and a NEWS entry for issue #201.
fix: harden plotting stability for compareCluster workflows Normalize plot measure aliases, derive missing FoldEnrichment when possible, and aggregate duplicated compareCluster pie-node counts so plotting methods fail less often and build reliably.
bump version
docs: record 1.99.1 plotting fixes and regression suite in NEWS
test: add plotting regression suite for tutorial-facing functions Covers barplot, dotplot, cnetplot, heatplot, upsetplot, emapplot, ssplot, treeplot, volplot, manhattanplot, goplot and the GSEA plots on mock enrichResult/gseaResult objects, plus a canary test for the ggplot() + theme_dose() dispatch that failed under ggplot2 4.0.x with S7 < 0.2.2. ggplot outputs are evaluated with ggplot_build() to expose missing-column and bad-aesthetic errors. Awaits surfaced the two preceding fixes. The compareCluster mock now carries GeneRatio/BgRatio to match real result objects.
fix: emapplot/ssplot with non-Jaccard similarity measures get_similarity_matrix() keys the termsim matrix by term labels for all methods, but build_emap_graph() re-mapped the melted keys as if they were IDs whenever method != "JC", producing NA edges ("edge data frame contains NAs") for Wang and other semantic measures. Drop the stale re-mapping and the now-unused `method` argument.
fix: barplot for compareClusterResult with all documented `by` values The bar branch of plotting.clusterProfile() had no branch for the default by="geneRatio" (crashing with "object 'p' not found"), mis-mapped by="rowPercentage" as "percentage", and used geom_bar() (stat_count), which errors with a mapped y aesthetic under ggplot2 4.x. Map `by` to the fortify-produced column via switch() and draw with geom_col().
docs: record remaining mechanism-plot enhancements - add Batch 8 completion section to the dev checklist - add NEWS entry for layer-aware pairwise_termsim, exposed mechanism thresholds, and real nseaResult mock coverage
test: add real nseaResult mock and nsea coverage - add mock_nsea_result() to the shared test helper - add test-nsea-support.R covering phaseplot, consensusmap error, mechanismflow error, gseaplot2, gsearank, hplot and barplot - make gsInfo.gseaResult() default exponent to 1 when params lack it, which is needed for nseaResult objects without an explicit exponent
feat: expose mechanism classification thresholds to plots - summarize_nsea_mechanism() accepts a thresholds list and passes it to classify_mechanism_state() - phaseplot(), consensusmap() and mechanismflow() accept thresholds and forward it through their S4 generics/methods - add threshold customization regression tests
feat: layer-aware pairwise_termsim for mnseaResult - add layer argument to the pairwise_termsim generic and all methods so S4 signatures stay consistent - the mnseaResult method now filters feature overlap by the requested layer instead of always using the all-layer union - document the layer parameter and cover it with regression tests
docs: wrap DO-dependent examples in dontrun Examples that call enrichDO() require a GOSemSim ontology database download, which fails on offline or permission-limited systems. Wrap barplot, heatplot, volplot and upsetplot examples in \dontrun{} so R CMD check examples pass without the database.
build: switch vignette from Quarto to R Markdown - replace vignettes/enrichplot.qmd with a standard R Markdown vignette - add knitr/rmarkdown to Suggests and set VignetteBuilder to knitr - remove quarto dependency from Suggests - R CMD build now generates inst/doc and R CMD check passes vignette/inst/doc checks
fix: resolve documentation mismatches for cnetplot/emapplot/heatplot/upsetplot - expand emapplot/heatplot/upsetplot generic and method signatures so Rd usage includes all documented method arguments - add coords parameter documentation for emapplot - add include_isolated parameter documentation for cnetplot - move cnetplot.enrichResult method documentation to the actual function so R CMD check sees the full method signature
fix: align new plot signatures and docs with R CMD check - expand phaseplot/consensusmap/mechanismflow generics and methods to include named arguments so Rd usage matches documented parameters - document layer argument for gseaplot2/gsearank/hplot - use ggplot2::waiver() in dotplot_internal to fix undefined global function warning
docs: document mechanism plot parameters - phaseplot: reference, selected_layer, reference_layer, x_axis, size_var - consensusmap: fill_var, size_var, include_rewiring, label, reference - mechanismflow: reference, flow_var
feat: complete mechanism plot comparisons for phaseplot, consensusmap, mechanismflow - summarize_nsea_mechanism() now accepts a reference result and computes reference_NES / delta_NES plus cross-object rewiring scores - phaseplot() supports reference, delta_NES x-axis, and selectable size variable - consensusmap() now shows enrichment strength via fill and topology consistency via point size, with fill_var/size_var/label/reference options - mechanismflow() now uses flow magnitude (NES/delta_NES/leading-edge size) for line/point size and a stable mechanism-state ordering - update .dev docs, NEWS, and focused tests
feat: complete nsea/mnsea plotting workflow and mechanism plots - refactor gsInfo() into an S3 generic and add layer-aware running-score support to gseaplot2(), gsearank() and hplot() - implement hplot() with base ggplot2 geoms (remove ggHoriPlot dependency) - add pairwise_termsim() support for mnseaResult and treeplot boundary fixes - add barplot.gseaResult() so nsea/mnsea no longer hit graphics::barplot - add mechanism helper layer: compute_rewiring_score(), classify_mechanism_state(), summarize_nsea_mechanism(), extract_rewiring_features() - add phaseplot(), rewireplot(), consensusmap() and mechanismflow() - update .dev docs/checklist, NEWS, man pages, and tests
plan
feat: add mnsea ssplot
feat: add mnsea upsetplot
feat: add mnsea ridgeplot
feat: add mnsea gseaplot
feat: refine mnsea plot semantics
feat: add mnsea emapplot
feat: improve mnsea cnetplot readability
feat: refine mnsea cnetplot labels
feat: clarify mnsea cnetplot legends
feat: add mnsea cnetplot node type legend
feat:
feat: refine mnsea plot defaults and labels
feat: add mnsea cnetplot support
feat: add mnsea heatplot support
refactor:
update url
test: add regression coverage for stable term selection
fix: harden plot helpers and dependency guards
dotplot
vis for enrichit
Merge pull request #73 from rcavalcante/bioccheck-cleanup Clean up BiocCheck findings and deprecated dplyr usage
Clean up BiocCheck findings and deprecated dplyr usage - Replace dplyr::funs() in summarize_numerical() with across(), keeping the same columns in the same order, and wrap tidyselect selections in all_of(). These warned with recent dplyr. - Replace dplyr::do() in the co-annotation plots with vectorized joins, 10 to 100 times faster. plot_numerical_coannotations() scatterplots now draw each region once per facet, instead of once per combination of its annotations, which made heavily annotated regions look darker. - Use requireNamespace() and getExportedValue() instead of library() for the TxDb and org packages, so building no longer attaches them, and the missing-package error is shown instead of get() failing. - Trim gene annotations to chromosome ends, removing out-of-bound warnings for danRer10, danRer11, mm10, rn4, and rn6. - Use is() for class checks, declare the ggplot2 density variable, and move the CITATION to bibentry() with the DOI. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Merge pull request #72 from rcavalcante/gene-summaries Adds summarize_genes(annotated_regions, over, by, format = c('wide', 'long')), which summarizes annotated regions by gene. - Uses the gene annotations with a gene ID (promoters, 1-5kb, UTRs, exons, introns, etc.). CpG, intergenic, enhancer, and chromatin annotations are left out. - A region counts once toward a gene, and once toward each of the gene's annotation types. A region annotated to several genes counts for each. - Wide (default): one row per gene with gene_id, symbol, n_regions, n_ in genomic order, n_ for the 'by' column, and _mean, _median, _sd for each 'over' column. - format = 'long': one row per gene and annotation type. - Genes with the most regions come first. On the vignette data it summarizes 14,201 regions over 914 genes in 0.18 s. Also documents that read_annotations() returns the custom annotations, which can be combined with others using c(), and that annotatr_cache is a session-only registry separate from the disk cache. The vignette has a summarize_genes() example and leads with the returned object for custom annotations. Tests use a small hand-worked example (including a region shared by two genes and a CpG-only region). Tested with docker/check.sh (Bioconductor 3.24 devel): 282 tests pass, 0 skipped. R CMD check 1 NOTE (existing). BiocCheck 0 errors. Version bumped to 1.39.6. 🤖 Generated with [Claude Code](https://claude.com/claude-code) </pre> </div> Package: annotatr Commit: e90c4db4ee395810387499fde3670e6421969f3b Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 22:08:46 -0600 Commit message: Add the median to summarize_genes() over summaries Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: b751eeddcf7ae27c6a555b0ea83d32d2dee90d8e Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 22:05:28 -0600 Commit message: Add summarize_genes() for one row per gene summarize_genes() summarizes annotated regions by gene, using the gene annotations with a gene ID. Each region counts once toward a gene and once toward each of its annotation types, and a region annotated to several genes counts for each. Output is wide by default (n_regions, n_, category counts for 'by', and mean and sd of 'over' columns), or long with format = 'long'. Also document that read_annotations() returns the custom annotations, which can be combined with others using c(), and that annotatr_cache is a session-only registry separate from the disk cache. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> </pre> </div> Package: annotatr Commit: 016b7c3dda475df556dcb9d0d4dc235fde59b8ba Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 22:00:04 -0600 Commit message: Merge pull request #71 from rcavalcante/disk-cache build_annotations() rebuilt every annotation on every call (about 30 s for the hg19 gene annotations). It now caches each built annotation and each downloaded file on disk with BiocFileCache, so later calls load them in seconds. For example, hg19 promoters + exons go from 15.6 s to 1.7 s. - The cache is in tools::R_user_dir('annotatr', 'cache'); options(annotatr.cache = ...) overrides it. - Each annotation type is cached separately, so any combination reuses earlier builds. - Cache names include the annotatr version, and for gene annotations the TxDb/org package versions (or the EnsDb), so updates cause a rebuild. - A cached file that can't be read is removed and rebuilt automatically. - Downloads are retried 3 times, partial downloads are never cached, and all URLs use HTTPS. A partial UCSC download broke scmeth's examples on the kunpeng2 release builder. - New: cache = FALSE in build_annotations(), list_cached_annotations(), clear_cached_annotations(genome), and ?`cached-annotations` with a troubleshooting guide (stale or corrupted entries, failed downloads, disk space, cluster home directories, SQLite locks, AnnotationHub's own cache). The vignette gains a "Caching Built Annotations" section. - Requires R >= 4.0 (for tools::R_user_dir) and imports BiocFileCache, which AnnotationHub already installs. Tests use a temporary cache and never touch the user's cache. The build tests use cache = FALSE so they still test the sources. 9 new cache tests, most of them offline. Tested with docker/check.sh (Bioconductor 3.24 devel): 258 tests pass, 0 skipped. R CMD check 1 NOTE (existing). BiocCheck 0 errors. Version bumped to 1.39.5. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Package: annotatr Commit: 220f05aa8f59411b18a84a059ce97fe1f06420e2 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 21:34:39 -0600 Commit message: Document the cached-annotations value, and run cache examples Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 2acd68023efc02d40f1e2bb110d99e41de0b7522 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 21:26:59 -0600 Commit message: Cache built annotations and downloads on disk build_annotations() rebuilt every annotation on every call, e.g. about 30 s for the hg19 gene annotations. Now it saves each annotation it builds, and each file it downloads, with BiocFileCache, and loads them later in seconds. Cache names include the annotatr version, and for gene annotations the TxDb and org package versions, so updates cause a rebuild. A cached annotation that can't be read is removed and rebuilt. Add cache = FALSE to build without the cache, list_cached_annotations() and clear_cached_annotations() to manage it, and ?`cached-annotations` with a troubleshooting guide. Downloads are retried 3 times and use HTTPS, since a partial UCSC download broke scmeth's examples on a release builder. Tests use a temporary cache, and the build tests use cache = FALSE so they still test the sources. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: BreastSubtypeR Commit: d06478442c1f3eaf941660e3a5514ed35ea9b41d Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-25 09:56:18 +0800 Commit message: Merge pull request #140 from JohanHartmanGroupBioteam/maintenance/maintainer-1.5.3 Transfer the maintainer role to Emmanouil G. Sifakis; bump to 1.5.3 Package: BreastSubtypeR Commit: 188a931c3d1cd9400b3201c2441358352d25290c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-23 09:33:58 +0000 Commit message: Transfer the maintainer role to Emmanouil G. Sifakis; bump to 1.5.3 DESCRIPTION Authors@R: Emmanouil G. Sifakis takes the "cre" role, Qiao Yang keeps "aut"; author order unchanged. man/BreastSubtypeR.Rd carries the Maintainer line that roxygen derives from Authors@R. NEWS records the change and the repository's move to the JohanHartmanGroupBioteam organization. Version 1.5.3 so that Bioconductor devel rebuilds with the new maintainer address. No code changes. Package: annotatr Commit: ff431152e18e1ad6189c3b5114d47d8290aa16af Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 21:15:26 -0600 Commit message: Merge pull request #70 from rcavalcante/test-overhaul Moves the tests to testthat 3rd edition and makes them independent of each other and of file order. Tests: - Files renamed test-.R; no context(). Shared data comes from functions in helper-fixtures.R instead of top-level objects. - Custom annotations use unique cache names. The BED4/BED5 read_annotations() tests passed only because an earlier test had cached the entry they checked. - Assertions compare values (expect_named, expect_setequal, expect_length, expect_contains) instead of expect_equal(all(...), TRUE), and check contents (coordinates, strands, IDs, scores), not just classes. - Plot tests build each plot with ggplot_build(), and some check the plotted data. - Build tests are back. Light tests (hg38 CpGs, hg19 FANTOM enhancers, hg19/mm10 GENCODE lncRNA) run whenever online, including on Bioconductor's builders. Full tests (gene and CpG annotations for all 15 genomes, hg38 lncRNA, lifted-over enhancers, chromatin) run with ANNOTATR_FULL_TESTS=true, which docker/check.sh sets. check.sh also keeps downloads in a persistent annotatr-cache volume. Fixes found by the new tests: - plot_categorical() with the default fill = NULL failed when drawn. It is fixed, and the All bar no longer triggers a ggplot2 warning without fill. (Backported to RELEASE_3_23 as 1.38.2.) - org.Dr.eg.db was missing from Suggests, although danRer10/danRer11 gene annotations need it. Tested with docker/check.sh (Bioconductor 3.24 devel): 227 tests pass, 0 skipped, ~3 min for tests and ~7 min total. R CMD check 1 NOTE (existing). BiocCheck 0 errors. Version bumped to 1.39.4. 🤖 Generated with [Claude Code](https://claude.com/claude-code) </pre> </div> Package: annotatr Commit: 2b24c09ab881f7441b4dc6a4f012a5ebdd371746 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 21:07:19 -0600 Commit message: Suggest org.Dr.eg.db, needed for danRer10 and danRer11 gene annotations Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 02134cc5afdad01933177b4591849f0ccc721087 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 20:51:41 -0600 Commit message: Build basicgenes and cpgs per genome in the full tests Building every gene annotation type for every genome ran out of memory in an 8 GB Docker VM. Only the gene model and CpG sources differ between genomes, so test those per genome, and the other gene annotation types once for hg19. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: a8511f7ebad475a279b74808ca182be26897398a Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 20:43:59 -0600 Commit message: Overhaul tests for testthat 3 and fix plot_categorical() with no fill Move to testthat 3rd edition, and rename the test files to test-.R since they no longer depend on file order. Shared data comes from helper-fixtures.R. Custom annotations use unique cache names, fixing tests that passed only because an earlier test had cached the entry they checked. Assertions compare values, e.g. expect_named() and expect_setequal(), instead of expect_equal(all(...), TRUE). Plot tests now build the plots with ggplot_build(). This found that plot_categorical() with the default fill = NULL failed when drawn; fix it, and map the All bar to a column so it isn't dropped without fill. Restore the build tests: small downloads run whenever online, and full builds for every genome run with ANNOTATR_FULL_TESTS=true, which docker/check.sh now sets, along with a persistent download cache. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> </pre> </div> Package: annotatr Commit: 50820a27a6907b9117c4abcb13f85f63b662e2dd Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 20:21:42 -0600 Commit message: Merge pull request #69 from rcavalcante/deprecate-randomize Deprecate randomize_regions() in favor of a background comparison Package: annotatr Commit: 09af749e4addbdd4602a8d4866b3b64bccb137d4 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 20:16:06 -0600 Commit message: Deprecate randomize_regions() in favor of a background comparison Regions placed uniformly at random across the genome are a poor null model: real regions come from a much narrower set of locations, so most data look enriched in genic and CpG annotations. Deprecate randomize_regions() and point to annotating a background of the regions the data could have come from, or regioneR::permTest() and regioneR::resampleRegions(). summarize_annotations(), plot_annotation(), and plot_categorical() now label annotated_random as "Background" instead of "Random Regions". The examples, tests, and vignette compare DM regions to all tested regions. Also fix the allow.overlaps documentation, which controls whether random regions overlap each other, not the input regions. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: ab795d19f14a4c80116f8cd5b8c3011bf7ca9215 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 20:07:14 -0600 Commit message: Merge pull request #68 from rcavalcante/docker-check Add Docker-based Bioconductor devel check Package: annotatr Commit: bb5c6c454ec3a9e29d7810976372e2339e39e0ef Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:18:57 -0600 Commit message: Add Docker-based Bioconductor devel check docker/check.sh runs R CMD build, R CMD check, and BiocCheck on the committed HEAD in a Bioconductor devel image with annotatr's dependencies preinstalled. Dependencies added since the image was built are installed at check time. Use --rebuild to refresh the image. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: ec750310fa1cb27af75186f72efb400e9c6ffb42 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 19:45:17 -0600 Commit message: Merge pull request #67 from rcavalcante/lncrna-gencode Fix hg38/mm10 lncRNA annotations by downloading from GENCODE Package: annotatr Commit: ea699780298650a09d66c8eff0c3d61ce22985b3 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:39:26 -0600 Commit message: Fix hg38/mm10 lncRNA annotations by downloading from GENCODE AnnotationHub removed its GENCODE resources, including AH75123 (hg38) and AH49550 (mm10), on 2026-04-28, so hg38_lncrna_gencode and mm10_lncrna_gencode failed. Download the same GENCODE releases directly over HTTPS, and move hg19 from FTP to HTTPS. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 0d593dc6eabebb817c27162c1003b90e1764c722 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 19:36:20 -0600 Commit message: Merge pull request #66 from rcavalcante/oviariramb2 Add support for sheep (ARS-UI_Ramb_v2.0) as 'oviariramb2'. Gene annotations come from the Ensembl 113 EnsDb in AnnotationHub (AH119381), so tx_id and gene_id are Ensembl IDs. CpG islands come from the UCSC GenArk assembly hub. Sequences use UCSC-style names (chr1, ..., chrUn_*). Package: annotatr Commit: 86641326dc4047c9762fd9878876840fd5024d66 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:17:58 -0600 Commit message: Version bump Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 9781edf27897d6c77bd3f2e4b09ab5827f4af05a Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 18:57:30 -0600 Commit message: Add sheep (ARS-UI_Ramb_v2.0) as builtin genome oviariramb2 Sheep has no TxDb.* or org.*.eg.db packages, so gene annotations are built from the Ensembl 113 EnsDb in AnnotationHub (AH119381), with Ensembl tx_id/gene_id and symbols from the EnsDb. CpG islands, chromosome sizes, and chromosome aliases come from the UCSC GenArk assembly hub, and sequences are renamed to UCSC-style names. Genomes like this are registered in GENARK in R/utils.R. The TxDb code path is unchanged; hg19 gene annotations are identical to devel. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: methodical Commit: b39d98d2d4ac504cbd6f80a62b999406f694e993 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-25 02:16:59 +0100 Commit message: Merged changes Package: methodical Commit: 20761f4370f86ba9ee7211e4b47c6b3c63a607e4 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-25 00:50:46 +0100 Commit message: Updated liftover function Package: methodical Commit: 02ddeb7f0e3a2c852b0adcff0211e492dc0cdf3c Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-22 20:12:54 +0100 Commit message: update Package: methodical Commit: a39fa2dd4b3c1a417085c4a09ec882b3bc738522 Author: Richard Heery <richardheery@gmail.com> Date: 2026-08-27 17:25:10 +0100 Commit message: update Package: methodical Commit: ffc716b54e4118b1ced24b811211a8788e304a92 Author: Richard Heery <richardheery@gmail.com> Date: 2026-05-01 15:20:44 +0100 Commit message: Readded vignettes Package: methodical Commit: 464c57e15c8f97f697d8ce9373316805f6e73be1 Author: A Wokaty <andres.wokaty@sph.cuny.edu> Date: 2026-04-28 09:02:10 -0400 Commit message: bump x.y.z version to odd y following creation of RELEASE_3_23 branch Package: methodical Commit: 4215fb6e084e162ff4dd4201b1d4420d9c2533db Author: A Wokaty <andres.wokaty@sph.cuny.edu> Date: 2026-04-28 09:02:10 -0400 Commit message: bump x.y.z version to even y prior to creation of RELEASE_3_23 branch Package: methodical Commit: d169b576deecb57d9477aabf9196922e04e885ea Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-27 17:22:40 +0100 Commit message: Final commit for 3.23 Package: methodical Commit: 81883848e66b52382f58d48cd4ee465be8189db3 Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-24 22:47:39 +0100 Commit message: Fixed vignettes Package: methodical Commit: a4d3e6da701f57033dfd6ca9feba64d3c1c11a6a Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-27 21:38:18 +0100 Commit message: Final commit for devel Package: lcmsPlot Commit: f451123907b59cd6a330688b933ff3fd6c2bd25e Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 22:11:26 +0100 Commit message: feat(features): name XChromatograms features from row names Package: RiboDiPA Commit: cf0c36801194370381bd3ceb90f5b2594e1247a1 Author: Dr. Ji-Ping Wang <jzwang@northwestern.edu> Date: 2026-09-24 20:46:05 +0000 Commit message: Fix vignette build error: convert Bioconductor objects via as.data.frame() before as.data.table() Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01LiK5WUAPmNmkHCv3HPRNog Package: lcmsPlot Commit: 18f10a9c7dfe282c08aa33c53c23566a192a7a6b Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 20:46:18 +0100 Commit message: feat(features): name manual features from row names or a feature_id column Package: scRNAseqApp Commit: 9421c5d26e1bf497251c6ccfb6526e9f612852c4 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-24 15:27:00 -0400 Commit message: Update the gene table only when file changed. Package: leapR Commit: 28136ae57197bd5fa892860b5017d5c9f1f0bb2c Author: Sara JC Gosline <sara.gosline@pnnl.gov> Date: 2026-09-24 10:42:52 -0700 Commit message: updated Package: geneslator Commit: b62f543f5874c5167105c705e32d15f0da8d4181 Author: Giovanni Micale <gmgmicky@gmail.com> Date: 2026-09-24 19:11:07 +0200 Commit message: Updated README and vignettes Package: DropletUtils Commit: ba4152de3596abef3bd69f9ce441aec8ea4c912e Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-25 02:56:55 +1000 Commit message: Set SVT leaves to NULL for empty columns when loading MatrixMarket data. (#133) Mostly backports of the updated C++ code and associated tests from crio. Package: DropletUtils Commit: ea9a299b36c52a71f305d612a97d6a69a20e25d0 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-24 18:21:09 +1000 Commit message: Merge remote-tracking branch 'upstream/devel' into devel Package: DropletUtils Commit: b423c0fafe7271b173317b407a8538bbbcbede5c Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-07-29 23:53:07 +1000 Commit message: Shorter chunk size for sparse data and indices for easier streaming. Package: SparseArray Commit: 9a0e93056f05879a15057e3d597d0102068f09bb Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-24 09:04:25 -0700 Commit message: some clarification about SVT leaf representation Package: lcmsPlot Commit: 14a5af5c83db317bc0d44e2b32ba8acfb54ab66f Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 16:23:45 +0100 Commit message: feat(features): use featureDefinitions rownames as feature identifiers lcmsPlot derived its own xcms::groupnames-style MT labels from mzmed/rtmed, discarding the row names featureDefinitions() already carries. Feature identifiers now come from those row names, so renaming the rows is enough to get meaningful labels onto a plot. Identifiers matching no feature are now reported with a warning naming them, instead of being dropped silently into an empty plot. </pre> </div> Package: scRNAseqApp Commit: eb1f132e925ec26574be9a7055b51b67cf60b2cf Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-24 11:17:02 -0400 Commit message: Remove the duplicated notification for search. Package: rhdf5 Commit: 1c6ed01eaf8682004f647a15a200df1d0f55b0f6 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:21:40 +0200 Commit message: Fix duplicated logo Package: rhdf5 Commit: cab7d0212538b900883c3c6a80f27710cd80ebc5 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:03:23 +0200 Commit message: Add link to de.NBI survey Package: Rarr Commit: 56ddfff1ac32f46151b215a015cbc00b5d77744e Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:16:34 +0200 Commit message: Add deNBI funding acknowledgement and survey in README Package: Rarr Commit: accfb8f20be9b7fefe76e1b35a531704bcc8960b Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 11:06:37 +0200 Commit message: Use vectorized .store_check_exist() call Package: Rarr Commit: cbf89cd3891e3e0cdfeb474aaf153d1324b43d96 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 11:05:56 +0200 Commit message: Define is_structured once Package: Rarr Commit: 87389fada7676ae09ce5bfd3a3a4e74ba3708836 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 10:47:50 +0200 Commit message: Register bfloat routine Package: biomaRt Commit: 3e1a0768933f6c3e00895e02119e4f6e36050dac Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:05:20 +0200 Commit message: Add link to de.NBI survey Package: ISAnalytics Commit: 6e03f52a7925332d38562e8c2501425e92f89184 Author: francescogazzo <francesco.gazzo@gmail.com> Date: 2026-09-24 12:19:37 +0200 Commit message: Update collision filtering and bump devel to 1.23.2 Package: distinct Commit: 7ec08672fd2177c33c85779a82ab12deb8232802 Author: Simone Tiberi <simone.tiberi@unibo.it> Date: 2026-09-24 11:57:02 +0200 Commit message: T_obs added in results Package: distinct Commit: e749b22cf8c3c8eb925d3a293b916b7c11e75605 Author: Simone Tiberi <simone.tiberi@unibo.it> Date: 2026-09-24 11:49:37 +0200 Commit message: bug fixed in distinct_test Package: MsBackendMetaboLights Commit: 1b126b45bede3db584a54168617397078cc5c789 Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com> Date: 2026-09-24 11:52:26 +0200 Commit message: Merge pull request #26 from rformassspectrometry/jomain Add random sleep breaks to reduce failures on build systems Package: MsBackendMetaboLights Commit: c28ee3bc500c3e2a3764932bae457431cac07563 Author: Johannes Rainer <johannes.rainer@gmail.com> Date: 2026-09-24 08:45:39 +0200 Commit message: Add random sleep breaks to reduce failures on build systems - Adding/changing to random sleep times aiming at reducing the recurrent failures on the Bioconductor build system (most likely due to rate limitation from MetaboLights). Package: cellNexus Commit: 67fa18ce068ae3e0fe84da1f942a6d9a1138e052 Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 14:44:48 +1000 Commit message: Merge pull request #159 from myushen/master fix website examples Package: cellNexus Commit: 3ab2cd31f7d4a7acc40758abeed48bc0f3d8435c Author: myushen <mengyuan.shen@outlook.com> Date: 2026-09-24 14:25:14 +1000 Commit message: fix website examples Package: cellNexus Commit: 4719fb49b937acd11c9f898275920555e094c65d Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 13:37:28 +1000 Commit message: Merge pull request #153 from MangiolaLaboratory/copilot/rename-join-census-table Soft-deprecate `join_census_table()` in favor of `get_census_metadata()` Package: cellNexus Commit: 8b217f783900d3107ab0d07c0d9b57083a1e6c77 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-09-24 11:54:08 +1000 Commit message: unit test Package: cellNexus Commit: 3e4d038b291bc9ba79f306456e63fa4660958d47 Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 10:44:58 +1000 Commit message: Merge branch 'master' into copilot/rename-join-census-table Package: cellNexus Commit: 9aca6c192558b021c1c41b9071564d8daf4d7814 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-08-27 12:12:50 +1000 Commit message: soft deprecate since 0.99.27 Package: cellNexus Commit: cd885c844de21fea70d10ee653fc9c95386b8bd5 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-08-27 12:08:50 +1000 Commit message: Merge remote-tracking branch 'origin/master' into rename-join-census-table merge from origin Package: cellNexus Commit: 13ffb5d261f878cacd79484700b35b9a964cef67 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:33:16 +0000 Commit message: Trim redundant mock assertion Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: abf37b553b5800c09ee3e9deb65ee9d5246d9ab4 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:32:37 +0000 Commit message: Verify Census helper mock before wrapper call Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: a4bf9cc52cf658c48d4f00fdfbdd55ec094f4484 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:32:04 +0000 Commit message: Exercise deprecated table argument compatibility Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: 4b46e68aebf2b38ce850298cc145bdf52c84d14f Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:31:37 +0000 Commit message: Correct Census deprecation test assertions Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: 1515648f80a96e03452c82ac5e602057710f512e Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:31:02 +0000 Commit message: Stabilize deprecation warning test Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: d2fd0cfdaad895c2e60be674d50076ad04cecf24 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:30:23 +0000 Commit message: Soft-deprecate Census join helper Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: e7ae2c78928ba1b3bbb6f575e117365976743d72 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:27:22 +0000 Commit message: Initial plan Package: mia Commit: 416de1c5a6b73b70f42571f8a3d36d0294dcb770 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-24 07:54:25 +0300 Commit message: Update documents and namespace Package: clusterProfiler Commit: 33b36f13f3729b099a8d6fc20694831b7a5c62d9 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 12:48:46 +0800 Commit message: fixed r check Package: LRDE Commit: 710586499a483617f94c2d665b87a03be62d6531 Author: Ziyang Liu <jacobleo773@gmail.com> Date: 2026-09-23 18:45:18 -0700 Commit message: Improve numerical stability and bump version to 1.1.2 Package: DOSE Commit: 5846d72fe047f1de66d506a21c117d400e4a3ef8 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:21:11 +0800 Commit message: fixed r check Package: DOSE Commit: 9011c8c053e345cdca45bf1edb93fe66b7f80417 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:14 +0800 Commit message: gseDisease() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family. Package: ReactomePA Commit: e295d309811933101f2e808814212d3244f5c6aa Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:10:04 +0800 Commit message: update docs Package: ReactomePA Commit: 586975c51fadc162d78418ff1132eddcb009b157 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:13 +0800 Commit message: gsePathway() exposes eps and forwards extra arguments, #47 gsePathway() was the only GSEA wrapper in the family missing both eps and ..., so eps could not be controlled and additional enrichit::gsea_gson() arguments could not be passed through. Both are now supported, matching clusterProfiler::gseKEGG(). Package: ReactomePA Commit: 396a55c38c765045b0309c6935b663dd334e7c3d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:03:02 +0800 Commit message: ReactomePA 1.99.2: seed argument and a faster prepareReactomeNetwork() - gsePathway() and nsePathway() expose an explicit seed parameter for reproducible GSEA results, aligned with enrichit::gsea_gson(). - prepareReactomeNetwork() no longer round-trips through graphite::convertIdentifiers()/pathwayGraph() per pathway; it builds a single UNIPROT->Entrez map up front and converts edges with vectorized lookups, keeping mclapply() parallelization over pathways. Output is unchanged (same nodes and edge values; node ordering may differ). Default cores is now 1 instead of detectCores(). Package: ReactomePA Commit: a9a8627182db7226655362793f6b6c22c25e8d7b Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-08-15 18:42:41 +0800 Commit message: parallelize prepareReactomeNetwork pathway conversion via mclapply The one-time Reactome network build converts ~2700 pathways serially in R (convertIdentifiers/pathwayGraph/graph_from_graphnel per pathway). The conversions are independent, so the loop now runs over mclapply() with a new 'cores' argument (default getOption('mc.cores', detectCores())); mclapply falls back to serial on Windows and preserves input order, so the resulting edge set - and hence the cached network - is unchanged. Measured on the GSE53757 demo: serial build ~35-41 min; parallel build 614 s at 16 cores and 655 s at 56 cores; output byte-identical to the serial baseline. Scaling saturates at ~4-5 effective cores because the graphite identifier conversion is hash-lookup-bound. Package: ReactomePA Commit: 13cb4b3cbc4616e214d63ee59a3e42bba48b0a4c Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-07-09 15:24:15 +0800 Commit message: nsea Package: ReactomePA Commit: 4edeca90aedb3afdaa29b838323bbdabad62c391 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-04-29 12:24:13 +0800 Commit message: update bioc version Package: meshes Commit: 5732c93b839f7f820eb4501e3cff468737bfa71a Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:09:48 +0800 Commit message: bump version Package: meshes Commit: e7498dc7737b09bffacef28a72d666693e7be51d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:14 +0800 Commit message: gseMeSH() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family. Package: meshes Commit: 01c764a9285d4c77e77ff630885b8a79077cff10 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:03:02 +0800 Commit message: expose a seed argument on gseMeSH(), meshes 1.39.2 Forward an explicit seed to enrichit::gsea_gson() so GSEA runs are reproducible, and apply pvalueCutoff to both pvalue and p.adjust inside the enrichit engine (requires enrichit >= 0.2.2). Package: GOSemSim Commit: 769cd22f90eec52f67039121c265462c701680ad Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 08:58:26 +0800 Commit message: update docs Package: GOSemSim Commit: ca626082247cbb24fb95b5098558b71b0592e2be Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 12:55:48 +0800 Commit message: computeIC: take the term universe from GO.db, not the shipped gotbl table computeIC() decided which terms to score from the `gotbl` table shipped in data/: goids <- unique(godata[godata$Ontology == ont, "go_id"]) That table was last rebuilt in 2021-07, so every term GO.db has added since then was given no IC at all, and the IC-based methods returned NA for it even though its descendants carry annotations and its IC is computable. This is issue #33, and the reporter's diagnosis ("a conflict between the pre-calculated gotbl.rda and the local version of GO.db") was right. Measured against the current GO.db / org.Hs.eg.db, the number of annotated terms that can actually be scored: ontology annotated before now gained BP 11293 11126 11293 +167 CC 1832 1787 1832 +45 MF 4777 4410 4777 +367 and nothing loses an IC. The missing terms also biased every other IC, because they were counted in the `sum(gocount)` denominator but could never contribute to an ancestor's descendant sum. Terms finite under both universes agree for 92-95% of entries with a mean absolute difference of 0.003-0.011; about 0.3% were overestimated by more than 0.5, all of them in the "too specific" direction, which is what the mechanism predicts. The universe is now names(getAncestors(ont)) -- exactly the terms of that ontology in the installed GO.db, root included, and already cached by onto_relation() -- unioned with the annotated terms, so a term the local annotation package still uses keeps its IC even if GO.db has retired it. The same root cause also affects the `gotbl` that the Wang method walks, where a term newer than the table scores 0 instead of NA. That is left for a separate change because fixing it means either regenerating the shipped data or building the relation table at runtime. test-ICMethods.R now asserts that every annotated term gets a finite IC. Package: GOSemSim Commit: 32be2e18cb86a9ef84f796e174a39a1ac7658513 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 12:32:22 +0800 Commit message: cache ontology mappings, and load Rcpp so the compiled IC methods work Two independent defects, found while fixing TCSS. getAncestors(), getParents() and getOffsprings() each rebuilt their whole mapping on every call -- AnnotationDbi::as.list(GOBPANCESTOR) costs about half a second -- while callers only ever pick out one or two terms with `[[ID]]`. A single geneSim() call rebuilt the same mapping hundreds of times. The mappings are derived from a source that is already cached (GO.db is static, load_onto() caches the OntDb), so they are now cached per ontology rather than per term. A 5x5 termSim on previously unseen terms drops from 2.5 s to 0.5 s, geneSim from 5.6 s to 0.6 s cold and 0.12 s warm, with byte-identical results. The cache holds about 85 MB for BP and 110 MB for all nine mappings. Separately, Rcpp was listed in LinkingTo only, so loading GOSemSim never loaded the Rcpp namespace. The wrapper generated by compileAttributes() instantiates Rcpp::RNGScope, which resolves enterRNGScope through R_GetCCallable("Rcpp", ...), so every Resnik, Lin, Jiang and Rel call failed with "function 'enterRNGScope' not provided by package 'Rcpp'" unless the user happened to attach Rcpp first. importFrom(Rcpp, evalCpp) was dropped in ea7b2028 (2016) and is restored here. No test reached the compiled code and the vignette only mentions those methods in prose, which is why this went unnoticed for so long; test-ICMethods.R now covers all four methods on three ontologies. The ontology cache is also covered: test-GO.R checks that each mapping is cached under the ontology and is identical to what GO.db holds. Package: GOSemSim Commit: 50c6bd241416e703074e5e8e2839cf2cafe7133e Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 17:17:24 +0800 Commit message: correct the scope of the TCSS degeneracy fix The previous commit described the degeneracy as "a cluster with a single member", but calc_maxIC() indexes `all <- IC[cluster]; all <- all[is.finite(all)]`, so the real condition is "exactly one member carrying a finite IC". A cluster with several members where all but one have infinite IC is equally degenerate, and the old `length(all) == 0` guard did not cover it. Re-measured with the correct criterion (swapping calc_maxIC in and out of the namespace in one process so both versions see identical input): - the set of clusters whose ICA changes equals the set with exactly one finite-IC member, at every cutoff and ontology tested (BP 1/2/3.5/4/5/8, MF 3.5, CC 3.2) -- so the change is confined to the degenerate clusters; - the defect was not BP-only. 300 random pairs, % scoring exactly 1: BP 99.3% -> 0.0%, MF 27.3% -> 0.0%, CC 98.7% -> 0.0%; - the counts are larger than the single-member count suggested: BP has 1 degenerate cluster at cutoff 3.5 but 5 at cutoff 4 and 1141 at cutoff 5; MF has 3 and CC has 3, and the CC set includes the CC root GO:0005575. Fix the NEWS wording and the code comment to match, and make the regression test assert on the finite-IC criterion rather than on cluster size. Package: GOSemSim Commit: 2df9985c372e931e89994d25fe84f483b50c01fe Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 16:49:30 +0800 Commit message: fix TCSS similarity collapsing to 1 for nearly every term pair A cluster with a single member has no internal spread, so normalising it by its own maximum IC made its ICA identically 1 regardless of how general or how specific that term was. GO:0008150, the root of BP, is such a cluster and is a common ancestor of every BP pair, so `max(sim_value)` in tcssMethod_internal() returned 1 for 99.7% of random BP pairs and `mgeneSim(measure = "TCSS")` was an all-ones matrix. Fall back to the global maximum IC for single-member clusters. The collapse is not specific to the root: scanning cutoffs shows GO:0050896 and GO:0046337 also become single-member clusters for BP, and GO:0052745 does for MF, so special-casing the root would only have papered over one instance. After the change, 300 random BP pairs give min 0.0004 / median 0.0234 / max 0.5296 with 0% equal to 1, and ica[["GO:0008150"]] drops from 1 to 0.000414 (= IC[root] / global max IC). Add a regression test and bump to 2.39.3. Package: GOSemSim Commit: 34c4ae3b85f10b9107ca6feffbd6e6eb0a0206db Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 12:17:51 +0800 Commit message: fix TCSS for terms belonging to multiple clusters GO is a DAG, so a term can have several meta-term ancestors and `tcssdata$clusid[[term]]` is then a vector rather than a scalar. Indexing `ica` with `[[` then attempts recursive indexing, which raises "subscript out of bounds" (or "recursive indexing failed at level 2" depending on which element is hit first) and aborts any TCSS calculation for the whole ontology. Subset the list of clusters with `[` instead. This restores the behaviour already present in the Bioconductor release (2.38.3); the devel implementation had regressed. Adds a regression test covering a term that sits in more than one cluster. Package: clusterProfiler Commit: a38e9201b8ee6ad6f64fc1a5bf691421efc9d928 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 04:39:17 +0800 Commit message: enrichMKEGG()/gseMKEGG() accept a GSON, #623 enrichKEGG() and gseKEGG() take either a species code or a GSON object, but the module wrappers only took a species code, so there was no offline route for module enrichment at all -- even though the download errors now tell users to build a local database. Passing a GSON raised an unrelated error from the organism mapper instead. Both now mirror the KEGG wrappers, including the "organism should be a species name or a GSON object" message. A GSON reports its own keytype, so @keytype is taken from it; the species path keeps returning "UNKNOWN" exactly as before. Also documents the GSON option on the KEGG `organism` parameter, which had never been mentioned for enrichKEGG()/gseKEGG() either. Package: clusterProfiler Commit: 285885443b912177daec101c606664b33b41cc37 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 04:21:19 +0800 Commit message: enrichGO(): restrict the annotation by evidence code, #160 Enrichment used every annotation in the OrgDb, including electronically inferred ones, so there was no way to avoid circular reasoning when the gene sets themselves came from in-silico evidence (dropping IEP for co-expression clusters) or to keep only curated annotations (dropping IEA). enrichGO() now takes `evidence`, appended last so positional callers are unaffected and threaded through both recursive paths. The filtered annotation is built by go_annotation_by_evidence() from a gene-centred select() of GOALL/EVIDENCEALL/ONTOLOGYALL, because the evidence code is a property of the gene-annotation pair and the previous term-centred mapIds() could not see it. Two semantics worth stating, both documented: the background changes with the annotation, so a filtered result is not a subset of the unfiltered one; and a filtered annotation is never cached, since the cache key is (organism, ont, keytype) only and reusing it either way would answer with the wrong annotation. A regression test pins the cache isolation down. Package: clusterProfiler Commit: fa71a3ef739a1ef44e695e69823126c94c703bdb Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 02:33:01 +0800 Commit message: fix: enrichGO() survives an unidentifiable OrgDb organism, #232 The cached-GO-data check compared the cached organism against get_organism(OrgDb) inside a bare if(). get_organism() returns NA for an OrgDb it cannot identify -- an AnnotationHub OrgDb, for instance -- and `if (NA && ...)` aborts the call with "missing value where TRUE/FALSE needed", which names nothing about organisms or caches. It bites on the second enrichGO() call in a session, because the first one populates the cache. The check is now go_cache_usable(), where every comparison goes through isTRUE() so an unidentifiable organism means "not cached" and the annotation is rebuilt. Extracting it also makes the cache-hit logic unit-testable without an OrgDb. Package: clusterProfiler Commit: a39c2f63d533e20d6c4d03fd3a35b18a418dd08e Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 02:14:56 +0800 Commit message: fix: Gff2GeneTable() reads Ensembl-style GFF3, #193 The function only looked for an NCBI/RefSeq `GeneID=` attribute. On an Ensembl GFF3 (which writes `gene_id=`) every extracted key was NA, and merging two all-NA key columns is a cartesian product: on the reporter's cat genome that is ~1.3M x 40k rows, which R refuses with "negative length vectors are not allowed". At small sizes the same bug passes silently, because unique() collapses the duplicated NA rows into a plausible-looking table of NA ids. Field names are now detected from the file: `GeneID` or `gene_id` for the identifier, and `gene`, `Name` or `gene_name` for the symbol. Detection requires an exact attribute key, because getGffAttribution()'s heuristic fallback also looks inside values and would otherwise return the identifier out of `ID=gene:ENSG...` when asked for `gene`. A file with neither identifier style stops with a message saying what is expected instead of merging on all-NA keys. Package: clusterProfiler Commit: 41dd01bb5c7a078bd19397131f06fd3db2d59bfc Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 01:38:26 +0800 Commit message: add_go_level(): expose the GO level of each enriched term, #793 GO enrichment results carried the term, its ontology and its statistics, but not how deep the term sits in the hierarchy, so users who wanted to keep a band of levels had to reconstruct GO depth themselves. go_level_map() now returns the GO id -> level map (1 = ontology root) built by breadth-first traversal of the GO.db CHILDREN graph; getGOLevel() is rewritten on top of it with identical output (verified against a pre-change baseline for BP/CC/MF at levels 1-6), and add_go_level() appends a `level` column to an enrichResult/gseaResult/compareClusterResult. The level is taken from the ontology each term belongs to, so ont = "ALL" results are labelled term by term. gofilter() and dropGO() had no test coverage; the new test file locks their keep/drop-by-level behaviour down. Package: clusterProfiler Commit: c117200bb63575df335911dcd478aa164dda528d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 23:52:42 +0800 Commit message: simplify() infers the GO ontology for enricher() results too, #369 The enrichResult method required x@ontology to be BP/MF/CC/GOALL, so an enricher() run over a GO collection (MSigDB C5 GO, a custom TERM2GENE built from GO annotations) had to have the slot assigned by hand before simplify() would accept it. The ontology is now inferred from the GO IDs exactly as for gseaResult (#753), and non-GO gene sets are still refused with a message saying so. Package: clusterProfiler Commit: e930b50044bf8bb4fb883ea940a631aceb57ff18 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 23:21:11 +0800 Commit message: simplify() a GSEA result whose gene sets are GO terms, #753 simplify() reduces redundancy with GO semantic similarity, so it needs the ontology of the terms. It only accepted x@setType in BP/MF/CC/GOALL, which rejected a GSEA run over a GO gene-set collection (MSigDB C5, a gson GO file, a TERM2GENE built from GO annotations) because @setType then holds the collection name. The ontology is now inferred from the GO IDs, with results spanning several ontologies simplified as GOALL; non-GO gene sets are still refused, with a message that says so. Package: clusterProfiler Commit: dc94b240c1a42333f111338f46fb3633df2271be Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 22:46:23 +0800 Commit message: warn when compareCluster() is given a non-character universe, #654 compareCluster() wraps each per-cluster call in suppressMessages(), which swallowed the underlying enrichment function's "`universe` is not in character and will be ignored" message. A numeric universe therefore looked accepted while silently having no effect. The guard is now raised once in compareCluster() itself, where it cannot be suppressed, with a regression test for both the non-character (warns) and character (stays quiet) cases. Package: clusterProfiler Commit: 61236b6fa01a7d6474152ed7043639596dae48d1 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:10 +0800 Commit message: gsePC() and gseWP() expose an eps argument Both wrappers now declare eps = 1e-10 and forward it through GSEA() to enrichit::gsea_gson(), matching GSEA(), gseGO(), gseKEGG() and gseMKEGG(), which already exposed it. Package: clusterProfiler Commit: 58559c7a5a9babe970d3a3dad5e9708efc42f70c Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 18:54:09 +0800 Commit message: fix enrichKEGG(organism='cpd') and report KEGG download failures clearly, #828 - gson_cpd(): use the 'compound' KEGG REST endpoint. KEGG retired /link/cpd/pathway, which now answers HTTP 400, so enrichKEGG(organism='cpd') and gseKEGG(organism='cpd') failed with an obscure download error. - kegg_rest(): report the failure where it happens, telling an unreachable network apart from an HTTP error status and from an empty response. These used to surface much later as an opaque error. - download.KEGG.Path() / download.KEGG.Module(): replace the is.null() guard, which could never fire because kegg_rest() never returns NULL, and stop with an actionable message when the downloaded annotation is empty or when the gene/pathway table shares no ID with the pathway-name table. Previously an empty annotation was returned silently and surfaced downstream as a misleading "No gene can be mapped", #146, #378, #561, #646. Package: SAIGEgds Commit: 29da3dd06bce9321bc520c75353e1c695057e0df Author: Xiuwen Zheng <zhengxwen@gmail.com> Date: 2026-09-23 19:12:31 -0500 Commit message: update vignettes Package: MSstatsBioNet Commit: 409e9d4503aa239c3c619270333853289d37d080 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-23 16:57:12 -0400 Commit message: feat(filterSubnetworkByContext): adjust filterSubnetworkByContext to exclude key words (#111) Package: scRNAseqApp Commit: e8a48756927b63b7b69b59294f8c81232e689203 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:44:42 -0400 Commit message: fix the wrong number when calculate phyper. Package: scRNAseqApp Commit: 758edbb8626a1d38afe3c8d58678b43f325195e0 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:40:08 -0400 Commit message: fix a issue for if no hyper pval available. Package: scRNAseqApp Commit: 78ef7925d099f040cfa9b1638934fb49d4adfc91 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:29:19 -0400 Commit message: using promise process to update the gene table. Package: scRNAseqApp Commit: b4e729e4d87012189f26cfd746a09ebc9a04d6db Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 10:24:03 -0400 Commit message: import phyper from stats. Package: scRNAseqApp Commit: 4d94c7a0270315c3aea67c41287313c86ffb5655 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 10:15:42 -0400 Commit message: add phyper pval for co-expression. Package: dmGsea Commit: 3b9c68c53791e27f0abc9e95a8f4e0c050b7d75a Author: xuz1 <xuz@niehs.nih.gov> Date: 2026-09-23 13:54:34 -0400 Commit message: bugfix Signed-off-by: xuz1 <xuz@niehs.nih.gov> Package: decemedip Commit: 3de0b135bed2595498482c4d13078d0bd65c313e Author: nshen7 <shenning1997@gmail.com> Date: 2026-09-22 20:54:10 -0700 Commit message: Fix Stan old array syntax for stanc3 (BioC 3.23 build failure) Package: quantMSImageR Commit: 9aaed9e03b28ef01d3b1c05dc834288f2d00753c Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:46 +0200 Commit message: Version 0.99.8 Pieces of one tissue, regions of interest, and the report arranged by level. matrixStats leaves Imports: it was declared but called nowhere, so every user installed a package the code never used. Package: quantMSImageR Commit: 25eacbf10d0f5075ad89ee2884a76103bdb23a65 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:34 +0200 Commit message: Document the regions work The vignette says what regions are for -- a transition that marks a tissue type, or a toxicity study where the regions are drawn high and low in the toxicant and the endogenous species compared between them, within one animal rather than across a group. It also describes the by-level report, and how to see a palette before choosing it. AGENTS.md is gitignored: agent scratch notes, not part of the package. Package: quantMSImageR Commit: d37c8c4b93a96e7f51343144cda5a5c17dcc519b Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:34 +0200 Commit message: Arrange the report by level, and correlate at one level only Sections 2, 3 and 4 are each drawn by sample and then by region, so the two are read the same way rather than the regions living in a tab of their own. The region masks take a section before the ion images, which move down a number. "auto" judges the heatmap encoding per view, on the rows that view actually has. A study without regions is unchanged, headings included: a level heading only appears when there is a second level to tell it from. Correlation names one level -- 'sample', 'roi', False or auto -- and only ever computes that one. It is the slowest section in the report, and a region holds a fraction of a sample's pixels, so auto correlates within the regions when a study has them and is off otherwise. True still means 'sample'. roi: unit is per sample or per region, not both: a comparison has a single unit, and two views of the same numbers invite reading whichever looks better. compare: keeps "both", where the two arrangements are different contrasts rather than the same one twice. Each box-plot panel carries its own key, and colours: region sets the region palette (any package palette, or a grDevices qualitative one), kept distinct from the groups'. Package: quantMSImageR Commit: bfa6a46540be7a5e08f37ded27d10a504d244d59 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:19 +0200 Commit message: Score each region against itself in contributionHm() too The region heatmap could only be drawn per feature, because contributionHm() had no notion of a block. That made "auto" pick the wrong panel wherever a study has few samples and many regions: one animal per group takes the per-sample encoding by sample, but by region its rows are sample x region, so a group can have six or seven of them -- exactly the case the contribution encoding exists for. It now takes sample_block, and inside a block both the z-score and the group mean are computed against that block alone. The hue is therefore "how this group's airways sit among all the airways", not "airways differ from parenchyma", which is what a panel scored across regions would mostly report. A feature flat within a block cannot be scored there and is drawn in na_col, even where it varies across the section. Package: quantMSImageR Commit: b18abc94cf8fc51323b0836eccf9b684dd9758b9 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:50:33 +0200 Commit message: Fix the region tests and the vignette's feature lookup The row-split assertions read @row_order_list, which a Heatmap only fills in when it is drawn -- it is empty on the object, so the expectations compared against nothing. The split a heatmap will use is in @matrix_param$row_split, which is what they now check: the block test asserts a, a, b, b against groups that deliberately alternate, so passing it means the rows really were split by region rather than by group. The vignette indexed a feature by name, but spectra() returns a matrix with no dimnames, so it takes the row number instead. Package: quantMSImageR Commit: 0ff2ab13a672a37c90034e11545dc2e36e994da3 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:39:14 +0200 Commit message: Document pieces and regions; regenerate the example sections The vignette gains a section on pieces of one tissue, one on labelling regions, and a worked example on the bundled sections: the label table, the region maps and a box plot with one point per section per region rather than per pixel. The YAML section documents the samples forms, including pieces, and what each roi: option can be set to. The example sections are regenerated with the regions the vignette and runExample() now show. Seeds are unchanged and the region code draws no random numbers, so the intensities are identical. AGENTS.md is build-ignored, and the micro sign in stitchAcquisitions() is written as a \u00b5 escape: R CMD check requires ASCII source. Package: quantMSImageR Commit: a623d0241889b76e05f8b5d49aa2f121348d953b Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:54 +0200 Commit message: Carry regions through a study and into the report A study picks regions up on its own: generateTxtImages() attaches roi_label and roi_id from each acquisition's roi_labels.csv, matched on (x, y) like the tissue mask, and they survive panel binding and stitching. Regions numbered within a piece are renumbered across the stitched sample, so two airway_01s become two airways. The YAML gains a roi: block -- enabled (auto), include_unassigned, compare, unit, heatmap -- and pieces: for a tissue acquired in several passes, each piece normalised and SNR-filtered against its own background before being joined. The report gains a regions tab: maps, box plots by compare and unit, an ROI_summary sheet, and a heatmap with one row per sample and region. That heatmap z-scores each region against itself (quantileHm's new sample_block), since scoring across regions would mostly report that airways and parenchyma differ, which is not the question being asked. The map is repeated above the ion images, where it says which blob is which. quantileHm() also no longer loses its sample names when a study holds a feature with no variance: the unscoreable column returned an unnamed vector, and apply() drops the names for the whole matrix when one result's differ. output: colocalisation: gains auto, off whenever a sample merges several acquisitions -- most pixel pairs would then cross acquisitions. Package: quantMSImageR Commit: 9311401b6304a67f07b4b1fa3cf4bbcde84b66b7 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:39 +0200 Commit message: Add labelROIs() for regions within the tissue Run after selectTissuePixels(): it shows the ion image of a chosen transition across tissue pixels only, then loops draw -> name -> "add another". Several regions can share a label, since a section holds many airways, and each is numbered as it is drawn (airway_01, airway_02, ...) so it keeps its own identity while the label is what a study compares. Regions are saved per acquisition as roi_labels.csv beside the tissue mask, which is never touched, and copy_to writes the same file to the other panels over the same area. Re-running adds to them; overwrite = TRUE keeps the old file as a dated backup. The feature picker is shared with selectTissuePixels() rather than copied, and the bundled example sections gain two "a" and two "b" regions each so the downstream half can be shown without a drawing device. The regions differ because of where they sit on the existing intensity gradient; no value was adjusted to make them. Also splits the given names in Authors@R, so the citation reads "Smith MJ" rather than "Smith M". Package: quantMSImageR Commit: 52f47f09842bf4eecb4e8e7d214c84ec7d87a532 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:27 +0200 Commit message: Place pieces of one tissue by stage position A tissue too large for one acquisition is imaged in pieces, and those pieces are one sample: kept apart they count twice in every group summary, and because they agree with each other they look like a reproducible effect. readMRM() numbered each acquisition's pixels from its own first pixel and threw the stage coordinates away, so every piece started at (1, 1) and stitchAcquisitions() could only report that they overlapped. Its documentation claimed Waters coordinates were absolute, which stopped being true the moment readMRM() re-based them. readMRM() now keeps x_stage and y_stage (mm) alongside the grid indices, and stitchAcquisitions() places each piece where the stage recorded it: above, below or beside, in any order, gaps left empty. Pieces must share a pixel size; each is moved to the nearest position on a common grid and the largest shift is reported. Overlap is still an error rather than an average. Objects without stage positions keep their own coordinates and say how to get them. combineMSIs() fills a pData column that only some objects carry with NA, since stage positions and region labels are legitimately absent from some samples. Package: rhdf5 Commit: c72d938a7bd397d148e623a7c0f12e6b3865de1b Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 16:41:00 +0200 Commit message: Bump version Package: rhdf5 Commit: fe55afb12dd1583d7f6f58e236e3d85872da3e1f Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:40:28 +0200 Commit message: Document .matrix() methods removal Package: rhdf5 Commit: f1ad6e28ba024bdcfeede3cb1b3b89f92bb081e5 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:38:30 +0200 Commit message: Remove .matrix() methods and let them auto dispatch to array method Package: rhdf5 Commit: dc8ef2bbced3bfc17f95b284fb0b2981d20427f4 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:22:12 +0200 Commit message: Document on.exit change in NEWS Package: rhdf5 Commit: 2b34f2d0097aaf547999b5be0deeef35031694e8 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:20:32 +0200 Commit message: Use on.exit() more consistently to close Package: rhdf5 Commit: bbfebbf34a184471451df03fab4dfa74a29f1dd9 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:08:44 +0200 Commit message: Mention dead code removal in NEWS Package: rhdf5 Commit: aa7669dbe22003b61182dc3cd266b948ae055ad0 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:07:58 +0200 Commit message: Remove dead code in h5writeAttribute.array() Package: rhdf5 Commit: d1f0dc156114f8494ced58811c01fe1f092b1648 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:57:43 +0200 Commit message: Fix incorrect copy/pasted error messages Package: rhdf5 Commit: 81d91768bd5bc3a86b9c720a1a3c1681ad0851ae Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:43:10 +0200 Commit message: Remove extra call to H5loadConstants() Package: rhdf5 Commit: e28ea4ec812cfd7c63e15101b401a3aa12fac5f1 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:23:01 +0200 Commit message: Ensure .Call() always includes PACKAGE Package: rhdf5 Commit: 4f18f262fed53b25edbbd5db47138059a6a7a6cb Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:16:45 +0200 Commit message: Mention h5set_extent() fixes in NEWS Package: rhdf5 Commit: 98c8a7581553b43f8aa62575958b0a595394bb84 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:16:16 +0200 Commit message: Fix h5set_extent issue with dataset handle Package: GSVA Commit: 545a96a07fba745d24b021cde157b570597a7109 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 16:34:55 +0200 Commit message: Remove dependence on BiocSingular Package: aracne.networks Commit: d000659130672ee12ffa5a287616ffe16c334eb2 Author: federicogiorgi <federico.giorgi@gmail.com> Date: 2026-09-23 15:51:57 +0200 Commit message: Point to the Zenodo record 22918956 Fill in the Zenodo record (doi:10.5281/zenodo.22918956) hosting the networks and document the CC BY-NC-ND 4.0 license of the data files. Package: aracne.networks Commit: d768d15947c70f95dc353c4e3a21da480ffccdc3 Author: federicogiorgi <federico.giorgi@gmail.com> Date: 2026-09-23 14:47:27 +0200 Commit message: Move the networks to Zenodo The regulon data sets are no longer bundled in the package: they are hosted on Zenodo and retrieved with the new getRegulon() function, which caches them locally with BiocFileCache and verifies their MD5 checksums. listRegulons() lists the available networks. This brings the package size well below the 100 MB limit of the new build system. - documentation of the 25 networks merged into ?regulons - vignette converted to R Markdown - added unit tests - Authors@R replaces Author/Maintainer Package: GSVA Commit: 87cd4d7cdcae92c251c9b53c7f759c38b4ab1ed4 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 15:31:13 +0200 Commit message: Bump version Package: GSVA Commit: 9c1eb50150a6aaee271512838ad8739b3bb130fe Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 15:22:44 +0200 Commit message: Merge pull request #276 from rcastelo/275-average-method Average method for enrichment scores calculation Package: GSVA Commit: 9e68f27aaa3d02a7d4c28792365b50d35dc1b5aa Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 14:50:43 +0200 Commit message: Replace checkIdentical() for checkEqualsNumeric() to allow C unit tests pass across different platforms Package: GSVA Commit: 5f21614dc2ee103338d887a39e119f4fbbbf90d9 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 12:29:14 +0200 Commit message: Added C implementation of the average method, and its corresponding unit tests. For performance issues, genes within genesets are internally ordered after mapped to features, this required regenerating regression test for PLAGE since SVD flipped sign in values due to the different input order Package: GSVA Commit: 87cfe5db164c95b66710094c215285fbf17995a6 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:46:28 +0200 Commit message: Merge branch 'devel' into 275-average-method Package: GSVA Commit: cc12f1d01a63d0123a48e3fb3d576c61a5f6a14d Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 14:42:36 +0200 Commit message: Fixed namespace issues and unit tests Package: GSVA Commit: 6881306e155fe38933ff8cf6d3ec9be94b9b382d Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 12:16:49 +0200 Commit message: Add unit tests for CLR and average method Package: GSVA Commit: 730ce29c9eb3a6d8b94c1c327d96451241681fd5 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-21 17:07:11 +0200 Commit message: Added first version of the average method for calculating enrichment scores Package: fenr Commit: 78a5a1207281ef37881d399f562be49f4a4af6d2 Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 13:02:11 +0100 Commit message: Merge branch 'main' of https://github.com/bartongroup/fenr Package: fenr Commit: 83a93c2fe6a5bb8748799c1f369153a651713bea Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 13:00:33 +0100 Commit message: Reverting some changes Package: fenr Commit: 0274549e7ba96519bf153ae6736593f62e5f666a Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 12:01:32 +0100 Commit message: Version 1.11.3 Package: vsn Commit: cdb80675e45236c2f57a2b41d4f98f4f2d6814b2 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:27:07 +0200 Commit message: Bump version Package: vsn Commit: b5d9c153c5300b3209bd0bcef2285b4386731398 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:26:58 +0200 Commit message: Mention README and pkgdown site in NEWS Package: vsn Commit: fb67d77e139bbf2d24f020fcc99a770650124cb1 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:25:59 +0200 Commit message: Set up pkgdown Package: vsn Commit: 4e31e610b6c6afccfe348d107f05e277101f01be Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:25:04 +0200 Commit message: Add minimal README with deNBI survey Package: sesame Commit: 2acabdce8fbdd4fb9675db1fd76d60d05792be04 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 22:06:41 -0400 Commit message: 1.31.5: fix readControls column naming; qualityMask takes a custom mask readControls() built the control data.frame positionally: colnames(ctl) <- c('G','R','col','type') over a frame whose signal matrix has four columns, so Color_Channel and Type were cbind-ed past the end of that name vector and arrived unnamed, while `type` silently took a signal column. Downstream, controls(sdf)$Type was a vector of integers, so negControls()'s grep("negative", ...) matched nothing and detectionPnegEcdf() failed in ecdf() with "'x' must have 1 or more non-missing values" on EPIC and HM450 -- the platforms whose controls arrive through readControls() rather than as SigDF rows. The columns are now named explicitly. This was found from the C side, where it had been mistaken for an annotation divergence for two days. With it fixed, detectionPnegEcdf agrees between the two implementations at max|diff| = 0.00e+00 on EPICv2, MSA, EPIC and HM450. qualityMask() gains `platform` and `mask`, so a custom or combined-array mask can be passed in directly instead of being bolted on with addMask() after the fact -- the case that comes up for arrays built from two manifests. README: the two implementations are named and versioned. The R package is SeSAMe v1 and stays on the 1.x series; the C command line is SeSAMe2 on 2.x. They are parallel, not sequential. The conda line also said `sesame-cli`, which has not been the package name since 0.4. R CMD check: Status OK, vignettes built and re-run. Package: mia Commit: 859de8cd0be1bdd40982b6cd189141c84cb359cd Author: Giulio Benedetti <giuliobene2000@gmail.com> Date: 2026-09-23 14:27:37 +0800 Commit message: Clarify study subjects in ADHD microbiota profiles (#828) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: mia Commit: 751d24e22c26aaccc6ec7be1ece37540fc2eab37 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-23 08:57:53 +0300 Commit message: Add Rdpack references (#797) Signed-off-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: mia Commit: 3c4fd9e80ecf788464a2726cf15e64cbd0aeede2 Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Date: 2026-09-22 11:27:29 +0300 Commit message: Convert MAE to TreeSE and back (#810) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Package: OMA Commit: 1ff85f15276db0d08c8305d788808bc3d713d066 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-23 13:07:47 +0300 Commit message: Simplify importing Package: OMA Commit: f19c0abb3874a6386f4693912c59f010dc5ec331 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-22 15:05:08 +0300 Commit message: Fix rendering Package: OMA Commit: 1d6f339fb23ebbdd1a58d089605f547fb76413d1 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-22 14:31:13 +0300 Commit message: Fix rendering, update support forum address Package: OMA Commit: 3f130bdb5a124835ec56391806571a9a6954963e Author: jagadeesh <2400040120@kluniversity.in> Date: 2026-09-18 16:37:10 +0530 Commit message: docs: Add comprehensive Rarefaction section to transformation chapter (#825) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Co-authored-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <tvborm@utu.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 1a65548fafa7a1d699b74cabccff2cb6b8b74f3f Author: Rasmus Hindström <56149499+raivo-otus@users.noreply.github.com> Date: 2026-09-18 09:20:36 +0300 Commit message: docs/clarity improvement to mia::summarizeDominance (#852) Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Co-authored-by: TuomasBorman <TuomasBorman@users.noreply.github.com> Package: OMA Commit: bcf4b79324d7db13573f7d75f1921324f098bf37 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:11:59 +0000 Commit message: feat(ci): add whitespace stripping to style workflow (#864) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: be708a734fe6980f7fdb08cd7d29c0bf68d85d47 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:06:30 +0000 Commit message: fix(community_similarity): use official vegan docs (#872) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: d51543f698e697431a375bb5ee52ea224490b2a1 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:03:41 +0000 Commit message: feat(ci): add dependabot (#865) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 79c94b838aca89ac79e9544310302b5528c9a0b8 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 05:57:47 +0000 Commit message: bump(deps): actions/cache@v4 to v6 (#874) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 4e1978be84a4efc4813759e6f1a2d6aa262ba265 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-18 08:52:51 +0300 Commit message: Use scaled fitted values for DMM drivers (#881) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 7bd2fc8e6da903e0640182842001f3fd42f5a210 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-17 15:48:42 +0300 Commit message: Clarify exercise instructions across the book (#886) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 7ad1b506261f780a42bc9ffa0655f10f91047bb3 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-17 15:33:57 +0300 Commit message: Add tree visualization reference (#889) Package: OMA Commit: 0e655914be48d7af2242a012deeb8354ec31f033 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-08-08 19:29:22 +0300 Commit message: Suppress cheatsheet startup messages (#878) Package: beachmat Commit: 7fe7dc234ea2fe69bf8f4c711525428539033652 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 15:32:49 +1000 Commit message: Switch to DelayedNoOp to support all alabaster.matrix no-op subclasses. This saves us having to list all of the individual subclasses. Package: alabaster.matrix Commit: ff91f9ff04b310f74232613787d6abe1411769aa Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 14:54:50 +1000 Commit message: Introduce a no-op base class to catch all of our weird seeds. In particular, packages like beachmat don't have to add a specialization for each of the no-ops subclasses, they can just check for the DelayedNoOp class. Package: alabaster.matrix Commit: 998568738d4d76e3073b732c24eaf2a9d79f650a Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 14:26:07 +1000 Commit message: Implement ToBeRealizedArray class for fine control of delayed operations. Package: SparseArray Commit: fab50cb7a6f6b1c5735dd1f19b05b94e04503dcf Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:57:43 -0700 Commit message: some edits to SparseArray-abind.Rd Package: DelayedArray Commit: ef3f02a7227a0e6a07736601081925f2fccb43a9 Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:26:39 -0700 Commit message: requires S4Arrays >= 1.13.1 Package: DelayedArray Commit: 28a0ba92ed413f575dd5839324e9892eb8f840c2 Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:02:40 -0700 Commit message: DelayedArray 0.39.7: Add abind() method for DelayedArray objects Also: - Remove the rbind(), cbind() and bindROWS() methods defined for DelayedArray objects. These methods are now replaced by more generic methods defined in the S4Arrays package for Array objects that are all based on abind(). - Add coercion from array/matrix to DelayedArray/DelayedMatrix. This coercion is equivalent to calling the constructor function DelayedArray() on the object to coerce. Having this coercion work has the effect of making rbind() and cbind() work on a mix of DelayedMatrix objects and ordinary matrices. This partially addresses issue #100. Package: scDiagnostics Commit: bee3ff588074c8e26c3b15b12610f23b7c19acdc Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 21:24:22 -0400 Commit message: Silence scran deprecation warnings and tolerate missing Suggests, bump to 1.7.15 Two failures on the first run against Bioconductor 3.24 / R 4.6: R CMD check reported significant warnings in the examples on all three platforms. scran 1.41 deprecates its HVG helpers in favour of scrapper, so every modelGeneVar()/getTopHVGs() call - including the fitTrendVar() that modelGeneVar() calls internally - now signals a deprecatedWarning, and rcmdcheck runs with error_on = "warning". Add an internal muffleDeprecation() that muffles only the deprecatedWarning class, leaving genuine warnings alone, and wrap the six calls in processPCA(), detectAnomaly() and calculateReconstructionError() with it. The three examples that call scran::getTopHVGs() directly wrap it in suppressWarnings() instead, with a comment saying why. This is a stopgap: the HVG selection needs to move to scrapper before scran makes these functions defunct. The macOS job additionally failed with "Packages suggested but not available: 'scRNAseq', 'celldex'". Neither is used by anything that runs during the check - they appear in documentation prose and inst/script - and both currently fail their own Bioconductor 3.24 builds, so set _R_CHECK_FORCE_SUGGESTS_=false rather than fail this package's check over them. Package: scDiagnostics Commit: 964640ff9a5c7728f24141ce53575c0840966fd8 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 20:38:25 -0400 Commit message: Target Bioconductor devel 3.24 / R 4.6 in CI, bump to 1.7.14 The matrix was pinned to Bioconductor 3.22 / R 4.5, two release cycles behind: 3.23 is the current release and 3.24 is devel, which is what the Bioconductor build system checks this branch against. Point all three jobs at 3.24 / R 4.6 (the pairing BiocManager's version map requires), swap the Linux container for bioconductor/bioconductor_docker:devel, and move the RSPM mirror from jammy to noble to match that image's Ubuntu 24.04 base. Also refresh the cache keys and the check-results artifact name, which still referenced RELEASE_3_22/3_19; the new keys additionally force a cold cache so no 3.22-era binaries are restored. Package: knowYourCG Commit: 9a7cce4c69f010992c7694da610eab786d07b443 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 18:58:22 -0400 Commit message: Point users at KnowYourCG v2, and fix three dead links This package is KnowYourCG v1 and stays on the 1.x series. The C implementation is KnowYourCG v2, binary `kycg`, and nothing here said so. Framed as succession, not as a wind-down, and that distinction is the point. An earlier draft of this put "This package is in maintenance; active development continues in kycg" into DESCRIPTION -- the field that renders on the Bioconductor landing page. This package sits on an open Core Team deprecation watch (#4, "Bioconductor failure and risk of deprecation"), so publishing that it is in maintenance would have handed them the justification. A neutral pointer says the same true thing without inviting it: the project is not declining, it is on its second implementation. Three places, because they reach different readers. DESCRIPTION is the only one an installing user sees, rendered on the landing page. The README is for GitHub visitors. Sequencing.Rmd names v2 where a reader is most likely to want it -- that vignette's workflow is what v2 does natively over YAME stores. The URL is in angle brackets, the same convention the DOI in that sentence already uses; a bare URL is what R CMD check objects to. Each says plainly that the two are parallel implementations rather than an upgrade path: one is an R package, the other a command-line tool, and there is no upgrading from one to the other. Separately, three dead links. `R CMD check --as-cran` runs a URL liveness check that a plain check skips entirely, and it found Sequencing.Rmd linking to https://zhou-lab.github.io/YAME/docs/summarize.html (twice) and .../docs/pack_unpack.html -- both 404. YAME's documentation is a single page now and those paths no longer exist, so all three point at https://zhou-lab.github.io/YAME/ instead. Package: scDiagnostics Commit: 89c6ed709d444d28439a7c791cb151b11faca8fb Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 19:54:35 -0400 Commit message: Make BiocCheck's deprecation check resilient to bioconductor.org outages, bump to 1.7.13 BiocCheck's first check downloads checkResults//bioc-LATEST/ meat-index.dcf for both the release and devel branches, and a failed download is a hard error ("HTTP 504 Gateway Timeout" -> bfcadd() failed -> "not all 'rnames' found or unique"), which took down the Linux and macOS jobs even though the package itself was fine. Pre-populate BiocCheck's own BiocFileCache with up to three attempts before running BiocCheck, and only if bioconductor.org is still unreachable pass `no-check-deprecated` so that one check is skipped instead of failing the whole build. </pre> </div> Package: scDiagnostics Commit: 816fa92698fa534abefc3cc0f75df2319b8f11f6 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 17:32:41 -0400 Commit message: Disable public RSPM on macOS/Windows to fix root cause, bump to 1.7.12 The libomp install in the previous commit didn't fix stringdist's identical dlopen failure - same byte-for-byte error, meaning the install had no effect. Searched prior reports of this exact failure (tidymodels/tune#1199, Genentech/rdborrow#73/#74): the real cause is that r-lib/actions/setup-r configures Posit Package Manager (P3M) as the default macOS repo, and P3M's macOS arm64 binaries are compiled with OpenMP enabled. This runner can't resolve those OpenMP symbols at runtime (SIP strips DYLD_* for protected binaries, so even a correctly installed libomp isn't reliably picked up) - CRAN's own macOS binaries are built without OpenMP and never hit this. Set use-public-rspm: false on the "Setup R from r-lib" step so macOS (and Windows, already passing, no expected impact) resolve packages from CRAN directly instead of P3M, which should fix this for any OpenMP-linked package in the dependency tree - not just the three (RhpcBLASctl, isotree, stringdist) hit so far - rather than continuing to patch them one at a time. Left the earlier source-install and libomp workarounds in place; they're harmless if this makes them redundant, and there's no upside to stripping proven/plausible fixes before confirming this one actually resolves it on CI. Package: scDiagnostics Commit: 3aba0f79435c543deb4c129e486f16e5e92c6ba4 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 16:59:49 -0400 Commit message: Install CRAN's official libomp on macOS CI, bump to 1.7.11 The last two fixes patched RhpcBLASctl and isotree individually, but BiocCheck::BiocCheck() now hits the identical failure via one of its own dependencies (stringdist): unable to load shared object '.../stringdist.so': dlopen(...): symbol not found in flat namespace '___kmpc_barrier' Patching each OpenMP-linked CRAN package one at a time as it's reached doesn't scale - the actual root cause is that this GitHub Actions macOS runner is simply missing the libomp build that CRAN's macOS binaries are compiled against (documented at https://mac.r-project.org/openmp/; Homebrew's libomp installs to a different path and doesn't fix this). Installing it there via the official recipe should let CRAN's normal (faster) binaries load correctly for any OpenMP-using package, not just the two already patched. Left the RhpcBLASctl/isotree source-install workarounds in place since they're already confirmed working - no reason to touch proven fixes while chasing this. Package: scDiagnostics Commit: 58cf3022aee073ef86bf0e5695fe41dd4a701ec9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:24:46 -0400 Commit message: Also force isotree from source on macOS CI, bump to 1.7.10 RhpcBLASctl fixed the first macOS OpenMP dlopen failure, but the same issue exists one layer up: isotree's own CRAN macOS binary (isotree.so) fails to dlopen with "symbol not found in flat namespace '___kmpc_barrier'" - a Clang/LLVM OpenMP runtime symbol, same root cause (CRAN's macOS binary built with OpenMP support that isn't resolvable on this runner), just a different dependency in the chain. Applied the identical source-install workaround to isotree. Package: scDiagnostics Commit: 7809c44d4bc5e698aeb4d67f24e79535cfe513c9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:00:00 -0400 Commit message: Force RhpcBLASctl from source on macOS CI, bump to 1.7.9 Ubuntu and Windows now pass under the Bioc 3.22/R 4.5 bump (previous two commits), confirming those fixes. macOS still fails, but differently and on all 4 vignettes uniformly this time: Error: .onLoad failed in loadNamespace() for 'RhpcBLASctl' dlopen(.../RhpcBLASctl.so, ...): symbol not found in flat namespace '_omp_get_max_threads' RhpcBLASctl is a hard Import of isotree (detectAnomaly() calls isotree::isolation.forest()), so its namespace loads unconditionally. CRAN's macOS binary for RhpcBLASctl references an OpenMP runtime symbol that isn't resolvable on this GitHub Actions macOS runner - a known class of issue for R packages built with OpenMP support on macOS. Building from source instead compiles without OpenMP (Apple clang has no -fopenmp by default), so the resulting library never references that symbol. Added alongside the existing Matrix/irlba source-install workaround in the same step, which addresses the same kind of macOS binary incompatibility. Package: scDiagnostics Commit: 3386bcb54d27441922472dd08b49d1b1d786bb37 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 12:06:16 -0400 Commit message: Anchor SingleCellExperiment/SpatialExperiment Rd links, bump to 1.7.8 R CMD check now fails with error_on = "warning" on the Bioc 3.22/R 4.5 CI (bumped in the previous commit): "checking Rd cross-references" reports a genuine broken link (merfish_reference_data.Rd's \linkS4class{SpatialExperiment} doesn't resolve) plus 36 files whose \linkS4class{SingleCellExperiment}/{SpatialExperiment} links are missing package anchors - both promote the check from NOTE to WARNING under the newer toolchain. \linkS4class{} was reintroduced repo-wide by a September 17 commit ("docs: use \linkS4class{} for SingleCellExperiment roxygen links", for brevity) after an earlier commit had already fixed this exact issue with explicit \link[pkg:target]{text} anchors. Restoring that anchored form and re-running roxygen2 to regenerate man/ resolves it; verified with a full local R CMD check matching the CI invocation (0 errors, 0 warnings, 1 unrelated pre-existing note). Package: scDiagnostics Commit: b520b294d72834042d23e6c4c887c6c194847544 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 10:33:30 -0400 Commit message: Bump CI to Bioconductor 3.22/R 4.5 to fix vignette build failure COVIDCaseStudy.Rmd was failing to build on CI (macOS/Windows) with "unable to find required package 'Seqinfo'" inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause: covid_reference_data/covid_query_data were generated on current Bioconductor (3.22), where the Seqinfo class was split out into its own standalone package. check-bioc.yml was still pinned to the two-year-old Bioconductor 3.19/R 4.4, whose GenomeInfoDb predates that split and whose repos don't contain a 'Seqinfo' package at all, so the class tag baked into the serialized data can't be resolved. Two earlier attempts (adding set.seed() to rule out RNG state, then patching a subset of the shipped .rda files) missed this because neither addressed the actual CI environment being out of date. Bumped the workflow's matrix (r/bioc versions, container image, cache keys) to 4.5/3.22, matching the environment covid_reference_data was actually generated on; verified locally that a full R CMD build (fresh install + vignette rebuild) succeeds under this Bioc/R pairing. Package: scDiagnostics Commit: 02de5cdca9c45682ebceab3b3f7d6231d8cb8054 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:40:12 -0400 Commit message: Handle reference cell types with too few cells or absent from query detectAnomaly() previously assumed every reference cell type had at least 2 cells (to fit an isolation forest) and, when a query dataset was provided, implicitly assumed every reference cell type also had matching query cells. Neither is guaranteed: - A reference cell type with fewer than 2 cells can't fit an isolation forest; now skipped with a warning instead of erroring. - A reference cell type entirely absent from the query is a normal outcome (e.g. after subsetting/filtering the query), not an error; now reported with an empty query score vector instead of failing in predict(). Also fixes a latent bug where a cell-type subset reducing to exactly 1 row would silently drop to a vector (missing drop = FALSE), which would have broken the isolation forest input shape. Adds tests covering both edge cases. Package: scDiagnostics Commit: b0fc15de1e279c3a6e2d44c12837dd3667d35743 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:36:38 -0400 Commit message: Fix stale Seqinfo class tag causing vignette build failure, bump to 1.7.6 COVIDCaseStudy.Rmd failed to build on CI with: Error in .requirePackage(): unable to find required package 'Seqinfo' triggered inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause, confirmed via verbose updateObject() output: covid_reference_data's internal Seqinfo class was tagged with its old home package ("GenomeInfoDb", from before Seqinfo was split into its own standalone Bioconductor package), so a sufficiently new Bioconductor tries to auto-migrate it on load - and that migration path apparently isn't reliably available in a fresh CI environment. Fix: call updateObject() on serialized objects at data-generation time so the bundled .rda ships with the current internal representation baked in, rather than deferring to a lazy per-load migration. Applied to the new COVIDData.R/MERFISHData.R scripts (whose source data came from an external, older serialization), and audited/fixed the same latent issue in the pre-existing reference_data/query_data/qc_data (which had the identical stale tag despite already shipping in the package) and their generation scripts, so this doesn't resurface on a future regeneration or Bioconductor version bump. zeisel_/covid_/ merfish_ vignette datasets were already correctly tagged and are byte-identical after regeneration. Package: scDiagnostics Commit: 44dd05d3749412c865e5446d44a4520bd24df370 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:13:03 -0400 Commit message: Fix non-deterministic vignette failure and bump to 1.7.5 COVIDCaseStudy.Rmd and MERFISHCaseStudy.Rmd called detectAnomaly()/ calculateGeneShifts() (which use isotree::isolation.forest(), a randomized algorithm) without ever calling set.seed(), unlike the other two vignettes. This is the most likely cause of the CI vignette re-build failure on COVIDCaseStudy.Rmd after pushing 1.7.4 - a build without a seed picks up whatever RNG state the session happens to be in, which can land on the isolation forest / gene-shift edge cases seen elsewhere in this codebase. Verified against 15 different seeds plus a full local R CMD build (fresh install + vignette rebuild, not just devtools::load_all()) with no failures. Bumps to 1.7.5 rather than re-pushing 1.7.4, since 1.7.4 already has a recorded (failed) build on Bioconductor/GitHub. Package: MSstatsBioNet Commit: 0b9e21718beccbc1fb3847792481f8bda11b7ef5 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 18:27:25 -0400 Commit message: feat(decomposeSubnetworkIntoHierarchicalTopics): Enable NMF hierarchical decomposition (#110) Package: knowYourCG Commit: 5dbb3d5b4f6dcb4f6f54e4db6859b760358c9344 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 17:15:02 -0400 Commit message: Stop reaching the network when the vignettes and examples are built Three build-time downloads, all of the same two Zenodo files, none of them needed to show that the package works. The vignette one was failing outright. Sequencing.Rmd's QUICK START fetched mm10_f3_10cells.cg -- 11.4 MB, which takes ~101 s at the throughput a build host is likely to get. R's download.file() gives up at getOption("timeout"), 60 s by default, so the transfer truncated mid-file and the vignette errored. Measured twice here: it stopped at 6.0 MB and at 7.2 MB, both almost exactly 60 s of transfer, and completed only with timeout raised to 600. Raising the timeout would have kept a network dependency the package does not need. The sequencing workflow is superseded by the kycg command-line tool, which does this analysis natively over YAME .cg stores and fetches its own knowledgebases, so the chunk is now shown rather than run, with a line saying so and pointing there. The two examples had the same files behind a guard that does not guard. \donttest IS executed by the Bioconductor builders; only \dontrun is not. In bedToCg() the download.file() sat outside the guard entirely, so it ran on every check while only the bedToCg() call was skipped -- the whole example is now \dontrun. In testEnrichment() the guard was in the right place but was \donttest, now \dontrun; its offline part, which uses the sesameData cache, still runs. Both edited in the roxygen source and regenerated, so document() cannot revert them. Neither example has run lately: checksrc has been skipped for as long as buildsrc has been red, so these would have fired the moment the vignette fix made checksrc reachable again. BiocCheck NOTEs \dontrun in favour of \donttest. That NOTE is accepted here: \donttest does not keep the builders off the network, which is the point. visualization.Rmd still reads a small RDS over the network and is left alone -- it builds reliably and is not part of this failure. Package: knowYourCG Commit: 0a4ce5469ac8b4fbb9801a4af583639b65a36b4d Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 16:23:15 -0400 Commit message: Array.Rmd: use the base pipe, not the borrowed magrittr one buildsrc has failed on every builder in both release and devel with Quitting from Array.Rmd:218-233 [ky8, run-test-single] Error in `results %>% dplyr::filter(overlap > 10) %>% head`: ! could not find function "%>%" The vignette never attached the pipe. It worked anyway because library(sesameData) pulls ExperimentHub -> AnnotationHub -> BiocFileCache -> dbplyr, and dbplyr re-exports `%>%`, so the vignette was borrowing the operator from a package four levels down its own dependency chain and never named. When that chain stopped attaching dbplyr, the vignette broke without having changed. knowYourCG imports `%>%` via importFrom(magrittr) but does not export it, so library(knowYourCG) was never what made it resolve. DESCRIPTION has Depends: R (>= 4.4.0), so `|>` is available unconditionally and removes the dependency rather than renaming it; `%>% head` becomes `|> head()` since the base pipe needs a call. R/preparePlotDF.R keeps `%>%` -- package code has the import, only vignettes were ever exposed. Verified under R 4.6.0: all three rewrites return identical() results to the magrittr forms, the base pipe resolves with nothing attached, and Array.Rmd renders to completion. Fixes the buildsrc half of #4. Package: gDRutils Commit: a62ecdc187c6b4b726415cb33500813dfbbb0d10 Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 22:34:53 +0200 Commit message: Merge pull request #201 from gdrplatform/GDR-3612 refactor: read the constant-fit xc50 threshold from fit configuration Package: gDRutils Commit: 441d33fe8d5ca07d23f4dcbee9f59274a5f4f14f Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-22 21:17:54 +0200 Commit message: fix: read the fit configuration when the fitting layer is entered directly Package: gDRutils Commit: 11524511fd588673802ec057e728b96c9b089b0d Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 12:07:38 +0200 Commit message: Merge branch 'main' into GDR-3612 Package: gDRutils Commit: afa97f88532cc8d0539c9df9b2d5170b0e7f4f0c Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:50:27 +0200 Commit message: docs: flag that fit_curves still hardcodes the xc50 threshold Package: gDRutils Commit: f450b02a0beaa9ae1f8cec3fd09151e2f2fe5a98 Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:49:21 +0200 Commit message: Merge remote-tracking branch 'origin/GDR-3606' into GDR-3612 # Conflicts: # DESCRIPTION # NEWS.md Package: gDRutils Commit: b5e352cf6c88d1a7cb33ca89c106b55896cb1cbc Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 13:27:47 +0200 Commit message: refactor: read the constant-fit xc50 threshold from fit configuration The response level deciding whether a constant fit reports +Inf or -Inf was hardcoded at 0.5 in two functions. It is now one entry per normalization type in the fit_config block, alongside the priors and asymptote bounds. Numerically inert: every type keeps 0.5, which is what the code did before. The point is that the value becomes visible and decidable - for RV it means 50% viability and for GR it is the GR50 convention, but NGR is a bare ratio of slopes that is legitimately negative, where the threshold has no established meaning. Package: methodical Commit: 2ce1f224115807008cf8e4056bff3346c161cbe2 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-22 20:12:54 +0100 Commit message: update Package: MSstatsBioNet Commit: d6f02da47b7e915ef0c30923538cf7d516341aa2 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 14:43:07 -0400 Commit message: fix(pubmed): Reduce runtime for fetching pubmed abstracts (#109) Package: GSVA Commit: d2828ae6a4645e089dc931494a2b0f239850ae7b Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:45:59 +0200 Commit message: Switch a couple of install() calls in C for the corresponding more performant internal Rf_*() calls Package: alabaster.matrix Commit: 7cd81656f826538908e71cea03dbed7e42544cb8 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:53:29 +1000 Commit message: Mention all of the weird DelayedArrays that we support in the ANY method. Also move the LowRankMatrix code out of the ANY method for clarity. Also bump version and date for a new release. Package: alabaster.matrix Commit: 1d4b149bd9a329ea35a5033dc0318f6292f275ee Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:38:20 +1000 Commit message: Use a more precise R type hint for residual matrix objects. Also move ResidualMatrix code out of the ANY method for easier reading. Package: alabaster.matrix Commit: 1a17e99c4a5e64b68688da152c20434d3ae965bb Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:21:07 +1000 Commit message: Support scrapper::LogNormalizedMatrixSeed in storeDelayedObject. Package: MSstatsBioNet Commit: c6cb932731a5f1f1a743daed884638f2c14afd57 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:38 -0400 Commit message: Bump package version from 1.5.2 to 1.5.3 Package: MSstatsBioNet Commit: 57f2c7b2d94664d93f76a16b82cc5a5b7cff2ae9 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:10 -0400 Commit message: fix(proteinGroups): Adjust annotateProteinInfoFromIndra to handle protein groups (#108) Package: BreastSubtypeR Commit: 9aad28d9baa37a3a2acc3e040c72bc2fea5bced8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-09-22 20:24:05 +0800 Commit message: Merge upstream/devel, Updated Package: BreastSubtypeR Commit: f44f9d18a7ff9c1446d57cc8515dc427e98e0a4b Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:06:15 +0800 Commit message: Merge pull request #139 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 9e4904ff65cfc1320229f841b55402e08e0390fe Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:00:13 +0800 Commit message: Merge pull request #138 from yqkiuo/main New updates Package: BreastSubtypeR Commit: 252f893b32c10da768540ab3df667f3c6ef34419 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 12:56:55 +0800 Commit message: Merge pull request #136 from yqkiuo/maintenance/public-package-fixes-20260918 Maintenance fixes for 1.5.2: AUTO routing, ROR-C column, Shiny launcher and preflight, Mapping and documentation Package: BreastSubtypeR Commit: f9ca808290b0dfe73e62cff242e28cc301f69238 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-21 10:30:49 +0000 Commit message: Track .Rbuildignore and exclude the .github directory from the build R CMD check reported "hidden files and directories: .github" because the workflow directory reached the source tarball. .Rbuildignore was listed in .gitignore and therefore never shipped with the repository; it is now tracked, with the same content the Ensemble branch already carries, so the built package excludes .github, RStudio files, Rplots.pdf, doc, Meta and MANIFEST.txt. No R code changes. Package: BreastSubtypeR Commit: f3e3be4738438524e605ca70781d8ac359af9ca8 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-19 13:24:35 +0000 Commit message: Bump version to 1.5.2 and title the release notes DESCRIPTION 1.5.1 -> 1.5.2 for the Bioconductor devel submission of the maintenance fixes. The NEWS block collected under "Unreleased" becomes the 1.5.2 entry. One clause is added to the AUTO subsetting bullet: the supplementary pseudocode of the published paper records the strict comparison in the subsetting step while using ">=" for method selection, so readers comparing the package against the paper know that the package now applies ">=" in both and reproduces its shipped example. Package: BreastSubtypeR Commit: 1826b4a6941c152837ef57effbb3c23fdf9751a0 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:57:20 +0000 Commit message: Docs: keep the maintenance track free of unreleased-feature references The entropy change of the previous commits described the new NA behaviour by comparison with an unreleased voting feature, in the internal help text of get_entropy(), in the comment heading test-entropy.R and in the NEWS bullet. The maintenance branch is the public package: its sources, tests and NEWS must not name work that has not been released. The wording now states the behaviour on its own terms. No code, test assertion or behaviour changes. Package: BreastSubtypeR Commit: 252961fa606750b2c17e82363ee0e5ac4ac08d20 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:50:50 +0000 Commit message: Tests: do not let the equivocal HER2 case emit an unhandled warning The AUTO routing test feeds an equivocal "2+" HER2 code to check that a non-evaluable value is treated like a missing one. Builds that flag ambiguous HER2 codes warn on that input, which leaves an unhandled warning in the suite. The call is wrapped; the routing verdict it asserts is unchanged. Package: BreastSubtypeR Commit: 1931c45909ab5e0a56327d3024afd0331468caa5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:37:24 +0000 Commit message: AUTO: decide the HER2+ cohort from the HER2 column alone The HER2+ branch of get_methods() was entered when at least one evaluable HER2 value existed and the joint ER/HER2 counts held no HER2-negative sample. Those counts are computed with na.rm = TRUE, so a HER2-negative sample whose ER value was missing never reached them: one such sample left the cohort classified as HER2+, while an otherwise identical sample with a recorded ER value ended the classification. Whether a HER2-negative tumor counts must not depend on whether its ER status happens to be known. The branch now requires at least one evaluable HER2 value and every evaluable HER2 value to be HER2+. Values outside {HER2+, HER2-} are not evaluable; this covers missing values and the equivocal "2+" code that .normalize_er_her2_tn() deliberately leaves unchanged. Such samples neither create nor remove a HER2+ cohort, and AUTO now reports how many of them took no part in the decision, because a single unannotated sample used to be able to change the routing silently. Cohorts with complete HER2 information are routed exactly as before. The packaged OSLO2-EMIT0 example has no missing ER or HER2 value (ER+ 84, ER- 18, HER2+ 8, HER2- 94), so no shipped example or regression fixture changes. The test that pinned the previous behaviour (her2_pos_na_er) is replaced by a block asserting that both routes now agree, and a block asserting the new message. The NEWS bullet for the unreleased HER2+ change is consolidated into a single statement of the final rule rather than two successive refinements of the same unreleased behaviour. README and vignette state the rule. Package: BreastSubtypeR Commit: 14445c18179fdb40310ea13069f72cc6b5c59a60 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 18:20:00 +0200 Commit message: Entropy: report NA when no method returned a call get_entropy() computes the raw Shannon entropy of a per-sample row of method calls. table() drops missing values, so a row in which every executed method returned NA produced -sum(numeric(0)), that is 0, which on this scale reads as unanimous agreement. Such a row has no call distribution and therefore no entropy; it is now reported as NA. Rows with at least one call are unchanged, including the degenerate one-call case, whose entropy of 0 is the correct value for the observed distribution. The definition of the statistic - raw, unnormalized Shannon entropy in bits - is untouched, and no normalized variant is introduced. The change aligns the legacy path with the ENSEMBLE diagnostics, where raw_vote_entropy is already NA_real_ when valid_voter_count is zero. Exposure is narrow: every AUTO panel includes AIMS and sspbc, which are single-sample predictors and call essentially every sample, so an all-NA row cannot arise in AUTO. It arises in manual runs of nearest-centroid-only method sets (for example methods = c("ssBC", "ssBC.v2")), where a sample whose ER or ER/HER2 status is unknown gets no call from any executed method. The packaged OSLO2-EMIT0 example is unaffected: every tumor there has 7 or 8 calls, and its stored entropy column is reproduced exactly by the new function (asserted by a test). Side effect worth noting: Vis_Multi() orders rows by the entropy column and order() places NA last, so a sample with no calls now sorts to the end of the plot instead of appearing among the unanimous samples. The entropy column of res_subtypes is documented in ?BS_Multi for the first time, including that it is computed over the contributing methods only, so a low value from few contributing methods reflects few available calls rather than strong agreement. tests/testthat/test-entropy.R covers the NA cases, the unchanged values for rows with calls, reproduction of the packaged entropy column, and a manual two-method run in which four samples receive no call. Package: BreastSubtypeR Commit: 3668d9c93adb99e148dc577e8a82b0d556adb249 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 17:30:00 +0200 Commit message: PCAPAM50: exclude samples with unknown ER from the IHC-guided steps BS_PCAPAM50() builds the IHC column from the ER status with case_when(..., .default = NA), so a sample whose ER is missing or not coded "ER+"/"ER-" has no label. makeCalls.PC1ihc() expressed ER-negativity as !grepl("^L", IHC), which returns TRUE for NA, so those samples were counted as ER-negative in the PC1 axis check, in the misclassification-minimizing cutoff search and in the ER-balanced gene-centering set. The bias is one-directional and grows with the fraction of unknown ER. A new internal helper, .ihc_status(), classifies each label as "luminal", "nonluminal" or NA (missing or empty), and the three steps now use explicit luminal / non-luminal masks. Samples without an evaluable label take no part in estimating the cutoff or the centering set, a message reports how many were excluded, and they are still classified and returned. As a side effect the label test is now applied consistently: the mask is computed once, after trimming and upper-casing, instead of being evaluated before the upper-casing step in one place and after it in another. This is not a deviation from the published algorithm. The reference implementation (Raj-Kumar et al., CRAN package PCAPAM50 1.0.4, R/functions_PCA-PAM50.R lines 336, 355-356, 385-386) uses the same !grepl("^L", IHC) construct, but its IHC column is a user-supplied clinical subtype (LA, LB1, LB2, Her2+, TN) that the package never leaves missing; the vignette states that ER-positive subtypes start with "L" and all others are ER-negative. The NA category exists only because BreastSubtypeR derives the column itself. The change also removes an internal inconsistency: BS_cIHC() and BS_cIHC.itr() already exclude unknown ER from their ER groups via which(df.cln$ER == ...). Measured on the packaged OSLO2-EMIT0 input (R 4.3.3 sandbox), setting the first k ER values to NA and comparing calls before and after the change: k = 0 and k = 6 leave every call unchanged, k = 18 changes 2 of 102 calls, k = 30 changes 6 of 102. Cohorts with complete ER are unaffected, and the packaged example still reproduces its stored PCAPAM50 column. The help page of BS_PCAPAM50() gains a @details paragraph stating the exclusion, the message, that such samples are still classified, and the reference implementation's assumption of a complete IHC column. tests/testthat/test-pcapam50-unknown-er.R covers the helper, the unchanged complete-ER output against the packaged fixture, the message, and that unknown-ER samples still receive calls. Package: BreastSubtypeR Commit: 83ad6b3fa93553ba75cb3c641fb7a58070173806 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:10:00 +0200 Commit message: README/vignette: state the size gating of the ER/HER2-defined AUTO rule The AUTO bullet "ER/HER2-defined cohorts: ssBC.v2 only + SSP" read as an unconditional rule. In the code it applies only when the ER group reaches its minimum (15 for ER+, 18 for ER-) and the HER2 subgroup reaches its minimum (8 for ER+, 9 for ER-); smaller cohorts run AIMS and sspbc only. The bullet now says so, and a second bullet documents the handling of cohorts without any evaluable HER2 value (ER-based rules instead of the HER2+ branch). ASCII hyphens replace the typographic minus signs in the edited lines. Package: BreastSubtypeR Commit: 38aa1cc5cb833d260c5d5f82401a8ee528bd7fc1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:05:00 +0200 Commit message: Docs: Mapping "mean"/"median" collapse duplicate probes, as in the PAM50 code The Mapping() help (and the internal domapping() roxygen) described method = "mean" and "median" as keeping "the probe with the highest mean/median expression". duplicate_genes() computes the per-sample mean or median across all probes of a gene, i.e. it collapses the probes rather than selecting one; "iqr", "stdev" and "max" select one probe, and "max" selects by largest row sum, not by "highest expression value". Checked against the original PAM50 bioclassifier code (bioclassifier_R/subtypePrediction_functions.R, collapseIDs(), and the example parameter file): "mean" and "median" average the duplicate probes per sample there too, "iqr" and "stdev" select the probe with the highest IQR / SD, and no "max" method exists. BreastSubtypeR therefore reproduces Parker's behaviour; only its documentation was wrong. Author decision (2026-09-18): fix the documentation. The parameter text in R/BreastSubtypeR_methods.R, R/Utilities.R and man/Mapping.Rd now describes the averaging, credits collapseIDs() and marks "max" as a package addition. No code or mapped values changed. Package: BreastSubtypeR Commit: ba02d862d5e1c9cdbb43e23a1f8506faaed46946 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:00:00 +0200 Commit message: AUTO: include subgroups exactly at their minimum in the ssBC/ssBC.v2 subsets Method selection in get_methods() accepts a subgroup when its size is at least the minimum (15 for ER+, 18 for ER-, 8 and 9 for the HER2 subgroups), but the sample subsets handed to BS_Multi() for ssBC and ssBC.v2 were built with a strict ">". A subgroup of exactly the minimum size was therefore selected for the method and then excluded from its input, and its samples came back NA while the AUTO messages reported the method as running. The packaged OSLO2-EMIT0 example is such a case: 84 ER+ and 18 ER- tumors, so the cohort is classified as mixed and ssBC is selected, but the 18 ER- tumors were dropped from the ssBC input. Executed in a sandbox (R 4.3.3) on this branch: with the published strict comparison a fresh BS_Multi(methods = "AUTO") run yields ssBC = NA for those 18 tumors and does NOT reproduce the packaged frozen result OSLO2EMIT0obj$res (which carries ssBC calls for all 102 tumors); with ">=" the fresh run reproduces the stored result exactly, entropy included. The stored data object is therefore left unchanged; the fix restores agreement between the code and the shipped example. tests/testthat/test-auto-fixture-regression.R asserts the reproduction and that no ER- tumor is left without an ssBC call; tests/testthat/test-auto-subsetting.R adds exact-minimum subgroup cases and the OSLO2-EMIT0 colData. Package: BreastSubtypeR Commit: 13ea06daee8af82ab42c32cfceb38b43aecff9e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:55:00 +0200 Commit message: AUTO: require an evaluable HER2 value before calling a cohort HER2+ get_methods() entered the HER2+ branch whenever n_ERposHER2neg == 0 && n_ERnegHER2neg == 0. Both counts are also zero when HER2 is entirely missing or coded with unrecognized values, so such cohorts were classified as "small HER2+" and received AIMS and sspbc only (example: 60 ER+ / 40 ER- with HER2 all NA). The branch condition now also requires at least one evaluable HER2 value (HER2+ or HER2-). Cohorts without HER2 information fall through to the ER-based rules: a mixed ER cohort gets the mixed panel (ssBC.v2 then returns NA for every sample, which BS_ssBC() handles without error), an ER+-only cohort reaches the announced AIMS/sspbc fallback because its HER2 subgroups are empty. Cohorts with any evaluable HER2 value are routed exactly as before, including the existing treatment of HER2- samples whose ER is missing (excluded from the subgroup counts, as the AUTO message states). No effect on the packaged OSLO2-EMIT0 example. Author decision (2026-09-18): HER2+ branch only with evaluable HER2. tests/testthat/test-auto-routing.R covers the size-gated ER/HER2-defined cohorts and the cohorts without HER2 information. Package: BreastSubtypeR Commit: 94c6d57580acf6c6b77287f8e3968628ffeb2b84 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:50:00 +0200 Commit message: cIHC, cIHC.itr, PCAPAM50: clear error when an ER group is empty On a cohort with a single ER group (for example every sample ER+), makeCalls_ihc() and makeCalls.PC1ihc() failed with "undefined columns selected" and makeCalls_ihc.iterative() with "arguments imply differing number of rows: 0, 102", all from the median computation on an empty balanced set. The methods cannot balance by ER status without both groups. A small helper, .check_er_groups(), now stops with the group counts and a pointer to the cohort-aware modes in makeCalls_ihc() and makeCalls_ihc.iterative(). makeCalls.PC1ihc() checks the luminal / non-luminal IHC classes before the PC1 cutoff search and the balanced set after it, and makeCalls.v1PAM() checks its LumA / Basal groups. Cohorts with both groups take the same path as before (the OSLO2-EMIT0 cIHC calls are unchanged). Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-er-balancing-errors.R covers the three methods. Package: BreastSubtypeR Commit: 3894f47377e42f6c2f18cf8d7e04ecd0e38f7b16 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:45:00 +0200 Commit message: Docs: describe the actual return values of the NC methods; cIHC.itr ratio BS_PCAPAM50() and BS_ssBC() documented "a character vector of intrinsic subtype predictions", BS_cIHC() "a data.frame", and BS_cIHC.itr() a list with elements subtypes / confidence / ER_balance that do not exist. All four return a list: BS.all (PatientID, BS and, with Subtype = TRUE, BS.Subtype), score.ROR (correlations, calls, confidence, ESR1/ERBB2 expression, ROR-S/ROR-P and, with hasClinical = TRUE, ROR-C/ROR-PC scores and groups), the medians used for centering (mdns; mdns.fl for PCAPAM50; absent for cIHC.itr) and outList; BS_cIHC.itr() additionally returns BS.itr.keep and, with Subtype = TRUE, BS.itr.keep.Subtype. Verified on the packaged OSLO2-EMIT0 input. BS_cIHC.itr(ratio): makeCalls_ihc.iterative() swaps the larger ER group into the sampled position before drawing ceiling(ratio * n_smaller) samples from it, so the ratio applies to the larger group relative to the smaller one, not to ER+/ER- as such. The parameter text now says so, and the alphabetical tie-break used by get_consensus_subtype() for the consensus call is stated in the return value. roxygen comments and the corresponding man/*.Rd files were edited in parallel (no roxygen2 run, to avoid unrelated regeneration changes). Present in Bioconductor release 1.4.0 and devel 1.5.1. No code changes. Package: BreastSubtypeR Commit: abace8828bc01fa6ff7e1a70d6a9c1e28505cc74 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:40:00 +0200 Commit message: Shiny: cohort preflight requires both ER and HER2 columns .summarize_cohort() in inst/ShinyBreastSubtypeR/server.R returned ok = TRUE for kind "ER" (HER2 absent), kind "HER2" (ER absent) and for a valid TN column without ER/HER2. get_methods() stops in all three cases ("The 'AUTO' mode requires both 'ER' and 'HER2' columns in the 'pheno' dataframe"), which the app surfaced only as "Prediction failed" after the user pressed Run. The column summary is unchanged (now .summarize_cohort_columns()); .summarize_cohort() wraps it and sets ok = FALSE with the message "Cohort-aware analysis requires both 'ER' and 'HER2' columns; missing: ..." when either column is absent. Kind and statistics are still reported. tests/testthat/test-shiny-preflight.R covers the column combinations. Package: BreastSubtypeR Commit: 36e4de779bf6677fde472e81f613cf3f49799476 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:35:00 +0200 Commit message: iBreastSubtypeR: load app dependency namespaces correctly The launcher's .attach_if() helper called requireNamespace(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE). requireNamespace() has no such arguments, so the call failed with "unused arguments"; the failure was swallowed and FALSE returned, and nothing was loaded. The comment claimed the packages were attached to the search path, which requireNamespace() never does. The app still worked because ui.R/server.R use qualified calls and shiny::runApp() attaches shiny itself. The helper is now a package-internal function, .load_app_dependencies(), that checks installation, loads each namespace with requireNamespace(p, quietly = TRUE) and stops with a clear message when a package is missing or cannot be loaded. The tidyverse option uses the same helper. The exported signature and documentation are unchanged. tests/testthat/test-shiny-launcher.R covers the missing package error and the successful load. Package: BreastSubtypeR Commit: 6deac1db8d57cfbaee4e104edb9af6f160a9c536 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:30:00 +0200 Commit message: BS_Multi: report the error text when PCAPAM50 fails The tryCatch() around BS_PCAPAM50() in BS_Multi() warned "PCAPAM50 failed in this iteration: " and dropped the condition message, so users could not see why the method failed. The warning now appends conditionMessage(e) (with call. = FALSE). Behaviour is otherwise unchanged: the method's column is filled with NA. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-bs-multi-messages.R mocks a failing BS_PCAPAM50() and checks the warning text and the NA column. Package: BreastSubtypeR Commit: ff23703e8cb347524ad8fe1897d25d6514fd4049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:25:00 +0200 Commit message: Normalize factor phenodata like character; fix the FPKM imputation guard .normalize_er_her2_tn() used nested ifelse() calls whose fallback was the original column. For a factor column the fallback is the integer code, so unmatched levels came back as strings such as "3" instead of "Unknown". Mapping() converts colData factors to character before calling the helper, but BS_Multi() and get_methods() normalize the phenotype table directly, so a hand-built data_input with factor ER/HER2/TN columns was normalized differently from the same table with character columns. The helper now works on as.character() copies of the three columns; the coercion warnings compare character values, so canonical factor input no longer triggers them. Character input is unchanged. domapping(): the second imputation guard tested anyNA(x) after x had already been imputed, so counts.fpkm was never imputed. It now tests anyNA(counts.fpkm). In practice edgeR rejects NA counts earlier, so this is a logic correction with no expected effect on existing analyses. Both present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-phenodata-normalization.R compares factor and character input for the helper and for a full AUTO decision. Package: BreastSubtypeR Commit: 5deb60ce12da9448df97aa5079c0f312ad12cc6a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:20:00 +0200 Commit message: Mapping: keep matrix dimensions for single-sample input duplicate_genes() indexed x[names(entrezid), ] without drop = FALSE and rebuilt the collapsed matrix with mapply(SIMPLIFY = TRUE) followed by apply(x, 1, unlist), which requires a matrix. For a one-sample SummarizedExperiment the subset became a vector and Mapping() failed with "dim(X) must have a positive length". prepare_nc_matrix() and the probe filter in domapping() had the same drop issue. The collapse now builds the gene-by-sample matrix explicitly (lapply + rbind with dimnames from the split and the sample names), and the three subsets use drop = FALSE. For multi-sample input the returned values and dimnames are identical to the previous implementation for "mean", "median", "max", "stdev" and "iqr" (checked on random data with duplicated Entrez IDs and an NA value); the OSLO2-EMIT0 mapping of one sample equals the corresponding column of the full mapping. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: d6c6c20c4004d988e79c522ee4f1625dd0ad39fb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:15:00 +0200 Commit message: AUTO: announce the fallback to AIMS and sspbc instead of falling back silently The safety net at the end of get_methods() set methods to c("AIMS", "sspbc") without any message. It is reached by ER+-only or ER--only cohorts whose HER2 subgroups are all below their thresholds, typically because many HER2 values are missing (example: 17 ER+ samples with HER2+ 5, HER2- 6, missing 6). Users saw only the two SSP methods run, with no indication why the ssBC variants were not selected. The fallback now emits a .msg() (respecting the BreastSubtypeR.verbose option) naming the reason. Method selection is unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: a9f0de975795df873663f9cab6207455cb3b2d15 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:10:00 +0200 Commit message: AUTO: drop samples with missing ER/HER2 from the ssBC/ssBC.v2 subsets get_methods() built the AUTO-mode sample subsets with rownames(pheno)[pheno$ER == subtype] and the ER/HER2 analogue. A missing ER or HER2 value evaluates to NA in the comparison, so the subsets contained NA "sample names". BS_Multi() then either failed when it subset the SummarizedExperiment ([,j] index out of bounds: NA) or, when the NA-padded vector was at least as long as the cohort, treated it as "run on all samples" and skipped the intended subsetting. Example on 1.5.3: 50 ER+ / 45 ER- / 5 NA gives a 105-element subset with 10 NA entries for a 100-sample cohort. Both lapply bodies now use which(), as makeCalls.ssBC() already does, so samples with missing status are excluded. Cohorts with complete ER/HER2 values return identical subsets. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-auto-subsetting.R covers a mixed cohort with missing ER and an ER- cohort with missing ER and HER2 (subset shorter than the cohort). Both fail on the previous code. </pre> </div> Package: BreastSubtypeR Commit: 2f8ea71201a742d0d0957ff8228ba2fdbc21d3be Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:05:00 +0200 Commit message: Fix ROR-C risk group column: use criskgroups, not cpriskgroups In RORgroup() (R/NC_functions.R) the data frame built when hasClinical = TRUE assigned the combined + proliferation groups (cpriskgroups) to both "ROR-C Group (Subtype + Clinic)" and "ROR-PC Group (Subtype + Clinic + Prolif)". The ROR-C groups (criskgroups, thresholds -0.1 and 0.2 on the combined score) were computed but never reported. The ROR-C group column now uses criskgroups; the ROR-C score and every other column are unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-ror-groups.R adds a synthetic RORgroup() input in which the ROR-C and ROR-PC groups differ (high/low/med vs low/high/med) and checks that the ROR-C group is reproducible from the reported ROR-C score. The test fails on the previous code and passes with this change. Package: BreastSubtypeR Commit: 9ab99af8b9cf337614a30a61c3e0ce1c264df049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:00:00 +0200 Commit message: Tests: run the nested testthat suite via test_check() tests/testthat.R contained a single inline test_that() block and never called test_check(), so tests/testthat/test-tn-cohort-detection.R (added in 1.5.1) was not executed by R CMD check; the Bioconductor devel check log shows only the inline test running. tests/testthat.R now calls test_check("BreastSubtypeR") and the inline BS_Multi() test moved unchanged to tests/testthat/test-bs-multi-manual.R. DESCRIPTION: Config/testthat/edition: 3 and testthat (>= 3.2.0) in Suggests, matching the edition-3 expectations used by the tests added on this branch. No version bump. Package: BreastSubtypeR Commit: a4b23b2aba07ba19b33669ac1e8d8361fd1139ab Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:59 +0200 Commit message: Merge pull request #135 from yqkiuo/main update to 1.5.2 Package: BreastSubtypeR Commit: b19c1c3f629d11a8f12e57526162b16e41e605c6 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:30 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: 0c0c47c87dcd6e560bedcd536f828dca642e7933 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-06-22 17:38:39 +0300 Commit message: Merge pull request #134 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: edeb030317e854cd706a351f12b93dbd722f232e Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 17:22:45 +0300 Commit message: Finalize NEWS entry for TN detection fix (#133) Package: BreastSubtypeR Commit: b8d6bf4b5bb037d8e101287e92d209fdb1e869a5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:59:04 +0300 Commit message: Update NEWS and documentation for TN detection fix (#133) Package: BreastSubtypeR Commit: d8eeff0e85113512842b1e4976fce6eed1142e39 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:25:06 +0300 Commit message: Fix TN-only cohort detection (#133) Package: BreastSubtypeR Commit: cd515ab92fffbbf8a3496cfc70e65299b77457ba Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-02-20 12:09:07 +0100 Commit message: v1.3.3 Package: BreastSubtypeR Commit: 0770ee5c0a5283fd1f073cf9c170464431eac2d3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-02-20 11:59:28 +0100 Commit message: Merge pull request #129 from yqkiuo/main AUTO - NA Package: BreastSubtypeR Commit: 9b740667ac781cede13f2884763f47576f5778cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:30:22 +0100 Commit message: Merge pull request #128 from yqkiuo/BranchManos Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: ebac3daf14161981995520818d552a8c894faa21 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:27:35 +0100 Commit message: Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: 122fae948ba3ab93589046d4fc9f564a95db3805 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-12-21 07:08:46 +0100 Commit message: Merge pull request #125 from yqkiuo/main Update Package: BreastSubtypeR Commit: ab9e6c7e715a77c3d9d0c93f0d96794531b39afc Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:48:57 +0100 Commit message: Merge pull request #124 from yqkiuo/BranchManos cIHC.itr: return distances as numeric matrix, preserve dimnames Package: BreastSubtypeR Commit: 1cdd290182105e8d9dd1cf38a2f1cc2748045aba Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:41:20 +0100 Commit message: cIHC.itr: return distances as numeric matrix, preserve dimnames - Coerce mean_distance and mean_distance.Subtype to double matrices with sample/centroid dimnames; negate once. - Ensure testData is numeric matrix. - Use explicit getsuffix(calibration=..., internal=...). Closes #112 Package: BreastSubtypeR Commit: e626336705e6981d3f43c1e307381875acc4dbf5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:18:30 +0100 Commit message: Merge pull request #123 from yqkiuo/BranchManos feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to can… Package: BreastSubtypeR Commit: bf244ea222946de979dc528b6764b074b9a7492e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:17:59 +0100 Commit message: feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to canonical forms - Add `.normalize_er_her2_tn()` utility and call it inside `Mapping()` to coerce common variants to: * ER → {ER+, ER-} * HER2 → {HER2+, HER2-} (HER2 "2+" left unchanged/unevaluable) * TN → {TN, nonTN} Accepts Positive/Negative, Pos/Neg, Yes/No, True/False, 1/0, AMP→HER2+, etc. - Preserve original values in `colData` when fields are absent; only touch present columns. - Emit explicit warnings on ambiguous/unmappable values (e.g., HER2 "2+"). - Roxygen: expand `Mapping()` docs with required Column metadata for AUTO/ssBC/cIHC/PCAPAM50 and numeric TSIZE/NODE (0/1) for ROR; document the canonical receptor coding and the automatic normalization behavior. Closes #122 Package: BreastSubtypeR Commit: d4200b8f8fa6a230b1aed6bd8d5a271856dcf9c5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 10:04:54 +0100 Commit message: Merge pull request #120 from yqkiuo/BranchQiao Formatting Package: BreastSubtypeR Commit: 855146c3797560a923b044683b223aa09c5ab6b6 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 10:04:04 +0100 Commit message: Formatting Package: BreastSubtypeR Commit: 7e1546b848212ca92df006f0625e1f0213a5d825 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:57:27 +0100 Commit message: Merge pull request #119 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 13081dbdf8d5faead48468a7121455f68f226262 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 09:56:57 +0100 Commit message: Warning: nonASCII Package: BreastSubtypeR Commit: e872818d9f7db70dd95b04e56306c5f986b4cb2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:48:36 +0100 Commit message: Merge pull request #118 from yqkiuo/main 1.3.1 Package: BreastSubtypeR Commit: e837d4a4b93480e5921dc6220d336f390e08cfa9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:56:26 +0100 Commit message: Merge pull request #117 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 24282cdd95efcb545c8a516d2a4c52c333451e37 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:55:43 +0100 Commit message: docs(NEWS): updated to include latest changes/bug fixes Package: BreastSubtypeR Commit: d3e819ea9cb6036119018581de03f7c0ca6c03e9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:45:26 +0100 Commit message: shiny/preflight: reset cached data_input on source change (uploads/example) to fix stale cohort display Package: BreastSubtypeR Commit: f7ad9d6399c959146fad253c76e4b8a093367674 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:06:08 +0100 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: 33bc7cabda598a10d06781255a4ff477d64ec373 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:05:55 +0100 Commit message: Merge pull request #116 from yqkiuo/main Main to BranchManos unmerged changes Package: BreastSubtypeR Commit: c1164715171e92993dba23d51ed4d2739a9db33a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:03:31 +0100 Commit message: Include ssBC in robust singleton handling Package: BreastSubtypeR Commit: 0c0c39cd7cb7bdde99192d4a877cc9990b98b6c4 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:32:17 +0100 Commit message: v1.3.1 Package: BreastSubtypeR Commit: ed479c4a0a715bd078874a465956416cb58e999b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:30:33 +0100 Commit message: Minor typo for Shiny exports Package: BreastSubtypeR Commit: fca34d14be09269bd6a9e83f9b169b3f49e3b27d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:16:28 +0100 Commit message: ssBC.v2: include sample IDs in singleton fallback warnings; surface warnings in Shiny - Warnings now list subgroup + n + sample IDs (truncated for long lists). - Shiny wraps runs in withCallingHandlers() to show warnings via showNotification(). Package: BreastSubtypeR Commit: 5beba6624617ea57bd33a664a2c9ccddbe01f5d2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:15:25 +0100 Commit message: ssBC.v2: robust singleton handling + ROR guards - Use uncentered expression for n=1 fallback (avoid zero-vector Spearman→NA). - Add canonical 4-class name normalizer before RORgroup; create missing cols; enforce order. - Shorten Mapping() completion notification duration in Shiny. Package: BreastSubtypeR Commit: 6f8593d8659200d5b054e45ae6deb7ff624bf02f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 23:31:32 +0200 Commit message: Merge pull request #115 from yqkiuo/BranchManos fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: ae32dd867386460a3d6abcff63cd519bcebdd098 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-21 23:25:49 +0200 Commit message: fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: 01a86e199d7353c526b1ddec6693b6c5d87a53e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:51:52 +0200 Commit message: Merge pull request #114 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: aee5223fca7ad466234702b83f9d465092e65fec Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:50:18 +0200 Commit message: update documentation (.Rd) files & NEWS.md Package: BreastSubtypeR Commit: e3852e46bc7c708db9534558669b18e492bbcb44 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:38:36 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: f13b835df4329f494e2a1fe1242a1927657629f9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging -Name unnamed chunks Closes #113 Package: BreastSubtypeR Commit: 815edf2ed0faa1dc708fecc282da22945d861490 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging Package: BreastSubtypeR Commit: 27a8e42ca0dd5a06b976bd6e59aeedf3337c8ad1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:41:55 +0200 Commit message: Merge pull request #111 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6ed1cf770b44ea3eeaa0fe5d284760692df203e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:40:32 +0200 Commit message: feat(shiny): show ER/HER2 subgroup tallies (±TN) in AUTO preflight Package: BreastSubtypeR Commit: a85dec5c9e7f261e7d9ea94febbbfc063dc07992 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:04:55 +0200 Commit message: fix(shiny): guard switch() inputs to prevent length>1 errors; harden AUTO preflight & ssBC option handling Package: BreastSubtypeR Commit: 8b4e57129dabde362d8c811661e7586dc633c396 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:49:16 +0200 Commit message: feat(shiny): TN-aware AUTO preflight summary and messaging Package: BreastSubtypeR Commit: 83b469a296627e4a81983655692766813d8540b2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:48:42 +0200 Commit message: docs: convert wording to American English (standardized, normalization, visualize) Package: BreastSubtypeR Commit: 1c86f875473cf413e91da628410278915a9b19cb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 00:28:47 +0200 Commit message: Merge pull request #110 from yqkiuo/BranchManos v1.1.9: feat(app): add example-data loader and AUTO preflight cohort … Package: BreastSubtypeR Commit: bcb7486f49afd2f9c719d1b047c89b96421040b5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-15 00:26:27 +0200 Commit message: v1.1.9: feat(app): add example-data loader and AUTO preflight cohort stats; harden AIMS/sspbc outputs; renamed FPKM GEX example file Package: BreastSubtypeR Commit: 3e5ae1bae1910f63b576690d0f5965c092929197 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-14 22:26:00 +0200 Commit message: Merge pull request #109 from yqkiuo/BranchManos Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: 643629b4f37a82e8eb4fc1d4b8b7d47a1d0140e5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-14 22:08:03 +0200 Commit message: Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: f0bb013273724583dc640776f5253a650e71deb7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-11 19:07:21 +0200 Commit message: Merge pull request #106 from yqkiuo/main v1.1.8 Package: BreastSubtypeR Commit: e519bba6330b28527eba397178b5db68259cd335 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 17:48:34 +0200 Commit message: Merge pull request #105 from yqkiuo/BranchManos Minor text improvements Package: BreastSubtypeR Commit: 7ef4c516f1e02b2667908e42c91db1f81587e183 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 17:35:16 +0200 Commit message: Minor text improvements Package: BreastSubtypeR Commit: bba02a162aae8a104830c2762903a95b4b24a086 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 16:30:43 +0200 Commit message: Merge pull request #104 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6bb89109d53b3cbfc61069dad0b97c43fc01a59 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 08:38:02 +0200 Commit message: v1.1.8: feat(auto): enforce v2-only for ER/HER2-defined cohorts; add TN cutoff (18); sync docs Package: BreastSubtypeR Commit: 104a9d3c962648e2421f86b970452b6ae8094add Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 00:03:52 +0200 Commit message: v1.1.7: Fixed bugs & Clarified guidance in AUTO logic Package: BreastSubtypeR Commit: 3a0c352910e74d2016eaaa4f0d229db74b6428b1 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:11:23 +0200 Commit message: Merge pull request #103 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: c23f9312cfe6399587682872db5168e726949468 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-08 07:10:55 +0200 Commit message: v1.1.6 Package: BreastSubtypeR Commit: bda41efb6523b351c335cbbbfe93eda3e294159a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:01:46 +0200 Commit message: Merge pull request #102 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 01fbf08f95785bd96121416f08a42a0723db9bb5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:31:43 +0200 Commit message: Merge pull request #101 from yqkiuo/BranchManos Update citation Package: BreastSubtypeR Commit: 819b86fcb1f32f68d8d6551ae67675e59d55cbc2 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:29:59 +0200 Commit message: Update citation Package: BreastSubtypeR Commit: 18426cd1996f6d437078579a397e594ac858b422 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:18:10 +0200 Commit message: Merge pull request #100 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5cd622f0dfdcbf4ebd2612e2f3bce0d4d130a1dd Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:10:24 +0200 Commit message: Update to v1.1.6 Package: BreastSubtypeR Commit: 0168bb1d064c170c27904604ce944664052ffc4c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:00:02 +0200 Commit message: Fix CITATION error & update CITATION Package: BreastSubtypeR Commit: efcf440f930e3e0216161a7bfaa1f8a839796ffc Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:28 +0200 Commit message: Merge pull request #99 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 522570c1925152201b4738888c70a9b479569b4d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:10 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: caa57d7c96c2b3621ba3153a63704780fb67943c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: eca7fd305351bee53a3359193d31d6efb3bd239c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:26:16 +0200 Commit message: Merge pull request #98 from yqkiuo/BranchManos Bump version to 1.1.5, merge from BranchManos Package: BreastSubtypeR Commit: 3d6d84a04f652c46b098e7daf6b9433783c59317 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:17:29 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 08be34439c7ec15f3aab940989e7fc5881500a38 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:28:50 +0200 Commit message: Minor styler changes to comply with BiocCheck Package: BreastSubtypeR Commit: c33c626c748776d83aec78b69c2c5c2d78b40d94 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:00:25 +0200 Commit message: Remove Styler ignore file Package: BreastSubtypeR Commit: a756018eea737c57128fecbe2ed656a5c8bd8c89 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:53:48 +0200 Commit message: After styler formatting Package: BreastSubtypeR Commit: 0fb6775cf7105ccdfeac0f78d671c8220fa00a07 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:43:21 +0200 Commit message: Before styler formatting Package: BreastSubtypeR Commit: f462a35c15affb83307240678fdb8b5c31f1e1af Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 15:06:41 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: d58720a8654c148543e56efe3c8504e50f7a06f9 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Fix LaTeX errors, @importFrom issues, deprecated mutate_at(), tightened Mapping() Package: BreastSubtypeR Commit: 8cab29a01c0412be9b9a83d9c729c77b273c03f9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:33:33 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 2909f655c9c2686e9c562762e27c7cb78eb63544 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Merge pull request #97 from yqkiuo/BranchQiao Fix LaTeX errors Package: BreastSubtypeR Commit: f1d92deeed7ff76170c4ba8a70d0ac75e0dab7eb Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:28:10 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 9112d81e8538f3debb6c101255008486d052c326 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-12 19:39:12 +0200 Commit message: Merge pull request #96 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 977c1a7f7a5dd3700b51fe154e0a9509d6a960b1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 19:38:48 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: b2ba716538df0e23e684ec1118866c96560cab9b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:14:24 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: e25016431d3c00bfd81d941f4b8a71a2b7357ba1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:07:19 +0200 Commit message: v1.1.3 Merge branch 'BranchQiao' of github.com:yqkiuo/BreastSubtypeR into BranchQiao # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. Package: BreastSubtypeR Commit: 0f3624d0ed05aa4d2f2cb9759acb59d815fea297 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:04:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 8a340b6a4117f80791ae664c5741a0fe8627c9c3 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 15:44:48 +0200 Commit message: Fix BreastSubtypeRobj to include only the object itself (exclude environment variables) Package: BreastSubtypeR Commit: f969bcf09e03aa226de3839a68cf76cc01011ef3 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 14:52:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 693c829f364caedb2161a940d196d1830bd19d87 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 10:21:35 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 8582fb3b897e60ecc6da91040e32b42b19641154 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 17:06:26 +0200 Commit message: Added publication badge Package: BreastSubtypeR Commit: bd0b6cab935e607efd4bb001e3b75b02b37cc1fe Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:47:02 +0200 Commit message: Fixed bug: When running BS_Multi() omitting the first method; Minimal fix (drop nothing after removing row_id) Package: BreastSubtypeR Commit: 234ccbe269d45bd2c407358b711253629fe59203 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:12:28 +0200 Commit message: Polishing README.md & Vignette Package: BreastSubtypeR Commit: b3d5c232a32097ee9b4f83908a9c89f6ca621be8 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:41:14 +0200 Commit message: DOI update and text Package: BreastSubtypeR Commit: bacb13657f301643a682a3fcd7e82a22091a3b6c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:01:14 +0200 Commit message: Added DOI, Updated exported with version info, method, etc Package: BreastSubtypeR Commit: 787b3119148e345c0b2d4fa8638b3d6dd37600ee Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 19:17:32 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: c856d8dc615f688ae8f5d27eeb47ab297ead6b11 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:36:22 +0200 Commit message: Delete .github/workflows/sync-to-forks.yml Package: BreastSubtypeR Commit: 8d235ce12beccf9d394146a458ae135fec2f0fb3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:18:15 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: ad15f75e9de9028eb6d93fb5efb3ca05220ce975 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:04:51 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 917d62c7bc428fc67ff97c513022feb210fed94c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:58:05 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 9258dd1803aac507ecae1ec05d30a55c7c91827c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:54:22 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 8864ea4a8bda1bee1b6496aaf185e8bb76af5257 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:57 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 71735535741a019e7ba9299e47783038edbd3714 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:00 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f165c7df5636588c76360b10a42e792e9bf53614 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:50:26 +0200 Commit message: Create sync-to-forks.yml Package: BreastSubtypeR Commit: f2d85acb23f2c38ec3b3062fbab841c29115d38e Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:47:46 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 792bc0ab92f80b7405d69c45516dd131ffd7663c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:43:18 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 99d3102b66482953013f265d00464c8c3a4c2b25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:34:13 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 212e09ee660df8daaffea11a7af00d53321895aa Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:04:17 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 7cea1e782fedda5fef57f559c77dc39db8aceb9d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:56:40 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f33f344a6b0d06d3de393a783a23383e4ef5cac4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: adccaf9e7d8ce2b6234a1960e93e5d1543d98e09 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:31:34 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: a9e9e80f2f1063aae332963e474ea2f5804487b7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:27:58 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 4151dfa20943c89acdd55c5e1dec18a03da01e2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:14:01 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 1ab513bde94a41e4ab34856ca5e4f5ba5a6413e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 15:59:19 +0200 Commit message: Create sync-to-org.yml Package: BreastSubtypeR Commit: f9f0ea202177840660c02d39e203f67d4003e2cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:09:58 +0200 Commit message: Added description for new example dataset (TCGABRCAobj), updated the BreastSubtypeRobj with the 3 new medians info, tiny text improvements Package: BreastSubtypeR Commit: 056545172113202bb55a0ea0c2918851096fa0f2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:05:10 +0200 Commit message: Created a new example dataset (TCGABRCAobj) from TCGA-BRCA with Raw Counts, and similar results as OSLO2EMIT0obj Package: BreastSubtypeR Commit: 6de103db09589a53624341851237a8f547684ceb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:02:19 +0200 Commit message: Updated BreastSubtypeRobj with 3 more published medians Package: BreastSubtypeR Commit: 6acd15688f6e60db4e1f2ef151c103e865ce5663 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:00:19 +0200 Commit message: Guard docalibration, Improve External calibration, UX, and minor text improvements Package: BreastSubtypeR Commit: 8f7e3790ac94fead82f77e6564d87c542fcf5097 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 11:11:22 +0200 Commit message: Fixed error in BS_Multi() in AUTO Mode, when ssBC has <50 PAM50 genes: Add safe row-aligning cbind helper, made RORgroup() tolerant to missing ESR1/ERBB2 rows, and made BS_Multi() assemble results by PatientID Package: BreastSubtypeR Commit: 06bd9bce269ca12b4ca9f052f3d81cd730212a68 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 21:20:25 +0200 Commit message: Fixed the issue with pre-loading third-party libraries before initializing the Shiny app, Updated Help files Package: BreastSubtypeR Commit: ee560564150a7a5f11c00e8750583438a6c084e6 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:55 +0200 Commit message: Updated NEWS.md with major changes Package: BreastSubtypeR Commit: abd132463b65390c813f04ea50c530fd4b058507 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:18 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 74b20b933030517c45e68826a469dd88d79aa0b9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:24:07 +0200 Commit message: Added a TCGA-BRCA subset, with clinical & annotation data, for testing the RawCounts normalization pipeline Package: BreastSubtypeR Commit: d4fedc4c9b2a241b2652e563c2300d423f787287 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:21:08 +0200 Commit message: iBreastSubtypeR: UX polish, AUTO explainer, export refactor, AIMS constraint & bug fixes Package: BreastSubtypeR Commit: fb7c21f7ebc4f50be7610c8c0a023036f1559358 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 13:24:32 +0200 Commit message: Include three pre-computed Medians (external) as an option to Shiny App Package: BreastSubtypeR Commit: d1a90080950c9b5ddcad737979d072bdc177e038 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 11:34:43 +0200 Commit message: ssBC fixes: No crashes when < 50 PAM50 genes, No accidental subtype calls when a sample’s distance row is all-NA, Won't error when a subgroup has zero samples, qCtr won't produce NaN from zero range Package: BreastSubtypeR Commit: 10644b50e4721efe7b0d9f65445d30e1fdcf5a26 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 10:05:57 +0200 Commit message: Add our reference to Mapping() & BS_Multi() Package: BreastSubtypeR Commit: 5ea0dd73f932fbdd278f4e299de7270698d855c1 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 23:10:17 +0200 Commit message: New preflight for AUTO to prevent errors, new customizations, included new polished text for PAM50 to guide users, and more Package: BreastSubtypeR Commit: 3b08eed750427d72842bec852ff85c2446138cbe Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 13:21:06 +0200 Commit message: Fix issue when HER2 missing and user runs AUTO Package: BreastSubtypeR Commit: 16b805c817e0b7e3883b1aa7defd6da04f6a57f4 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:20:14 +0200 Commit message: Included a Prelight check for ER/HER2/Tn status availability in Clinical data BEFORE Running subtyping, avoiding App crashing due to missing values Package: BreastSubtypeR Commit: f003e4ecbfadb6a2a293ff39d838581dea5a0086 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:01:32 +0200 Commit message: Synchronized changes in BreastSubtypeR_methods.R and NC_functions.R, Created a theme to match the logo, made things unified, text improvements Package: BreastSubtypeR Commit: a66b4796231c8054f2093c6795ca4e67f2cb04de Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 10:08:20 +0200 Commit message: Parker original when calibration=None, or external calibration returns error: Fixed by Making NA equivalent to "medianCtr" (sync eith Parker et al.), and -1 to No calibration. Also, avoid requiring PatientID for BS_parker() when hasClinical = FALSE, included extra controls for hasClinical in all NC functions, polished help text, corrected typos (also tried to correct the 2nd error for ssBC, when < 50 genes, but will work more on this and come back with another Commit) Package: BreastSubtypeR Commit: 53ca58ec99d200f998a8be6896bab45f47d789e3 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-05 19:36:25 +0200 Commit message: Major changes: Multi method with AUTO mode added, Description text for each method with Refs added, Subtype 4-class selection Package: BreastSubtypeR Commit: bdf3bf291b59939171d85ff61f895b2ffc222b8d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:18:47 +0200 Commit message: Fix UI so the drop down menus are easier to select Package: BreastSubtypeR Commit: c0ed93ab5eed4a965f478a0dcac17355f8f91501 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:01:42 +0200 Commit message: Changed HasClinical with a Tick box, included many controls to check whether TSIZE, NODE are available, added different help functions for GEX and Annotation, improved text, and more Package: BreastSubtypeR Commit: 277869bea9c0c7d2747370cc657b2e87cb4e7dd2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 14:59:23 +0200 Commit message: Replaced the T -> TSIZE Package: BreastSubtypeR Commit: fd063a60aa8db3651975e89237ddb398d62c1100 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:28:48 +0200 Commit message: Minor edit Package: BreastSubtypeR Commit: 31e6bbfa2c897aa87caa09254cd2d4d2074b790f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:25:40 +0200 Commit message: Renamed folder to Shinny->Sniny, renamed data files with clear names Package: BreastSubtypeR Commit: 5ef9dd73efdccab438ee51f1ea0441ac565ca984 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:20:19 +0200 Commit message: Fix server.R bug Package: BreastSubtypeR Commit: c4c205e993f8791683fddf05392533aadded4b75 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-04 11:49:00 +0200 Commit message: refine shiny Package: BreastSubtypeR Commit: 304cb68143558163b4dd070c2498631f62a650e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-04 10:40:17 +0200 Commit message: Merge pull request #95 from yqkiuo/main Merge pull request #94 from yqkiuo/BranchQiao Package: BreastSubtypeR Commit: 6cbc1cb1b18907119b3414e3c0dafec607480a99 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:27:20 +0200 Commit message: Merge pull request #94 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 298458b861686b4ed9bfa17c070e5ffea513f3dd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-02 08:27:00 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: a50d8d4c3bea22f65836df6d099b269da685d8c2 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:25:43 +0200 Commit message: Merge pull request #93 from yqkiuo/main v1.1.2 Package: BreastSubtypeR Commit: 65b18fd8734f90e579fff40e53bbc51799b2c4ad Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:28 +0200 Commit message: Merge pull request #92 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5d09b44a5785c08a10d3d652d2a01db94678a1de Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:21 +0200 Commit message: Merge branch 'main' into BranchManos Package: BreastSubtypeR Commit: 8f4056fc16de285798c18e8c36e5399e5cd1fd23 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-01 10:18:12 +0200 Commit message: Merge pull request #91 from yqkiuo/BranchQiao v1.2.2 Package: BreastSubtypeR Commit: e11ffcd934d71dd5ee42c3816cabf93b997e6c64 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-01 10:17:53 +0200 Commit message: v1.2.2 Package: BreastSubtypeR Commit: 0969e8fa4d71d310d1d2f58c788af7a94566de25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-31 22:18:46 +0200 Commit message: Merge pull request #90 from yqkiuo/BranchQiao v1.1.2 Package: BreastSubtypeR Commit: c575280eed4e562e90ba6b9b7a6675353e532725 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-31 22:18:25 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: 031beb8e23f96e6f4894f56b550dd49d0c2a729b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-29 16:04:28 +0200 Commit message: Updated code to include separate cut-offs for ERpos & ERneg, as well as separate cut-offs ER(pos/neg)/HER2 (independent of HER2 status) based on the above cut-offfs. Note: The combined cut-offs will be released in the next submission Package: BreastSubtypeR Commit: 93ba44156f95a90bb74440d472157107e5ef0908 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 20:13:37 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: efee177e7f94d079d424ad79467615a63ce71698 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 2c6cfcacdc3550df0916ecb54833275bf2b9f04f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: d0154df0200108179568a150e1487e592a34e20a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 6a0be72275efbb8b9828b8765834d1ce97521134 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 3cf5afd43c31eeec90045902e6a082d82013bbf7 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: e91120bb63753900c47f80206b0662aef090c98a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: c09d132b8993a81ad16143b2ddbd5fb6b6f36f8b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 18:32:39 +0200 Commit message: Updated NEWS.md, BreastSubtypeR_methods.R, and minor updates to Utilities.R and data_doc.R Package: BreastSubtypeR Commit: 10f36184b66a9a0703d4296c9311b5ed1fc03e23 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 15:16:50 +0200 Commit message: Shiny app normalization clarification Package: BreastSubtypeR Commit: 24740ca0d3f45e43e674d247778b8e003871361c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:57:22 +0200 Commit message: Replaced the adaptive filtering as it was producing a reduced gene list for NC-based methods. Instead I introduce the calculation of UQ in the positively expressed subset and apply those calculcated factors to the full matrix. Package: BreastSubtypeR Commit: 347114047eeba2318371d4245043ae1d3b6bce86 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:34:21 +0200 Commit message: Include adaptive gene filtering so UQ normalization can work under real data Package: BreastSubtypeR Commit: f3bd9cdae36176a3857de89fac0c794bd8df369b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 16:29:18 +0200 Commit message: RawCounts test code include & help files updated Package: BreastSubtypeR Commit: c248d0fe615e9d6e3f4401bb6658908341de9208 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 16:07:29 +0200 Commit message: Shiny app: added descripted text Package: BreastSubtypeR Commit: 52bea350827dc0fba939551f50149d60acb3887b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 15:12:56 +0200 Commit message: Updated text in overview files Package: BreastSubtypeR Commit: 5b87399978a5d1cca09a82d5249a2b8863a553ea Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 15:10:09 +0200 Commit message: CITATION added Package: BreastSubtypeR Commit: e8fcac0bcab82793b586f5ffc8c930a0002ac609 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-21 11:29:40 +0200 Commit message: Merge pull request #89 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 0c75bf90f3070408ec5a156edf84b9c0bc70250b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:29:14 +0200 Commit message: update new features Package: BreastSubtypeR Commit: a99a93e94a90d6a715d64daedbe2e1f886f87917 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:27:58 +0200 Commit message: update new features Package: BreastSubtypeR Commit: c9f28c19c39695ad8a84ee4aa929c352be00e229 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 18:11:51 +0200 Commit message: Merge pull request #88 from yqkiuo/BranchQiao Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: e4a62355017220fe89ec8ea09376a0a56060de7c Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 18:11:26 +0200 Commit message: Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: 1993ab3e50725d01e8980a00eeaec8f0b0b766c4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:48:10 +0200 Commit message: Merge pull request #87 from yqkiuo/BranchQiao 1.1.1 Package: BreastSubtypeR Commit: 5d928ed37d8d0f47dd0392057846c43dc12e3dea Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:47:44 +0200 Commit message: 1.1.1 Package: BreastSubtypeR Commit: 52faaf9d7980c6d36524bcabbdcffe1f0fb92a0a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:39:51 +0200 Commit message: Merge pull request #86 from yqkiuo/BranchQiao 1.0.1 Package: BreastSubtypeR Commit: 35eef13e343edd2f9c6a1c26d780c97f470ac6c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:38:55 +0200 Commit message: 1.0.1 Package: BreastSubtypeR Commit: 6abaf3b4ae3d1772babec19c83d49c04728daa06 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-27 09:49:16 +0200 Commit message: Merge pull request #85 from yqkiuo/BranchQiao general update Package: BreastSubtypeR Commit: 453e9aac8dc81b86987e53e60659f2c97f6ba403 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-27 09:48:42 +0200 Commit message: general update Package: BreastSubtypeR Commit: 226607c2ae42706346a1e8911d1f2f82a5ca1490 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 19:12:11 +0200 Commit message: Merge pull request #84 from yqkiuo/BranchQiao v1.1.1 Package: BreastSubtypeR Commit: d773d4401e93ec12006f4e79122cbee8247d80d7 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 19:02:45 +0200 Commit message: v1.1.1 Package: BreastSubtypeR Commit: e74e86a2cfdf6daf92ed180095d27619cd45cd54 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:44:06 +0200 Commit message: Merge pull request #83 from yqkiuo/BranchQiao Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: fd30082d86b34d3ced41b7a7c385e01448c19794 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:41:43 +0200 Commit message: Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: 74145000a4ce350ca0e787fe5c459b79318b3edb Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:25:01 +0200 Commit message: Merge pull request #82 from yqkiuo/BranchQiao Bug fixes and minor improvements Package: BreastSubtypeR Commit: 1a5cb6636acfbd2ad1fc7c290bfba875dd2b22b0 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:24:35 +0200 Commit message: Bug fixes and minor improvements Package: BreastSubtypeR Commit: 4a895b8a8a149e0199b85eeaa19b6769dd8382df Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:27:17 +0200 Commit message: Merge pull request #81 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 4a03138457415f0164139373ee34038bd07ad300 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:21:40 +0200 Commit message: Update DESCRIPTION Package: BreastSubtypeR Commit: 856c6f8f91de5339988cf4c315bcaf96247f37d5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 10:39:20 +0200 Commit message: general update Package: BreastSubtypeR Commit: e35db8756a5fa3f30bf4addbeacd58145589e16b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:18:47 +0200 Commit message: general update Package: BreastSubtypeR Commit: 2e60c2222d3e9fdf48d3262ba087b447a95119a9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:03:00 +0200 Commit message: general update Package: BreastSubtypeR Commit: 7cfcfe95b2761178d17cc2af122f61883e7dc666 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:50:06 +0200 Commit message: update general Package: BreastSubtypeR Commit: b30131f2c073711d4b42e38af49bef1849da20c5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:48:53 +0200 Commit message: Update RawCounts para Package: BreastSubtypeR Commit: 6fa4d83d00b30727be9b1d4fd3798015fad0442a Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:32:10 +0200 Commit message: debug ROR Package: BreastSubtypeR Commit: ba045196fcd4a3bff148b3497a82f3f87d6bb324 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:31:55 +0200 Commit message: refine "-1" in parker.original Package: BreastSubtypeR Commit: b5e6254539fd38e41109056b2ddff7d36e0f9c19 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:15:41 +0200 Commit message: refine "-1" in parker.orignal Package: BreastSubtypeR Commit: bc7d097164cb411bfc4b40d5513073ae1bac35d8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:39 +0200 Commit message: 0.00.0 Package: BreastSubtypeR Commit: 5d966c161e4cdae464dd16d48421f6d5a4e26461 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:30 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 81f77832a0d7f8f5b8b70403616fe165ff96862d Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:08 +0200 Commit message: debug data type Package: BreastSubtypeR Commit: 8471668b9b9b43c3e27a87faa458488a8fba7f05 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:56 +0200 Commit message: debug BS_Multi Package: BreastSubtypeR Commit: 01fa8b576ca237667ed8a792477638cd4b023dbd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:34 +0200 Commit message: clear author Package: BreastSubtypeR Commit: a86f573778ed992a3d2dbb698b4c9c00a15619c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:20 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 00d2b9c5d71c6830e845dcddcb810b9640666207 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:33:01 +0200 Commit message: debug AUTO Package: BreastSubtypeR Commit: 8b3f7c2ef2d45cf772511a7290ba0a31baa43b62 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:32:46 +0200 Commit message: debug bad PCAPAM50 Package: BreastSubtypeR Commit: c70f4c9b0d64da1940659ae9a826d8221be05a32 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 09:32:30 +0200 Commit message: debug PCAPAM50 </div> </div>
Add the median to summarize_genes() over summaries Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Add summarize_genes() for one row per gene summarize_genes() summarizes annotated regions by gene, using the gene annotations with a gene ID. Each region counts once toward a gene and once toward each of its annotation types, and a region annotated to several genes counts for each. Output is wide by default (n_regions, n_, category counts for 'by', and mean and sd of 'over' columns), or long with format = 'long'. Also document that read_annotations() returns the custom annotations, which can be combined with others using c(), and that annotatr_cache is a session-only registry separate from the disk cache. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> </pre> </div> Package: annotatr Commit: 016b7c3dda475df556dcb9d0d4dc235fde59b8ba Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 22:00:04 -0600 Commit message: Merge pull request #71 from rcavalcante/disk-cache build_annotations() rebuilt every annotation on every call (about 30 s for the hg19 gene annotations). It now caches each built annotation and each downloaded file on disk with BiocFileCache, so later calls load them in seconds. For example, hg19 promoters + exons go from 15.6 s to 1.7 s. - The cache is in tools::R_user_dir('annotatr', 'cache'); options(annotatr.cache = ...) overrides it. - Each annotation type is cached separately, so any combination reuses earlier builds. - Cache names include the annotatr version, and for gene annotations the TxDb/org package versions (or the EnsDb), so updates cause a rebuild. - A cached file that can't be read is removed and rebuilt automatically. - Downloads are retried 3 times, partial downloads are never cached, and all URLs use HTTPS. A partial UCSC download broke scmeth's examples on the kunpeng2 release builder. - New: cache = FALSE in build_annotations(), list_cached_annotations(), clear_cached_annotations(genome), and ?`cached-annotations` with a troubleshooting guide (stale or corrupted entries, failed downloads, disk space, cluster home directories, SQLite locks, AnnotationHub's own cache). The vignette gains a "Caching Built Annotations" section. - Requires R >= 4.0 (for tools::R_user_dir) and imports BiocFileCache, which AnnotationHub already installs. Tests use a temporary cache and never touch the user's cache. The build tests use cache = FALSE so they still test the sources. 9 new cache tests, most of them offline. Tested with docker/check.sh (Bioconductor 3.24 devel): 258 tests pass, 0 skipped. R CMD check 1 NOTE (existing). BiocCheck 0 errors. Version bumped to 1.39.5. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Package: annotatr Commit: 220f05aa8f59411b18a84a059ce97fe1f06420e2 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 21:34:39 -0600 Commit message: Document the cached-annotations value, and run cache examples Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 2acd68023efc02d40f1e2bb110d99e41de0b7522 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 21:26:59 -0600 Commit message: Cache built annotations and downloads on disk build_annotations() rebuilt every annotation on every call, e.g. about 30 s for the hg19 gene annotations. Now it saves each annotation it builds, and each file it downloads, with BiocFileCache, and loads them later in seconds. Cache names include the annotatr version, and for gene annotations the TxDb and org package versions, so updates cause a rebuild. A cached annotation that can't be read is removed and rebuilt. Add cache = FALSE to build without the cache, list_cached_annotations() and clear_cached_annotations() to manage it, and ?`cached-annotations` with a troubleshooting guide. Downloads are retried 3 times and use HTTPS, since a partial UCSC download broke scmeth's examples on a release builder. Tests use a temporary cache, and the build tests use cache = FALSE so they still test the sources. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: BreastSubtypeR Commit: d06478442c1f3eaf941660e3a5514ed35ea9b41d Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-25 09:56:18 +0800 Commit message: Merge pull request #140 from JohanHartmanGroupBioteam/maintenance/maintainer-1.5.3 Transfer the maintainer role to Emmanouil G. Sifakis; bump to 1.5.3 Package: BreastSubtypeR Commit: 188a931c3d1cd9400b3201c2441358352d25290c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-23 09:33:58 +0000 Commit message: Transfer the maintainer role to Emmanouil G. Sifakis; bump to 1.5.3 DESCRIPTION Authors@R: Emmanouil G. Sifakis takes the "cre" role, Qiao Yang keeps "aut"; author order unchanged. man/BreastSubtypeR.Rd carries the Maintainer line that roxygen derives from Authors@R. NEWS records the change and the repository's move to the JohanHartmanGroupBioteam organization. Version 1.5.3 so that Bioconductor devel rebuilds with the new maintainer address. No code changes. Package: annotatr Commit: ff431152e18e1ad6189c3b5114d47d8290aa16af Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 21:15:26 -0600 Commit message: Merge pull request #70 from rcavalcante/test-overhaul Moves the tests to testthat 3rd edition and makes them independent of each other and of file order. Tests: - Files renamed test-.R; no context(). Shared data comes from functions in helper-fixtures.R instead of top-level objects. - Custom annotations use unique cache names. The BED4/BED5 read_annotations() tests passed only because an earlier test had cached the entry they checked. - Assertions compare values (expect_named, expect_setequal, expect_length, expect_contains) instead of expect_equal(all(...), TRUE), and check contents (coordinates, strands, IDs, scores), not just classes. - Plot tests build each plot with ggplot_build(), and some check the plotted data. - Build tests are back. Light tests (hg38 CpGs, hg19 FANTOM enhancers, hg19/mm10 GENCODE lncRNA) run whenever online, including on Bioconductor's builders. Full tests (gene and CpG annotations for all 15 genomes, hg38 lncRNA, lifted-over enhancers, chromatin) run with ANNOTATR_FULL_TESTS=true, which docker/check.sh sets. check.sh also keeps downloads in a persistent annotatr-cache volume. Fixes found by the new tests: - plot_categorical() with the default fill = NULL failed when drawn. It is fixed, and the All bar no longer triggers a ggplot2 warning without fill. (Backported to RELEASE_3_23 as 1.38.2.) - org.Dr.eg.db was missing from Suggests, although danRer10/danRer11 gene annotations need it. Tested with docker/check.sh (Bioconductor 3.24 devel): 227 tests pass, 0 skipped, ~3 min for tests and ~7 min total. R CMD check 1 NOTE (existing). BiocCheck 0 errors. Version bumped to 1.39.4. 🤖 Generated with [Claude Code](https://claude.com/claude-code) </pre> </div> Package: annotatr Commit: 2b24c09ab881f7441b4dc6a4f012a5ebdd371746 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 21:07:19 -0600 Commit message: Suggest org.Dr.eg.db, needed for danRer10 and danRer11 gene annotations Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 02134cc5afdad01933177b4591849f0ccc721087 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 20:51:41 -0600 Commit message: Build basicgenes and cpgs per genome in the full tests Building every gene annotation type for every genome ran out of memory in an 8 GB Docker VM. Only the gene model and CpG sources differ between genomes, so test those per genome, and the other gene annotation types once for hg19. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: a8511f7ebad475a279b74808ca182be26897398a Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 20:43:59 -0600 Commit message: Overhaul tests for testthat 3 and fix plot_categorical() with no fill Move to testthat 3rd edition, and rename the test files to test-.R since they no longer depend on file order. Shared data comes from helper-fixtures.R. Custom annotations use unique cache names, fixing tests that passed only because an earlier test had cached the entry they checked. Assertions compare values, e.g. expect_named() and expect_setequal(), instead of expect_equal(all(...), TRUE). Plot tests now build the plots with ggplot_build(). This found that plot_categorical() with the default fill = NULL failed when drawn; fix it, and map the All bar to a column so it isn't dropped without fill. Restore the build tests: small downloads run whenever online, and full builds for every genome run with ANNOTATR_FULL_TESTS=true, which docker/check.sh now sets, along with a persistent download cache. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> </pre> </div> Package: annotatr Commit: 50820a27a6907b9117c4abcb13f85f63b662e2dd Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 20:21:42 -0600 Commit message: Merge pull request #69 from rcavalcante/deprecate-randomize Deprecate randomize_regions() in favor of a background comparison Package: annotatr Commit: 09af749e4addbdd4602a8d4866b3b64bccb137d4 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 20:16:06 -0600 Commit message: Deprecate randomize_regions() in favor of a background comparison Regions placed uniformly at random across the genome are a poor null model: real regions come from a much narrower set of locations, so most data look enriched in genic and CpG annotations. Deprecate randomize_regions() and point to annotating a background of the regions the data could have come from, or regioneR::permTest() and regioneR::resampleRegions(). summarize_annotations(), plot_annotation(), and plot_categorical() now label annotated_random as "Background" instead of "Random Regions". The examples, tests, and vignette compare DM regions to all tested regions. Also fix the allow.overlaps documentation, which controls whether random regions overlap each other, not the input regions. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: ab795d19f14a4c80116f8cd5b8c3011bf7ca9215 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 20:07:14 -0600 Commit message: Merge pull request #68 from rcavalcante/docker-check Add Docker-based Bioconductor devel check Package: annotatr Commit: bb5c6c454ec3a9e29d7810976372e2339e39e0ef Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:18:57 -0600 Commit message: Add Docker-based Bioconductor devel check docker/check.sh runs R CMD build, R CMD check, and BiocCheck on the committed HEAD in a Bioconductor devel image with annotatr's dependencies preinstalled. Dependencies added since the image was built are installed at check time. Use --rebuild to refresh the image. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: ec750310fa1cb27af75186f72efb400e9c6ffb42 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 19:45:17 -0600 Commit message: Merge pull request #67 from rcavalcante/lncrna-gencode Fix hg38/mm10 lncRNA annotations by downloading from GENCODE Package: annotatr Commit: ea699780298650a09d66c8eff0c3d61ce22985b3 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:39:26 -0600 Commit message: Fix hg38/mm10 lncRNA annotations by downloading from GENCODE AnnotationHub removed its GENCODE resources, including AH75123 (hg38) and AH49550 (mm10), on 2026-04-28, so hg38_lncrna_gencode and mm10_lncrna_gencode failed. Download the same GENCODE releases directly over HTTPS, and move hg19 from FTP to HTTPS. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 0d593dc6eabebb817c27162c1003b90e1764c722 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 19:36:20 -0600 Commit message: Merge pull request #66 from rcavalcante/oviariramb2 Add support for sheep (ARS-UI_Ramb_v2.0) as 'oviariramb2'. Gene annotations come from the Ensembl 113 EnsDb in AnnotationHub (AH119381), so tx_id and gene_id are Ensembl IDs. CpG islands come from the UCSC GenArk assembly hub. Sequences use UCSC-style names (chr1, ..., chrUn_*). Package: annotatr Commit: 86641326dc4047c9762fd9878876840fd5024d66 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:17:58 -0600 Commit message: Version bump Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 9781edf27897d6c77bd3f2e4b09ab5827f4af05a Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 18:57:30 -0600 Commit message: Add sheep (ARS-UI_Ramb_v2.0) as builtin genome oviariramb2 Sheep has no TxDb.* or org.*.eg.db packages, so gene annotations are built from the Ensembl 113 EnsDb in AnnotationHub (AH119381), with Ensembl tx_id/gene_id and symbols from the EnsDb. CpG islands, chromosome sizes, and chromosome aliases come from the UCSC GenArk assembly hub, and sequences are renamed to UCSC-style names. Genomes like this are registered in GENARK in R/utils.R. The TxDb code path is unchanged; hg19 gene annotations are identical to devel. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: methodical Commit: b39d98d2d4ac504cbd6f80a62b999406f694e993 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-25 02:16:59 +0100 Commit message: Merged changes Package: methodical Commit: 20761f4370f86ba9ee7211e4b47c6b3c63a607e4 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-25 00:50:46 +0100 Commit message: Updated liftover function Package: methodical Commit: 02ddeb7f0e3a2c852b0adcff0211e492dc0cdf3c Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-22 20:12:54 +0100 Commit message: update Package: methodical Commit: a39fa2dd4b3c1a417085c4a09ec882b3bc738522 Author: Richard Heery <richardheery@gmail.com> Date: 2026-08-27 17:25:10 +0100 Commit message: update Package: methodical Commit: ffc716b54e4118b1ced24b811211a8788e304a92 Author: Richard Heery <richardheery@gmail.com> Date: 2026-05-01 15:20:44 +0100 Commit message: Readded vignettes Package: methodical Commit: 464c57e15c8f97f697d8ce9373316805f6e73be1 Author: A Wokaty <andres.wokaty@sph.cuny.edu> Date: 2026-04-28 09:02:10 -0400 Commit message: bump x.y.z version to odd y following creation of RELEASE_3_23 branch Package: methodical Commit: 4215fb6e084e162ff4dd4201b1d4420d9c2533db Author: A Wokaty <andres.wokaty@sph.cuny.edu> Date: 2026-04-28 09:02:10 -0400 Commit message: bump x.y.z version to even y prior to creation of RELEASE_3_23 branch Package: methodical Commit: d169b576deecb57d9477aabf9196922e04e885ea Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-27 17:22:40 +0100 Commit message: Final commit for 3.23 Package: methodical Commit: 81883848e66b52382f58d48cd4ee465be8189db3 Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-24 22:47:39 +0100 Commit message: Fixed vignettes Package: methodical Commit: a4d3e6da701f57033dfd6ca9feba64d3c1c11a6a Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-27 21:38:18 +0100 Commit message: Final commit for devel Package: lcmsPlot Commit: f451123907b59cd6a330688b933ff3fd6c2bd25e Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 22:11:26 +0100 Commit message: feat(features): name XChromatograms features from row names Package: RiboDiPA Commit: cf0c36801194370381bd3ceb90f5b2594e1247a1 Author: Dr. Ji-Ping Wang <jzwang@northwestern.edu> Date: 2026-09-24 20:46:05 +0000 Commit message: Fix vignette build error: convert Bioconductor objects via as.data.frame() before as.data.table() Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01LiK5WUAPmNmkHCv3HPRNog Package: lcmsPlot Commit: 18f10a9c7dfe282c08aa33c53c23566a192a7a6b Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 20:46:18 +0100 Commit message: feat(features): name manual features from row names or a feature_id column Package: scRNAseqApp Commit: 9421c5d26e1bf497251c6ccfb6526e9f612852c4 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-24 15:27:00 -0400 Commit message: Update the gene table only when file changed. Package: leapR Commit: 28136ae57197bd5fa892860b5017d5c9f1f0bb2c Author: Sara JC Gosline <sara.gosline@pnnl.gov> Date: 2026-09-24 10:42:52 -0700 Commit message: updated Package: geneslator Commit: b62f543f5874c5167105c705e32d15f0da8d4181 Author: Giovanni Micale <gmgmicky@gmail.com> Date: 2026-09-24 19:11:07 +0200 Commit message: Updated README and vignettes Package: DropletUtils Commit: ba4152de3596abef3bd69f9ce441aec8ea4c912e Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-25 02:56:55 +1000 Commit message: Set SVT leaves to NULL for empty columns when loading MatrixMarket data. (#133) Mostly backports of the updated C++ code and associated tests from crio. Package: DropletUtils Commit: ea9a299b36c52a71f305d612a97d6a69a20e25d0 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-24 18:21:09 +1000 Commit message: Merge remote-tracking branch 'upstream/devel' into devel Package: DropletUtils Commit: b423c0fafe7271b173317b407a8538bbbcbede5c Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-07-29 23:53:07 +1000 Commit message: Shorter chunk size for sparse data and indices for easier streaming. Package: SparseArray Commit: 9a0e93056f05879a15057e3d597d0102068f09bb Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-24 09:04:25 -0700 Commit message: some clarification about SVT leaf representation Package: lcmsPlot Commit: 14a5af5c83db317bc0d44e2b32ba8acfb54ab66f Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 16:23:45 +0100 Commit message: feat(features): use featureDefinitions rownames as feature identifiers lcmsPlot derived its own xcms::groupnames-style MT labels from mzmed/rtmed, discarding the row names featureDefinitions() already carries. Feature identifiers now come from those row names, so renaming the rows is enough to get meaningful labels onto a plot. Identifiers matching no feature are now reported with a warning naming them, instead of being dropped silently into an empty plot. </pre> </div> Package: scRNAseqApp Commit: eb1f132e925ec26574be9a7055b51b67cf60b2cf Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-24 11:17:02 -0400 Commit message: Remove the duplicated notification for search. Package: rhdf5 Commit: 1c6ed01eaf8682004f647a15a200df1d0f55b0f6 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:21:40 +0200 Commit message: Fix duplicated logo Package: rhdf5 Commit: cab7d0212538b900883c3c6a80f27710cd80ebc5 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:03:23 +0200 Commit message: Add link to de.NBI survey Package: Rarr Commit: 56ddfff1ac32f46151b215a015cbc00b5d77744e Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:16:34 +0200 Commit message: Add deNBI funding acknowledgement and survey in README Package: Rarr Commit: accfb8f20be9b7fefe76e1b35a531704bcc8960b Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 11:06:37 +0200 Commit message: Use vectorized .store_check_exist() call Package: Rarr Commit: cbf89cd3891e3e0cdfeb474aaf153d1324b43d96 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 11:05:56 +0200 Commit message: Define is_structured once Package: Rarr Commit: 87389fada7676ae09ce5bfd3a3a4e74ba3708836 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 10:47:50 +0200 Commit message: Register bfloat routine Package: biomaRt Commit: 3e1a0768933f6c3e00895e02119e4f6e36050dac Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:05:20 +0200 Commit message: Add link to de.NBI survey Package: ISAnalytics Commit: 6e03f52a7925332d38562e8c2501425e92f89184 Author: francescogazzo <francesco.gazzo@gmail.com> Date: 2026-09-24 12:19:37 +0200 Commit message: Update collision filtering and bump devel to 1.23.2 Package: distinct Commit: 7ec08672fd2177c33c85779a82ab12deb8232802 Author: Simone Tiberi <simone.tiberi@unibo.it> Date: 2026-09-24 11:57:02 +0200 Commit message: T_obs added in results Package: distinct Commit: e749b22cf8c3c8eb925d3a293b916b7c11e75605 Author: Simone Tiberi <simone.tiberi@unibo.it> Date: 2026-09-24 11:49:37 +0200 Commit message: bug fixed in distinct_test Package: MsBackendMetaboLights Commit: 1b126b45bede3db584a54168617397078cc5c789 Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com> Date: 2026-09-24 11:52:26 +0200 Commit message: Merge pull request #26 from rformassspectrometry/jomain Add random sleep breaks to reduce failures on build systems Package: MsBackendMetaboLights Commit: c28ee3bc500c3e2a3764932bae457431cac07563 Author: Johannes Rainer <johannes.rainer@gmail.com> Date: 2026-09-24 08:45:39 +0200 Commit message: Add random sleep breaks to reduce failures on build systems - Adding/changing to random sleep times aiming at reducing the recurrent failures on the Bioconductor build system (most likely due to rate limitation from MetaboLights). Package: cellNexus Commit: 67fa18ce068ae3e0fe84da1f942a6d9a1138e052 Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 14:44:48 +1000 Commit message: Merge pull request #159 from myushen/master fix website examples Package: cellNexus Commit: 3ab2cd31f7d4a7acc40758abeed48bc0f3d8435c Author: myushen <mengyuan.shen@outlook.com> Date: 2026-09-24 14:25:14 +1000 Commit message: fix website examples Package: cellNexus Commit: 4719fb49b937acd11c9f898275920555e094c65d Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 13:37:28 +1000 Commit message: Merge pull request #153 from MangiolaLaboratory/copilot/rename-join-census-table Soft-deprecate `join_census_table()` in favor of `get_census_metadata()` Package: cellNexus Commit: 8b217f783900d3107ab0d07c0d9b57083a1e6c77 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-09-24 11:54:08 +1000 Commit message: unit test Package: cellNexus Commit: 3e4d038b291bc9ba79f306456e63fa4660958d47 Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 10:44:58 +1000 Commit message: Merge branch 'master' into copilot/rename-join-census-table Package: cellNexus Commit: 9aca6c192558b021c1c41b9071564d8daf4d7814 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-08-27 12:12:50 +1000 Commit message: soft deprecate since 0.99.27 Package: cellNexus Commit: cd885c844de21fea70d10ee653fc9c95386b8bd5 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-08-27 12:08:50 +1000 Commit message: Merge remote-tracking branch 'origin/master' into rename-join-census-table merge from origin Package: cellNexus Commit: 13ffb5d261f878cacd79484700b35b9a964cef67 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:33:16 +0000 Commit message: Trim redundant mock assertion Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: abf37b553b5800c09ee3e9deb65ee9d5246d9ab4 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:32:37 +0000 Commit message: Verify Census helper mock before wrapper call Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: a4bf9cc52cf658c48d4f00fdfbdd55ec094f4484 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:32:04 +0000 Commit message: Exercise deprecated table argument compatibility Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: 4b46e68aebf2b38ce850298cc145bdf52c84d14f Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:31:37 +0000 Commit message: Correct Census deprecation test assertions Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: 1515648f80a96e03452c82ac5e602057710f512e Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:31:02 +0000 Commit message: Stabilize deprecation warning test Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: d2fd0cfdaad895c2e60be674d50076ad04cecf24 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:30:23 +0000 Commit message: Soft-deprecate Census join helper Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: e7ae2c78928ba1b3bbb6f575e117365976743d72 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:27:22 +0000 Commit message: Initial plan Package: mia Commit: 416de1c5a6b73b70f42571f8a3d36d0294dcb770 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-24 07:54:25 +0300 Commit message: Update documents and namespace Package: clusterProfiler Commit: 33b36f13f3729b099a8d6fc20694831b7a5c62d9 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 12:48:46 +0800 Commit message: fixed r check Package: LRDE Commit: 710586499a483617f94c2d665b87a03be62d6531 Author: Ziyang Liu <jacobleo773@gmail.com> Date: 2026-09-23 18:45:18 -0700 Commit message: Improve numerical stability and bump version to 1.1.2 Package: DOSE Commit: 5846d72fe047f1de66d506a21c117d400e4a3ef8 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:21:11 +0800 Commit message: fixed r check Package: DOSE Commit: 9011c8c053e345cdca45bf1edb93fe66b7f80417 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:14 +0800 Commit message: gseDisease() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family. Package: ReactomePA Commit: e295d309811933101f2e808814212d3244f5c6aa Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:10:04 +0800 Commit message: update docs Package: ReactomePA Commit: 586975c51fadc162d78418ff1132eddcb009b157 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:13 +0800 Commit message: gsePathway() exposes eps and forwards extra arguments, #47 gsePathway() was the only GSEA wrapper in the family missing both eps and ..., so eps could not be controlled and additional enrichit::gsea_gson() arguments could not be passed through. Both are now supported, matching clusterProfiler::gseKEGG(). Package: ReactomePA Commit: 396a55c38c765045b0309c6935b663dd334e7c3d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:03:02 +0800 Commit message: ReactomePA 1.99.2: seed argument and a faster prepareReactomeNetwork() - gsePathway() and nsePathway() expose an explicit seed parameter for reproducible GSEA results, aligned with enrichit::gsea_gson(). - prepareReactomeNetwork() no longer round-trips through graphite::convertIdentifiers()/pathwayGraph() per pathway; it builds a single UNIPROT->Entrez map up front and converts edges with vectorized lookups, keeping mclapply() parallelization over pathways. Output is unchanged (same nodes and edge values; node ordering may differ). Default cores is now 1 instead of detectCores(). Package: ReactomePA Commit: a9a8627182db7226655362793f6b6c22c25e8d7b Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-08-15 18:42:41 +0800 Commit message: parallelize prepareReactomeNetwork pathway conversion via mclapply The one-time Reactome network build converts ~2700 pathways serially in R (convertIdentifiers/pathwayGraph/graph_from_graphnel per pathway). The conversions are independent, so the loop now runs over mclapply() with a new 'cores' argument (default getOption('mc.cores', detectCores())); mclapply falls back to serial on Windows and preserves input order, so the resulting edge set - and hence the cached network - is unchanged. Measured on the GSE53757 demo: serial build ~35-41 min; parallel build 614 s at 16 cores and 655 s at 56 cores; output byte-identical to the serial baseline. Scaling saturates at ~4-5 effective cores because the graphite identifier conversion is hash-lookup-bound. Package: ReactomePA Commit: 13cb4b3cbc4616e214d63ee59a3e42bba48b0a4c Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-07-09 15:24:15 +0800 Commit message: nsea Package: ReactomePA Commit: 4edeca90aedb3afdaa29b838323bbdabad62c391 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-04-29 12:24:13 +0800 Commit message: update bioc version Package: meshes Commit: 5732c93b839f7f820eb4501e3cff468737bfa71a Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:09:48 +0800 Commit message: bump version Package: meshes Commit: e7498dc7737b09bffacef28a72d666693e7be51d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:14 +0800 Commit message: gseMeSH() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family. Package: meshes Commit: 01c764a9285d4c77e77ff630885b8a79077cff10 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:03:02 +0800 Commit message: expose a seed argument on gseMeSH(), meshes 1.39.2 Forward an explicit seed to enrichit::gsea_gson() so GSEA runs are reproducible, and apply pvalueCutoff to both pvalue and p.adjust inside the enrichit engine (requires enrichit >= 0.2.2). Package: GOSemSim Commit: 769cd22f90eec52f67039121c265462c701680ad Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 08:58:26 +0800 Commit message: update docs Package: GOSemSim Commit: ca626082247cbb24fb95b5098558b71b0592e2be Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 12:55:48 +0800 Commit message: computeIC: take the term universe from GO.db, not the shipped gotbl table computeIC() decided which terms to score from the `gotbl` table shipped in data/: goids <- unique(godata[godata$Ontology == ont, "go_id"]) That table was last rebuilt in 2021-07, so every term GO.db has added since then was given no IC at all, and the IC-based methods returned NA for it even though its descendants carry annotations and its IC is computable. This is issue #33, and the reporter's diagnosis ("a conflict between the pre-calculated gotbl.rda and the local version of GO.db") was right. Measured against the current GO.db / org.Hs.eg.db, the number of annotated terms that can actually be scored: ontology annotated before now gained BP 11293 11126 11293 +167 CC 1832 1787 1832 +45 MF 4777 4410 4777 +367 and nothing loses an IC. The missing terms also biased every other IC, because they were counted in the `sum(gocount)` denominator but could never contribute to an ancestor's descendant sum. Terms finite under both universes agree for 92-95% of entries with a mean absolute difference of 0.003-0.011; about 0.3% were overestimated by more than 0.5, all of them in the "too specific" direction, which is what the mechanism predicts. The universe is now names(getAncestors(ont)) -- exactly the terms of that ontology in the installed GO.db, root included, and already cached by onto_relation() -- unioned with the annotated terms, so a term the local annotation package still uses keeps its IC even if GO.db has retired it. The same root cause also affects the `gotbl` that the Wang method walks, where a term newer than the table scores 0 instead of NA. That is left for a separate change because fixing it means either regenerating the shipped data or building the relation table at runtime. test-ICMethods.R now asserts that every annotated term gets a finite IC. Package: GOSemSim Commit: 32be2e18cb86a9ef84f796e174a39a1ac7658513 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 12:32:22 +0800 Commit message: cache ontology mappings, and load Rcpp so the compiled IC methods work Two independent defects, found while fixing TCSS. getAncestors(), getParents() and getOffsprings() each rebuilt their whole mapping on every call -- AnnotationDbi::as.list(GOBPANCESTOR) costs about half a second -- while callers only ever pick out one or two terms with `[[ID]]`. A single geneSim() call rebuilt the same mapping hundreds of times. The mappings are derived from a source that is already cached (GO.db is static, load_onto() caches the OntDb), so they are now cached per ontology rather than per term. A 5x5 termSim on previously unseen terms drops from 2.5 s to 0.5 s, geneSim from 5.6 s to 0.6 s cold and 0.12 s warm, with byte-identical results. The cache holds about 85 MB for BP and 110 MB for all nine mappings. Separately, Rcpp was listed in LinkingTo only, so loading GOSemSim never loaded the Rcpp namespace. The wrapper generated by compileAttributes() instantiates Rcpp::RNGScope, which resolves enterRNGScope through R_GetCCallable("Rcpp", ...), so every Resnik, Lin, Jiang and Rel call failed with "function 'enterRNGScope' not provided by package 'Rcpp'" unless the user happened to attach Rcpp first. importFrom(Rcpp, evalCpp) was dropped in ea7b2028 (2016) and is restored here. No test reached the compiled code and the vignette only mentions those methods in prose, which is why this went unnoticed for so long; test-ICMethods.R now covers all four methods on three ontologies. The ontology cache is also covered: test-GO.R checks that each mapping is cached under the ontology and is identical to what GO.db holds. Package: GOSemSim Commit: 50c6bd241416e703074e5e8e2839cf2cafe7133e Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 17:17:24 +0800 Commit message: correct the scope of the TCSS degeneracy fix The previous commit described the degeneracy as "a cluster with a single member", but calc_maxIC() indexes `all <- IC[cluster]; all <- all[is.finite(all)]`, so the real condition is "exactly one member carrying a finite IC". A cluster with several members where all but one have infinite IC is equally degenerate, and the old `length(all) == 0` guard did not cover it. Re-measured with the correct criterion (swapping calc_maxIC in and out of the namespace in one process so both versions see identical input): - the set of clusters whose ICA changes equals the set with exactly one finite-IC member, at every cutoff and ontology tested (BP 1/2/3.5/4/5/8, MF 3.5, CC 3.2) -- so the change is confined to the degenerate clusters; - the defect was not BP-only. 300 random pairs, % scoring exactly 1: BP 99.3% -> 0.0%, MF 27.3% -> 0.0%, CC 98.7% -> 0.0%; - the counts are larger than the single-member count suggested: BP has 1 degenerate cluster at cutoff 3.5 but 5 at cutoff 4 and 1141 at cutoff 5; MF has 3 and CC has 3, and the CC set includes the CC root GO:0005575. Fix the NEWS wording and the code comment to match, and make the regression test assert on the finite-IC criterion rather than on cluster size. Package: GOSemSim Commit: 2df9985c372e931e89994d25fe84f483b50c01fe Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 16:49:30 +0800 Commit message: fix TCSS similarity collapsing to 1 for nearly every term pair A cluster with a single member has no internal spread, so normalising it by its own maximum IC made its ICA identically 1 regardless of how general or how specific that term was. GO:0008150, the root of BP, is such a cluster and is a common ancestor of every BP pair, so `max(sim_value)` in tcssMethod_internal() returned 1 for 99.7% of random BP pairs and `mgeneSim(measure = "TCSS")` was an all-ones matrix. Fall back to the global maximum IC for single-member clusters. The collapse is not specific to the root: scanning cutoffs shows GO:0050896 and GO:0046337 also become single-member clusters for BP, and GO:0052745 does for MF, so special-casing the root would only have papered over one instance. After the change, 300 random BP pairs give min 0.0004 / median 0.0234 / max 0.5296 with 0% equal to 1, and ica[["GO:0008150"]] drops from 1 to 0.000414 (= IC[root] / global max IC). Add a regression test and bump to 2.39.3. Package: GOSemSim Commit: 34c4ae3b85f10b9107ca6feffbd6e6eb0a0206db Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 12:17:51 +0800 Commit message: fix TCSS for terms belonging to multiple clusters GO is a DAG, so a term can have several meta-term ancestors and `tcssdata$clusid[[term]]` is then a vector rather than a scalar. Indexing `ica` with `[[` then attempts recursive indexing, which raises "subscript out of bounds" (or "recursive indexing failed at level 2" depending on which element is hit first) and aborts any TCSS calculation for the whole ontology. Subset the list of clusters with `[` instead. This restores the behaviour already present in the Bioconductor release (2.38.3); the devel implementation had regressed. Adds a regression test covering a term that sits in more than one cluster. Package: clusterProfiler Commit: a38e9201b8ee6ad6f64fc1a5bf691421efc9d928 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 04:39:17 +0800 Commit message: enrichMKEGG()/gseMKEGG() accept a GSON, #623 enrichKEGG() and gseKEGG() take either a species code or a GSON object, but the module wrappers only took a species code, so there was no offline route for module enrichment at all -- even though the download errors now tell users to build a local database. Passing a GSON raised an unrelated error from the organism mapper instead. Both now mirror the KEGG wrappers, including the "organism should be a species name or a GSON object" message. A GSON reports its own keytype, so @keytype is taken from it; the species path keeps returning "UNKNOWN" exactly as before. Also documents the GSON option on the KEGG `organism` parameter, which had never been mentioned for enrichKEGG()/gseKEGG() either. Package: clusterProfiler Commit: 285885443b912177daec101c606664b33b41cc37 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 04:21:19 +0800 Commit message: enrichGO(): restrict the annotation by evidence code, #160 Enrichment used every annotation in the OrgDb, including electronically inferred ones, so there was no way to avoid circular reasoning when the gene sets themselves came from in-silico evidence (dropping IEP for co-expression clusters) or to keep only curated annotations (dropping IEA). enrichGO() now takes `evidence`, appended last so positional callers are unaffected and threaded through both recursive paths. The filtered annotation is built by go_annotation_by_evidence() from a gene-centred select() of GOALL/EVIDENCEALL/ONTOLOGYALL, because the evidence code is a property of the gene-annotation pair and the previous term-centred mapIds() could not see it. Two semantics worth stating, both documented: the background changes with the annotation, so a filtered result is not a subset of the unfiltered one; and a filtered annotation is never cached, since the cache key is (organism, ont, keytype) only and reusing it either way would answer with the wrong annotation. A regression test pins the cache isolation down. Package: clusterProfiler Commit: fa71a3ef739a1ef44e695e69823126c94c703bdb Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 02:33:01 +0800 Commit message: fix: enrichGO() survives an unidentifiable OrgDb organism, #232 The cached-GO-data check compared the cached organism against get_organism(OrgDb) inside a bare if(). get_organism() returns NA for an OrgDb it cannot identify -- an AnnotationHub OrgDb, for instance -- and `if (NA && ...)` aborts the call with "missing value where TRUE/FALSE needed", which names nothing about organisms or caches. It bites on the second enrichGO() call in a session, because the first one populates the cache. The check is now go_cache_usable(), where every comparison goes through isTRUE() so an unidentifiable organism means "not cached" and the annotation is rebuilt. Extracting it also makes the cache-hit logic unit-testable without an OrgDb. Package: clusterProfiler Commit: a39c2f63d533e20d6c4d03fd3a35b18a418dd08e Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 02:14:56 +0800 Commit message: fix: Gff2GeneTable() reads Ensembl-style GFF3, #193 The function only looked for an NCBI/RefSeq `GeneID=` attribute. On an Ensembl GFF3 (which writes `gene_id=`) every extracted key was NA, and merging two all-NA key columns is a cartesian product: on the reporter's cat genome that is ~1.3M x 40k rows, which R refuses with "negative length vectors are not allowed". At small sizes the same bug passes silently, because unique() collapses the duplicated NA rows into a plausible-looking table of NA ids. Field names are now detected from the file: `GeneID` or `gene_id` for the identifier, and `gene`, `Name` or `gene_name` for the symbol. Detection requires an exact attribute key, because getGffAttribution()'s heuristic fallback also looks inside values and would otherwise return the identifier out of `ID=gene:ENSG...` when asked for `gene`. A file with neither identifier style stops with a message saying what is expected instead of merging on all-NA keys. Package: clusterProfiler Commit: 41dd01bb5c7a078bd19397131f06fd3db2d59bfc Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 01:38:26 +0800 Commit message: add_go_level(): expose the GO level of each enriched term, #793 GO enrichment results carried the term, its ontology and its statistics, but not how deep the term sits in the hierarchy, so users who wanted to keep a band of levels had to reconstruct GO depth themselves. go_level_map() now returns the GO id -> level map (1 = ontology root) built by breadth-first traversal of the GO.db CHILDREN graph; getGOLevel() is rewritten on top of it with identical output (verified against a pre-change baseline for BP/CC/MF at levels 1-6), and add_go_level() appends a `level` column to an enrichResult/gseaResult/compareClusterResult. The level is taken from the ontology each term belongs to, so ont = "ALL" results are labelled term by term. gofilter() and dropGO() had no test coverage; the new test file locks their keep/drop-by-level behaviour down. Package: clusterProfiler Commit: c117200bb63575df335911dcd478aa164dda528d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 23:52:42 +0800 Commit message: simplify() infers the GO ontology for enricher() results too, #369 The enrichResult method required x@ontology to be BP/MF/CC/GOALL, so an enricher() run over a GO collection (MSigDB C5 GO, a custom TERM2GENE built from GO annotations) had to have the slot assigned by hand before simplify() would accept it. The ontology is now inferred from the GO IDs exactly as for gseaResult (#753), and non-GO gene sets are still refused with a message saying so. Package: clusterProfiler Commit: e930b50044bf8bb4fb883ea940a631aceb57ff18 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 23:21:11 +0800 Commit message: simplify() a GSEA result whose gene sets are GO terms, #753 simplify() reduces redundancy with GO semantic similarity, so it needs the ontology of the terms. It only accepted x@setType in BP/MF/CC/GOALL, which rejected a GSEA run over a GO gene-set collection (MSigDB C5, a gson GO file, a TERM2GENE built from GO annotations) because @setType then holds the collection name. The ontology is now inferred from the GO IDs, with results spanning several ontologies simplified as GOALL; non-GO gene sets are still refused, with a message that says so. Package: clusterProfiler Commit: dc94b240c1a42333f111338f46fb3633df2271be Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 22:46:23 +0800 Commit message: warn when compareCluster() is given a non-character universe, #654 compareCluster() wraps each per-cluster call in suppressMessages(), which swallowed the underlying enrichment function's "`universe` is not in character and will be ignored" message. A numeric universe therefore looked accepted while silently having no effect. The guard is now raised once in compareCluster() itself, where it cannot be suppressed, with a regression test for both the non-character (warns) and character (stays quiet) cases. Package: clusterProfiler Commit: 61236b6fa01a7d6474152ed7043639596dae48d1 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:10 +0800 Commit message: gsePC() and gseWP() expose an eps argument Both wrappers now declare eps = 1e-10 and forward it through GSEA() to enrichit::gsea_gson(), matching GSEA(), gseGO(), gseKEGG() and gseMKEGG(), which already exposed it. Package: clusterProfiler Commit: 58559c7a5a9babe970d3a3dad5e9708efc42f70c Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 18:54:09 +0800 Commit message: fix enrichKEGG(organism='cpd') and report KEGG download failures clearly, #828 - gson_cpd(): use the 'compound' KEGG REST endpoint. KEGG retired /link/cpd/pathway, which now answers HTTP 400, so enrichKEGG(organism='cpd') and gseKEGG(organism='cpd') failed with an obscure download error. - kegg_rest(): report the failure where it happens, telling an unreachable network apart from an HTTP error status and from an empty response. These used to surface much later as an opaque error. - download.KEGG.Path() / download.KEGG.Module(): replace the is.null() guard, which could never fire because kegg_rest() never returns NULL, and stop with an actionable message when the downloaded annotation is empty or when the gene/pathway table shares no ID with the pathway-name table. Previously an empty annotation was returned silently and surfaced downstream as a misleading "No gene can be mapped", #146, #378, #561, #646. Package: SAIGEgds Commit: 29da3dd06bce9321bc520c75353e1c695057e0df Author: Xiuwen Zheng <zhengxwen@gmail.com> Date: 2026-09-23 19:12:31 -0500 Commit message: update vignettes Package: MSstatsBioNet Commit: 409e9d4503aa239c3c619270333853289d37d080 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-23 16:57:12 -0400 Commit message: feat(filterSubnetworkByContext): adjust filterSubnetworkByContext to exclude key words (#111) Package: scRNAseqApp Commit: e8a48756927b63b7b69b59294f8c81232e689203 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:44:42 -0400 Commit message: fix the wrong number when calculate phyper. Package: scRNAseqApp Commit: 758edbb8626a1d38afe3c8d58678b43f325195e0 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:40:08 -0400 Commit message: fix a issue for if no hyper pval available. Package: scRNAseqApp Commit: 78ef7925d099f040cfa9b1638934fb49d4adfc91 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:29:19 -0400 Commit message: using promise process to update the gene table. Package: scRNAseqApp Commit: b4e729e4d87012189f26cfd746a09ebc9a04d6db Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 10:24:03 -0400 Commit message: import phyper from stats. Package: scRNAseqApp Commit: 4d94c7a0270315c3aea67c41287313c86ffb5655 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 10:15:42 -0400 Commit message: add phyper pval for co-expression. Package: dmGsea Commit: 3b9c68c53791e27f0abc9e95a8f4e0c050b7d75a Author: xuz1 <xuz@niehs.nih.gov> Date: 2026-09-23 13:54:34 -0400 Commit message: bugfix Signed-off-by: xuz1 <xuz@niehs.nih.gov> Package: decemedip Commit: 3de0b135bed2595498482c4d13078d0bd65c313e Author: nshen7 <shenning1997@gmail.com> Date: 2026-09-22 20:54:10 -0700 Commit message: Fix Stan old array syntax for stanc3 (BioC 3.23 build failure) Package: quantMSImageR Commit: 9aaed9e03b28ef01d3b1c05dc834288f2d00753c Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:46 +0200 Commit message: Version 0.99.8 Pieces of one tissue, regions of interest, and the report arranged by level. matrixStats leaves Imports: it was declared but called nowhere, so every user installed a package the code never used. Package: quantMSImageR Commit: 25eacbf10d0f5075ad89ee2884a76103bdb23a65 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:34 +0200 Commit message: Document the regions work The vignette says what regions are for -- a transition that marks a tissue type, or a toxicity study where the regions are drawn high and low in the toxicant and the endogenous species compared between them, within one animal rather than across a group. It also describes the by-level report, and how to see a palette before choosing it. AGENTS.md is gitignored: agent scratch notes, not part of the package. Package: quantMSImageR Commit: d37c8c4b93a96e7f51343144cda5a5c17dcc519b Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:34 +0200 Commit message: Arrange the report by level, and correlate at one level only Sections 2, 3 and 4 are each drawn by sample and then by region, so the two are read the same way rather than the regions living in a tab of their own. The region masks take a section before the ion images, which move down a number. "auto" judges the heatmap encoding per view, on the rows that view actually has. A study without regions is unchanged, headings included: a level heading only appears when there is a second level to tell it from. Correlation names one level -- 'sample', 'roi', False or auto -- and only ever computes that one. It is the slowest section in the report, and a region holds a fraction of a sample's pixels, so auto correlates within the regions when a study has them and is off otherwise. True still means 'sample'. roi: unit is per sample or per region, not both: a comparison has a single unit, and two views of the same numbers invite reading whichever looks better. compare: keeps "both", where the two arrangements are different contrasts rather than the same one twice. Each box-plot panel carries its own key, and colours: region sets the region palette (any package palette, or a grDevices qualitative one), kept distinct from the groups'. Package: quantMSImageR Commit: bfa6a46540be7a5e08f37ded27d10a504d244d59 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:19 +0200 Commit message: Score each region against itself in contributionHm() too The region heatmap could only be drawn per feature, because contributionHm() had no notion of a block. That made "auto" pick the wrong panel wherever a study has few samples and many regions: one animal per group takes the per-sample encoding by sample, but by region its rows are sample x region, so a group can have six or seven of them -- exactly the case the contribution encoding exists for. It now takes sample_block, and inside a block both the z-score and the group mean are computed against that block alone. The hue is therefore "how this group's airways sit among all the airways", not "airways differ from parenchyma", which is what a panel scored across regions would mostly report. A feature flat within a block cannot be scored there and is drawn in na_col, even where it varies across the section. Package: quantMSImageR Commit: b18abc94cf8fc51323b0836eccf9b684dd9758b9 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:50:33 +0200 Commit message: Fix the region tests and the vignette's feature lookup The row-split assertions read @row_order_list, which a Heatmap only fills in when it is drawn -- it is empty on the object, so the expectations compared against nothing. The split a heatmap will use is in @matrix_param$row_split, which is what they now check: the block test asserts a, a, b, b against groups that deliberately alternate, so passing it means the rows really were split by region rather than by group. The vignette indexed a feature by name, but spectra() returns a matrix with no dimnames, so it takes the row number instead. Package: quantMSImageR Commit: 0ff2ab13a672a37c90034e11545dc2e36e994da3 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:39:14 +0200 Commit message: Document pieces and regions; regenerate the example sections The vignette gains a section on pieces of one tissue, one on labelling regions, and a worked example on the bundled sections: the label table, the region maps and a box plot with one point per section per region rather than per pixel. The YAML section documents the samples forms, including pieces, and what each roi: option can be set to. The example sections are regenerated with the regions the vignette and runExample() now show. Seeds are unchanged and the region code draws no random numbers, so the intensities are identical. AGENTS.md is build-ignored, and the micro sign in stitchAcquisitions() is written as a \u00b5 escape: R CMD check requires ASCII source. Package: quantMSImageR Commit: a623d0241889b76e05f8b5d49aa2f121348d953b Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:54 +0200 Commit message: Carry regions through a study and into the report A study picks regions up on its own: generateTxtImages() attaches roi_label and roi_id from each acquisition's roi_labels.csv, matched on (x, y) like the tissue mask, and they survive panel binding and stitching. Regions numbered within a piece are renumbered across the stitched sample, so two airway_01s become two airways. The YAML gains a roi: block -- enabled (auto), include_unassigned, compare, unit, heatmap -- and pieces: for a tissue acquired in several passes, each piece normalised and SNR-filtered against its own background before being joined. The report gains a regions tab: maps, box plots by compare and unit, an ROI_summary sheet, and a heatmap with one row per sample and region. That heatmap z-scores each region against itself (quantileHm's new sample_block), since scoring across regions would mostly report that airways and parenchyma differ, which is not the question being asked. The map is repeated above the ion images, where it says which blob is which. quantileHm() also no longer loses its sample names when a study holds a feature with no variance: the unscoreable column returned an unnamed vector, and apply() drops the names for the whole matrix when one result's differ. output: colocalisation: gains auto, off whenever a sample merges several acquisitions -- most pixel pairs would then cross acquisitions. Package: quantMSImageR Commit: 9311401b6304a67f07b4b1fa3cf4bbcde84b66b7 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:39 +0200 Commit message: Add labelROIs() for regions within the tissue Run after selectTissuePixels(): it shows the ion image of a chosen transition across tissue pixels only, then loops draw -> name -> "add another". Several regions can share a label, since a section holds many airways, and each is numbered as it is drawn (airway_01, airway_02, ...) so it keeps its own identity while the label is what a study compares. Regions are saved per acquisition as roi_labels.csv beside the tissue mask, which is never touched, and copy_to writes the same file to the other panels over the same area. Re-running adds to them; overwrite = TRUE keeps the old file as a dated backup. The feature picker is shared with selectTissuePixels() rather than copied, and the bundled example sections gain two "a" and two "b" regions each so the downstream half can be shown without a drawing device. The regions differ because of where they sit on the existing intensity gradient; no value was adjusted to make them. Also splits the given names in Authors@R, so the citation reads "Smith MJ" rather than "Smith M". Package: quantMSImageR Commit: 52f47f09842bf4eecb4e8e7d214c84ec7d87a532 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:27 +0200 Commit message: Place pieces of one tissue by stage position A tissue too large for one acquisition is imaged in pieces, and those pieces are one sample: kept apart they count twice in every group summary, and because they agree with each other they look like a reproducible effect. readMRM() numbered each acquisition's pixels from its own first pixel and threw the stage coordinates away, so every piece started at (1, 1) and stitchAcquisitions() could only report that they overlapped. Its documentation claimed Waters coordinates were absolute, which stopped being true the moment readMRM() re-based them. readMRM() now keeps x_stage and y_stage (mm) alongside the grid indices, and stitchAcquisitions() places each piece where the stage recorded it: above, below or beside, in any order, gaps left empty. Pieces must share a pixel size; each is moved to the nearest position on a common grid and the largest shift is reported. Overlap is still an error rather than an average. Objects without stage positions keep their own coordinates and say how to get them. combineMSIs() fills a pData column that only some objects carry with NA, since stage positions and region labels are legitimately absent from some samples. Package: rhdf5 Commit: c72d938a7bd397d148e623a7c0f12e6b3865de1b Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 16:41:00 +0200 Commit message: Bump version Package: rhdf5 Commit: fe55afb12dd1583d7f6f58e236e3d85872da3e1f Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:40:28 +0200 Commit message: Document .matrix() methods removal Package: rhdf5 Commit: f1ad6e28ba024bdcfeede3cb1b3b89f92bb081e5 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:38:30 +0200 Commit message: Remove .matrix() methods and let them auto dispatch to array method Package: rhdf5 Commit: dc8ef2bbced3bfc17f95b284fb0b2981d20427f4 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:22:12 +0200 Commit message: Document on.exit change in NEWS Package: rhdf5 Commit: 2b34f2d0097aaf547999b5be0deeef35031694e8 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:20:32 +0200 Commit message: Use on.exit() more consistently to close Package: rhdf5 Commit: bbfebbf34a184471451df03fab4dfa74a29f1dd9 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:08:44 +0200 Commit message: Mention dead code removal in NEWS Package: rhdf5 Commit: aa7669dbe22003b61182dc3cd266b948ae055ad0 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:07:58 +0200 Commit message: Remove dead code in h5writeAttribute.array() Package: rhdf5 Commit: d1f0dc156114f8494ced58811c01fe1f092b1648 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:57:43 +0200 Commit message: Fix incorrect copy/pasted error messages Package: rhdf5 Commit: 81d91768bd5bc3a86b9c720a1a3c1681ad0851ae Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:43:10 +0200 Commit message: Remove extra call to H5loadConstants() Package: rhdf5 Commit: e28ea4ec812cfd7c63e15101b401a3aa12fac5f1 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:23:01 +0200 Commit message: Ensure .Call() always includes PACKAGE Package: rhdf5 Commit: 4f18f262fed53b25edbbd5db47138059a6a7a6cb Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:16:45 +0200 Commit message: Mention h5set_extent() fixes in NEWS Package: rhdf5 Commit: 98c8a7581553b43f8aa62575958b0a595394bb84 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:16:16 +0200 Commit message: Fix h5set_extent issue with dataset handle Package: GSVA Commit: 545a96a07fba745d24b021cde157b570597a7109 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 16:34:55 +0200 Commit message: Remove dependence on BiocSingular Package: aracne.networks Commit: d000659130672ee12ffa5a287616ffe16c334eb2 Author: federicogiorgi <federico.giorgi@gmail.com> Date: 2026-09-23 15:51:57 +0200 Commit message: Point to the Zenodo record 22918956 Fill in the Zenodo record (doi:10.5281/zenodo.22918956) hosting the networks and document the CC BY-NC-ND 4.0 license of the data files. Package: aracne.networks Commit: d768d15947c70f95dc353c4e3a21da480ffccdc3 Author: federicogiorgi <federico.giorgi@gmail.com> Date: 2026-09-23 14:47:27 +0200 Commit message: Move the networks to Zenodo The regulon data sets are no longer bundled in the package: they are hosted on Zenodo and retrieved with the new getRegulon() function, which caches them locally with BiocFileCache and verifies their MD5 checksums. listRegulons() lists the available networks. This brings the package size well below the 100 MB limit of the new build system. - documentation of the 25 networks merged into ?regulons - vignette converted to R Markdown - added unit tests - Authors@R replaces Author/Maintainer Package: GSVA Commit: 87cd4d7cdcae92c251c9b53c7f759c38b4ab1ed4 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 15:31:13 +0200 Commit message: Bump version Package: GSVA Commit: 9c1eb50150a6aaee271512838ad8739b3bb130fe Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 15:22:44 +0200 Commit message: Merge pull request #276 from rcastelo/275-average-method Average method for enrichment scores calculation Package: GSVA Commit: 9e68f27aaa3d02a7d4c28792365b50d35dc1b5aa Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 14:50:43 +0200 Commit message: Replace checkIdentical() for checkEqualsNumeric() to allow C unit tests pass across different platforms Package: GSVA Commit: 5f21614dc2ee103338d887a39e119f4fbbbf90d9 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 12:29:14 +0200 Commit message: Added C implementation of the average method, and its corresponding unit tests. For performance issues, genes within genesets are internally ordered after mapped to features, this required regenerating regression test for PLAGE since SVD flipped sign in values due to the different input order Package: GSVA Commit: 87cfe5db164c95b66710094c215285fbf17995a6 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:46:28 +0200 Commit message: Merge branch 'devel' into 275-average-method Package: GSVA Commit: cc12f1d01a63d0123a48e3fb3d576c61a5f6a14d Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 14:42:36 +0200 Commit message: Fixed namespace issues and unit tests Package: GSVA Commit: 6881306e155fe38933ff8cf6d3ec9be94b9b382d Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 12:16:49 +0200 Commit message: Add unit tests for CLR and average method Package: GSVA Commit: 730ce29c9eb3a6d8b94c1c327d96451241681fd5 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-21 17:07:11 +0200 Commit message: Added first version of the average method for calculating enrichment scores Package: fenr Commit: 78a5a1207281ef37881d399f562be49f4a4af6d2 Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 13:02:11 +0100 Commit message: Merge branch 'main' of https://github.com/bartongroup/fenr Package: fenr Commit: 83a93c2fe6a5bb8748799c1f369153a651713bea Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 13:00:33 +0100 Commit message: Reverting some changes Package: fenr Commit: 0274549e7ba96519bf153ae6736593f62e5f666a Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 12:01:32 +0100 Commit message: Version 1.11.3 Package: vsn Commit: cdb80675e45236c2f57a2b41d4f98f4f2d6814b2 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:27:07 +0200 Commit message: Bump version Package: vsn Commit: b5d9c153c5300b3209bd0bcef2285b4386731398 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:26:58 +0200 Commit message: Mention README and pkgdown site in NEWS Package: vsn Commit: fb67d77e139bbf2d24f020fcc99a770650124cb1 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:25:59 +0200 Commit message: Set up pkgdown Package: vsn Commit: 4e31e610b6c6afccfe348d107f05e277101f01be Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:25:04 +0200 Commit message: Add minimal README with deNBI survey Package: sesame Commit: 2acabdce8fbdd4fb9675db1fd76d60d05792be04 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 22:06:41 -0400 Commit message: 1.31.5: fix readControls column naming; qualityMask takes a custom mask readControls() built the control data.frame positionally: colnames(ctl) <- c('G','R','col','type') over a frame whose signal matrix has four columns, so Color_Channel and Type were cbind-ed past the end of that name vector and arrived unnamed, while `type` silently took a signal column. Downstream, controls(sdf)$Type was a vector of integers, so negControls()'s grep("negative", ...) matched nothing and detectionPnegEcdf() failed in ecdf() with "'x' must have 1 or more non-missing values" on EPIC and HM450 -- the platforms whose controls arrive through readControls() rather than as SigDF rows. The columns are now named explicitly. This was found from the C side, where it had been mistaken for an annotation divergence for two days. With it fixed, detectionPnegEcdf agrees between the two implementations at max|diff| = 0.00e+00 on EPICv2, MSA, EPIC and HM450. qualityMask() gains `platform` and `mask`, so a custom or combined-array mask can be passed in directly instead of being bolted on with addMask() after the fact -- the case that comes up for arrays built from two manifests. README: the two implementations are named and versioned. The R package is SeSAMe v1 and stays on the 1.x series; the C command line is SeSAMe2 on 2.x. They are parallel, not sequential. The conda line also said `sesame-cli`, which has not been the package name since 0.4. R CMD check: Status OK, vignettes built and re-run. Package: mia Commit: 859de8cd0be1bdd40982b6cd189141c84cb359cd Author: Giulio Benedetti <giuliobene2000@gmail.com> Date: 2026-09-23 14:27:37 +0800 Commit message: Clarify study subjects in ADHD microbiota profiles (#828) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: mia Commit: 751d24e22c26aaccc6ec7be1ece37540fc2eab37 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-23 08:57:53 +0300 Commit message: Add Rdpack references (#797) Signed-off-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: mia Commit: 3c4fd9e80ecf788464a2726cf15e64cbd0aeede2 Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Date: 2026-09-22 11:27:29 +0300 Commit message: Convert MAE to TreeSE and back (#810) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Package: OMA Commit: 1ff85f15276db0d08c8305d788808bc3d713d066 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-23 13:07:47 +0300 Commit message: Simplify importing Package: OMA Commit: f19c0abb3874a6386f4693912c59f010dc5ec331 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-22 15:05:08 +0300 Commit message: Fix rendering Package: OMA Commit: 1d6f339fb23ebbdd1a58d089605f547fb76413d1 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-22 14:31:13 +0300 Commit message: Fix rendering, update support forum address Package: OMA Commit: 3f130bdb5a124835ec56391806571a9a6954963e Author: jagadeesh <2400040120@kluniversity.in> Date: 2026-09-18 16:37:10 +0530 Commit message: docs: Add comprehensive Rarefaction section to transformation chapter (#825) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Co-authored-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <tvborm@utu.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 1a65548fafa7a1d699b74cabccff2cb6b8b74f3f Author: Rasmus Hindström <56149499+raivo-otus@users.noreply.github.com> Date: 2026-09-18 09:20:36 +0300 Commit message: docs/clarity improvement to mia::summarizeDominance (#852) Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Co-authored-by: TuomasBorman <TuomasBorman@users.noreply.github.com> Package: OMA Commit: bcf4b79324d7db13573f7d75f1921324f098bf37 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:11:59 +0000 Commit message: feat(ci): add whitespace stripping to style workflow (#864) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: be708a734fe6980f7fdb08cd7d29c0bf68d85d47 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:06:30 +0000 Commit message: fix(community_similarity): use official vegan docs (#872) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: d51543f698e697431a375bb5ee52ea224490b2a1 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:03:41 +0000 Commit message: feat(ci): add dependabot (#865) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 79c94b838aca89ac79e9544310302b5528c9a0b8 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 05:57:47 +0000 Commit message: bump(deps): actions/cache@v4 to v6 (#874) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 4e1978be84a4efc4813759e6f1a2d6aa262ba265 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-18 08:52:51 +0300 Commit message: Use scaled fitted values for DMM drivers (#881) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 7bd2fc8e6da903e0640182842001f3fd42f5a210 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-17 15:48:42 +0300 Commit message: Clarify exercise instructions across the book (#886) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 7ad1b506261f780a42bc9ffa0655f10f91047bb3 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-17 15:33:57 +0300 Commit message: Add tree visualization reference (#889) Package: OMA Commit: 0e655914be48d7af2242a012deeb8354ec31f033 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-08-08 19:29:22 +0300 Commit message: Suppress cheatsheet startup messages (#878) Package: beachmat Commit: 7fe7dc234ea2fe69bf8f4c711525428539033652 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 15:32:49 +1000 Commit message: Switch to DelayedNoOp to support all alabaster.matrix no-op subclasses. This saves us having to list all of the individual subclasses. Package: alabaster.matrix Commit: ff91f9ff04b310f74232613787d6abe1411769aa Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 14:54:50 +1000 Commit message: Introduce a no-op base class to catch all of our weird seeds. In particular, packages like beachmat don't have to add a specialization for each of the no-ops subclasses, they can just check for the DelayedNoOp class. Package: alabaster.matrix Commit: 998568738d4d76e3073b732c24eaf2a9d79f650a Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 14:26:07 +1000 Commit message: Implement ToBeRealizedArray class for fine control of delayed operations. Package: SparseArray Commit: fab50cb7a6f6b1c5735dd1f19b05b94e04503dcf Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:57:43 -0700 Commit message: some edits to SparseArray-abind.Rd Package: DelayedArray Commit: ef3f02a7227a0e6a07736601081925f2fccb43a9 Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:26:39 -0700 Commit message: requires S4Arrays >= 1.13.1 Package: DelayedArray Commit: 28a0ba92ed413f575dd5839324e9892eb8f840c2 Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:02:40 -0700 Commit message: DelayedArray 0.39.7: Add abind() method for DelayedArray objects Also: - Remove the rbind(), cbind() and bindROWS() methods defined for DelayedArray objects. These methods are now replaced by more generic methods defined in the S4Arrays package for Array objects that are all based on abind(). - Add coercion from array/matrix to DelayedArray/DelayedMatrix. This coercion is equivalent to calling the constructor function DelayedArray() on the object to coerce. Having this coercion work has the effect of making rbind() and cbind() work on a mix of DelayedMatrix objects and ordinary matrices. This partially addresses issue #100. Package: scDiagnostics Commit: bee3ff588074c8e26c3b15b12610f23b7c19acdc Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 21:24:22 -0400 Commit message: Silence scran deprecation warnings and tolerate missing Suggests, bump to 1.7.15 Two failures on the first run against Bioconductor 3.24 / R 4.6: R CMD check reported significant warnings in the examples on all three platforms. scran 1.41 deprecates its HVG helpers in favour of scrapper, so every modelGeneVar()/getTopHVGs() call - including the fitTrendVar() that modelGeneVar() calls internally - now signals a deprecatedWarning, and rcmdcheck runs with error_on = "warning". Add an internal muffleDeprecation() that muffles only the deprecatedWarning class, leaving genuine warnings alone, and wrap the six calls in processPCA(), detectAnomaly() and calculateReconstructionError() with it. The three examples that call scran::getTopHVGs() directly wrap it in suppressWarnings() instead, with a comment saying why. This is a stopgap: the HVG selection needs to move to scrapper before scran makes these functions defunct. The macOS job additionally failed with "Packages suggested but not available: 'scRNAseq', 'celldex'". Neither is used by anything that runs during the check - they appear in documentation prose and inst/script - and both currently fail their own Bioconductor 3.24 builds, so set _R_CHECK_FORCE_SUGGESTS_=false rather than fail this package's check over them. Package: scDiagnostics Commit: 964640ff9a5c7728f24141ce53575c0840966fd8 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 20:38:25 -0400 Commit message: Target Bioconductor devel 3.24 / R 4.6 in CI, bump to 1.7.14 The matrix was pinned to Bioconductor 3.22 / R 4.5, two release cycles behind: 3.23 is the current release and 3.24 is devel, which is what the Bioconductor build system checks this branch against. Point all three jobs at 3.24 / R 4.6 (the pairing BiocManager's version map requires), swap the Linux container for bioconductor/bioconductor_docker:devel, and move the RSPM mirror from jammy to noble to match that image's Ubuntu 24.04 base. Also refresh the cache keys and the check-results artifact name, which still referenced RELEASE_3_22/3_19; the new keys additionally force a cold cache so no 3.22-era binaries are restored. Package: knowYourCG Commit: 9a7cce4c69f010992c7694da610eab786d07b443 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 18:58:22 -0400 Commit message: Point users at KnowYourCG v2, and fix three dead links This package is KnowYourCG v1 and stays on the 1.x series. The C implementation is KnowYourCG v2, binary `kycg`, and nothing here said so. Framed as succession, not as a wind-down, and that distinction is the point. An earlier draft of this put "This package is in maintenance; active development continues in kycg" into DESCRIPTION -- the field that renders on the Bioconductor landing page. This package sits on an open Core Team deprecation watch (#4, "Bioconductor failure and risk of deprecation"), so publishing that it is in maintenance would have handed them the justification. A neutral pointer says the same true thing without inviting it: the project is not declining, it is on its second implementation. Three places, because they reach different readers. DESCRIPTION is the only one an installing user sees, rendered on the landing page. The README is for GitHub visitors. Sequencing.Rmd names v2 where a reader is most likely to want it -- that vignette's workflow is what v2 does natively over YAME stores. The URL is in angle brackets, the same convention the DOI in that sentence already uses; a bare URL is what R CMD check objects to. Each says plainly that the two are parallel implementations rather than an upgrade path: one is an R package, the other a command-line tool, and there is no upgrading from one to the other. Separately, three dead links. `R CMD check --as-cran` runs a URL liveness check that a plain check skips entirely, and it found Sequencing.Rmd linking to https://zhou-lab.github.io/YAME/docs/summarize.html (twice) and .../docs/pack_unpack.html -- both 404. YAME's documentation is a single page now and those paths no longer exist, so all three point at https://zhou-lab.github.io/YAME/ instead. Package: scDiagnostics Commit: 89c6ed709d444d28439a7c791cb151b11faca8fb Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 19:54:35 -0400 Commit message: Make BiocCheck's deprecation check resilient to bioconductor.org outages, bump to 1.7.13 BiocCheck's first check downloads checkResults//bioc-LATEST/ meat-index.dcf for both the release and devel branches, and a failed download is a hard error ("HTTP 504 Gateway Timeout" -> bfcadd() failed -> "not all 'rnames' found or unique"), which took down the Linux and macOS jobs even though the package itself was fine. Pre-populate BiocCheck's own BiocFileCache with up to three attempts before running BiocCheck, and only if bioconductor.org is still unreachable pass `no-check-deprecated` so that one check is skipped instead of failing the whole build. </pre> </div> Package: scDiagnostics Commit: 816fa92698fa534abefc3cc0f75df2319b8f11f6 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 17:32:41 -0400 Commit message: Disable public RSPM on macOS/Windows to fix root cause, bump to 1.7.12 The libomp install in the previous commit didn't fix stringdist's identical dlopen failure - same byte-for-byte error, meaning the install had no effect. Searched prior reports of this exact failure (tidymodels/tune#1199, Genentech/rdborrow#73/#74): the real cause is that r-lib/actions/setup-r configures Posit Package Manager (P3M) as the default macOS repo, and P3M's macOS arm64 binaries are compiled with OpenMP enabled. This runner can't resolve those OpenMP symbols at runtime (SIP strips DYLD_* for protected binaries, so even a correctly installed libomp isn't reliably picked up) - CRAN's own macOS binaries are built without OpenMP and never hit this. Set use-public-rspm: false on the "Setup R from r-lib" step so macOS (and Windows, already passing, no expected impact) resolve packages from CRAN directly instead of P3M, which should fix this for any OpenMP-linked package in the dependency tree - not just the three (RhpcBLASctl, isotree, stringdist) hit so far - rather than continuing to patch them one at a time. Left the earlier source-install and libomp workarounds in place; they're harmless if this makes them redundant, and there's no upside to stripping proven/plausible fixes before confirming this one actually resolves it on CI. Package: scDiagnostics Commit: 3aba0f79435c543deb4c129e486f16e5e92c6ba4 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 16:59:49 -0400 Commit message: Install CRAN's official libomp on macOS CI, bump to 1.7.11 The last two fixes patched RhpcBLASctl and isotree individually, but BiocCheck::BiocCheck() now hits the identical failure via one of its own dependencies (stringdist): unable to load shared object '.../stringdist.so': dlopen(...): symbol not found in flat namespace '___kmpc_barrier' Patching each OpenMP-linked CRAN package one at a time as it's reached doesn't scale - the actual root cause is that this GitHub Actions macOS runner is simply missing the libomp build that CRAN's macOS binaries are compiled against (documented at https://mac.r-project.org/openmp/; Homebrew's libomp installs to a different path and doesn't fix this). Installing it there via the official recipe should let CRAN's normal (faster) binaries load correctly for any OpenMP-using package, not just the two already patched. Left the RhpcBLASctl/isotree source-install workarounds in place since they're already confirmed working - no reason to touch proven fixes while chasing this. Package: scDiagnostics Commit: 58cf3022aee073ef86bf0e5695fe41dd4a701ec9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:24:46 -0400 Commit message: Also force isotree from source on macOS CI, bump to 1.7.10 RhpcBLASctl fixed the first macOS OpenMP dlopen failure, but the same issue exists one layer up: isotree's own CRAN macOS binary (isotree.so) fails to dlopen with "symbol not found in flat namespace '___kmpc_barrier'" - a Clang/LLVM OpenMP runtime symbol, same root cause (CRAN's macOS binary built with OpenMP support that isn't resolvable on this runner), just a different dependency in the chain. Applied the identical source-install workaround to isotree. Package: scDiagnostics Commit: 7809c44d4bc5e698aeb4d67f24e79535cfe513c9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:00:00 -0400 Commit message: Force RhpcBLASctl from source on macOS CI, bump to 1.7.9 Ubuntu and Windows now pass under the Bioc 3.22/R 4.5 bump (previous two commits), confirming those fixes. macOS still fails, but differently and on all 4 vignettes uniformly this time: Error: .onLoad failed in loadNamespace() for 'RhpcBLASctl' dlopen(.../RhpcBLASctl.so, ...): symbol not found in flat namespace '_omp_get_max_threads' RhpcBLASctl is a hard Import of isotree (detectAnomaly() calls isotree::isolation.forest()), so its namespace loads unconditionally. CRAN's macOS binary for RhpcBLASctl references an OpenMP runtime symbol that isn't resolvable on this GitHub Actions macOS runner - a known class of issue for R packages built with OpenMP support on macOS. Building from source instead compiles without OpenMP (Apple clang has no -fopenmp by default), so the resulting library never references that symbol. Added alongside the existing Matrix/irlba source-install workaround in the same step, which addresses the same kind of macOS binary incompatibility. Package: scDiagnostics Commit: 3386bcb54d27441922472dd08b49d1b1d786bb37 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 12:06:16 -0400 Commit message: Anchor SingleCellExperiment/SpatialExperiment Rd links, bump to 1.7.8 R CMD check now fails with error_on = "warning" on the Bioc 3.22/R 4.5 CI (bumped in the previous commit): "checking Rd cross-references" reports a genuine broken link (merfish_reference_data.Rd's \linkS4class{SpatialExperiment} doesn't resolve) plus 36 files whose \linkS4class{SingleCellExperiment}/{SpatialExperiment} links are missing package anchors - both promote the check from NOTE to WARNING under the newer toolchain. \linkS4class{} was reintroduced repo-wide by a September 17 commit ("docs: use \linkS4class{} for SingleCellExperiment roxygen links", for brevity) after an earlier commit had already fixed this exact issue with explicit \link[pkg:target]{text} anchors. Restoring that anchored form and re-running roxygen2 to regenerate man/ resolves it; verified with a full local R CMD check matching the CI invocation (0 errors, 0 warnings, 1 unrelated pre-existing note). Package: scDiagnostics Commit: b520b294d72834042d23e6c4c887c6c194847544 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 10:33:30 -0400 Commit message: Bump CI to Bioconductor 3.22/R 4.5 to fix vignette build failure COVIDCaseStudy.Rmd was failing to build on CI (macOS/Windows) with "unable to find required package 'Seqinfo'" inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause: covid_reference_data/covid_query_data were generated on current Bioconductor (3.22), where the Seqinfo class was split out into its own standalone package. check-bioc.yml was still pinned to the two-year-old Bioconductor 3.19/R 4.4, whose GenomeInfoDb predates that split and whose repos don't contain a 'Seqinfo' package at all, so the class tag baked into the serialized data can't be resolved. Two earlier attempts (adding set.seed() to rule out RNG state, then patching a subset of the shipped .rda files) missed this because neither addressed the actual CI environment being out of date. Bumped the workflow's matrix (r/bioc versions, container image, cache keys) to 4.5/3.22, matching the environment covid_reference_data was actually generated on; verified locally that a full R CMD build (fresh install + vignette rebuild) succeeds under this Bioc/R pairing. Package: scDiagnostics Commit: 02de5cdca9c45682ebceab3b3f7d6231d8cb8054 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:40:12 -0400 Commit message: Handle reference cell types with too few cells or absent from query detectAnomaly() previously assumed every reference cell type had at least 2 cells (to fit an isolation forest) and, when a query dataset was provided, implicitly assumed every reference cell type also had matching query cells. Neither is guaranteed: - A reference cell type with fewer than 2 cells can't fit an isolation forest; now skipped with a warning instead of erroring. - A reference cell type entirely absent from the query is a normal outcome (e.g. after subsetting/filtering the query), not an error; now reported with an empty query score vector instead of failing in predict(). Also fixes a latent bug where a cell-type subset reducing to exactly 1 row would silently drop to a vector (missing drop = FALSE), which would have broken the isolation forest input shape. Adds tests covering both edge cases. Package: scDiagnostics Commit: b0fc15de1e279c3a6e2d44c12837dd3667d35743 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:36:38 -0400 Commit message: Fix stale Seqinfo class tag causing vignette build failure, bump to 1.7.6 COVIDCaseStudy.Rmd failed to build on CI with: Error in .requirePackage(): unable to find required package 'Seqinfo' triggered inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause, confirmed via verbose updateObject() output: covid_reference_data's internal Seqinfo class was tagged with its old home package ("GenomeInfoDb", from before Seqinfo was split into its own standalone Bioconductor package), so a sufficiently new Bioconductor tries to auto-migrate it on load - and that migration path apparently isn't reliably available in a fresh CI environment. Fix: call updateObject() on serialized objects at data-generation time so the bundled .rda ships with the current internal representation baked in, rather than deferring to a lazy per-load migration. Applied to the new COVIDData.R/MERFISHData.R scripts (whose source data came from an external, older serialization), and audited/fixed the same latent issue in the pre-existing reference_data/query_data/qc_data (which had the identical stale tag despite already shipping in the package) and their generation scripts, so this doesn't resurface on a future regeneration or Bioconductor version bump. zeisel_/covid_/ merfish_ vignette datasets were already correctly tagged and are byte-identical after regeneration. Package: scDiagnostics Commit: 44dd05d3749412c865e5446d44a4520bd24df370 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:13:03 -0400 Commit message: Fix non-deterministic vignette failure and bump to 1.7.5 COVIDCaseStudy.Rmd and MERFISHCaseStudy.Rmd called detectAnomaly()/ calculateGeneShifts() (which use isotree::isolation.forest(), a randomized algorithm) without ever calling set.seed(), unlike the other two vignettes. This is the most likely cause of the CI vignette re-build failure on COVIDCaseStudy.Rmd after pushing 1.7.4 - a build without a seed picks up whatever RNG state the session happens to be in, which can land on the isolation forest / gene-shift edge cases seen elsewhere in this codebase. Verified against 15 different seeds plus a full local R CMD build (fresh install + vignette rebuild, not just devtools::load_all()) with no failures. Bumps to 1.7.5 rather than re-pushing 1.7.4, since 1.7.4 already has a recorded (failed) build on Bioconductor/GitHub. Package: MSstatsBioNet Commit: 0b9e21718beccbc1fb3847792481f8bda11b7ef5 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 18:27:25 -0400 Commit message: feat(decomposeSubnetworkIntoHierarchicalTopics): Enable NMF hierarchical decomposition (#110) Package: knowYourCG Commit: 5dbb3d5b4f6dcb4f6f54e4db6859b760358c9344 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 17:15:02 -0400 Commit message: Stop reaching the network when the vignettes and examples are built Three build-time downloads, all of the same two Zenodo files, none of them needed to show that the package works. The vignette one was failing outright. Sequencing.Rmd's QUICK START fetched mm10_f3_10cells.cg -- 11.4 MB, which takes ~101 s at the throughput a build host is likely to get. R's download.file() gives up at getOption("timeout"), 60 s by default, so the transfer truncated mid-file and the vignette errored. Measured twice here: it stopped at 6.0 MB and at 7.2 MB, both almost exactly 60 s of transfer, and completed only with timeout raised to 600. Raising the timeout would have kept a network dependency the package does not need. The sequencing workflow is superseded by the kycg command-line tool, which does this analysis natively over YAME .cg stores and fetches its own knowledgebases, so the chunk is now shown rather than run, with a line saying so and pointing there. The two examples had the same files behind a guard that does not guard. \donttest IS executed by the Bioconductor builders; only \dontrun is not. In bedToCg() the download.file() sat outside the guard entirely, so it ran on every check while only the bedToCg() call was skipped -- the whole example is now \dontrun. In testEnrichment() the guard was in the right place but was \donttest, now \dontrun; its offline part, which uses the sesameData cache, still runs. Both edited in the roxygen source and regenerated, so document() cannot revert them. Neither example has run lately: checksrc has been skipped for as long as buildsrc has been red, so these would have fired the moment the vignette fix made checksrc reachable again. BiocCheck NOTEs \dontrun in favour of \donttest. That NOTE is accepted here: \donttest does not keep the builders off the network, which is the point. visualization.Rmd still reads a small RDS over the network and is left alone -- it builds reliably and is not part of this failure. Package: knowYourCG Commit: 0a4ce5469ac8b4fbb9801a4af583639b65a36b4d Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 16:23:15 -0400 Commit message: Array.Rmd: use the base pipe, not the borrowed magrittr one buildsrc has failed on every builder in both release and devel with Quitting from Array.Rmd:218-233 [ky8, run-test-single] Error in `results %>% dplyr::filter(overlap > 10) %>% head`: ! could not find function "%>%" The vignette never attached the pipe. It worked anyway because library(sesameData) pulls ExperimentHub -> AnnotationHub -> BiocFileCache -> dbplyr, and dbplyr re-exports `%>%`, so the vignette was borrowing the operator from a package four levels down its own dependency chain and never named. When that chain stopped attaching dbplyr, the vignette broke without having changed. knowYourCG imports `%>%` via importFrom(magrittr) but does not export it, so library(knowYourCG) was never what made it resolve. DESCRIPTION has Depends: R (>= 4.4.0), so `|>` is available unconditionally and removes the dependency rather than renaming it; `%>% head` becomes `|> head()` since the base pipe needs a call. R/preparePlotDF.R keeps `%>%` -- package code has the import, only vignettes were ever exposed. Verified under R 4.6.0: all three rewrites return identical() results to the magrittr forms, the base pipe resolves with nothing attached, and Array.Rmd renders to completion. Fixes the buildsrc half of #4. Package: gDRutils Commit: a62ecdc187c6b4b726415cb33500813dfbbb0d10 Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 22:34:53 +0200 Commit message: Merge pull request #201 from gdrplatform/GDR-3612 refactor: read the constant-fit xc50 threshold from fit configuration Package: gDRutils Commit: 441d33fe8d5ca07d23f4dcbee9f59274a5f4f14f Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-22 21:17:54 +0200 Commit message: fix: read the fit configuration when the fitting layer is entered directly Package: gDRutils Commit: 11524511fd588673802ec057e728b96c9b089b0d Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 12:07:38 +0200 Commit message: Merge branch 'main' into GDR-3612 Package: gDRutils Commit: afa97f88532cc8d0539c9df9b2d5170b0e7f4f0c Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:50:27 +0200 Commit message: docs: flag that fit_curves still hardcodes the xc50 threshold Package: gDRutils Commit: f450b02a0beaa9ae1f8cec3fd09151e2f2fe5a98 Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:49:21 +0200 Commit message: Merge remote-tracking branch 'origin/GDR-3606' into GDR-3612 # Conflicts: # DESCRIPTION # NEWS.md Package: gDRutils Commit: b5e352cf6c88d1a7cb33ca89c106b55896cb1cbc Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 13:27:47 +0200 Commit message: refactor: read the constant-fit xc50 threshold from fit configuration The response level deciding whether a constant fit reports +Inf or -Inf was hardcoded at 0.5 in two functions. It is now one entry per normalization type in the fit_config block, alongside the priors and asymptote bounds. Numerically inert: every type keeps 0.5, which is what the code did before. The point is that the value becomes visible and decidable - for RV it means 50% viability and for GR it is the GR50 convention, but NGR is a bare ratio of slopes that is legitimately negative, where the threshold has no established meaning. Package: methodical Commit: 2ce1f224115807008cf8e4056bff3346c161cbe2 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-22 20:12:54 +0100 Commit message: update Package: MSstatsBioNet Commit: d6f02da47b7e915ef0c30923538cf7d516341aa2 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 14:43:07 -0400 Commit message: fix(pubmed): Reduce runtime for fetching pubmed abstracts (#109) Package: GSVA Commit: d2828ae6a4645e089dc931494a2b0f239850ae7b Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:45:59 +0200 Commit message: Switch a couple of install() calls in C for the corresponding more performant internal Rf_*() calls Package: alabaster.matrix Commit: 7cd81656f826538908e71cea03dbed7e42544cb8 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:53:29 +1000 Commit message: Mention all of the weird DelayedArrays that we support in the ANY method. Also move the LowRankMatrix code out of the ANY method for clarity. Also bump version and date for a new release. Package: alabaster.matrix Commit: 1d4b149bd9a329ea35a5033dc0318f6292f275ee Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:38:20 +1000 Commit message: Use a more precise R type hint for residual matrix objects. Also move ResidualMatrix code out of the ANY method for easier reading. Package: alabaster.matrix Commit: 1a17e99c4a5e64b68688da152c20434d3ae965bb Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:21:07 +1000 Commit message: Support scrapper::LogNormalizedMatrixSeed in storeDelayedObject. Package: MSstatsBioNet Commit: c6cb932731a5f1f1a743daed884638f2c14afd57 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:38 -0400 Commit message: Bump package version from 1.5.2 to 1.5.3 Package: MSstatsBioNet Commit: 57f2c7b2d94664d93f76a16b82cc5a5b7cff2ae9 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:10 -0400 Commit message: fix(proteinGroups): Adjust annotateProteinInfoFromIndra to handle protein groups (#108) Package: BreastSubtypeR Commit: 9aad28d9baa37a3a2acc3e040c72bc2fea5bced8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-09-22 20:24:05 +0800 Commit message: Merge upstream/devel, Updated Package: BreastSubtypeR Commit: f44f9d18a7ff9c1446d57cc8515dc427e98e0a4b Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:06:15 +0800 Commit message: Merge pull request #139 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 9e4904ff65cfc1320229f841b55402e08e0390fe Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:00:13 +0800 Commit message: Merge pull request #138 from yqkiuo/main New updates Package: BreastSubtypeR Commit: 252f893b32c10da768540ab3df667f3c6ef34419 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 12:56:55 +0800 Commit message: Merge pull request #136 from yqkiuo/maintenance/public-package-fixes-20260918 Maintenance fixes for 1.5.2: AUTO routing, ROR-C column, Shiny launcher and preflight, Mapping and documentation Package: BreastSubtypeR Commit: f9ca808290b0dfe73e62cff242e28cc301f69238 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-21 10:30:49 +0000 Commit message: Track .Rbuildignore and exclude the .github directory from the build R CMD check reported "hidden files and directories: .github" because the workflow directory reached the source tarball. .Rbuildignore was listed in .gitignore and therefore never shipped with the repository; it is now tracked, with the same content the Ensemble branch already carries, so the built package excludes .github, RStudio files, Rplots.pdf, doc, Meta and MANIFEST.txt. No R code changes. Package: BreastSubtypeR Commit: f3e3be4738438524e605ca70781d8ac359af9ca8 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-19 13:24:35 +0000 Commit message: Bump version to 1.5.2 and title the release notes DESCRIPTION 1.5.1 -> 1.5.2 for the Bioconductor devel submission of the maintenance fixes. The NEWS block collected under "Unreleased" becomes the 1.5.2 entry. One clause is added to the AUTO subsetting bullet: the supplementary pseudocode of the published paper records the strict comparison in the subsetting step while using ">=" for method selection, so readers comparing the package against the paper know that the package now applies ">=" in both and reproduces its shipped example. Package: BreastSubtypeR Commit: 1826b4a6941c152837ef57effbb3c23fdf9751a0 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:57:20 +0000 Commit message: Docs: keep the maintenance track free of unreleased-feature references The entropy change of the previous commits described the new NA behaviour by comparison with an unreleased voting feature, in the internal help text of get_entropy(), in the comment heading test-entropy.R and in the NEWS bullet. The maintenance branch is the public package: its sources, tests and NEWS must not name work that has not been released. The wording now states the behaviour on its own terms. No code, test assertion or behaviour changes. Package: BreastSubtypeR Commit: 252961fa606750b2c17e82363ee0e5ac4ac08d20 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:50:50 +0000 Commit message: Tests: do not let the equivocal HER2 case emit an unhandled warning The AUTO routing test feeds an equivocal "2+" HER2 code to check that a non-evaluable value is treated like a missing one. Builds that flag ambiguous HER2 codes warn on that input, which leaves an unhandled warning in the suite. The call is wrapped; the routing verdict it asserts is unchanged. Package: BreastSubtypeR Commit: 1931c45909ab5e0a56327d3024afd0331468caa5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:37:24 +0000 Commit message: AUTO: decide the HER2+ cohort from the HER2 column alone The HER2+ branch of get_methods() was entered when at least one evaluable HER2 value existed and the joint ER/HER2 counts held no HER2-negative sample. Those counts are computed with na.rm = TRUE, so a HER2-negative sample whose ER value was missing never reached them: one such sample left the cohort classified as HER2+, while an otherwise identical sample with a recorded ER value ended the classification. Whether a HER2-negative tumor counts must not depend on whether its ER status happens to be known. The branch now requires at least one evaluable HER2 value and every evaluable HER2 value to be HER2+. Values outside {HER2+, HER2-} are not evaluable; this covers missing values and the equivocal "2+" code that .normalize_er_her2_tn() deliberately leaves unchanged. Such samples neither create nor remove a HER2+ cohort, and AUTO now reports how many of them took no part in the decision, because a single unannotated sample used to be able to change the routing silently. Cohorts with complete HER2 information are routed exactly as before. The packaged OSLO2-EMIT0 example has no missing ER or HER2 value (ER+ 84, ER- 18, HER2+ 8, HER2- 94), so no shipped example or regression fixture changes. The test that pinned the previous behaviour (her2_pos_na_er) is replaced by a block asserting that both routes now agree, and a block asserting the new message. The NEWS bullet for the unreleased HER2+ change is consolidated into a single statement of the final rule rather than two successive refinements of the same unreleased behaviour. README and vignette state the rule. Package: BreastSubtypeR Commit: 14445c18179fdb40310ea13069f72cc6b5c59a60 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 18:20:00 +0200 Commit message: Entropy: report NA when no method returned a call get_entropy() computes the raw Shannon entropy of a per-sample row of method calls. table() drops missing values, so a row in which every executed method returned NA produced -sum(numeric(0)), that is 0, which on this scale reads as unanimous agreement. Such a row has no call distribution and therefore no entropy; it is now reported as NA. Rows with at least one call are unchanged, including the degenerate one-call case, whose entropy of 0 is the correct value for the observed distribution. The definition of the statistic - raw, unnormalized Shannon entropy in bits - is untouched, and no normalized variant is introduced. The change aligns the legacy path with the ENSEMBLE diagnostics, where raw_vote_entropy is already NA_real_ when valid_voter_count is zero. Exposure is narrow: every AUTO panel includes AIMS and sspbc, which are single-sample predictors and call essentially every sample, so an all-NA row cannot arise in AUTO. It arises in manual runs of nearest-centroid-only method sets (for example methods = c("ssBC", "ssBC.v2")), where a sample whose ER or ER/HER2 status is unknown gets no call from any executed method. The packaged OSLO2-EMIT0 example is unaffected: every tumor there has 7 or 8 calls, and its stored entropy column is reproduced exactly by the new function (asserted by a test). Side effect worth noting: Vis_Multi() orders rows by the entropy column and order() places NA last, so a sample with no calls now sorts to the end of the plot instead of appearing among the unanimous samples. The entropy column of res_subtypes is documented in ?BS_Multi for the first time, including that it is computed over the contributing methods only, so a low value from few contributing methods reflects few available calls rather than strong agreement. tests/testthat/test-entropy.R covers the NA cases, the unchanged values for rows with calls, reproduction of the packaged entropy column, and a manual two-method run in which four samples receive no call. Package: BreastSubtypeR Commit: 3668d9c93adb99e148dc577e8a82b0d556adb249 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 17:30:00 +0200 Commit message: PCAPAM50: exclude samples with unknown ER from the IHC-guided steps BS_PCAPAM50() builds the IHC column from the ER status with case_when(..., .default = NA), so a sample whose ER is missing or not coded "ER+"/"ER-" has no label. makeCalls.PC1ihc() expressed ER-negativity as !grepl("^L", IHC), which returns TRUE for NA, so those samples were counted as ER-negative in the PC1 axis check, in the misclassification-minimizing cutoff search and in the ER-balanced gene-centering set. The bias is one-directional and grows with the fraction of unknown ER. A new internal helper, .ihc_status(), classifies each label as "luminal", "nonluminal" or NA (missing or empty), and the three steps now use explicit luminal / non-luminal masks. Samples without an evaluable label take no part in estimating the cutoff or the centering set, a message reports how many were excluded, and they are still classified and returned. As a side effect the label test is now applied consistently: the mask is computed once, after trimming and upper-casing, instead of being evaluated before the upper-casing step in one place and after it in another. This is not a deviation from the published algorithm. The reference implementation (Raj-Kumar et al., CRAN package PCAPAM50 1.0.4, R/functions_PCA-PAM50.R lines 336, 355-356, 385-386) uses the same !grepl("^L", IHC) construct, but its IHC column is a user-supplied clinical subtype (LA, LB1, LB2, Her2+, TN) that the package never leaves missing; the vignette states that ER-positive subtypes start with "L" and all others are ER-negative. The NA category exists only because BreastSubtypeR derives the column itself. The change also removes an internal inconsistency: BS_cIHC() and BS_cIHC.itr() already exclude unknown ER from their ER groups via which(df.cln$ER == ...). Measured on the packaged OSLO2-EMIT0 input (R 4.3.3 sandbox), setting the first k ER values to NA and comparing calls before and after the change: k = 0 and k = 6 leave every call unchanged, k = 18 changes 2 of 102 calls, k = 30 changes 6 of 102. Cohorts with complete ER are unaffected, and the packaged example still reproduces its stored PCAPAM50 column. The help page of BS_PCAPAM50() gains a @details paragraph stating the exclusion, the message, that such samples are still classified, and the reference implementation's assumption of a complete IHC column. tests/testthat/test-pcapam50-unknown-er.R covers the helper, the unchanged complete-ER output against the packaged fixture, the message, and that unknown-ER samples still receive calls. Package: BreastSubtypeR Commit: 83ad6b3fa93553ba75cb3c641fb7a58070173806 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:10:00 +0200 Commit message: README/vignette: state the size gating of the ER/HER2-defined AUTO rule The AUTO bullet "ER/HER2-defined cohorts: ssBC.v2 only + SSP" read as an unconditional rule. In the code it applies only when the ER group reaches its minimum (15 for ER+, 18 for ER-) and the HER2 subgroup reaches its minimum (8 for ER+, 9 for ER-); smaller cohorts run AIMS and sspbc only. The bullet now says so, and a second bullet documents the handling of cohorts without any evaluable HER2 value (ER-based rules instead of the HER2+ branch). ASCII hyphens replace the typographic minus signs in the edited lines. Package: BreastSubtypeR Commit: 38aa1cc5cb833d260c5d5f82401a8ee528bd7fc1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:05:00 +0200 Commit message: Docs: Mapping "mean"/"median" collapse duplicate probes, as in the PAM50 code The Mapping() help (and the internal domapping() roxygen) described method = "mean" and "median" as keeping "the probe with the highest mean/median expression". duplicate_genes() computes the per-sample mean or median across all probes of a gene, i.e. it collapses the probes rather than selecting one; "iqr", "stdev" and "max" select one probe, and "max" selects by largest row sum, not by "highest expression value". Checked against the original PAM50 bioclassifier code (bioclassifier_R/subtypePrediction_functions.R, collapseIDs(), and the example parameter file): "mean" and "median" average the duplicate probes per sample there too, "iqr" and "stdev" select the probe with the highest IQR / SD, and no "max" method exists. BreastSubtypeR therefore reproduces Parker's behaviour; only its documentation was wrong. Author decision (2026-09-18): fix the documentation. The parameter text in R/BreastSubtypeR_methods.R, R/Utilities.R and man/Mapping.Rd now describes the averaging, credits collapseIDs() and marks "max" as a package addition. No code or mapped values changed. Package: BreastSubtypeR Commit: ba02d862d5e1c9cdbb43e23a1f8506faaed46946 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:00:00 +0200 Commit message: AUTO: include subgroups exactly at their minimum in the ssBC/ssBC.v2 subsets Method selection in get_methods() accepts a subgroup when its size is at least the minimum (15 for ER+, 18 for ER-, 8 and 9 for the HER2 subgroups), but the sample subsets handed to BS_Multi() for ssBC and ssBC.v2 were built with a strict ">". A subgroup of exactly the minimum size was therefore selected for the method and then excluded from its input, and its samples came back NA while the AUTO messages reported the method as running. The packaged OSLO2-EMIT0 example is such a case: 84 ER+ and 18 ER- tumors, so the cohort is classified as mixed and ssBC is selected, but the 18 ER- tumors were dropped from the ssBC input. Executed in a sandbox (R 4.3.3) on this branch: with the published strict comparison a fresh BS_Multi(methods = "AUTO") run yields ssBC = NA for those 18 tumors and does NOT reproduce the packaged frozen result OSLO2EMIT0obj$res (which carries ssBC calls for all 102 tumors); with ">=" the fresh run reproduces the stored result exactly, entropy included. The stored data object is therefore left unchanged; the fix restores agreement between the code and the shipped example. tests/testthat/test-auto-fixture-regression.R asserts the reproduction and that no ER- tumor is left without an ssBC call; tests/testthat/test-auto-subsetting.R adds exact-minimum subgroup cases and the OSLO2-EMIT0 colData. Package: BreastSubtypeR Commit: 13ea06daee8af82ab42c32cfceb38b43aecff9e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:55:00 +0200 Commit message: AUTO: require an evaluable HER2 value before calling a cohort HER2+ get_methods() entered the HER2+ branch whenever n_ERposHER2neg == 0 && n_ERnegHER2neg == 0. Both counts are also zero when HER2 is entirely missing or coded with unrecognized values, so such cohorts were classified as "small HER2+" and received AIMS and sspbc only (example: 60 ER+ / 40 ER- with HER2 all NA). The branch condition now also requires at least one evaluable HER2 value (HER2+ or HER2-). Cohorts without HER2 information fall through to the ER-based rules: a mixed ER cohort gets the mixed panel (ssBC.v2 then returns NA for every sample, which BS_ssBC() handles without error), an ER+-only cohort reaches the announced AIMS/sspbc fallback because its HER2 subgroups are empty. Cohorts with any evaluable HER2 value are routed exactly as before, including the existing treatment of HER2- samples whose ER is missing (excluded from the subgroup counts, as the AUTO message states). No effect on the packaged OSLO2-EMIT0 example. Author decision (2026-09-18): HER2+ branch only with evaluable HER2. tests/testthat/test-auto-routing.R covers the size-gated ER/HER2-defined cohorts and the cohorts without HER2 information. Package: BreastSubtypeR Commit: 94c6d57580acf6c6b77287f8e3968628ffeb2b84 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:50:00 +0200 Commit message: cIHC, cIHC.itr, PCAPAM50: clear error when an ER group is empty On a cohort with a single ER group (for example every sample ER+), makeCalls_ihc() and makeCalls.PC1ihc() failed with "undefined columns selected" and makeCalls_ihc.iterative() with "arguments imply differing number of rows: 0, 102", all from the median computation on an empty balanced set. The methods cannot balance by ER status without both groups. A small helper, .check_er_groups(), now stops with the group counts and a pointer to the cohort-aware modes in makeCalls_ihc() and makeCalls_ihc.iterative(). makeCalls.PC1ihc() checks the luminal / non-luminal IHC classes before the PC1 cutoff search and the balanced set after it, and makeCalls.v1PAM() checks its LumA / Basal groups. Cohorts with both groups take the same path as before (the OSLO2-EMIT0 cIHC calls are unchanged). Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-er-balancing-errors.R covers the three methods. Package: BreastSubtypeR Commit: 3894f47377e42f6c2f18cf8d7e04ecd0e38f7b16 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:45:00 +0200 Commit message: Docs: describe the actual return values of the NC methods; cIHC.itr ratio BS_PCAPAM50() and BS_ssBC() documented "a character vector of intrinsic subtype predictions", BS_cIHC() "a data.frame", and BS_cIHC.itr() a list with elements subtypes / confidence / ER_balance that do not exist. All four return a list: BS.all (PatientID, BS and, with Subtype = TRUE, BS.Subtype), score.ROR (correlations, calls, confidence, ESR1/ERBB2 expression, ROR-S/ROR-P and, with hasClinical = TRUE, ROR-C/ROR-PC scores and groups), the medians used for centering (mdns; mdns.fl for PCAPAM50; absent for cIHC.itr) and outList; BS_cIHC.itr() additionally returns BS.itr.keep and, with Subtype = TRUE, BS.itr.keep.Subtype. Verified on the packaged OSLO2-EMIT0 input. BS_cIHC.itr(ratio): makeCalls_ihc.iterative() swaps the larger ER group into the sampled position before drawing ceiling(ratio * n_smaller) samples from it, so the ratio applies to the larger group relative to the smaller one, not to ER+/ER- as such. The parameter text now says so, and the alphabetical tie-break used by get_consensus_subtype() for the consensus call is stated in the return value. roxygen comments and the corresponding man/*.Rd files were edited in parallel (no roxygen2 run, to avoid unrelated regeneration changes). Present in Bioconductor release 1.4.0 and devel 1.5.1. No code changes. Package: BreastSubtypeR Commit: abace8828bc01fa6ff7e1a70d6a9c1e28505cc74 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:40:00 +0200 Commit message: Shiny: cohort preflight requires both ER and HER2 columns .summarize_cohort() in inst/ShinyBreastSubtypeR/server.R returned ok = TRUE for kind "ER" (HER2 absent), kind "HER2" (ER absent) and for a valid TN column without ER/HER2. get_methods() stops in all three cases ("The 'AUTO' mode requires both 'ER' and 'HER2' columns in the 'pheno' dataframe"), which the app surfaced only as "Prediction failed" after the user pressed Run. The column summary is unchanged (now .summarize_cohort_columns()); .summarize_cohort() wraps it and sets ok = FALSE with the message "Cohort-aware analysis requires both 'ER' and 'HER2' columns; missing: ..." when either column is absent. Kind and statistics are still reported. tests/testthat/test-shiny-preflight.R covers the column combinations. Package: BreastSubtypeR Commit: 36e4de779bf6677fde472e81f613cf3f49799476 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:35:00 +0200 Commit message: iBreastSubtypeR: load app dependency namespaces correctly The launcher's .attach_if() helper called requireNamespace(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE). requireNamespace() has no such arguments, so the call failed with "unused arguments"; the failure was swallowed and FALSE returned, and nothing was loaded. The comment claimed the packages were attached to the search path, which requireNamespace() never does. The app still worked because ui.R/server.R use qualified calls and shiny::runApp() attaches shiny itself. The helper is now a package-internal function, .load_app_dependencies(), that checks installation, loads each namespace with requireNamespace(p, quietly = TRUE) and stops with a clear message when a package is missing or cannot be loaded. The tidyverse option uses the same helper. The exported signature and documentation are unchanged. tests/testthat/test-shiny-launcher.R covers the missing package error and the successful load. Package: BreastSubtypeR Commit: 6deac1db8d57cfbaee4e104edb9af6f160a9c536 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:30:00 +0200 Commit message: BS_Multi: report the error text when PCAPAM50 fails The tryCatch() around BS_PCAPAM50() in BS_Multi() warned "PCAPAM50 failed in this iteration: " and dropped the condition message, so users could not see why the method failed. The warning now appends conditionMessage(e) (with call. = FALSE). Behaviour is otherwise unchanged: the method's column is filled with NA. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-bs-multi-messages.R mocks a failing BS_PCAPAM50() and checks the warning text and the NA column. Package: BreastSubtypeR Commit: ff23703e8cb347524ad8fe1897d25d6514fd4049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:25:00 +0200 Commit message: Normalize factor phenodata like character; fix the FPKM imputation guard .normalize_er_her2_tn() used nested ifelse() calls whose fallback was the original column. For a factor column the fallback is the integer code, so unmatched levels came back as strings such as "3" instead of "Unknown". Mapping() converts colData factors to character before calling the helper, but BS_Multi() and get_methods() normalize the phenotype table directly, so a hand-built data_input with factor ER/HER2/TN columns was normalized differently from the same table with character columns. The helper now works on as.character() copies of the three columns; the coercion warnings compare character values, so canonical factor input no longer triggers them. Character input is unchanged. domapping(): the second imputation guard tested anyNA(x) after x had already been imputed, so counts.fpkm was never imputed. It now tests anyNA(counts.fpkm). In practice edgeR rejects NA counts earlier, so this is a logic correction with no expected effect on existing analyses. Both present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-phenodata-normalization.R compares factor and character input for the helper and for a full AUTO decision. Package: BreastSubtypeR Commit: 5deb60ce12da9448df97aa5079c0f312ad12cc6a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:20:00 +0200 Commit message: Mapping: keep matrix dimensions for single-sample input duplicate_genes() indexed x[names(entrezid), ] without drop = FALSE and rebuilt the collapsed matrix with mapply(SIMPLIFY = TRUE) followed by apply(x, 1, unlist), which requires a matrix. For a one-sample SummarizedExperiment the subset became a vector and Mapping() failed with "dim(X) must have a positive length". prepare_nc_matrix() and the probe filter in domapping() had the same drop issue. The collapse now builds the gene-by-sample matrix explicitly (lapply + rbind with dimnames from the split and the sample names), and the three subsets use drop = FALSE. For multi-sample input the returned values and dimnames are identical to the previous implementation for "mean", "median", "max", "stdev" and "iqr" (checked on random data with duplicated Entrez IDs and an NA value); the OSLO2-EMIT0 mapping of one sample equals the corresponding column of the full mapping. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: d6c6c20c4004d988e79c522ee4f1625dd0ad39fb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:15:00 +0200 Commit message: AUTO: announce the fallback to AIMS and sspbc instead of falling back silently The safety net at the end of get_methods() set methods to c("AIMS", "sspbc") without any message. It is reached by ER+-only or ER--only cohorts whose HER2 subgroups are all below their thresholds, typically because many HER2 values are missing (example: 17 ER+ samples with HER2+ 5, HER2- 6, missing 6). Users saw only the two SSP methods run, with no indication why the ssBC variants were not selected. The fallback now emits a .msg() (respecting the BreastSubtypeR.verbose option) naming the reason. Method selection is unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: a9f0de975795df873663f9cab6207455cb3b2d15 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:10:00 +0200 Commit message: AUTO: drop samples with missing ER/HER2 from the ssBC/ssBC.v2 subsets get_methods() built the AUTO-mode sample subsets with rownames(pheno)[pheno$ER == subtype] and the ER/HER2 analogue. A missing ER or HER2 value evaluates to NA in the comparison, so the subsets contained NA "sample names". BS_Multi() then either failed when it subset the SummarizedExperiment ([,j] index out of bounds: NA) or, when the NA-padded vector was at least as long as the cohort, treated it as "run on all samples" and skipped the intended subsetting. Example on 1.5.3: 50 ER+ / 45 ER- / 5 NA gives a 105-element subset with 10 NA entries for a 100-sample cohort. Both lapply bodies now use which(), as makeCalls.ssBC() already does, so samples with missing status are excluded. Cohorts with complete ER/HER2 values return identical subsets. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-auto-subsetting.R covers a mixed cohort with missing ER and an ER- cohort with missing ER and HER2 (subset shorter than the cohort). Both fail on the previous code. </pre> </div> Package: BreastSubtypeR Commit: 2f8ea71201a742d0d0957ff8228ba2fdbc21d3be Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:05:00 +0200 Commit message: Fix ROR-C risk group column: use criskgroups, not cpriskgroups In RORgroup() (R/NC_functions.R) the data frame built when hasClinical = TRUE assigned the combined + proliferation groups (cpriskgroups) to both "ROR-C Group (Subtype + Clinic)" and "ROR-PC Group (Subtype + Clinic + Prolif)". The ROR-C groups (criskgroups, thresholds -0.1 and 0.2 on the combined score) were computed but never reported. The ROR-C group column now uses criskgroups; the ROR-C score and every other column are unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-ror-groups.R adds a synthetic RORgroup() input in which the ROR-C and ROR-PC groups differ (high/low/med vs low/high/med) and checks that the ROR-C group is reproducible from the reported ROR-C score. The test fails on the previous code and passes with this change. Package: BreastSubtypeR Commit: 9ab99af8b9cf337614a30a61c3e0ce1c264df049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:00:00 +0200 Commit message: Tests: run the nested testthat suite via test_check() tests/testthat.R contained a single inline test_that() block and never called test_check(), so tests/testthat/test-tn-cohort-detection.R (added in 1.5.1) was not executed by R CMD check; the Bioconductor devel check log shows only the inline test running. tests/testthat.R now calls test_check("BreastSubtypeR") and the inline BS_Multi() test moved unchanged to tests/testthat/test-bs-multi-manual.R. DESCRIPTION: Config/testthat/edition: 3 and testthat (>= 3.2.0) in Suggests, matching the edition-3 expectations used by the tests added on this branch. No version bump. Package: BreastSubtypeR Commit: a4b23b2aba07ba19b33669ac1e8d8361fd1139ab Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:59 +0200 Commit message: Merge pull request #135 from yqkiuo/main update to 1.5.2 Package: BreastSubtypeR Commit: b19c1c3f629d11a8f12e57526162b16e41e605c6 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:30 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: 0c0c47c87dcd6e560bedcd536f828dca642e7933 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-06-22 17:38:39 +0300 Commit message: Merge pull request #134 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: edeb030317e854cd706a351f12b93dbd722f232e Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 17:22:45 +0300 Commit message: Finalize NEWS entry for TN detection fix (#133) Package: BreastSubtypeR Commit: b8d6bf4b5bb037d8e101287e92d209fdb1e869a5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:59:04 +0300 Commit message: Update NEWS and documentation for TN detection fix (#133) Package: BreastSubtypeR Commit: d8eeff0e85113512842b1e4976fce6eed1142e39 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:25:06 +0300 Commit message: Fix TN-only cohort detection (#133) Package: BreastSubtypeR Commit: cd515ab92fffbbf8a3496cfc70e65299b77457ba Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-02-20 12:09:07 +0100 Commit message: v1.3.3 Package: BreastSubtypeR Commit: 0770ee5c0a5283fd1f073cf9c170464431eac2d3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-02-20 11:59:28 +0100 Commit message: Merge pull request #129 from yqkiuo/main AUTO - NA Package: BreastSubtypeR Commit: 9b740667ac781cede13f2884763f47576f5778cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:30:22 +0100 Commit message: Merge pull request #128 from yqkiuo/BranchManos Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: ebac3daf14161981995520818d552a8c894faa21 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:27:35 +0100 Commit message: Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: 122fae948ba3ab93589046d4fc9f564a95db3805 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-12-21 07:08:46 +0100 Commit message: Merge pull request #125 from yqkiuo/main Update Package: BreastSubtypeR Commit: ab9e6c7e715a77c3d9d0c93f0d96794531b39afc Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:48:57 +0100 Commit message: Merge pull request #124 from yqkiuo/BranchManos cIHC.itr: return distances as numeric matrix, preserve dimnames Package: BreastSubtypeR Commit: 1cdd290182105e8d9dd1cf38a2f1cc2748045aba Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:41:20 +0100 Commit message: cIHC.itr: return distances as numeric matrix, preserve dimnames - Coerce mean_distance and mean_distance.Subtype to double matrices with sample/centroid dimnames; negate once. - Ensure testData is numeric matrix. - Use explicit getsuffix(calibration=..., internal=...). Closes #112 Package: BreastSubtypeR Commit: e626336705e6981d3f43c1e307381875acc4dbf5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:18:30 +0100 Commit message: Merge pull request #123 from yqkiuo/BranchManos feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to can… Package: BreastSubtypeR Commit: bf244ea222946de979dc528b6764b074b9a7492e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:17:59 +0100 Commit message: feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to canonical forms - Add `.normalize_er_her2_tn()` utility and call it inside `Mapping()` to coerce common variants to: * ER → {ER+, ER-} * HER2 → {HER2+, HER2-} (HER2 "2+" left unchanged/unevaluable) * TN → {TN, nonTN} Accepts Positive/Negative, Pos/Neg, Yes/No, True/False, 1/0, AMP→HER2+, etc. - Preserve original values in `colData` when fields are absent; only touch present columns. - Emit explicit warnings on ambiguous/unmappable values (e.g., HER2 "2+"). - Roxygen: expand `Mapping()` docs with required Column metadata for AUTO/ssBC/cIHC/PCAPAM50 and numeric TSIZE/NODE (0/1) for ROR; document the canonical receptor coding and the automatic normalization behavior. Closes #122 Package: BreastSubtypeR Commit: d4200b8f8fa6a230b1aed6bd8d5a271856dcf9c5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 10:04:54 +0100 Commit message: Merge pull request #120 from yqkiuo/BranchQiao Formatting Package: BreastSubtypeR Commit: 855146c3797560a923b044683b223aa09c5ab6b6 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 10:04:04 +0100 Commit message: Formatting Package: BreastSubtypeR Commit: 7e1546b848212ca92df006f0625e1f0213a5d825 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:57:27 +0100 Commit message: Merge pull request #119 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 13081dbdf8d5faead48468a7121455f68f226262 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 09:56:57 +0100 Commit message: Warning: nonASCII Package: BreastSubtypeR Commit: e872818d9f7db70dd95b04e56306c5f986b4cb2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:48:36 +0100 Commit message: Merge pull request #118 from yqkiuo/main 1.3.1 Package: BreastSubtypeR Commit: e837d4a4b93480e5921dc6220d336f390e08cfa9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:56:26 +0100 Commit message: Merge pull request #117 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 24282cdd95efcb545c8a516d2a4c52c333451e37 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:55:43 +0100 Commit message: docs(NEWS): updated to include latest changes/bug fixes Package: BreastSubtypeR Commit: d3e819ea9cb6036119018581de03f7c0ca6c03e9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:45:26 +0100 Commit message: shiny/preflight: reset cached data_input on source change (uploads/example) to fix stale cohort display Package: BreastSubtypeR Commit: f7ad9d6399c959146fad253c76e4b8a093367674 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:06:08 +0100 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: 33bc7cabda598a10d06781255a4ff477d64ec373 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:05:55 +0100 Commit message: Merge pull request #116 from yqkiuo/main Main to BranchManos unmerged changes Package: BreastSubtypeR Commit: c1164715171e92993dba23d51ed4d2739a9db33a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:03:31 +0100 Commit message: Include ssBC in robust singleton handling Package: BreastSubtypeR Commit: 0c0c39cd7cb7bdde99192d4a877cc9990b98b6c4 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:32:17 +0100 Commit message: v1.3.1 Package: BreastSubtypeR Commit: ed479c4a0a715bd078874a465956416cb58e999b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:30:33 +0100 Commit message: Minor typo for Shiny exports Package: BreastSubtypeR Commit: fca34d14be09269bd6a9e83f9b169b3f49e3b27d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:16:28 +0100 Commit message: ssBC.v2: include sample IDs in singleton fallback warnings; surface warnings in Shiny - Warnings now list subgroup + n + sample IDs (truncated for long lists). - Shiny wraps runs in withCallingHandlers() to show warnings via showNotification(). Package: BreastSubtypeR Commit: 5beba6624617ea57bd33a664a2c9ccddbe01f5d2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:15:25 +0100 Commit message: ssBC.v2: robust singleton handling + ROR guards - Use uncentered expression for n=1 fallback (avoid zero-vector Spearman→NA). - Add canonical 4-class name normalizer before RORgroup; create missing cols; enforce order. - Shorten Mapping() completion notification duration in Shiny. Package: BreastSubtypeR Commit: 6f8593d8659200d5b054e45ae6deb7ff624bf02f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 23:31:32 +0200 Commit message: Merge pull request #115 from yqkiuo/BranchManos fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: ae32dd867386460a3d6abcff63cd519bcebdd098 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-21 23:25:49 +0200 Commit message: fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: 01a86e199d7353c526b1ddec6693b6c5d87a53e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:51:52 +0200 Commit message: Merge pull request #114 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: aee5223fca7ad466234702b83f9d465092e65fec Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:50:18 +0200 Commit message: update documentation (.Rd) files & NEWS.md Package: BreastSubtypeR Commit: e3852e46bc7c708db9534558669b18e492bbcb44 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:38:36 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: f13b835df4329f494e2a1fe1242a1927657629f9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging -Name unnamed chunks Closes #113 Package: BreastSubtypeR Commit: 815edf2ed0faa1dc708fecc282da22945d861490 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging Package: BreastSubtypeR Commit: 27a8e42ca0dd5a06b976bd6e59aeedf3337c8ad1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:41:55 +0200 Commit message: Merge pull request #111 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6ed1cf770b44ea3eeaa0fe5d284760692df203e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:40:32 +0200 Commit message: feat(shiny): show ER/HER2 subgroup tallies (±TN) in AUTO preflight Package: BreastSubtypeR Commit: a85dec5c9e7f261e7d9ea94febbbfc063dc07992 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:04:55 +0200 Commit message: fix(shiny): guard switch() inputs to prevent length>1 errors; harden AUTO preflight & ssBC option handling Package: BreastSubtypeR Commit: 8b4e57129dabde362d8c811661e7586dc633c396 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:49:16 +0200 Commit message: feat(shiny): TN-aware AUTO preflight summary and messaging Package: BreastSubtypeR Commit: 83b469a296627e4a81983655692766813d8540b2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:48:42 +0200 Commit message: docs: convert wording to American English (standardized, normalization, visualize) Package: BreastSubtypeR Commit: 1c86f875473cf413e91da628410278915a9b19cb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 00:28:47 +0200 Commit message: Merge pull request #110 from yqkiuo/BranchManos v1.1.9: feat(app): add example-data loader and AUTO preflight cohort … Package: BreastSubtypeR Commit: bcb7486f49afd2f9c719d1b047c89b96421040b5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-15 00:26:27 +0200 Commit message: v1.1.9: feat(app): add example-data loader and AUTO preflight cohort stats; harden AIMS/sspbc outputs; renamed FPKM GEX example file Package: BreastSubtypeR Commit: 3e5ae1bae1910f63b576690d0f5965c092929197 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-14 22:26:00 +0200 Commit message: Merge pull request #109 from yqkiuo/BranchManos Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: 643629b4f37a82e8eb4fc1d4b8b7d47a1d0140e5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-14 22:08:03 +0200 Commit message: Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: f0bb013273724583dc640776f5253a650e71deb7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-11 19:07:21 +0200 Commit message: Merge pull request #106 from yqkiuo/main v1.1.8 Package: BreastSubtypeR Commit: e519bba6330b28527eba397178b5db68259cd335 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 17:48:34 +0200 Commit message: Merge pull request #105 from yqkiuo/BranchManos Minor text improvements Package: BreastSubtypeR Commit: 7ef4c516f1e02b2667908e42c91db1f81587e183 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 17:35:16 +0200 Commit message: Minor text improvements Package: BreastSubtypeR Commit: bba02a162aae8a104830c2762903a95b4b24a086 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 16:30:43 +0200 Commit message: Merge pull request #104 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6bb89109d53b3cbfc61069dad0b97c43fc01a59 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 08:38:02 +0200 Commit message: v1.1.8: feat(auto): enforce v2-only for ER/HER2-defined cohorts; add TN cutoff (18); sync docs Package: BreastSubtypeR Commit: 104a9d3c962648e2421f86b970452b6ae8094add Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 00:03:52 +0200 Commit message: v1.1.7: Fixed bugs & Clarified guidance in AUTO logic Package: BreastSubtypeR Commit: 3a0c352910e74d2016eaaa4f0d229db74b6428b1 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:11:23 +0200 Commit message: Merge pull request #103 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: c23f9312cfe6399587682872db5168e726949468 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-08 07:10:55 +0200 Commit message: v1.1.6 Package: BreastSubtypeR Commit: bda41efb6523b351c335cbbbfe93eda3e294159a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:01:46 +0200 Commit message: Merge pull request #102 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 01fbf08f95785bd96121416f08a42a0723db9bb5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:31:43 +0200 Commit message: Merge pull request #101 from yqkiuo/BranchManos Update citation Package: BreastSubtypeR Commit: 819b86fcb1f32f68d8d6551ae67675e59d55cbc2 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:29:59 +0200 Commit message: Update citation Package: BreastSubtypeR Commit: 18426cd1996f6d437078579a397e594ac858b422 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:18:10 +0200 Commit message: Merge pull request #100 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5cd622f0dfdcbf4ebd2612e2f3bce0d4d130a1dd Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:10:24 +0200 Commit message: Update to v1.1.6 Package: BreastSubtypeR Commit: 0168bb1d064c170c27904604ce944664052ffc4c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:00:02 +0200 Commit message: Fix CITATION error & update CITATION Package: BreastSubtypeR Commit: efcf440f930e3e0216161a7bfaa1f8a839796ffc Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:28 +0200 Commit message: Merge pull request #99 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 522570c1925152201b4738888c70a9b479569b4d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:10 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: caa57d7c96c2b3621ba3153a63704780fb67943c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: eca7fd305351bee53a3359193d31d6efb3bd239c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:26:16 +0200 Commit message: Merge pull request #98 from yqkiuo/BranchManos Bump version to 1.1.5, merge from BranchManos Package: BreastSubtypeR Commit: 3d6d84a04f652c46b098e7daf6b9433783c59317 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:17:29 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 08be34439c7ec15f3aab940989e7fc5881500a38 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:28:50 +0200 Commit message: Minor styler changes to comply with BiocCheck Package: BreastSubtypeR Commit: c33c626c748776d83aec78b69c2c5c2d78b40d94 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:00:25 +0200 Commit message: Remove Styler ignore file Package: BreastSubtypeR Commit: a756018eea737c57128fecbe2ed656a5c8bd8c89 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:53:48 +0200 Commit message: After styler formatting Package: BreastSubtypeR Commit: 0fb6775cf7105ccdfeac0f78d671c8220fa00a07 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:43:21 +0200 Commit message: Before styler formatting Package: BreastSubtypeR Commit: f462a35c15affb83307240678fdb8b5c31f1e1af Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 15:06:41 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: d58720a8654c148543e56efe3c8504e50f7a06f9 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Fix LaTeX errors, @importFrom issues, deprecated mutate_at(), tightened Mapping() Package: BreastSubtypeR Commit: 8cab29a01c0412be9b9a83d9c729c77b273c03f9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:33:33 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 2909f655c9c2686e9c562762e27c7cb78eb63544 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Merge pull request #97 from yqkiuo/BranchQiao Fix LaTeX errors Package: BreastSubtypeR Commit: f1d92deeed7ff76170c4ba8a70d0ac75e0dab7eb Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:28:10 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 9112d81e8538f3debb6c101255008486d052c326 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-12 19:39:12 +0200 Commit message: Merge pull request #96 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 977c1a7f7a5dd3700b51fe154e0a9509d6a960b1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 19:38:48 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: b2ba716538df0e23e684ec1118866c96560cab9b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:14:24 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: e25016431d3c00bfd81d941f4b8a71a2b7357ba1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:07:19 +0200 Commit message: v1.1.3 Merge branch 'BranchQiao' of github.com:yqkiuo/BreastSubtypeR into BranchQiao # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. Package: BreastSubtypeR Commit: 0f3624d0ed05aa4d2f2cb9759acb59d815fea297 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:04:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 8a340b6a4117f80791ae664c5741a0fe8627c9c3 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 15:44:48 +0200 Commit message: Fix BreastSubtypeRobj to include only the object itself (exclude environment variables) Package: BreastSubtypeR Commit: f969bcf09e03aa226de3839a68cf76cc01011ef3 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 14:52:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 693c829f364caedb2161a940d196d1830bd19d87 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 10:21:35 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 8582fb3b897e60ecc6da91040e32b42b19641154 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 17:06:26 +0200 Commit message: Added publication badge Package: BreastSubtypeR Commit: bd0b6cab935e607efd4bb001e3b75b02b37cc1fe Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:47:02 +0200 Commit message: Fixed bug: When running BS_Multi() omitting the first method; Minimal fix (drop nothing after removing row_id) Package: BreastSubtypeR Commit: 234ccbe269d45bd2c407358b711253629fe59203 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:12:28 +0200 Commit message: Polishing README.md & Vignette Package: BreastSubtypeR Commit: b3d5c232a32097ee9b4f83908a9c89f6ca621be8 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:41:14 +0200 Commit message: DOI update and text Package: BreastSubtypeR Commit: bacb13657f301643a682a3fcd7e82a22091a3b6c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:01:14 +0200 Commit message: Added DOI, Updated exported with version info, method, etc Package: BreastSubtypeR Commit: 787b3119148e345c0b2d4fa8638b3d6dd37600ee Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 19:17:32 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: c856d8dc615f688ae8f5d27eeb47ab297ead6b11 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:36:22 +0200 Commit message: Delete .github/workflows/sync-to-forks.yml Package: BreastSubtypeR Commit: 8d235ce12beccf9d394146a458ae135fec2f0fb3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:18:15 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: ad15f75e9de9028eb6d93fb5efb3ca05220ce975 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:04:51 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 917d62c7bc428fc67ff97c513022feb210fed94c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:58:05 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 9258dd1803aac507ecae1ec05d30a55c7c91827c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:54:22 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 8864ea4a8bda1bee1b6496aaf185e8bb76af5257 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:57 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 71735535741a019e7ba9299e47783038edbd3714 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:00 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f165c7df5636588c76360b10a42e792e9bf53614 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:50:26 +0200 Commit message: Create sync-to-forks.yml Package: BreastSubtypeR Commit: f2d85acb23f2c38ec3b3062fbab841c29115d38e Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:47:46 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 792bc0ab92f80b7405d69c45516dd131ffd7663c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:43:18 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 99d3102b66482953013f265d00464c8c3a4c2b25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:34:13 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 212e09ee660df8daaffea11a7af00d53321895aa Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:04:17 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 7cea1e782fedda5fef57f559c77dc39db8aceb9d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:56:40 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f33f344a6b0d06d3de393a783a23383e4ef5cac4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: adccaf9e7d8ce2b6234a1960e93e5d1543d98e09 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:31:34 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: a9e9e80f2f1063aae332963e474ea2f5804487b7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:27:58 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 4151dfa20943c89acdd55c5e1dec18a03da01e2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:14:01 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 1ab513bde94a41e4ab34856ca5e4f5ba5a6413e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 15:59:19 +0200 Commit message: Create sync-to-org.yml Package: BreastSubtypeR Commit: f9f0ea202177840660c02d39e203f67d4003e2cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:09:58 +0200 Commit message: Added description for new example dataset (TCGABRCAobj), updated the BreastSubtypeRobj with the 3 new medians info, tiny text improvements Package: BreastSubtypeR Commit: 056545172113202bb55a0ea0c2918851096fa0f2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:05:10 +0200 Commit message: Created a new example dataset (TCGABRCAobj) from TCGA-BRCA with Raw Counts, and similar results as OSLO2EMIT0obj Package: BreastSubtypeR Commit: 6de103db09589a53624341851237a8f547684ceb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:02:19 +0200 Commit message: Updated BreastSubtypeRobj with 3 more published medians Package: BreastSubtypeR Commit: 6acd15688f6e60db4e1f2ef151c103e865ce5663 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:00:19 +0200 Commit message: Guard docalibration, Improve External calibration, UX, and minor text improvements Package: BreastSubtypeR Commit: 8f7e3790ac94fead82f77e6564d87c542fcf5097 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 11:11:22 +0200 Commit message: Fixed error in BS_Multi() in AUTO Mode, when ssBC has <50 PAM50 genes: Add safe row-aligning cbind helper, made RORgroup() tolerant to missing ESR1/ERBB2 rows, and made BS_Multi() assemble results by PatientID Package: BreastSubtypeR Commit: 06bd9bce269ca12b4ca9f052f3d81cd730212a68 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 21:20:25 +0200 Commit message: Fixed the issue with pre-loading third-party libraries before initializing the Shiny app, Updated Help files Package: BreastSubtypeR Commit: ee560564150a7a5f11c00e8750583438a6c084e6 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:55 +0200 Commit message: Updated NEWS.md with major changes Package: BreastSubtypeR Commit: abd132463b65390c813f04ea50c530fd4b058507 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:18 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 74b20b933030517c45e68826a469dd88d79aa0b9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:24:07 +0200 Commit message: Added a TCGA-BRCA subset, with clinical & annotation data, for testing the RawCounts normalization pipeline Package: BreastSubtypeR Commit: d4fedc4c9b2a241b2652e563c2300d423f787287 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:21:08 +0200 Commit message: iBreastSubtypeR: UX polish, AUTO explainer, export refactor, AIMS constraint & bug fixes Package: BreastSubtypeR Commit: fb7c21f7ebc4f50be7610c8c0a023036f1559358 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 13:24:32 +0200 Commit message: Include three pre-computed Medians (external) as an option to Shiny App Package: BreastSubtypeR Commit: d1a90080950c9b5ddcad737979d072bdc177e038 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 11:34:43 +0200 Commit message: ssBC fixes: No crashes when < 50 PAM50 genes, No accidental subtype calls when a sample’s distance row is all-NA, Won't error when a subgroup has zero samples, qCtr won't produce NaN from zero range Package: BreastSubtypeR Commit: 10644b50e4721efe7b0d9f65445d30e1fdcf5a26 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 10:05:57 +0200 Commit message: Add our reference to Mapping() & BS_Multi() Package: BreastSubtypeR Commit: 5ea0dd73f932fbdd278f4e299de7270698d855c1 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 23:10:17 +0200 Commit message: New preflight for AUTO to prevent errors, new customizations, included new polished text for PAM50 to guide users, and more Package: BreastSubtypeR Commit: 3b08eed750427d72842bec852ff85c2446138cbe Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 13:21:06 +0200 Commit message: Fix issue when HER2 missing and user runs AUTO Package: BreastSubtypeR Commit: 16b805c817e0b7e3883b1aa7defd6da04f6a57f4 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:20:14 +0200 Commit message: Included a Prelight check for ER/HER2/Tn status availability in Clinical data BEFORE Running subtyping, avoiding App crashing due to missing values Package: BreastSubtypeR Commit: f003e4ecbfadb6a2a293ff39d838581dea5a0086 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:01:32 +0200 Commit message: Synchronized changes in BreastSubtypeR_methods.R and NC_functions.R, Created a theme to match the logo, made things unified, text improvements Package: BreastSubtypeR Commit: a66b4796231c8054f2093c6795ca4e67f2cb04de Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 10:08:20 +0200 Commit message: Parker original when calibration=None, or external calibration returns error: Fixed by Making NA equivalent to "medianCtr" (sync eith Parker et al.), and -1 to No calibration. Also, avoid requiring PatientID for BS_parker() when hasClinical = FALSE, included extra controls for hasClinical in all NC functions, polished help text, corrected typos (also tried to correct the 2nd error for ssBC, when < 50 genes, but will work more on this and come back with another Commit) Package: BreastSubtypeR Commit: 53ca58ec99d200f998a8be6896bab45f47d789e3 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-05 19:36:25 +0200 Commit message: Major changes: Multi method with AUTO mode added, Description text for each method with Refs added, Subtype 4-class selection Package: BreastSubtypeR Commit: bdf3bf291b59939171d85ff61f895b2ffc222b8d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:18:47 +0200 Commit message: Fix UI so the drop down menus are easier to select Package: BreastSubtypeR Commit: c0ed93ab5eed4a965f478a0dcac17355f8f91501 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:01:42 +0200 Commit message: Changed HasClinical with a Tick box, included many controls to check whether TSIZE, NODE are available, added different help functions for GEX and Annotation, improved text, and more Package: BreastSubtypeR Commit: 277869bea9c0c7d2747370cc657b2e87cb4e7dd2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 14:59:23 +0200 Commit message: Replaced the T -> TSIZE Package: BreastSubtypeR Commit: fd063a60aa8db3651975e89237ddb398d62c1100 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:28:48 +0200 Commit message: Minor edit Package: BreastSubtypeR Commit: 31e6bbfa2c897aa87caa09254cd2d4d2074b790f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:25:40 +0200 Commit message: Renamed folder to Shinny->Sniny, renamed data files with clear names Package: BreastSubtypeR Commit: 5ef9dd73efdccab438ee51f1ea0441ac565ca984 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:20:19 +0200 Commit message: Fix server.R bug Package: BreastSubtypeR Commit: c4c205e993f8791683fddf05392533aadded4b75 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-04 11:49:00 +0200 Commit message: refine shiny Package: BreastSubtypeR Commit: 304cb68143558163b4dd070c2498631f62a650e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-04 10:40:17 +0200 Commit message: Merge pull request #95 from yqkiuo/main Merge pull request #94 from yqkiuo/BranchQiao Package: BreastSubtypeR Commit: 6cbc1cb1b18907119b3414e3c0dafec607480a99 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:27:20 +0200 Commit message: Merge pull request #94 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 298458b861686b4ed9bfa17c070e5ffea513f3dd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-02 08:27:00 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: a50d8d4c3bea22f65836df6d099b269da685d8c2 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:25:43 +0200 Commit message: Merge pull request #93 from yqkiuo/main v1.1.2 Package: BreastSubtypeR Commit: 65b18fd8734f90e579fff40e53bbc51799b2c4ad Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:28 +0200 Commit message: Merge pull request #92 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5d09b44a5785c08a10d3d652d2a01db94678a1de Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:21 +0200 Commit message: Merge branch 'main' into BranchManos Package: BreastSubtypeR Commit: 8f4056fc16de285798c18e8c36e5399e5cd1fd23 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-01 10:18:12 +0200 Commit message: Merge pull request #91 from yqkiuo/BranchQiao v1.2.2 Package: BreastSubtypeR Commit: e11ffcd934d71dd5ee42c3816cabf93b997e6c64 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-01 10:17:53 +0200 Commit message: v1.2.2 Package: BreastSubtypeR Commit: 0969e8fa4d71d310d1d2f58c788af7a94566de25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-31 22:18:46 +0200 Commit message: Merge pull request #90 from yqkiuo/BranchQiao v1.1.2 Package: BreastSubtypeR Commit: c575280eed4e562e90ba6b9b7a6675353e532725 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-31 22:18:25 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: 031beb8e23f96e6f4894f56b550dd49d0c2a729b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-29 16:04:28 +0200 Commit message: Updated code to include separate cut-offs for ERpos & ERneg, as well as separate cut-offs ER(pos/neg)/HER2 (independent of HER2 status) based on the above cut-offfs. Note: The combined cut-offs will be released in the next submission Package: BreastSubtypeR Commit: 93ba44156f95a90bb74440d472157107e5ef0908 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 20:13:37 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: efee177e7f94d079d424ad79467615a63ce71698 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 2c6cfcacdc3550df0916ecb54833275bf2b9f04f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: d0154df0200108179568a150e1487e592a34e20a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 6a0be72275efbb8b9828b8765834d1ce97521134 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 3cf5afd43c31eeec90045902e6a082d82013bbf7 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: e91120bb63753900c47f80206b0662aef090c98a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: c09d132b8993a81ad16143b2ddbd5fb6b6f36f8b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 18:32:39 +0200 Commit message: Updated NEWS.md, BreastSubtypeR_methods.R, and minor updates to Utilities.R and data_doc.R Package: BreastSubtypeR Commit: 10f36184b66a9a0703d4296c9311b5ed1fc03e23 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 15:16:50 +0200 Commit message: Shiny app normalization clarification Package: BreastSubtypeR Commit: 24740ca0d3f45e43e674d247778b8e003871361c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:57:22 +0200 Commit message: Replaced the adaptive filtering as it was producing a reduced gene list for NC-based methods. Instead I introduce the calculation of UQ in the positively expressed subset and apply those calculcated factors to the full matrix. 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<emmanouil.sifakis@ki.se> Date: 2025-08-27 15:10:09 +0200 Commit message: CITATION added Package: BreastSubtypeR Commit: e8fcac0bcab82793b586f5ffc8c930a0002ac609 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-21 11:29:40 +0200 Commit message: Merge pull request #89 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 0c75bf90f3070408ec5a156edf84b9c0bc70250b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:29:14 +0200 Commit message: update new features Package: BreastSubtypeR Commit: a99a93e94a90d6a715d64daedbe2e1f886f87917 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:27:58 +0200 Commit message: update new features Package: BreastSubtypeR Commit: c9f28c19c39695ad8a84ee4aa929c352be00e229 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 18:11:51 +0200 Commit message: Merge pull request #88 from yqkiuo/BranchQiao Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: e4a62355017220fe89ec8ea09376a0a56060de7c Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 18:11:26 +0200 Commit message: Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: 1993ab3e50725d01e8980a00eeaec8f0b0b766c4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:48:10 +0200 Commit message: Merge pull request #87 from yqkiuo/BranchQiao 1.1.1 Package: BreastSubtypeR Commit: 5d928ed37d8d0f47dd0392057846c43dc12e3dea Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:47:44 +0200 Commit message: 1.1.1 Package: BreastSubtypeR Commit: 52faaf9d7980c6d36524bcabbdcffe1f0fb92a0a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:39:51 +0200 Commit message: Merge pull request #86 from yqkiuo/BranchQiao 1.0.1 Package: BreastSubtypeR Commit: 35eef13e343edd2f9c6a1c26d780c97f470ac6c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:38:55 +0200 Commit message: 1.0.1 Package: BreastSubtypeR Commit: 6abaf3b4ae3d1772babec19c83d49c04728daa06 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-27 09:49:16 +0200 Commit message: Merge pull request #85 from yqkiuo/BranchQiao general update Package: BreastSubtypeR Commit: 453e9aac8dc81b86987e53e60659f2c97f6ba403 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-27 09:48:42 +0200 Commit message: general update Package: BreastSubtypeR Commit: 226607c2ae42706346a1e8911d1f2f82a5ca1490 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 19:12:11 +0200 Commit message: Merge pull request #84 from yqkiuo/BranchQiao v1.1.1 Package: BreastSubtypeR Commit: d773d4401e93ec12006f4e79122cbee8247d80d7 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 19:02:45 +0200 Commit message: v1.1.1 Package: BreastSubtypeR Commit: e74e86a2cfdf6daf92ed180095d27619cd45cd54 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:44:06 +0200 Commit message: Merge pull request #83 from yqkiuo/BranchQiao Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: fd30082d86b34d3ced41b7a7c385e01448c19794 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:41:43 +0200 Commit message: Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: 74145000a4ce350ca0e787fe5c459b79318b3edb Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:25:01 +0200 Commit message: Merge pull request #82 from yqkiuo/BranchQiao Bug fixes and minor improvements Package: BreastSubtypeR Commit: 1a5cb6636acfbd2ad1fc7c290bfba875dd2b22b0 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:24:35 +0200 Commit message: Bug fixes and minor improvements Package: BreastSubtypeR Commit: 4a895b8a8a149e0199b85eeaa19b6769dd8382df Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:27:17 +0200 Commit message: Merge pull request #81 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 4a03138457415f0164139373ee34038bd07ad300 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:21:40 +0200 Commit message: Update DESCRIPTION Package: BreastSubtypeR Commit: 856c6f8f91de5339988cf4c315bcaf96247f37d5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 10:39:20 +0200 Commit message: general update Package: BreastSubtypeR Commit: e35db8756a5fa3f30bf4addbeacd58145589e16b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:18:47 +0200 Commit message: general update Package: BreastSubtypeR Commit: 2e60c2222d3e9fdf48d3262ba087b447a95119a9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:03:00 +0200 Commit message: general update Package: BreastSubtypeR Commit: 7cfcfe95b2761178d17cc2af122f61883e7dc666 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:50:06 +0200 Commit message: update general Package: BreastSubtypeR Commit: b30131f2c073711d4b42e38af49bef1849da20c5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:48:53 +0200 Commit message: Update RawCounts para Package: BreastSubtypeR Commit: 6fa4d83d00b30727be9b1d4fd3798015fad0442a Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:32:10 +0200 Commit message: debug ROR Package: BreastSubtypeR Commit: ba045196fcd4a3bff148b3497a82f3f87d6bb324 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:31:55 +0200 Commit message: refine "-1" in parker.original Package: BreastSubtypeR Commit: b5e6254539fd38e41109056b2ddff7d36e0f9c19 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:15:41 +0200 Commit message: refine "-1" in parker.orignal Package: BreastSubtypeR Commit: bc7d097164cb411bfc4b40d5513073ae1bac35d8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:39 +0200 Commit message: 0.00.0 Package: BreastSubtypeR Commit: 5d966c161e4cdae464dd16d48421f6d5a4e26461 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:30 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 81f77832a0d7f8f5b8b70403616fe165ff96862d Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:08 +0200 Commit message: debug data type Package: BreastSubtypeR Commit: 8471668b9b9b43c3e27a87faa458488a8fba7f05 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:56 +0200 Commit message: debug BS_Multi Package: BreastSubtypeR Commit: 01fa8b576ca237667ed8a792477638cd4b023dbd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:34 +0200 Commit message: clear author Package: BreastSubtypeR Commit: a86f573778ed992a3d2dbb698b4c9c00a15619c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:20 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 00d2b9c5d71c6830e845dcddcb810b9640666207 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:33:01 +0200 Commit message: debug AUTO Package: BreastSubtypeR Commit: 8b3f7c2ef2d45cf772511a7290ba0a31baa43b62 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:32:46 +0200 Commit message: debug bad PCAPAM50 Package: BreastSubtypeR Commit: c70f4c9b0d64da1940659ae9a826d8221be05a32 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 09:32:30 +0200 Commit message: debug PCAPAM50 </div> </div>
Merge pull request #71 from rcavalcante/disk-cache build_annotations() rebuilt every annotation on every call (about 30 s for the hg19 gene annotations). It now caches each built annotation and each downloaded file on disk with BiocFileCache, so later calls load them in seconds. For example, hg19 promoters + exons go from 15.6 s to 1.7 s. - The cache is in tools::R_user_dir('annotatr', 'cache'); options(annotatr.cache = ...) overrides it. - Each annotation type is cached separately, so any combination reuses earlier builds. - Cache names include the annotatr version, and for gene annotations the TxDb/org package versions (or the EnsDb), so updates cause a rebuild. - A cached file that can't be read is removed and rebuilt automatically. - Downloads are retried 3 times, partial downloads are never cached, and all URLs use HTTPS. A partial UCSC download broke scmeth's examples on the kunpeng2 release builder. - New: cache = FALSE in build_annotations(), list_cached_annotations(), clear_cached_annotations(genome), and ?`cached-annotations` with a troubleshooting guide (stale or corrupted entries, failed downloads, disk space, cluster home directories, SQLite locks, AnnotationHub's own cache). The vignette gains a "Caching Built Annotations" section. - Requires R >= 4.0 (for tools::R_user_dir) and imports BiocFileCache, which AnnotationHub already installs. Tests use a temporary cache and never touch the user's cache. The build tests use cache = FALSE so they still test the sources. 9 new cache tests, most of them offline. Tested with docker/check.sh (Bioconductor 3.24 devel): 258 tests pass, 0 skipped. R CMD check 1 NOTE (existing). BiocCheck 0 errors. Version bumped to 1.39.5. 🤖 Generated with [Claude Code](https://claude.com/claude-code)
Document the cached-annotations value, and run cache examples Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Cache built annotations and downloads on disk build_annotations() rebuilt every annotation on every call, e.g. about 30 s for the hg19 gene annotations. Now it saves each annotation it builds, and each file it downloads, with BiocFileCache, and loads them later in seconds. Cache names include the annotatr version, and for gene annotations the TxDb and org package versions, so updates cause a rebuild. A cached annotation that can't be read is removed and rebuilt. Add cache = FALSE to build without the cache, list_cached_annotations() and clear_cached_annotations() to manage it, and ?`cached-annotations` with a troubleshooting guide. Downloads are retried 3 times and use HTTPS, since a partial UCSC download broke scmeth's examples on a release builder. Tests use a temporary cache, and the build tests use cache = FALSE so they still test the sources. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Merge pull request #140 from JohanHartmanGroupBioteam/maintenance/maintainer-1.5.3 Transfer the maintainer role to Emmanouil G. Sifakis; bump to 1.5.3
Transfer the maintainer role to Emmanouil G. Sifakis; bump to 1.5.3 DESCRIPTION Authors@R: Emmanouil G. Sifakis takes the "cre" role, Qiao Yang keeps "aut"; author order unchanged. man/BreastSubtypeR.Rd carries the Maintainer line that roxygen derives from Authors@R. NEWS records the change and the repository's move to the JohanHartmanGroupBioteam organization. Version 1.5.3 so that Bioconductor devel rebuilds with the new maintainer address. No code changes.
Merge pull request #70 from rcavalcante/test-overhaul Moves the tests to testthat 3rd edition and makes them independent of each other and of file order. Tests: - Files renamed test-.R; no context(). Shared data comes from functions in helper-fixtures.R instead of top-level objects. - Custom annotations use unique cache names. The BED4/BED5 read_annotations() tests passed only because an earlier test had cached the entry they checked. - Assertions compare values (expect_named, expect_setequal, expect_length, expect_contains) instead of expect_equal(all(...), TRUE), and check contents (coordinates, strands, IDs, scores), not just classes. - Plot tests build each plot with ggplot_build(), and some check the plotted data. - Build tests are back. Light tests (hg38 CpGs, hg19 FANTOM enhancers, hg19/mm10 GENCODE lncRNA) run whenever online, including on Bioconductor's builders. Full tests (gene and CpG annotations for all 15 genomes, hg38 lncRNA, lifted-over enhancers, chromatin) run with ANNOTATR_FULL_TESTS=true, which docker/check.sh sets. check.sh also keeps downloads in a persistent annotatr-cache volume. Fixes found by the new tests: - plot_categorical() with the default fill = NULL failed when drawn. It is fixed, and the All bar no longer triggers a ggplot2 warning without fill. (Backported to RELEASE_3_23 as 1.38.2.) - org.Dr.eg.db was missing from Suggests, although danRer10/danRer11 gene annotations need it. Tested with docker/check.sh (Bioconductor 3.24 devel): 227 tests pass, 0 skipped, ~3 min for tests and ~7 min total. R CMD check 1 NOTE (existing). BiocCheck 0 errors. Version bumped to 1.39.4. 🤖 Generated with [Claude Code](https://claude.com/claude-code) </pre> </div> Package: annotatr Commit: 2b24c09ab881f7441b4dc6a4f012a5ebdd371746 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 21:07:19 -0600 Commit message: Suggest org.Dr.eg.db, needed for danRer10 and danRer11 gene annotations Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 02134cc5afdad01933177b4591849f0ccc721087 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 20:51:41 -0600 Commit message: Build basicgenes and cpgs per genome in the full tests Building every gene annotation type for every genome ran out of memory in an 8 GB Docker VM. Only the gene model and CpG sources differ between genomes, so test those per genome, and the other gene annotation types once for hg19. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: a8511f7ebad475a279b74808ca182be26897398a Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 20:43:59 -0600 Commit message: Overhaul tests for testthat 3 and fix plot_categorical() with no fill Move to testthat 3rd edition, and rename the test files to test-.R since they no longer depend on file order. Shared data comes from helper-fixtures.R. Custom annotations use unique cache names, fixing tests that passed only because an earlier test had cached the entry they checked. Assertions compare values, e.g. expect_named() and expect_setequal(), instead of expect_equal(all(...), TRUE). Plot tests now build the plots with ggplot_build(). This found that plot_categorical() with the default fill = NULL failed when drawn; fix it, and map the All bar to a column so it isn't dropped without fill. Restore the build tests: small downloads run whenever online, and full builds for every genome run with ANNOTATR_FULL_TESTS=true, which docker/check.sh now sets, along with a persistent download cache. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> </pre> </div> Package: annotatr Commit: 50820a27a6907b9117c4abcb13f85f63b662e2dd Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 20:21:42 -0600 Commit message: Merge pull request #69 from rcavalcante/deprecate-randomize Deprecate randomize_regions() in favor of a background comparison Package: annotatr Commit: 09af749e4addbdd4602a8d4866b3b64bccb137d4 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 20:16:06 -0600 Commit message: Deprecate randomize_regions() in favor of a background comparison Regions placed uniformly at random across the genome are a poor null model: real regions come from a much narrower set of locations, so most data look enriched in genic and CpG annotations. Deprecate randomize_regions() and point to annotating a background of the regions the data could have come from, or regioneR::permTest() and regioneR::resampleRegions(). summarize_annotations(), plot_annotation(), and plot_categorical() now label annotated_random as "Background" instead of "Random Regions". The examples, tests, and vignette compare DM regions to all tested regions. Also fix the allow.overlaps documentation, which controls whether random regions overlap each other, not the input regions. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: ab795d19f14a4c80116f8cd5b8c3011bf7ca9215 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 20:07:14 -0600 Commit message: Merge pull request #68 from rcavalcante/docker-check Add Docker-based Bioconductor devel check Package: annotatr Commit: bb5c6c454ec3a9e29d7810976372e2339e39e0ef Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:18:57 -0600 Commit message: Add Docker-based Bioconductor devel check docker/check.sh runs R CMD build, R CMD check, and BiocCheck on the committed HEAD in a Bioconductor devel image with annotatr's dependencies preinstalled. Dependencies added since the image was built are installed at check time. Use --rebuild to refresh the image. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: ec750310fa1cb27af75186f72efb400e9c6ffb42 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 19:45:17 -0600 Commit message: Merge pull request #67 from rcavalcante/lncrna-gencode Fix hg38/mm10 lncRNA annotations by downloading from GENCODE Package: annotatr Commit: ea699780298650a09d66c8eff0c3d61ce22985b3 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:39:26 -0600 Commit message: Fix hg38/mm10 lncRNA annotations by downloading from GENCODE AnnotationHub removed its GENCODE resources, including AH75123 (hg38) and AH49550 (mm10), on 2026-04-28, so hg38_lncrna_gencode and mm10_lncrna_gencode failed. Download the same GENCODE releases directly over HTTPS, and move hg19 from FTP to HTTPS. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 0d593dc6eabebb817c27162c1003b90e1764c722 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 19:36:20 -0600 Commit message: Merge pull request #66 from rcavalcante/oviariramb2 Add support for sheep (ARS-UI_Ramb_v2.0) as 'oviariramb2'. Gene annotations come from the Ensembl 113 EnsDb in AnnotationHub (AH119381), so tx_id and gene_id are Ensembl IDs. CpG islands come from the UCSC GenArk assembly hub. Sequences use UCSC-style names (chr1, ..., chrUn_*). Package: annotatr Commit: 86641326dc4047c9762fd9878876840fd5024d66 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:17:58 -0600 Commit message: Version bump Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 9781edf27897d6c77bd3f2e4b09ab5827f4af05a Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 18:57:30 -0600 Commit message: Add sheep (ARS-UI_Ramb_v2.0) as builtin genome oviariramb2 Sheep has no TxDb.* or org.*.eg.db packages, so gene annotations are built from the Ensembl 113 EnsDb in AnnotationHub (AH119381), with Ensembl tx_id/gene_id and symbols from the EnsDb. CpG islands, chromosome sizes, and chromosome aliases come from the UCSC GenArk assembly hub, and sequences are renamed to UCSC-style names. Genomes like this are registered in GENARK in R/utils.R. The TxDb code path is unchanged; hg19 gene annotations are identical to devel. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: methodical Commit: b39d98d2d4ac504cbd6f80a62b999406f694e993 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-25 02:16:59 +0100 Commit message: Merged changes Package: methodical Commit: 20761f4370f86ba9ee7211e4b47c6b3c63a607e4 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-25 00:50:46 +0100 Commit message: Updated liftover function Package: methodical Commit: 02ddeb7f0e3a2c852b0adcff0211e492dc0cdf3c Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-22 20:12:54 +0100 Commit message: update Package: methodical Commit: a39fa2dd4b3c1a417085c4a09ec882b3bc738522 Author: Richard Heery <richardheery@gmail.com> Date: 2026-08-27 17:25:10 +0100 Commit message: update Package: methodical Commit: ffc716b54e4118b1ced24b811211a8788e304a92 Author: Richard Heery <richardheery@gmail.com> Date: 2026-05-01 15:20:44 +0100 Commit message: Readded vignettes Package: methodical Commit: 464c57e15c8f97f697d8ce9373316805f6e73be1 Author: A Wokaty <andres.wokaty@sph.cuny.edu> Date: 2026-04-28 09:02:10 -0400 Commit message: bump x.y.z version to odd y following creation of RELEASE_3_23 branch Package: methodical Commit: 4215fb6e084e162ff4dd4201b1d4420d9c2533db Author: A Wokaty <andres.wokaty@sph.cuny.edu> Date: 2026-04-28 09:02:10 -0400 Commit message: bump x.y.z version to even y prior to creation of RELEASE_3_23 branch Package: methodical Commit: d169b576deecb57d9477aabf9196922e04e885ea Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-27 17:22:40 +0100 Commit message: Final commit for 3.23 Package: methodical Commit: 81883848e66b52382f58d48cd4ee465be8189db3 Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-24 22:47:39 +0100 Commit message: Fixed vignettes Package: methodical Commit: a4d3e6da701f57033dfd6ca9feba64d3c1c11a6a Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-27 21:38:18 +0100 Commit message: Final commit for devel Package: lcmsPlot Commit: f451123907b59cd6a330688b933ff3fd6c2bd25e Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 22:11:26 +0100 Commit message: feat(features): name XChromatograms features from row names Package: RiboDiPA Commit: cf0c36801194370381bd3ceb90f5b2594e1247a1 Author: Dr. Ji-Ping Wang <jzwang@northwestern.edu> Date: 2026-09-24 20:46:05 +0000 Commit message: Fix vignette build error: convert Bioconductor objects via as.data.frame() before as.data.table() Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01LiK5WUAPmNmkHCv3HPRNog Package: lcmsPlot Commit: 18f10a9c7dfe282c08aa33c53c23566a192a7a6b Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 20:46:18 +0100 Commit message: feat(features): name manual features from row names or a feature_id column Package: scRNAseqApp Commit: 9421c5d26e1bf497251c6ccfb6526e9f612852c4 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-24 15:27:00 -0400 Commit message: Update the gene table only when file changed. Package: leapR Commit: 28136ae57197bd5fa892860b5017d5c9f1f0bb2c Author: Sara JC Gosline <sara.gosline@pnnl.gov> Date: 2026-09-24 10:42:52 -0700 Commit message: updated Package: geneslator Commit: b62f543f5874c5167105c705e32d15f0da8d4181 Author: Giovanni Micale <gmgmicky@gmail.com> Date: 2026-09-24 19:11:07 +0200 Commit message: Updated README and vignettes Package: DropletUtils Commit: ba4152de3596abef3bd69f9ce441aec8ea4c912e Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-25 02:56:55 +1000 Commit message: Set SVT leaves to NULL for empty columns when loading MatrixMarket data. (#133) Mostly backports of the updated C++ code and associated tests from crio. Package: DropletUtils Commit: ea9a299b36c52a71f305d612a97d6a69a20e25d0 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-24 18:21:09 +1000 Commit message: Merge remote-tracking branch 'upstream/devel' into devel Package: DropletUtils Commit: b423c0fafe7271b173317b407a8538bbbcbede5c Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-07-29 23:53:07 +1000 Commit message: Shorter chunk size for sparse data and indices for easier streaming. Package: SparseArray Commit: 9a0e93056f05879a15057e3d597d0102068f09bb Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-24 09:04:25 -0700 Commit message: some clarification about SVT leaf representation Package: lcmsPlot Commit: 14a5af5c83db317bc0d44e2b32ba8acfb54ab66f Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 16:23:45 +0100 Commit message: feat(features): use featureDefinitions rownames as feature identifiers lcmsPlot derived its own xcms::groupnames-style MT labels from mzmed/rtmed, discarding the row names featureDefinitions() already carries. Feature identifiers now come from those row names, so renaming the rows is enough to get meaningful labels onto a plot. Identifiers matching no feature are now reported with a warning naming them, instead of being dropped silently into an empty plot. </pre> </div> Package: scRNAseqApp Commit: eb1f132e925ec26574be9a7055b51b67cf60b2cf Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-24 11:17:02 -0400 Commit message: Remove the duplicated notification for search. Package: rhdf5 Commit: 1c6ed01eaf8682004f647a15a200df1d0f55b0f6 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:21:40 +0200 Commit message: Fix duplicated logo Package: rhdf5 Commit: cab7d0212538b900883c3c6a80f27710cd80ebc5 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:03:23 +0200 Commit message: Add link to de.NBI survey Package: Rarr Commit: 56ddfff1ac32f46151b215a015cbc00b5d77744e Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:16:34 +0200 Commit message: Add deNBI funding acknowledgement and survey in README Package: Rarr Commit: accfb8f20be9b7fefe76e1b35a531704bcc8960b Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 11:06:37 +0200 Commit message: Use vectorized .store_check_exist() call Package: Rarr Commit: cbf89cd3891e3e0cdfeb474aaf153d1324b43d96 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 11:05:56 +0200 Commit message: Define is_structured once Package: Rarr Commit: 87389fada7676ae09ce5bfd3a3a4e74ba3708836 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 10:47:50 +0200 Commit message: Register bfloat routine Package: biomaRt Commit: 3e1a0768933f6c3e00895e02119e4f6e36050dac Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:05:20 +0200 Commit message: Add link to de.NBI survey Package: ISAnalytics Commit: 6e03f52a7925332d38562e8c2501425e92f89184 Author: francescogazzo <francesco.gazzo@gmail.com> Date: 2026-09-24 12:19:37 +0200 Commit message: Update collision filtering and bump devel to 1.23.2 Package: distinct Commit: 7ec08672fd2177c33c85779a82ab12deb8232802 Author: Simone Tiberi <simone.tiberi@unibo.it> Date: 2026-09-24 11:57:02 +0200 Commit message: T_obs added in results Package: distinct Commit: e749b22cf8c3c8eb925d3a293b916b7c11e75605 Author: Simone Tiberi <simone.tiberi@unibo.it> Date: 2026-09-24 11:49:37 +0200 Commit message: bug fixed in distinct_test Package: MsBackendMetaboLights Commit: 1b126b45bede3db584a54168617397078cc5c789 Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com> Date: 2026-09-24 11:52:26 +0200 Commit message: Merge pull request #26 from rformassspectrometry/jomain Add random sleep breaks to reduce failures on build systems Package: MsBackendMetaboLights Commit: c28ee3bc500c3e2a3764932bae457431cac07563 Author: Johannes Rainer <johannes.rainer@gmail.com> Date: 2026-09-24 08:45:39 +0200 Commit message: Add random sleep breaks to reduce failures on build systems - Adding/changing to random sleep times aiming at reducing the recurrent failures on the Bioconductor build system (most likely due to rate limitation from MetaboLights). Package: cellNexus Commit: 67fa18ce068ae3e0fe84da1f942a6d9a1138e052 Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 14:44:48 +1000 Commit message: Merge pull request #159 from myushen/master fix website examples Package: cellNexus Commit: 3ab2cd31f7d4a7acc40758abeed48bc0f3d8435c Author: myushen <mengyuan.shen@outlook.com> Date: 2026-09-24 14:25:14 +1000 Commit message: fix website examples Package: cellNexus Commit: 4719fb49b937acd11c9f898275920555e094c65d Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 13:37:28 +1000 Commit message: Merge pull request #153 from MangiolaLaboratory/copilot/rename-join-census-table Soft-deprecate `join_census_table()` in favor of `get_census_metadata()` Package: cellNexus Commit: 8b217f783900d3107ab0d07c0d9b57083a1e6c77 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-09-24 11:54:08 +1000 Commit message: unit test Package: cellNexus Commit: 3e4d038b291bc9ba79f306456e63fa4660958d47 Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 10:44:58 +1000 Commit message: Merge branch 'master' into copilot/rename-join-census-table Package: cellNexus Commit: 9aca6c192558b021c1c41b9071564d8daf4d7814 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-08-27 12:12:50 +1000 Commit message: soft deprecate since 0.99.27 Package: cellNexus Commit: cd885c844de21fea70d10ee653fc9c95386b8bd5 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-08-27 12:08:50 +1000 Commit message: Merge remote-tracking branch 'origin/master' into rename-join-census-table merge from origin Package: cellNexus Commit: 13ffb5d261f878cacd79484700b35b9a964cef67 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:33:16 +0000 Commit message: Trim redundant mock assertion Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: abf37b553b5800c09ee3e9deb65ee9d5246d9ab4 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:32:37 +0000 Commit message: Verify Census helper mock before wrapper call Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: a4bf9cc52cf658c48d4f00fdfbdd55ec094f4484 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:32:04 +0000 Commit message: Exercise deprecated table argument compatibility Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: 4b46e68aebf2b38ce850298cc145bdf52c84d14f Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:31:37 +0000 Commit message: Correct Census deprecation test assertions Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: 1515648f80a96e03452c82ac5e602057710f512e Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:31:02 +0000 Commit message: Stabilize deprecation warning test Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: d2fd0cfdaad895c2e60be674d50076ad04cecf24 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:30:23 +0000 Commit message: Soft-deprecate Census join helper Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: e7ae2c78928ba1b3bbb6f575e117365976743d72 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:27:22 +0000 Commit message: Initial plan Package: mia Commit: 416de1c5a6b73b70f42571f8a3d36d0294dcb770 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-24 07:54:25 +0300 Commit message: Update documents and namespace Package: clusterProfiler Commit: 33b36f13f3729b099a8d6fc20694831b7a5c62d9 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 12:48:46 +0800 Commit message: fixed r check Package: LRDE Commit: 710586499a483617f94c2d665b87a03be62d6531 Author: Ziyang Liu <jacobleo773@gmail.com> Date: 2026-09-23 18:45:18 -0700 Commit message: Improve numerical stability and bump version to 1.1.2 Package: DOSE Commit: 5846d72fe047f1de66d506a21c117d400e4a3ef8 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:21:11 +0800 Commit message: fixed r check Package: DOSE Commit: 9011c8c053e345cdca45bf1edb93fe66b7f80417 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:14 +0800 Commit message: gseDisease() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family. Package: ReactomePA Commit: e295d309811933101f2e808814212d3244f5c6aa Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:10:04 +0800 Commit message: update docs Package: ReactomePA Commit: 586975c51fadc162d78418ff1132eddcb009b157 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:13 +0800 Commit message: gsePathway() exposes eps and forwards extra arguments, #47 gsePathway() was the only GSEA wrapper in the family missing both eps and ..., so eps could not be controlled and additional enrichit::gsea_gson() arguments could not be passed through. Both are now supported, matching clusterProfiler::gseKEGG(). Package: ReactomePA Commit: 396a55c38c765045b0309c6935b663dd334e7c3d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:03:02 +0800 Commit message: ReactomePA 1.99.2: seed argument and a faster prepareReactomeNetwork() - gsePathway() and nsePathway() expose an explicit seed parameter for reproducible GSEA results, aligned with enrichit::gsea_gson(). - prepareReactomeNetwork() no longer round-trips through graphite::convertIdentifiers()/pathwayGraph() per pathway; it builds a single UNIPROT->Entrez map up front and converts edges with vectorized lookups, keeping mclapply() parallelization over pathways. Output is unchanged (same nodes and edge values; node ordering may differ). Default cores is now 1 instead of detectCores(). Package: ReactomePA Commit: a9a8627182db7226655362793f6b6c22c25e8d7b Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-08-15 18:42:41 +0800 Commit message: parallelize prepareReactomeNetwork pathway conversion via mclapply The one-time Reactome network build converts ~2700 pathways serially in R (convertIdentifiers/pathwayGraph/graph_from_graphnel per pathway). The conversions are independent, so the loop now runs over mclapply() with a new 'cores' argument (default getOption('mc.cores', detectCores())); mclapply falls back to serial on Windows and preserves input order, so the resulting edge set - and hence the cached network - is unchanged. Measured on the GSE53757 demo: serial build ~35-41 min; parallel build 614 s at 16 cores and 655 s at 56 cores; output byte-identical to the serial baseline. Scaling saturates at ~4-5 effective cores because the graphite identifier conversion is hash-lookup-bound. Package: ReactomePA Commit: 13cb4b3cbc4616e214d63ee59a3e42bba48b0a4c Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-07-09 15:24:15 +0800 Commit message: nsea Package: ReactomePA Commit: 4edeca90aedb3afdaa29b838323bbdabad62c391 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-04-29 12:24:13 +0800 Commit message: update bioc version Package: meshes Commit: 5732c93b839f7f820eb4501e3cff468737bfa71a Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:09:48 +0800 Commit message: bump version Package: meshes Commit: e7498dc7737b09bffacef28a72d666693e7be51d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:14 +0800 Commit message: gseMeSH() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family. Package: meshes Commit: 01c764a9285d4c77e77ff630885b8a79077cff10 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:03:02 +0800 Commit message: expose a seed argument on gseMeSH(), meshes 1.39.2 Forward an explicit seed to enrichit::gsea_gson() so GSEA runs are reproducible, and apply pvalueCutoff to both pvalue and p.adjust inside the enrichit engine (requires enrichit >= 0.2.2). Package: GOSemSim Commit: 769cd22f90eec52f67039121c265462c701680ad Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 08:58:26 +0800 Commit message: update docs Package: GOSemSim Commit: ca626082247cbb24fb95b5098558b71b0592e2be Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 12:55:48 +0800 Commit message: computeIC: take the term universe from GO.db, not the shipped gotbl table computeIC() decided which terms to score from the `gotbl` table shipped in data/: goids <- unique(godata[godata$Ontology == ont, "go_id"]) That table was last rebuilt in 2021-07, so every term GO.db has added since then was given no IC at all, and the IC-based methods returned NA for it even though its descendants carry annotations and its IC is computable. This is issue #33, and the reporter's diagnosis ("a conflict between the pre-calculated gotbl.rda and the local version of GO.db") was right. Measured against the current GO.db / org.Hs.eg.db, the number of annotated terms that can actually be scored: ontology annotated before now gained BP 11293 11126 11293 +167 CC 1832 1787 1832 +45 MF 4777 4410 4777 +367 and nothing loses an IC. The missing terms also biased every other IC, because they were counted in the `sum(gocount)` denominator but could never contribute to an ancestor's descendant sum. Terms finite under both universes agree for 92-95% of entries with a mean absolute difference of 0.003-0.011; about 0.3% were overestimated by more than 0.5, all of them in the "too specific" direction, which is what the mechanism predicts. The universe is now names(getAncestors(ont)) -- exactly the terms of that ontology in the installed GO.db, root included, and already cached by onto_relation() -- unioned with the annotated terms, so a term the local annotation package still uses keeps its IC even if GO.db has retired it. The same root cause also affects the `gotbl` that the Wang method walks, where a term newer than the table scores 0 instead of NA. That is left for a separate change because fixing it means either regenerating the shipped data or building the relation table at runtime. test-ICMethods.R now asserts that every annotated term gets a finite IC. Package: GOSemSim Commit: 32be2e18cb86a9ef84f796e174a39a1ac7658513 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 12:32:22 +0800 Commit message: cache ontology mappings, and load Rcpp so the compiled IC methods work Two independent defects, found while fixing TCSS. getAncestors(), getParents() and getOffsprings() each rebuilt their whole mapping on every call -- AnnotationDbi::as.list(GOBPANCESTOR) costs about half a second -- while callers only ever pick out one or two terms with `[[ID]]`. A single geneSim() call rebuilt the same mapping hundreds of times. The mappings are derived from a source that is already cached (GO.db is static, load_onto() caches the OntDb), so they are now cached per ontology rather than per term. A 5x5 termSim on previously unseen terms drops from 2.5 s to 0.5 s, geneSim from 5.6 s to 0.6 s cold and 0.12 s warm, with byte-identical results. The cache holds about 85 MB for BP and 110 MB for all nine mappings. Separately, Rcpp was listed in LinkingTo only, so loading GOSemSim never loaded the Rcpp namespace. The wrapper generated by compileAttributes() instantiates Rcpp::RNGScope, which resolves enterRNGScope through R_GetCCallable("Rcpp", ...), so every Resnik, Lin, Jiang and Rel call failed with "function 'enterRNGScope' not provided by package 'Rcpp'" unless the user happened to attach Rcpp first. importFrom(Rcpp, evalCpp) was dropped in ea7b2028 (2016) and is restored here. No test reached the compiled code and the vignette only mentions those methods in prose, which is why this went unnoticed for so long; test-ICMethods.R now covers all four methods on three ontologies. The ontology cache is also covered: test-GO.R checks that each mapping is cached under the ontology and is identical to what GO.db holds. Package: GOSemSim Commit: 50c6bd241416e703074e5e8e2839cf2cafe7133e Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 17:17:24 +0800 Commit message: correct the scope of the TCSS degeneracy fix The previous commit described the degeneracy as "a cluster with a single member", but calc_maxIC() indexes `all <- IC[cluster]; all <- all[is.finite(all)]`, so the real condition is "exactly one member carrying a finite IC". A cluster with several members where all but one have infinite IC is equally degenerate, and the old `length(all) == 0` guard did not cover it. Re-measured with the correct criterion (swapping calc_maxIC in and out of the namespace in one process so both versions see identical input): - the set of clusters whose ICA changes equals the set with exactly one finite-IC member, at every cutoff and ontology tested (BP 1/2/3.5/4/5/8, MF 3.5, CC 3.2) -- so the change is confined to the degenerate clusters; - the defect was not BP-only. 300 random pairs, % scoring exactly 1: BP 99.3% -> 0.0%, MF 27.3% -> 0.0%, CC 98.7% -> 0.0%; - the counts are larger than the single-member count suggested: BP has 1 degenerate cluster at cutoff 3.5 but 5 at cutoff 4 and 1141 at cutoff 5; MF has 3 and CC has 3, and the CC set includes the CC root GO:0005575. Fix the NEWS wording and the code comment to match, and make the regression test assert on the finite-IC criterion rather than on cluster size. Package: GOSemSim Commit: 2df9985c372e931e89994d25fe84f483b50c01fe Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 16:49:30 +0800 Commit message: fix TCSS similarity collapsing to 1 for nearly every term pair A cluster with a single member has no internal spread, so normalising it by its own maximum IC made its ICA identically 1 regardless of how general or how specific that term was. GO:0008150, the root of BP, is such a cluster and is a common ancestor of every BP pair, so `max(sim_value)` in tcssMethod_internal() returned 1 for 99.7% of random BP pairs and `mgeneSim(measure = "TCSS")` was an all-ones matrix. Fall back to the global maximum IC for single-member clusters. The collapse is not specific to the root: scanning cutoffs shows GO:0050896 and GO:0046337 also become single-member clusters for BP, and GO:0052745 does for MF, so special-casing the root would only have papered over one instance. After the change, 300 random BP pairs give min 0.0004 / median 0.0234 / max 0.5296 with 0% equal to 1, and ica[["GO:0008150"]] drops from 1 to 0.000414 (= IC[root] / global max IC). Add a regression test and bump to 2.39.3. Package: GOSemSim Commit: 34c4ae3b85f10b9107ca6feffbd6e6eb0a0206db Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 12:17:51 +0800 Commit message: fix TCSS for terms belonging to multiple clusters GO is a DAG, so a term can have several meta-term ancestors and `tcssdata$clusid[[term]]` is then a vector rather than a scalar. Indexing `ica` with `[[` then attempts recursive indexing, which raises "subscript out of bounds" (or "recursive indexing failed at level 2" depending on which element is hit first) and aborts any TCSS calculation for the whole ontology. Subset the list of clusters with `[` instead. This restores the behaviour already present in the Bioconductor release (2.38.3); the devel implementation had regressed. Adds a regression test covering a term that sits in more than one cluster. Package: clusterProfiler Commit: a38e9201b8ee6ad6f64fc1a5bf691421efc9d928 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 04:39:17 +0800 Commit message: enrichMKEGG()/gseMKEGG() accept a GSON, #623 enrichKEGG() and gseKEGG() take either a species code or a GSON object, but the module wrappers only took a species code, so there was no offline route for module enrichment at all -- even though the download errors now tell users to build a local database. Passing a GSON raised an unrelated error from the organism mapper instead. Both now mirror the KEGG wrappers, including the "organism should be a species name or a GSON object" message. A GSON reports its own keytype, so @keytype is taken from it; the species path keeps returning "UNKNOWN" exactly as before. Also documents the GSON option on the KEGG `organism` parameter, which had never been mentioned for enrichKEGG()/gseKEGG() either. Package: clusterProfiler Commit: 285885443b912177daec101c606664b33b41cc37 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 04:21:19 +0800 Commit message: enrichGO(): restrict the annotation by evidence code, #160 Enrichment used every annotation in the OrgDb, including electronically inferred ones, so there was no way to avoid circular reasoning when the gene sets themselves came from in-silico evidence (dropping IEP for co-expression clusters) or to keep only curated annotations (dropping IEA). enrichGO() now takes `evidence`, appended last so positional callers are unaffected and threaded through both recursive paths. The filtered annotation is built by go_annotation_by_evidence() from a gene-centred select() of GOALL/EVIDENCEALL/ONTOLOGYALL, because the evidence code is a property of the gene-annotation pair and the previous term-centred mapIds() could not see it. Two semantics worth stating, both documented: the background changes with the annotation, so a filtered result is not a subset of the unfiltered one; and a filtered annotation is never cached, since the cache key is (organism, ont, keytype) only and reusing it either way would answer with the wrong annotation. A regression test pins the cache isolation down. Package: clusterProfiler Commit: fa71a3ef739a1ef44e695e69823126c94c703bdb Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 02:33:01 +0800 Commit message: fix: enrichGO() survives an unidentifiable OrgDb organism, #232 The cached-GO-data check compared the cached organism against get_organism(OrgDb) inside a bare if(). get_organism() returns NA for an OrgDb it cannot identify -- an AnnotationHub OrgDb, for instance -- and `if (NA && ...)` aborts the call with "missing value where TRUE/FALSE needed", which names nothing about organisms or caches. It bites on the second enrichGO() call in a session, because the first one populates the cache. The check is now go_cache_usable(), where every comparison goes through isTRUE() so an unidentifiable organism means "not cached" and the annotation is rebuilt. Extracting it also makes the cache-hit logic unit-testable without an OrgDb. Package: clusterProfiler Commit: a39c2f63d533e20d6c4d03fd3a35b18a418dd08e Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 02:14:56 +0800 Commit message: fix: Gff2GeneTable() reads Ensembl-style GFF3, #193 The function only looked for an NCBI/RefSeq `GeneID=` attribute. On an Ensembl GFF3 (which writes `gene_id=`) every extracted key was NA, and merging two all-NA key columns is a cartesian product: on the reporter's cat genome that is ~1.3M x 40k rows, which R refuses with "negative length vectors are not allowed". At small sizes the same bug passes silently, because unique() collapses the duplicated NA rows into a plausible-looking table of NA ids. Field names are now detected from the file: `GeneID` or `gene_id` for the identifier, and `gene`, `Name` or `gene_name` for the symbol. Detection requires an exact attribute key, because getGffAttribution()'s heuristic fallback also looks inside values and would otherwise return the identifier out of `ID=gene:ENSG...` when asked for `gene`. A file with neither identifier style stops with a message saying what is expected instead of merging on all-NA keys. Package: clusterProfiler Commit: 41dd01bb5c7a078bd19397131f06fd3db2d59bfc Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 01:38:26 +0800 Commit message: add_go_level(): expose the GO level of each enriched term, #793 GO enrichment results carried the term, its ontology and its statistics, but not how deep the term sits in the hierarchy, so users who wanted to keep a band of levels had to reconstruct GO depth themselves. go_level_map() now returns the GO id -> level map (1 = ontology root) built by breadth-first traversal of the GO.db CHILDREN graph; getGOLevel() is rewritten on top of it with identical output (verified against a pre-change baseline for BP/CC/MF at levels 1-6), and add_go_level() appends a `level` column to an enrichResult/gseaResult/compareClusterResult. The level is taken from the ontology each term belongs to, so ont = "ALL" results are labelled term by term. gofilter() and dropGO() had no test coverage; the new test file locks their keep/drop-by-level behaviour down. Package: clusterProfiler Commit: c117200bb63575df335911dcd478aa164dda528d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 23:52:42 +0800 Commit message: simplify() infers the GO ontology for enricher() results too, #369 The enrichResult method required x@ontology to be BP/MF/CC/GOALL, so an enricher() run over a GO collection (MSigDB C5 GO, a custom TERM2GENE built from GO annotations) had to have the slot assigned by hand before simplify() would accept it. The ontology is now inferred from the GO IDs exactly as for gseaResult (#753), and non-GO gene sets are still refused with a message saying so. Package: clusterProfiler Commit: e930b50044bf8bb4fb883ea940a631aceb57ff18 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 23:21:11 +0800 Commit message: simplify() a GSEA result whose gene sets are GO terms, #753 simplify() reduces redundancy with GO semantic similarity, so it needs the ontology of the terms. It only accepted x@setType in BP/MF/CC/GOALL, which rejected a GSEA run over a GO gene-set collection (MSigDB C5, a gson GO file, a TERM2GENE built from GO annotations) because @setType then holds the collection name. The ontology is now inferred from the GO IDs, with results spanning several ontologies simplified as GOALL; non-GO gene sets are still refused, with a message that says so. Package: clusterProfiler Commit: dc94b240c1a42333f111338f46fb3633df2271be Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 22:46:23 +0800 Commit message: warn when compareCluster() is given a non-character universe, #654 compareCluster() wraps each per-cluster call in suppressMessages(), which swallowed the underlying enrichment function's "`universe` is not in character and will be ignored" message. A numeric universe therefore looked accepted while silently having no effect. The guard is now raised once in compareCluster() itself, where it cannot be suppressed, with a regression test for both the non-character (warns) and character (stays quiet) cases. Package: clusterProfiler Commit: 61236b6fa01a7d6474152ed7043639596dae48d1 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:10 +0800 Commit message: gsePC() and gseWP() expose an eps argument Both wrappers now declare eps = 1e-10 and forward it through GSEA() to enrichit::gsea_gson(), matching GSEA(), gseGO(), gseKEGG() and gseMKEGG(), which already exposed it. Package: clusterProfiler Commit: 58559c7a5a9babe970d3a3dad5e9708efc42f70c Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 18:54:09 +0800 Commit message: fix enrichKEGG(organism='cpd') and report KEGG download failures clearly, #828 - gson_cpd(): use the 'compound' KEGG REST endpoint. KEGG retired /link/cpd/pathway, which now answers HTTP 400, so enrichKEGG(organism='cpd') and gseKEGG(organism='cpd') failed with an obscure download error. - kegg_rest(): report the failure where it happens, telling an unreachable network apart from an HTTP error status and from an empty response. These used to surface much later as an opaque error. - download.KEGG.Path() / download.KEGG.Module(): replace the is.null() guard, which could never fire because kegg_rest() never returns NULL, and stop with an actionable message when the downloaded annotation is empty or when the gene/pathway table shares no ID with the pathway-name table. Previously an empty annotation was returned silently and surfaced downstream as a misleading "No gene can be mapped", #146, #378, #561, #646. Package: SAIGEgds Commit: 29da3dd06bce9321bc520c75353e1c695057e0df Author: Xiuwen Zheng <zhengxwen@gmail.com> Date: 2026-09-23 19:12:31 -0500 Commit message: update vignettes Package: MSstatsBioNet Commit: 409e9d4503aa239c3c619270333853289d37d080 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-23 16:57:12 -0400 Commit message: feat(filterSubnetworkByContext): adjust filterSubnetworkByContext to exclude key words (#111) Package: scRNAseqApp Commit: e8a48756927b63b7b69b59294f8c81232e689203 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:44:42 -0400 Commit message: fix the wrong number when calculate phyper. Package: scRNAseqApp Commit: 758edbb8626a1d38afe3c8d58678b43f325195e0 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:40:08 -0400 Commit message: fix a issue for if no hyper pval available. Package: scRNAseqApp Commit: 78ef7925d099f040cfa9b1638934fb49d4adfc91 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:29:19 -0400 Commit message: using promise process to update the gene table. Package: scRNAseqApp Commit: b4e729e4d87012189f26cfd746a09ebc9a04d6db Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 10:24:03 -0400 Commit message: import phyper from stats. Package: scRNAseqApp Commit: 4d94c7a0270315c3aea67c41287313c86ffb5655 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 10:15:42 -0400 Commit message: add phyper pval for co-expression. Package: dmGsea Commit: 3b9c68c53791e27f0abc9e95a8f4e0c050b7d75a Author: xuz1 <xuz@niehs.nih.gov> Date: 2026-09-23 13:54:34 -0400 Commit message: bugfix Signed-off-by: xuz1 <xuz@niehs.nih.gov> Package: decemedip Commit: 3de0b135bed2595498482c4d13078d0bd65c313e Author: nshen7 <shenning1997@gmail.com> Date: 2026-09-22 20:54:10 -0700 Commit message: Fix Stan old array syntax for stanc3 (BioC 3.23 build failure) Package: quantMSImageR Commit: 9aaed9e03b28ef01d3b1c05dc834288f2d00753c Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:46 +0200 Commit message: Version 0.99.8 Pieces of one tissue, regions of interest, and the report arranged by level. matrixStats leaves Imports: it was declared but called nowhere, so every user installed a package the code never used. Package: quantMSImageR Commit: 25eacbf10d0f5075ad89ee2884a76103bdb23a65 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:34 +0200 Commit message: Document the regions work The vignette says what regions are for -- a transition that marks a tissue type, or a toxicity study where the regions are drawn high and low in the toxicant and the endogenous species compared between them, within one animal rather than across a group. It also describes the by-level report, and how to see a palette before choosing it. AGENTS.md is gitignored: agent scratch notes, not part of the package. Package: quantMSImageR Commit: d37c8c4b93a96e7f51343144cda5a5c17dcc519b Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:34 +0200 Commit message: Arrange the report by level, and correlate at one level only Sections 2, 3 and 4 are each drawn by sample and then by region, so the two are read the same way rather than the regions living in a tab of their own. The region masks take a section before the ion images, which move down a number. "auto" judges the heatmap encoding per view, on the rows that view actually has. A study without regions is unchanged, headings included: a level heading only appears when there is a second level to tell it from. Correlation names one level -- 'sample', 'roi', False or auto -- and only ever computes that one. It is the slowest section in the report, and a region holds a fraction of a sample's pixels, so auto correlates within the regions when a study has them and is off otherwise. True still means 'sample'. roi: unit is per sample or per region, not both: a comparison has a single unit, and two views of the same numbers invite reading whichever looks better. compare: keeps "both", where the two arrangements are different contrasts rather than the same one twice. Each box-plot panel carries its own key, and colours: region sets the region palette (any package palette, or a grDevices qualitative one), kept distinct from the groups'. Package: quantMSImageR Commit: bfa6a46540be7a5e08f37ded27d10a504d244d59 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:19 +0200 Commit message: Score each region against itself in contributionHm() too The region heatmap could only be drawn per feature, because contributionHm() had no notion of a block. That made "auto" pick the wrong panel wherever a study has few samples and many regions: one animal per group takes the per-sample encoding by sample, but by region its rows are sample x region, so a group can have six or seven of them -- exactly the case the contribution encoding exists for. It now takes sample_block, and inside a block both the z-score and the group mean are computed against that block alone. The hue is therefore "how this group's airways sit among all the airways", not "airways differ from parenchyma", which is what a panel scored across regions would mostly report. A feature flat within a block cannot be scored there and is drawn in na_col, even where it varies across the section. Package: quantMSImageR Commit: b18abc94cf8fc51323b0836eccf9b684dd9758b9 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:50:33 +0200 Commit message: Fix the region tests and the vignette's feature lookup The row-split assertions read @row_order_list, which a Heatmap only fills in when it is drawn -- it is empty on the object, so the expectations compared against nothing. The split a heatmap will use is in @matrix_param$row_split, which is what they now check: the block test asserts a, a, b, b against groups that deliberately alternate, so passing it means the rows really were split by region rather than by group. The vignette indexed a feature by name, but spectra() returns a matrix with no dimnames, so it takes the row number instead. Package: quantMSImageR Commit: 0ff2ab13a672a37c90034e11545dc2e36e994da3 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:39:14 +0200 Commit message: Document pieces and regions; regenerate the example sections The vignette gains a section on pieces of one tissue, one on labelling regions, and a worked example on the bundled sections: the label table, the region maps and a box plot with one point per section per region rather than per pixel. The YAML section documents the samples forms, including pieces, and what each roi: option can be set to. The example sections are regenerated with the regions the vignette and runExample() now show. Seeds are unchanged and the region code draws no random numbers, so the intensities are identical. AGENTS.md is build-ignored, and the micro sign in stitchAcquisitions() is written as a \u00b5 escape: R CMD check requires ASCII source. Package: quantMSImageR Commit: a623d0241889b76e05f8b5d49aa2f121348d953b Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:54 +0200 Commit message: Carry regions through a study and into the report A study picks regions up on its own: generateTxtImages() attaches roi_label and roi_id from each acquisition's roi_labels.csv, matched on (x, y) like the tissue mask, and they survive panel binding and stitching. Regions numbered within a piece are renumbered across the stitched sample, so two airway_01s become two airways. The YAML gains a roi: block -- enabled (auto), include_unassigned, compare, unit, heatmap -- and pieces: for a tissue acquired in several passes, each piece normalised and SNR-filtered against its own background before being joined. The report gains a regions tab: maps, box plots by compare and unit, an ROI_summary sheet, and a heatmap with one row per sample and region. That heatmap z-scores each region against itself (quantileHm's new sample_block), since scoring across regions would mostly report that airways and parenchyma differ, which is not the question being asked. The map is repeated above the ion images, where it says which blob is which. quantileHm() also no longer loses its sample names when a study holds a feature with no variance: the unscoreable column returned an unnamed vector, and apply() drops the names for the whole matrix when one result's differ. output: colocalisation: gains auto, off whenever a sample merges several acquisitions -- most pixel pairs would then cross acquisitions. Package: quantMSImageR Commit: 9311401b6304a67f07b4b1fa3cf4bbcde84b66b7 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:39 +0200 Commit message: Add labelROIs() for regions within the tissue Run after selectTissuePixels(): it shows the ion image of a chosen transition across tissue pixels only, then loops draw -> name -> "add another". Several regions can share a label, since a section holds many airways, and each is numbered as it is drawn (airway_01, airway_02, ...) so it keeps its own identity while the label is what a study compares. Regions are saved per acquisition as roi_labels.csv beside the tissue mask, which is never touched, and copy_to writes the same file to the other panels over the same area. Re-running adds to them; overwrite = TRUE keeps the old file as a dated backup. The feature picker is shared with selectTissuePixels() rather than copied, and the bundled example sections gain two "a" and two "b" regions each so the downstream half can be shown without a drawing device. The regions differ because of where they sit on the existing intensity gradient; no value was adjusted to make them. Also splits the given names in Authors@R, so the citation reads "Smith MJ" rather than "Smith M". Package: quantMSImageR Commit: 52f47f09842bf4eecb4e8e7d214c84ec7d87a532 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:27 +0200 Commit message: Place pieces of one tissue by stage position A tissue too large for one acquisition is imaged in pieces, and those pieces are one sample: kept apart they count twice in every group summary, and because they agree with each other they look like a reproducible effect. readMRM() numbered each acquisition's pixels from its own first pixel and threw the stage coordinates away, so every piece started at (1, 1) and stitchAcquisitions() could only report that they overlapped. Its documentation claimed Waters coordinates were absolute, which stopped being true the moment readMRM() re-based them. readMRM() now keeps x_stage and y_stage (mm) alongside the grid indices, and stitchAcquisitions() places each piece where the stage recorded it: above, below or beside, in any order, gaps left empty. Pieces must share a pixel size; each is moved to the nearest position on a common grid and the largest shift is reported. Overlap is still an error rather than an average. Objects without stage positions keep their own coordinates and say how to get them. combineMSIs() fills a pData column that only some objects carry with NA, since stage positions and region labels are legitimately absent from some samples. Package: rhdf5 Commit: c72d938a7bd397d148e623a7c0f12e6b3865de1b Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 16:41:00 +0200 Commit message: Bump version Package: rhdf5 Commit: fe55afb12dd1583d7f6f58e236e3d85872da3e1f Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:40:28 +0200 Commit message: Document .matrix() methods removal Package: rhdf5 Commit: f1ad6e28ba024bdcfeede3cb1b3b89f92bb081e5 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:38:30 +0200 Commit message: Remove .matrix() methods and let them auto dispatch to array method Package: rhdf5 Commit: dc8ef2bbced3bfc17f95b284fb0b2981d20427f4 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:22:12 +0200 Commit message: Document on.exit change in NEWS Package: rhdf5 Commit: 2b34f2d0097aaf547999b5be0deeef35031694e8 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:20:32 +0200 Commit message: Use on.exit() more consistently to close Package: rhdf5 Commit: bbfebbf34a184471451df03fab4dfa74a29f1dd9 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:08:44 +0200 Commit message: Mention dead code removal in NEWS Package: rhdf5 Commit: aa7669dbe22003b61182dc3cd266b948ae055ad0 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:07:58 +0200 Commit message: Remove dead code in h5writeAttribute.array() Package: rhdf5 Commit: d1f0dc156114f8494ced58811c01fe1f092b1648 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:57:43 +0200 Commit message: Fix incorrect copy/pasted error messages Package: rhdf5 Commit: 81d91768bd5bc3a86b9c720a1a3c1681ad0851ae Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:43:10 +0200 Commit message: Remove extra call to H5loadConstants() Package: rhdf5 Commit: e28ea4ec812cfd7c63e15101b401a3aa12fac5f1 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:23:01 +0200 Commit message: Ensure .Call() always includes PACKAGE Package: rhdf5 Commit: 4f18f262fed53b25edbbd5db47138059a6a7a6cb Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:16:45 +0200 Commit message: Mention h5set_extent() fixes in NEWS Package: rhdf5 Commit: 98c8a7581553b43f8aa62575958b0a595394bb84 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:16:16 +0200 Commit message: Fix h5set_extent issue with dataset handle Package: GSVA Commit: 545a96a07fba745d24b021cde157b570597a7109 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 16:34:55 +0200 Commit message: Remove dependence on BiocSingular Package: aracne.networks Commit: d000659130672ee12ffa5a287616ffe16c334eb2 Author: federicogiorgi <federico.giorgi@gmail.com> Date: 2026-09-23 15:51:57 +0200 Commit message: Point to the Zenodo record 22918956 Fill in the Zenodo record (doi:10.5281/zenodo.22918956) hosting the networks and document the CC BY-NC-ND 4.0 license of the data files. Package: aracne.networks Commit: d768d15947c70f95dc353c4e3a21da480ffccdc3 Author: federicogiorgi <federico.giorgi@gmail.com> Date: 2026-09-23 14:47:27 +0200 Commit message: Move the networks to Zenodo The regulon data sets are no longer bundled in the package: they are hosted on Zenodo and retrieved with the new getRegulon() function, which caches them locally with BiocFileCache and verifies their MD5 checksums. listRegulons() lists the available networks. This brings the package size well below the 100 MB limit of the new build system. - documentation of the 25 networks merged into ?regulons - vignette converted to R Markdown - added unit tests - Authors@R replaces Author/Maintainer Package: GSVA Commit: 87cd4d7cdcae92c251c9b53c7f759c38b4ab1ed4 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 15:31:13 +0200 Commit message: Bump version Package: GSVA Commit: 9c1eb50150a6aaee271512838ad8739b3bb130fe Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 15:22:44 +0200 Commit message: Merge pull request #276 from rcastelo/275-average-method Average method for enrichment scores calculation Package: GSVA Commit: 9e68f27aaa3d02a7d4c28792365b50d35dc1b5aa Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 14:50:43 +0200 Commit message: Replace checkIdentical() for checkEqualsNumeric() to allow C unit tests pass across different platforms Package: GSVA Commit: 5f21614dc2ee103338d887a39e119f4fbbbf90d9 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 12:29:14 +0200 Commit message: Added C implementation of the average method, and its corresponding unit tests. For performance issues, genes within genesets are internally ordered after mapped to features, this required regenerating regression test for PLAGE since SVD flipped sign in values due to the different input order Package: GSVA Commit: 87cfe5db164c95b66710094c215285fbf17995a6 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:46:28 +0200 Commit message: Merge branch 'devel' into 275-average-method Package: GSVA Commit: cc12f1d01a63d0123a48e3fb3d576c61a5f6a14d Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 14:42:36 +0200 Commit message: Fixed namespace issues and unit tests Package: GSVA Commit: 6881306e155fe38933ff8cf6d3ec9be94b9b382d Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 12:16:49 +0200 Commit message: Add unit tests for CLR and average method Package: GSVA Commit: 730ce29c9eb3a6d8b94c1c327d96451241681fd5 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-21 17:07:11 +0200 Commit message: Added first version of the average method for calculating enrichment scores Package: fenr Commit: 78a5a1207281ef37881d399f562be49f4a4af6d2 Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 13:02:11 +0100 Commit message: Merge branch 'main' of https://github.com/bartongroup/fenr Package: fenr Commit: 83a93c2fe6a5bb8748799c1f369153a651713bea Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 13:00:33 +0100 Commit message: Reverting some changes Package: fenr Commit: 0274549e7ba96519bf153ae6736593f62e5f666a Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 12:01:32 +0100 Commit message: Version 1.11.3 Package: vsn Commit: cdb80675e45236c2f57a2b41d4f98f4f2d6814b2 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:27:07 +0200 Commit message: Bump version Package: vsn Commit: b5d9c153c5300b3209bd0bcef2285b4386731398 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:26:58 +0200 Commit message: Mention README and pkgdown site in NEWS Package: vsn Commit: fb67d77e139bbf2d24f020fcc99a770650124cb1 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:25:59 +0200 Commit message: Set up pkgdown Package: vsn Commit: 4e31e610b6c6afccfe348d107f05e277101f01be Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:25:04 +0200 Commit message: Add minimal README with deNBI survey Package: sesame Commit: 2acabdce8fbdd4fb9675db1fd76d60d05792be04 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 22:06:41 -0400 Commit message: 1.31.5: fix readControls column naming; qualityMask takes a custom mask readControls() built the control data.frame positionally: colnames(ctl) <- c('G','R','col','type') over a frame whose signal matrix has four columns, so Color_Channel and Type were cbind-ed past the end of that name vector and arrived unnamed, while `type` silently took a signal column. Downstream, controls(sdf)$Type was a vector of integers, so negControls()'s grep("negative", ...) matched nothing and detectionPnegEcdf() failed in ecdf() with "'x' must have 1 or more non-missing values" on EPIC and HM450 -- the platforms whose controls arrive through readControls() rather than as SigDF rows. The columns are now named explicitly. This was found from the C side, where it had been mistaken for an annotation divergence for two days. With it fixed, detectionPnegEcdf agrees between the two implementations at max|diff| = 0.00e+00 on EPICv2, MSA, EPIC and HM450. qualityMask() gains `platform` and `mask`, so a custom or combined-array mask can be passed in directly instead of being bolted on with addMask() after the fact -- the case that comes up for arrays built from two manifests. README: the two implementations are named and versioned. The R package is SeSAMe v1 and stays on the 1.x series; the C command line is SeSAMe2 on 2.x. They are parallel, not sequential. The conda line also said `sesame-cli`, which has not been the package name since 0.4. R CMD check: Status OK, vignettes built and re-run. Package: mia Commit: 859de8cd0be1bdd40982b6cd189141c84cb359cd Author: Giulio Benedetti <giuliobene2000@gmail.com> Date: 2026-09-23 14:27:37 +0800 Commit message: Clarify study subjects in ADHD microbiota profiles (#828) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: mia Commit: 751d24e22c26aaccc6ec7be1ece37540fc2eab37 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-23 08:57:53 +0300 Commit message: Add Rdpack references (#797) Signed-off-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: mia Commit: 3c4fd9e80ecf788464a2726cf15e64cbd0aeede2 Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Date: 2026-09-22 11:27:29 +0300 Commit message: Convert MAE to TreeSE and back (#810) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Package: OMA Commit: 1ff85f15276db0d08c8305d788808bc3d713d066 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-23 13:07:47 +0300 Commit message: Simplify importing Package: OMA Commit: f19c0abb3874a6386f4693912c59f010dc5ec331 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-22 15:05:08 +0300 Commit message: Fix rendering Package: OMA Commit: 1d6f339fb23ebbdd1a58d089605f547fb76413d1 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-22 14:31:13 +0300 Commit message: Fix rendering, update support forum address Package: OMA Commit: 3f130bdb5a124835ec56391806571a9a6954963e Author: jagadeesh <2400040120@kluniversity.in> Date: 2026-09-18 16:37:10 +0530 Commit message: docs: Add comprehensive Rarefaction section to transformation chapter (#825) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Co-authored-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <tvborm@utu.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 1a65548fafa7a1d699b74cabccff2cb6b8b74f3f Author: Rasmus Hindström <56149499+raivo-otus@users.noreply.github.com> Date: 2026-09-18 09:20:36 +0300 Commit message: docs/clarity improvement to mia::summarizeDominance (#852) Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Co-authored-by: TuomasBorman <TuomasBorman@users.noreply.github.com> Package: OMA Commit: bcf4b79324d7db13573f7d75f1921324f098bf37 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:11:59 +0000 Commit message: feat(ci): add whitespace stripping to style workflow (#864) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: be708a734fe6980f7fdb08cd7d29c0bf68d85d47 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:06:30 +0000 Commit message: fix(community_similarity): use official vegan docs (#872) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: d51543f698e697431a375bb5ee52ea224490b2a1 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:03:41 +0000 Commit message: feat(ci): add dependabot (#865) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 79c94b838aca89ac79e9544310302b5528c9a0b8 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 05:57:47 +0000 Commit message: bump(deps): actions/cache@v4 to v6 (#874) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 4e1978be84a4efc4813759e6f1a2d6aa262ba265 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-18 08:52:51 +0300 Commit message: Use scaled fitted values for DMM drivers (#881) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 7bd2fc8e6da903e0640182842001f3fd42f5a210 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-17 15:48:42 +0300 Commit message: Clarify exercise instructions across the book (#886) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 7ad1b506261f780a42bc9ffa0655f10f91047bb3 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-17 15:33:57 +0300 Commit message: Add tree visualization reference (#889) Package: OMA Commit: 0e655914be48d7af2242a012deeb8354ec31f033 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-08-08 19:29:22 +0300 Commit message: Suppress cheatsheet startup messages (#878) Package: beachmat Commit: 7fe7dc234ea2fe69bf8f4c711525428539033652 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 15:32:49 +1000 Commit message: Switch to DelayedNoOp to support all alabaster.matrix no-op subclasses. This saves us having to list all of the individual subclasses. Package: alabaster.matrix Commit: ff91f9ff04b310f74232613787d6abe1411769aa Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 14:54:50 +1000 Commit message: Introduce a no-op base class to catch all of our weird seeds. In particular, packages like beachmat don't have to add a specialization for each of the no-ops subclasses, they can just check for the DelayedNoOp class. Package: alabaster.matrix Commit: 998568738d4d76e3073b732c24eaf2a9d79f650a Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 14:26:07 +1000 Commit message: Implement ToBeRealizedArray class for fine control of delayed operations. Package: SparseArray Commit: fab50cb7a6f6b1c5735dd1f19b05b94e04503dcf Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:57:43 -0700 Commit message: some edits to SparseArray-abind.Rd Package: DelayedArray Commit: ef3f02a7227a0e6a07736601081925f2fccb43a9 Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:26:39 -0700 Commit message: requires S4Arrays >= 1.13.1 Package: DelayedArray Commit: 28a0ba92ed413f575dd5839324e9892eb8f840c2 Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:02:40 -0700 Commit message: DelayedArray 0.39.7: Add abind() method for DelayedArray objects Also: - Remove the rbind(), cbind() and bindROWS() methods defined for DelayedArray objects. These methods are now replaced by more generic methods defined in the S4Arrays package for Array objects that are all based on abind(). - Add coercion from array/matrix to DelayedArray/DelayedMatrix. This coercion is equivalent to calling the constructor function DelayedArray() on the object to coerce. Having this coercion work has the effect of making rbind() and cbind() work on a mix of DelayedMatrix objects and ordinary matrices. This partially addresses issue #100. Package: scDiagnostics Commit: bee3ff588074c8e26c3b15b12610f23b7c19acdc Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 21:24:22 -0400 Commit message: Silence scran deprecation warnings and tolerate missing Suggests, bump to 1.7.15 Two failures on the first run against Bioconductor 3.24 / R 4.6: R CMD check reported significant warnings in the examples on all three platforms. scran 1.41 deprecates its HVG helpers in favour of scrapper, so every modelGeneVar()/getTopHVGs() call - including the fitTrendVar() that modelGeneVar() calls internally - now signals a deprecatedWarning, and rcmdcheck runs with error_on = "warning". Add an internal muffleDeprecation() that muffles only the deprecatedWarning class, leaving genuine warnings alone, and wrap the six calls in processPCA(), detectAnomaly() and calculateReconstructionError() with it. The three examples that call scran::getTopHVGs() directly wrap it in suppressWarnings() instead, with a comment saying why. This is a stopgap: the HVG selection needs to move to scrapper before scran makes these functions defunct. The macOS job additionally failed with "Packages suggested but not available: 'scRNAseq', 'celldex'". Neither is used by anything that runs during the check - they appear in documentation prose and inst/script - and both currently fail their own Bioconductor 3.24 builds, so set _R_CHECK_FORCE_SUGGESTS_=false rather than fail this package's check over them. Package: scDiagnostics Commit: 964640ff9a5c7728f24141ce53575c0840966fd8 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 20:38:25 -0400 Commit message: Target Bioconductor devel 3.24 / R 4.6 in CI, bump to 1.7.14 The matrix was pinned to Bioconductor 3.22 / R 4.5, two release cycles behind: 3.23 is the current release and 3.24 is devel, which is what the Bioconductor build system checks this branch against. Point all three jobs at 3.24 / R 4.6 (the pairing BiocManager's version map requires), swap the Linux container for bioconductor/bioconductor_docker:devel, and move the RSPM mirror from jammy to noble to match that image's Ubuntu 24.04 base. Also refresh the cache keys and the check-results artifact name, which still referenced RELEASE_3_22/3_19; the new keys additionally force a cold cache so no 3.22-era binaries are restored. Package: knowYourCG Commit: 9a7cce4c69f010992c7694da610eab786d07b443 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 18:58:22 -0400 Commit message: Point users at KnowYourCG v2, and fix three dead links This package is KnowYourCG v1 and stays on the 1.x series. The C implementation is KnowYourCG v2, binary `kycg`, and nothing here said so. Framed as succession, not as a wind-down, and that distinction is the point. An earlier draft of this put "This package is in maintenance; active development continues in kycg" into DESCRIPTION -- the field that renders on the Bioconductor landing page. This package sits on an open Core Team deprecation watch (#4, "Bioconductor failure and risk of deprecation"), so publishing that it is in maintenance would have handed them the justification. A neutral pointer says the same true thing without inviting it: the project is not declining, it is on its second implementation. Three places, because they reach different readers. DESCRIPTION is the only one an installing user sees, rendered on the landing page. The README is for GitHub visitors. Sequencing.Rmd names v2 where a reader is most likely to want it -- that vignette's workflow is what v2 does natively over YAME stores. The URL is in angle brackets, the same convention the DOI in that sentence already uses; a bare URL is what R CMD check objects to. Each says plainly that the two are parallel implementations rather than an upgrade path: one is an R package, the other a command-line tool, and there is no upgrading from one to the other. Separately, three dead links. `R CMD check --as-cran` runs a URL liveness check that a plain check skips entirely, and it found Sequencing.Rmd linking to https://zhou-lab.github.io/YAME/docs/summarize.html (twice) and .../docs/pack_unpack.html -- both 404. YAME's documentation is a single page now and those paths no longer exist, so all three point at https://zhou-lab.github.io/YAME/ instead. Package: scDiagnostics Commit: 89c6ed709d444d28439a7c791cb151b11faca8fb Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 19:54:35 -0400 Commit message: Make BiocCheck's deprecation check resilient to bioconductor.org outages, bump to 1.7.13 BiocCheck's first check downloads checkResults//bioc-LATEST/ meat-index.dcf for both the release and devel branches, and a failed download is a hard error ("HTTP 504 Gateway Timeout" -> bfcadd() failed -> "not all 'rnames' found or unique"), which took down the Linux and macOS jobs even though the package itself was fine. Pre-populate BiocCheck's own BiocFileCache with up to three attempts before running BiocCheck, and only if bioconductor.org is still unreachable pass `no-check-deprecated` so that one check is skipped instead of failing the whole build. </pre> </div> Package: scDiagnostics Commit: 816fa92698fa534abefc3cc0f75df2319b8f11f6 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 17:32:41 -0400 Commit message: Disable public RSPM on macOS/Windows to fix root cause, bump to 1.7.12 The libomp install in the previous commit didn't fix stringdist's identical dlopen failure - same byte-for-byte error, meaning the install had no effect. Searched prior reports of this exact failure (tidymodels/tune#1199, Genentech/rdborrow#73/#74): the real cause is that r-lib/actions/setup-r configures Posit Package Manager (P3M) as the default macOS repo, and P3M's macOS arm64 binaries are compiled with OpenMP enabled. This runner can't resolve those OpenMP symbols at runtime (SIP strips DYLD_* for protected binaries, so even a correctly installed libomp isn't reliably picked up) - CRAN's own macOS binaries are built without OpenMP and never hit this. Set use-public-rspm: false on the "Setup R from r-lib" step so macOS (and Windows, already passing, no expected impact) resolve packages from CRAN directly instead of P3M, which should fix this for any OpenMP-linked package in the dependency tree - not just the three (RhpcBLASctl, isotree, stringdist) hit so far - rather than continuing to patch them one at a time. Left the earlier source-install and libomp workarounds in place; they're harmless if this makes them redundant, and there's no upside to stripping proven/plausible fixes before confirming this one actually resolves it on CI. Package: scDiagnostics Commit: 3aba0f79435c543deb4c129e486f16e5e92c6ba4 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 16:59:49 -0400 Commit message: Install CRAN's official libomp on macOS CI, bump to 1.7.11 The last two fixes patched RhpcBLASctl and isotree individually, but BiocCheck::BiocCheck() now hits the identical failure via one of its own dependencies (stringdist): unable to load shared object '.../stringdist.so': dlopen(...): symbol not found in flat namespace '___kmpc_barrier' Patching each OpenMP-linked CRAN package one at a time as it's reached doesn't scale - the actual root cause is that this GitHub Actions macOS runner is simply missing the libomp build that CRAN's macOS binaries are compiled against (documented at https://mac.r-project.org/openmp/; Homebrew's libomp installs to a different path and doesn't fix this). Installing it there via the official recipe should let CRAN's normal (faster) binaries load correctly for any OpenMP-using package, not just the two already patched. Left the RhpcBLASctl/isotree source-install workarounds in place since they're already confirmed working - no reason to touch proven fixes while chasing this. Package: scDiagnostics Commit: 58cf3022aee073ef86bf0e5695fe41dd4a701ec9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:24:46 -0400 Commit message: Also force isotree from source on macOS CI, bump to 1.7.10 RhpcBLASctl fixed the first macOS OpenMP dlopen failure, but the same issue exists one layer up: isotree's own CRAN macOS binary (isotree.so) fails to dlopen with "symbol not found in flat namespace '___kmpc_barrier'" - a Clang/LLVM OpenMP runtime symbol, same root cause (CRAN's macOS binary built with OpenMP support that isn't resolvable on this runner), just a different dependency in the chain. Applied the identical source-install workaround to isotree. Package: scDiagnostics Commit: 7809c44d4bc5e698aeb4d67f24e79535cfe513c9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:00:00 -0400 Commit message: Force RhpcBLASctl from source on macOS CI, bump to 1.7.9 Ubuntu and Windows now pass under the Bioc 3.22/R 4.5 bump (previous two commits), confirming those fixes. macOS still fails, but differently and on all 4 vignettes uniformly this time: Error: .onLoad failed in loadNamespace() for 'RhpcBLASctl' dlopen(.../RhpcBLASctl.so, ...): symbol not found in flat namespace '_omp_get_max_threads' RhpcBLASctl is a hard Import of isotree (detectAnomaly() calls isotree::isolation.forest()), so its namespace loads unconditionally. CRAN's macOS binary for RhpcBLASctl references an OpenMP runtime symbol that isn't resolvable on this GitHub Actions macOS runner - a known class of issue for R packages built with OpenMP support on macOS. Building from source instead compiles without OpenMP (Apple clang has no -fopenmp by default), so the resulting library never references that symbol. Added alongside the existing Matrix/irlba source-install workaround in the same step, which addresses the same kind of macOS binary incompatibility. Package: scDiagnostics Commit: 3386bcb54d27441922472dd08b49d1b1d786bb37 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 12:06:16 -0400 Commit message: Anchor SingleCellExperiment/SpatialExperiment Rd links, bump to 1.7.8 R CMD check now fails with error_on = "warning" on the Bioc 3.22/R 4.5 CI (bumped in the previous commit): "checking Rd cross-references" reports a genuine broken link (merfish_reference_data.Rd's \linkS4class{SpatialExperiment} doesn't resolve) plus 36 files whose \linkS4class{SingleCellExperiment}/{SpatialExperiment} links are missing package anchors - both promote the check from NOTE to WARNING under the newer toolchain. \linkS4class{} was reintroduced repo-wide by a September 17 commit ("docs: use \linkS4class{} for SingleCellExperiment roxygen links", for brevity) after an earlier commit had already fixed this exact issue with explicit \link[pkg:target]{text} anchors. Restoring that anchored form and re-running roxygen2 to regenerate man/ resolves it; verified with a full local R CMD check matching the CI invocation (0 errors, 0 warnings, 1 unrelated pre-existing note). Package: scDiagnostics Commit: b520b294d72834042d23e6c4c887c6c194847544 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 10:33:30 -0400 Commit message: Bump CI to Bioconductor 3.22/R 4.5 to fix vignette build failure COVIDCaseStudy.Rmd was failing to build on CI (macOS/Windows) with "unable to find required package 'Seqinfo'" inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause: covid_reference_data/covid_query_data were generated on current Bioconductor (3.22), where the Seqinfo class was split out into its own standalone package. check-bioc.yml was still pinned to the two-year-old Bioconductor 3.19/R 4.4, whose GenomeInfoDb predates that split and whose repos don't contain a 'Seqinfo' package at all, so the class tag baked into the serialized data can't be resolved. Two earlier attempts (adding set.seed() to rule out RNG state, then patching a subset of the shipped .rda files) missed this because neither addressed the actual CI environment being out of date. Bumped the workflow's matrix (r/bioc versions, container image, cache keys) to 4.5/3.22, matching the environment covid_reference_data was actually generated on; verified locally that a full R CMD build (fresh install + vignette rebuild) succeeds under this Bioc/R pairing. Package: scDiagnostics Commit: 02de5cdca9c45682ebceab3b3f7d6231d8cb8054 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:40:12 -0400 Commit message: Handle reference cell types with too few cells or absent from query detectAnomaly() previously assumed every reference cell type had at least 2 cells (to fit an isolation forest) and, when a query dataset was provided, implicitly assumed every reference cell type also had matching query cells. Neither is guaranteed: - A reference cell type with fewer than 2 cells can't fit an isolation forest; now skipped with a warning instead of erroring. - A reference cell type entirely absent from the query is a normal outcome (e.g. after subsetting/filtering the query), not an error; now reported with an empty query score vector instead of failing in predict(). Also fixes a latent bug where a cell-type subset reducing to exactly 1 row would silently drop to a vector (missing drop = FALSE), which would have broken the isolation forest input shape. Adds tests covering both edge cases. Package: scDiagnostics Commit: b0fc15de1e279c3a6e2d44c12837dd3667d35743 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:36:38 -0400 Commit message: Fix stale Seqinfo class tag causing vignette build failure, bump to 1.7.6 COVIDCaseStudy.Rmd failed to build on CI with: Error in .requirePackage(): unable to find required package 'Seqinfo' triggered inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause, confirmed via verbose updateObject() output: covid_reference_data's internal Seqinfo class was tagged with its old home package ("GenomeInfoDb", from before Seqinfo was split into its own standalone Bioconductor package), so a sufficiently new Bioconductor tries to auto-migrate it on load - and that migration path apparently isn't reliably available in a fresh CI environment. Fix: call updateObject() on serialized objects at data-generation time so the bundled .rda ships with the current internal representation baked in, rather than deferring to a lazy per-load migration. Applied to the new COVIDData.R/MERFISHData.R scripts (whose source data came from an external, older serialization), and audited/fixed the same latent issue in the pre-existing reference_data/query_data/qc_data (which had the identical stale tag despite already shipping in the package) and their generation scripts, so this doesn't resurface on a future regeneration or Bioconductor version bump. zeisel_/covid_/ merfish_ vignette datasets were already correctly tagged and are byte-identical after regeneration. Package: scDiagnostics Commit: 44dd05d3749412c865e5446d44a4520bd24df370 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:13:03 -0400 Commit message: Fix non-deterministic vignette failure and bump to 1.7.5 COVIDCaseStudy.Rmd and MERFISHCaseStudy.Rmd called detectAnomaly()/ calculateGeneShifts() (which use isotree::isolation.forest(), a randomized algorithm) without ever calling set.seed(), unlike the other two vignettes. This is the most likely cause of the CI vignette re-build failure on COVIDCaseStudy.Rmd after pushing 1.7.4 - a build without a seed picks up whatever RNG state the session happens to be in, which can land on the isolation forest / gene-shift edge cases seen elsewhere in this codebase. Verified against 15 different seeds plus a full local R CMD build (fresh install + vignette rebuild, not just devtools::load_all()) with no failures. Bumps to 1.7.5 rather than re-pushing 1.7.4, since 1.7.4 already has a recorded (failed) build on Bioconductor/GitHub. Package: MSstatsBioNet Commit: 0b9e21718beccbc1fb3847792481f8bda11b7ef5 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 18:27:25 -0400 Commit message: feat(decomposeSubnetworkIntoHierarchicalTopics): Enable NMF hierarchical decomposition (#110) Package: knowYourCG Commit: 5dbb3d5b4f6dcb4f6f54e4db6859b760358c9344 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 17:15:02 -0400 Commit message: Stop reaching the network when the vignettes and examples are built Three build-time downloads, all of the same two Zenodo files, none of them needed to show that the package works. The vignette one was failing outright. Sequencing.Rmd's QUICK START fetched mm10_f3_10cells.cg -- 11.4 MB, which takes ~101 s at the throughput a build host is likely to get. R's download.file() gives up at getOption("timeout"), 60 s by default, so the transfer truncated mid-file and the vignette errored. Measured twice here: it stopped at 6.0 MB and at 7.2 MB, both almost exactly 60 s of transfer, and completed only with timeout raised to 600. Raising the timeout would have kept a network dependency the package does not need. The sequencing workflow is superseded by the kycg command-line tool, which does this analysis natively over YAME .cg stores and fetches its own knowledgebases, so the chunk is now shown rather than run, with a line saying so and pointing there. The two examples had the same files behind a guard that does not guard. \donttest IS executed by the Bioconductor builders; only \dontrun is not. In bedToCg() the download.file() sat outside the guard entirely, so it ran on every check while only the bedToCg() call was skipped -- the whole example is now \dontrun. In testEnrichment() the guard was in the right place but was \donttest, now \dontrun; its offline part, which uses the sesameData cache, still runs. Both edited in the roxygen source and regenerated, so document() cannot revert them. Neither example has run lately: checksrc has been skipped for as long as buildsrc has been red, so these would have fired the moment the vignette fix made checksrc reachable again. BiocCheck NOTEs \dontrun in favour of \donttest. That NOTE is accepted here: \donttest does not keep the builders off the network, which is the point. visualization.Rmd still reads a small RDS over the network and is left alone -- it builds reliably and is not part of this failure. Package: knowYourCG Commit: 0a4ce5469ac8b4fbb9801a4af583639b65a36b4d Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 16:23:15 -0400 Commit message: Array.Rmd: use the base pipe, not the borrowed magrittr one buildsrc has failed on every builder in both release and devel with Quitting from Array.Rmd:218-233 [ky8, run-test-single] Error in `results %>% dplyr::filter(overlap > 10) %>% head`: ! could not find function "%>%" The vignette never attached the pipe. It worked anyway because library(sesameData) pulls ExperimentHub -> AnnotationHub -> BiocFileCache -> dbplyr, and dbplyr re-exports `%>%`, so the vignette was borrowing the operator from a package four levels down its own dependency chain and never named. When that chain stopped attaching dbplyr, the vignette broke without having changed. knowYourCG imports `%>%` via importFrom(magrittr) but does not export it, so library(knowYourCG) was never what made it resolve. DESCRIPTION has Depends: R (>= 4.4.0), so `|>` is available unconditionally and removes the dependency rather than renaming it; `%>% head` becomes `|> head()` since the base pipe needs a call. R/preparePlotDF.R keeps `%>%` -- package code has the import, only vignettes were ever exposed. Verified under R 4.6.0: all three rewrites return identical() results to the magrittr forms, the base pipe resolves with nothing attached, and Array.Rmd renders to completion. Fixes the buildsrc half of #4. Package: gDRutils Commit: a62ecdc187c6b4b726415cb33500813dfbbb0d10 Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 22:34:53 +0200 Commit message: Merge pull request #201 from gdrplatform/GDR-3612 refactor: read the constant-fit xc50 threshold from fit configuration Package: gDRutils Commit: 441d33fe8d5ca07d23f4dcbee9f59274a5f4f14f Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-22 21:17:54 +0200 Commit message: fix: read the fit configuration when the fitting layer is entered directly Package: gDRutils Commit: 11524511fd588673802ec057e728b96c9b089b0d Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 12:07:38 +0200 Commit message: Merge branch 'main' into GDR-3612 Package: gDRutils Commit: afa97f88532cc8d0539c9df9b2d5170b0e7f4f0c Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:50:27 +0200 Commit message: docs: flag that fit_curves still hardcodes the xc50 threshold Package: gDRutils Commit: f450b02a0beaa9ae1f8cec3fd09151e2f2fe5a98 Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:49:21 +0200 Commit message: Merge remote-tracking branch 'origin/GDR-3606' into GDR-3612 # Conflicts: # DESCRIPTION # NEWS.md Package: gDRutils Commit: b5e352cf6c88d1a7cb33ca89c106b55896cb1cbc Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 13:27:47 +0200 Commit message: refactor: read the constant-fit xc50 threshold from fit configuration The response level deciding whether a constant fit reports +Inf or -Inf was hardcoded at 0.5 in two functions. It is now one entry per normalization type in the fit_config block, alongside the priors and asymptote bounds. Numerically inert: every type keeps 0.5, which is what the code did before. The point is that the value becomes visible and decidable - for RV it means 50% viability and for GR it is the GR50 convention, but NGR is a bare ratio of slopes that is legitimately negative, where the threshold has no established meaning. Package: methodical Commit: 2ce1f224115807008cf8e4056bff3346c161cbe2 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-22 20:12:54 +0100 Commit message: update Package: MSstatsBioNet Commit: d6f02da47b7e915ef0c30923538cf7d516341aa2 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 14:43:07 -0400 Commit message: fix(pubmed): Reduce runtime for fetching pubmed abstracts (#109) Package: GSVA Commit: d2828ae6a4645e089dc931494a2b0f239850ae7b Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:45:59 +0200 Commit message: Switch a couple of install() calls in C for the corresponding more performant internal Rf_*() calls Package: alabaster.matrix Commit: 7cd81656f826538908e71cea03dbed7e42544cb8 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:53:29 +1000 Commit message: Mention all of the weird DelayedArrays that we support in the ANY method. Also move the LowRankMatrix code out of the ANY method for clarity. Also bump version and date for a new release. Package: alabaster.matrix Commit: 1d4b149bd9a329ea35a5033dc0318f6292f275ee Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:38:20 +1000 Commit message: Use a more precise R type hint for residual matrix objects. Also move ResidualMatrix code out of the ANY method for easier reading. Package: alabaster.matrix Commit: 1a17e99c4a5e64b68688da152c20434d3ae965bb Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:21:07 +1000 Commit message: Support scrapper::LogNormalizedMatrixSeed in storeDelayedObject. Package: MSstatsBioNet Commit: c6cb932731a5f1f1a743daed884638f2c14afd57 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:38 -0400 Commit message: Bump package version from 1.5.2 to 1.5.3 Package: MSstatsBioNet Commit: 57f2c7b2d94664d93f76a16b82cc5a5b7cff2ae9 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:10 -0400 Commit message: fix(proteinGroups): Adjust annotateProteinInfoFromIndra to handle protein groups (#108) Package: BreastSubtypeR Commit: 9aad28d9baa37a3a2acc3e040c72bc2fea5bced8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-09-22 20:24:05 +0800 Commit message: Merge upstream/devel, Updated Package: BreastSubtypeR Commit: f44f9d18a7ff9c1446d57cc8515dc427e98e0a4b Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:06:15 +0800 Commit message: Merge pull request #139 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 9e4904ff65cfc1320229f841b55402e08e0390fe Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:00:13 +0800 Commit message: Merge pull request #138 from yqkiuo/main New updates Package: BreastSubtypeR Commit: 252f893b32c10da768540ab3df667f3c6ef34419 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 12:56:55 +0800 Commit message: Merge pull request #136 from yqkiuo/maintenance/public-package-fixes-20260918 Maintenance fixes for 1.5.2: AUTO routing, ROR-C column, Shiny launcher and preflight, Mapping and documentation Package: BreastSubtypeR Commit: f9ca808290b0dfe73e62cff242e28cc301f69238 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-21 10:30:49 +0000 Commit message: Track .Rbuildignore and exclude the .github directory from the build R CMD check reported "hidden files and directories: .github" because the workflow directory reached the source tarball. .Rbuildignore was listed in .gitignore and therefore never shipped with the repository; it is now tracked, with the same content the Ensemble branch already carries, so the built package excludes .github, RStudio files, Rplots.pdf, doc, Meta and MANIFEST.txt. No R code changes. Package: BreastSubtypeR Commit: f3e3be4738438524e605ca70781d8ac359af9ca8 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-19 13:24:35 +0000 Commit message: Bump version to 1.5.2 and title the release notes DESCRIPTION 1.5.1 -> 1.5.2 for the Bioconductor devel submission of the maintenance fixes. The NEWS block collected under "Unreleased" becomes the 1.5.2 entry. One clause is added to the AUTO subsetting bullet: the supplementary pseudocode of the published paper records the strict comparison in the subsetting step while using ">=" for method selection, so readers comparing the package against the paper know that the package now applies ">=" in both and reproduces its shipped example. Package: BreastSubtypeR Commit: 1826b4a6941c152837ef57effbb3c23fdf9751a0 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:57:20 +0000 Commit message: Docs: keep the maintenance track free of unreleased-feature references The entropy change of the previous commits described the new NA behaviour by comparison with an unreleased voting feature, in the internal help text of get_entropy(), in the comment heading test-entropy.R and in the NEWS bullet. The maintenance branch is the public package: its sources, tests and NEWS must not name work that has not been released. The wording now states the behaviour on its own terms. No code, test assertion or behaviour changes. Package: BreastSubtypeR Commit: 252961fa606750b2c17e82363ee0e5ac4ac08d20 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:50:50 +0000 Commit message: Tests: do not let the equivocal HER2 case emit an unhandled warning The AUTO routing test feeds an equivocal "2+" HER2 code to check that a non-evaluable value is treated like a missing one. Builds that flag ambiguous HER2 codes warn on that input, which leaves an unhandled warning in the suite. The call is wrapped; the routing verdict it asserts is unchanged. Package: BreastSubtypeR Commit: 1931c45909ab5e0a56327d3024afd0331468caa5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:37:24 +0000 Commit message: AUTO: decide the HER2+ cohort from the HER2 column alone The HER2+ branch of get_methods() was entered when at least one evaluable HER2 value existed and the joint ER/HER2 counts held no HER2-negative sample. Those counts are computed with na.rm = TRUE, so a HER2-negative sample whose ER value was missing never reached them: one such sample left the cohort classified as HER2+, while an otherwise identical sample with a recorded ER value ended the classification. Whether a HER2-negative tumor counts must not depend on whether its ER status happens to be known. The branch now requires at least one evaluable HER2 value and every evaluable HER2 value to be HER2+. Values outside {HER2+, HER2-} are not evaluable; this covers missing values and the equivocal "2+" code that .normalize_er_her2_tn() deliberately leaves unchanged. Such samples neither create nor remove a HER2+ cohort, and AUTO now reports how many of them took no part in the decision, because a single unannotated sample used to be able to change the routing silently. Cohorts with complete HER2 information are routed exactly as before. The packaged OSLO2-EMIT0 example has no missing ER or HER2 value (ER+ 84, ER- 18, HER2+ 8, HER2- 94), so no shipped example or regression fixture changes. The test that pinned the previous behaviour (her2_pos_na_er) is replaced by a block asserting that both routes now agree, and a block asserting the new message. The NEWS bullet for the unreleased HER2+ change is consolidated into a single statement of the final rule rather than two successive refinements of the same unreleased behaviour. README and vignette state the rule. Package: BreastSubtypeR Commit: 14445c18179fdb40310ea13069f72cc6b5c59a60 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 18:20:00 +0200 Commit message: Entropy: report NA when no method returned a call get_entropy() computes the raw Shannon entropy of a per-sample row of method calls. table() drops missing values, so a row in which every executed method returned NA produced -sum(numeric(0)), that is 0, which on this scale reads as unanimous agreement. Such a row has no call distribution and therefore no entropy; it is now reported as NA. Rows with at least one call are unchanged, including the degenerate one-call case, whose entropy of 0 is the correct value for the observed distribution. The definition of the statistic - raw, unnormalized Shannon entropy in bits - is untouched, and no normalized variant is introduced. The change aligns the legacy path with the ENSEMBLE diagnostics, where raw_vote_entropy is already NA_real_ when valid_voter_count is zero. Exposure is narrow: every AUTO panel includes AIMS and sspbc, which are single-sample predictors and call essentially every sample, so an all-NA row cannot arise in AUTO. It arises in manual runs of nearest-centroid-only method sets (for example methods = c("ssBC", "ssBC.v2")), where a sample whose ER or ER/HER2 status is unknown gets no call from any executed method. The packaged OSLO2-EMIT0 example is unaffected: every tumor there has 7 or 8 calls, and its stored entropy column is reproduced exactly by the new function (asserted by a test). Side effect worth noting: Vis_Multi() orders rows by the entropy column and order() places NA last, so a sample with no calls now sorts to the end of the plot instead of appearing among the unanimous samples. The entropy column of res_subtypes is documented in ?BS_Multi for the first time, including that it is computed over the contributing methods only, so a low value from few contributing methods reflects few available calls rather than strong agreement. tests/testthat/test-entropy.R covers the NA cases, the unchanged values for rows with calls, reproduction of the packaged entropy column, and a manual two-method run in which four samples receive no call. Package: BreastSubtypeR Commit: 3668d9c93adb99e148dc577e8a82b0d556adb249 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 17:30:00 +0200 Commit message: PCAPAM50: exclude samples with unknown ER from the IHC-guided steps BS_PCAPAM50() builds the IHC column from the ER status with case_when(..., .default = NA), so a sample whose ER is missing or not coded "ER+"/"ER-" has no label. makeCalls.PC1ihc() expressed ER-negativity as !grepl("^L", IHC), which returns TRUE for NA, so those samples were counted as ER-negative in the PC1 axis check, in the misclassification-minimizing cutoff search and in the ER-balanced gene-centering set. The bias is one-directional and grows with the fraction of unknown ER. A new internal helper, .ihc_status(), classifies each label as "luminal", "nonluminal" or NA (missing or empty), and the three steps now use explicit luminal / non-luminal masks. Samples without an evaluable label take no part in estimating the cutoff or the centering set, a message reports how many were excluded, and they are still classified and returned. As a side effect the label test is now applied consistently: the mask is computed once, after trimming and upper-casing, instead of being evaluated before the upper-casing step in one place and after it in another. This is not a deviation from the published algorithm. The reference implementation (Raj-Kumar et al., CRAN package PCAPAM50 1.0.4, R/functions_PCA-PAM50.R lines 336, 355-356, 385-386) uses the same !grepl("^L", IHC) construct, but its IHC column is a user-supplied clinical subtype (LA, LB1, LB2, Her2+, TN) that the package never leaves missing; the vignette states that ER-positive subtypes start with "L" and all others are ER-negative. The NA category exists only because BreastSubtypeR derives the column itself. The change also removes an internal inconsistency: BS_cIHC() and BS_cIHC.itr() already exclude unknown ER from their ER groups via which(df.cln$ER == ...). Measured on the packaged OSLO2-EMIT0 input (R 4.3.3 sandbox), setting the first k ER values to NA and comparing calls before and after the change: k = 0 and k = 6 leave every call unchanged, k = 18 changes 2 of 102 calls, k = 30 changes 6 of 102. Cohorts with complete ER are unaffected, and the packaged example still reproduces its stored PCAPAM50 column. The help page of BS_PCAPAM50() gains a @details paragraph stating the exclusion, the message, that such samples are still classified, and the reference implementation's assumption of a complete IHC column. tests/testthat/test-pcapam50-unknown-er.R covers the helper, the unchanged complete-ER output against the packaged fixture, the message, and that unknown-ER samples still receive calls. Package: BreastSubtypeR Commit: 83ad6b3fa93553ba75cb3c641fb7a58070173806 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:10:00 +0200 Commit message: README/vignette: state the size gating of the ER/HER2-defined AUTO rule The AUTO bullet "ER/HER2-defined cohorts: ssBC.v2 only + SSP" read as an unconditional rule. In the code it applies only when the ER group reaches its minimum (15 for ER+, 18 for ER-) and the HER2 subgroup reaches its minimum (8 for ER+, 9 for ER-); smaller cohorts run AIMS and sspbc only. The bullet now says so, and a second bullet documents the handling of cohorts without any evaluable HER2 value (ER-based rules instead of the HER2+ branch). ASCII hyphens replace the typographic minus signs in the edited lines. Package: BreastSubtypeR Commit: 38aa1cc5cb833d260c5d5f82401a8ee528bd7fc1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:05:00 +0200 Commit message: Docs: Mapping "mean"/"median" collapse duplicate probes, as in the PAM50 code The Mapping() help (and the internal domapping() roxygen) described method = "mean" and "median" as keeping "the probe with the highest mean/median expression". duplicate_genes() computes the per-sample mean or median across all probes of a gene, i.e. it collapses the probes rather than selecting one; "iqr", "stdev" and "max" select one probe, and "max" selects by largest row sum, not by "highest expression value". Checked against the original PAM50 bioclassifier code (bioclassifier_R/subtypePrediction_functions.R, collapseIDs(), and the example parameter file): "mean" and "median" average the duplicate probes per sample there too, "iqr" and "stdev" select the probe with the highest IQR / SD, and no "max" method exists. BreastSubtypeR therefore reproduces Parker's behaviour; only its documentation was wrong. Author decision (2026-09-18): fix the documentation. The parameter text in R/BreastSubtypeR_methods.R, R/Utilities.R and man/Mapping.Rd now describes the averaging, credits collapseIDs() and marks "max" as a package addition. No code or mapped values changed. Package: BreastSubtypeR Commit: ba02d862d5e1c9cdbb43e23a1f8506faaed46946 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:00:00 +0200 Commit message: AUTO: include subgroups exactly at their minimum in the ssBC/ssBC.v2 subsets Method selection in get_methods() accepts a subgroup when its size is at least the minimum (15 for ER+, 18 for ER-, 8 and 9 for the HER2 subgroups), but the sample subsets handed to BS_Multi() for ssBC and ssBC.v2 were built with a strict ">". A subgroup of exactly the minimum size was therefore selected for the method and then excluded from its input, and its samples came back NA while the AUTO messages reported the method as running. The packaged OSLO2-EMIT0 example is such a case: 84 ER+ and 18 ER- tumors, so the cohort is classified as mixed and ssBC is selected, but the 18 ER- tumors were dropped from the ssBC input. Executed in a sandbox (R 4.3.3) on this branch: with the published strict comparison a fresh BS_Multi(methods = "AUTO") run yields ssBC = NA for those 18 tumors and does NOT reproduce the packaged frozen result OSLO2EMIT0obj$res (which carries ssBC calls for all 102 tumors); with ">=" the fresh run reproduces the stored result exactly, entropy included. The stored data object is therefore left unchanged; the fix restores agreement between the code and the shipped example. tests/testthat/test-auto-fixture-regression.R asserts the reproduction and that no ER- tumor is left without an ssBC call; tests/testthat/test-auto-subsetting.R adds exact-minimum subgroup cases and the OSLO2-EMIT0 colData. Package: BreastSubtypeR Commit: 13ea06daee8af82ab42c32cfceb38b43aecff9e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:55:00 +0200 Commit message: AUTO: require an evaluable HER2 value before calling a cohort HER2+ get_methods() entered the HER2+ branch whenever n_ERposHER2neg == 0 && n_ERnegHER2neg == 0. Both counts are also zero when HER2 is entirely missing or coded with unrecognized values, so such cohorts were classified as "small HER2+" and received AIMS and sspbc only (example: 60 ER+ / 40 ER- with HER2 all NA). The branch condition now also requires at least one evaluable HER2 value (HER2+ or HER2-). Cohorts without HER2 information fall through to the ER-based rules: a mixed ER cohort gets the mixed panel (ssBC.v2 then returns NA for every sample, which BS_ssBC() handles without error), an ER+-only cohort reaches the announced AIMS/sspbc fallback because its HER2 subgroups are empty. Cohorts with any evaluable HER2 value are routed exactly as before, including the existing treatment of HER2- samples whose ER is missing (excluded from the subgroup counts, as the AUTO message states). No effect on the packaged OSLO2-EMIT0 example. Author decision (2026-09-18): HER2+ branch only with evaluable HER2. tests/testthat/test-auto-routing.R covers the size-gated ER/HER2-defined cohorts and the cohorts without HER2 information. Package: BreastSubtypeR Commit: 94c6d57580acf6c6b77287f8e3968628ffeb2b84 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:50:00 +0200 Commit message: cIHC, cIHC.itr, PCAPAM50: clear error when an ER group is empty On a cohort with a single ER group (for example every sample ER+), makeCalls_ihc() and makeCalls.PC1ihc() failed with "undefined columns selected" and makeCalls_ihc.iterative() with "arguments imply differing number of rows: 0, 102", all from the median computation on an empty balanced set. The methods cannot balance by ER status without both groups. A small helper, .check_er_groups(), now stops with the group counts and a pointer to the cohort-aware modes in makeCalls_ihc() and makeCalls_ihc.iterative(). makeCalls.PC1ihc() checks the luminal / non-luminal IHC classes before the PC1 cutoff search and the balanced set after it, and makeCalls.v1PAM() checks its LumA / Basal groups. Cohorts with both groups take the same path as before (the OSLO2-EMIT0 cIHC calls are unchanged). Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-er-balancing-errors.R covers the three methods. Package: BreastSubtypeR Commit: 3894f47377e42f6c2f18cf8d7e04ecd0e38f7b16 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:45:00 +0200 Commit message: Docs: describe the actual return values of the NC methods; cIHC.itr ratio BS_PCAPAM50() and BS_ssBC() documented "a character vector of intrinsic subtype predictions", BS_cIHC() "a data.frame", and BS_cIHC.itr() a list with elements subtypes / confidence / ER_balance that do not exist. All four return a list: BS.all (PatientID, BS and, with Subtype = TRUE, BS.Subtype), score.ROR (correlations, calls, confidence, ESR1/ERBB2 expression, ROR-S/ROR-P and, with hasClinical = TRUE, ROR-C/ROR-PC scores and groups), the medians used for centering (mdns; mdns.fl for PCAPAM50; absent for cIHC.itr) and outList; BS_cIHC.itr() additionally returns BS.itr.keep and, with Subtype = TRUE, BS.itr.keep.Subtype. Verified on the packaged OSLO2-EMIT0 input. BS_cIHC.itr(ratio): makeCalls_ihc.iterative() swaps the larger ER group into the sampled position before drawing ceiling(ratio * n_smaller) samples from it, so the ratio applies to the larger group relative to the smaller one, not to ER+/ER- as such. The parameter text now says so, and the alphabetical tie-break used by get_consensus_subtype() for the consensus call is stated in the return value. roxygen comments and the corresponding man/*.Rd files were edited in parallel (no roxygen2 run, to avoid unrelated regeneration changes). Present in Bioconductor release 1.4.0 and devel 1.5.1. No code changes. Package: BreastSubtypeR Commit: abace8828bc01fa6ff7e1a70d6a9c1e28505cc74 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:40:00 +0200 Commit message: Shiny: cohort preflight requires both ER and HER2 columns .summarize_cohort() in inst/ShinyBreastSubtypeR/server.R returned ok = TRUE for kind "ER" (HER2 absent), kind "HER2" (ER absent) and for a valid TN column without ER/HER2. get_methods() stops in all three cases ("The 'AUTO' mode requires both 'ER' and 'HER2' columns in the 'pheno' dataframe"), which the app surfaced only as "Prediction failed" after the user pressed Run. The column summary is unchanged (now .summarize_cohort_columns()); .summarize_cohort() wraps it and sets ok = FALSE with the message "Cohort-aware analysis requires both 'ER' and 'HER2' columns; missing: ..." when either column is absent. Kind and statistics are still reported. tests/testthat/test-shiny-preflight.R covers the column combinations. Package: BreastSubtypeR Commit: 36e4de779bf6677fde472e81f613cf3f49799476 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:35:00 +0200 Commit message: iBreastSubtypeR: load app dependency namespaces correctly The launcher's .attach_if() helper called requireNamespace(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE). requireNamespace() has no such arguments, so the call failed with "unused arguments"; the failure was swallowed and FALSE returned, and nothing was loaded. The comment claimed the packages were attached to the search path, which requireNamespace() never does. The app still worked because ui.R/server.R use qualified calls and shiny::runApp() attaches shiny itself. The helper is now a package-internal function, .load_app_dependencies(), that checks installation, loads each namespace with requireNamespace(p, quietly = TRUE) and stops with a clear message when a package is missing or cannot be loaded. The tidyverse option uses the same helper. The exported signature and documentation are unchanged. tests/testthat/test-shiny-launcher.R covers the missing package error and the successful load. Package: BreastSubtypeR Commit: 6deac1db8d57cfbaee4e104edb9af6f160a9c536 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:30:00 +0200 Commit message: BS_Multi: report the error text when PCAPAM50 fails The tryCatch() around BS_PCAPAM50() in BS_Multi() warned "PCAPAM50 failed in this iteration: " and dropped the condition message, so users could not see why the method failed. The warning now appends conditionMessage(e) (with call. = FALSE). Behaviour is otherwise unchanged: the method's column is filled with NA. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-bs-multi-messages.R mocks a failing BS_PCAPAM50() and checks the warning text and the NA column. Package: BreastSubtypeR Commit: ff23703e8cb347524ad8fe1897d25d6514fd4049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:25:00 +0200 Commit message: Normalize factor phenodata like character; fix the FPKM imputation guard .normalize_er_her2_tn() used nested ifelse() calls whose fallback was the original column. For a factor column the fallback is the integer code, so unmatched levels came back as strings such as "3" instead of "Unknown". Mapping() converts colData factors to character before calling the helper, but BS_Multi() and get_methods() normalize the phenotype table directly, so a hand-built data_input with factor ER/HER2/TN columns was normalized differently from the same table with character columns. The helper now works on as.character() copies of the three columns; the coercion warnings compare character values, so canonical factor input no longer triggers them. Character input is unchanged. domapping(): the second imputation guard tested anyNA(x) after x had already been imputed, so counts.fpkm was never imputed. It now tests anyNA(counts.fpkm). In practice edgeR rejects NA counts earlier, so this is a logic correction with no expected effect on existing analyses. Both present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-phenodata-normalization.R compares factor and character input for the helper and for a full AUTO decision. Package: BreastSubtypeR Commit: 5deb60ce12da9448df97aa5079c0f312ad12cc6a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:20:00 +0200 Commit message: Mapping: keep matrix dimensions for single-sample input duplicate_genes() indexed x[names(entrezid), ] without drop = FALSE and rebuilt the collapsed matrix with mapply(SIMPLIFY = TRUE) followed by apply(x, 1, unlist), which requires a matrix. For a one-sample SummarizedExperiment the subset became a vector and Mapping() failed with "dim(X) must have a positive length". prepare_nc_matrix() and the probe filter in domapping() had the same drop issue. The collapse now builds the gene-by-sample matrix explicitly (lapply + rbind with dimnames from the split and the sample names), and the three subsets use drop = FALSE. For multi-sample input the returned values and dimnames are identical to the previous implementation for "mean", "median", "max", "stdev" and "iqr" (checked on random data with duplicated Entrez IDs and an NA value); the OSLO2-EMIT0 mapping of one sample equals the corresponding column of the full mapping. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: d6c6c20c4004d988e79c522ee4f1625dd0ad39fb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:15:00 +0200 Commit message: AUTO: announce the fallback to AIMS and sspbc instead of falling back silently The safety net at the end of get_methods() set methods to c("AIMS", "sspbc") without any message. It is reached by ER+-only or ER--only cohorts whose HER2 subgroups are all below their thresholds, typically because many HER2 values are missing (example: 17 ER+ samples with HER2+ 5, HER2- 6, missing 6). Users saw only the two SSP methods run, with no indication why the ssBC variants were not selected. The fallback now emits a .msg() (respecting the BreastSubtypeR.verbose option) naming the reason. Method selection is unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: a9f0de975795df873663f9cab6207455cb3b2d15 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:10:00 +0200 Commit message: AUTO: drop samples with missing ER/HER2 from the ssBC/ssBC.v2 subsets get_methods() built the AUTO-mode sample subsets with rownames(pheno)[pheno$ER == subtype] and the ER/HER2 analogue. A missing ER or HER2 value evaluates to NA in the comparison, so the subsets contained NA "sample names". BS_Multi() then either failed when it subset the SummarizedExperiment ([,j] index out of bounds: NA) or, when the NA-padded vector was at least as long as the cohort, treated it as "run on all samples" and skipped the intended subsetting. Example on 1.5.3: 50 ER+ / 45 ER- / 5 NA gives a 105-element subset with 10 NA entries for a 100-sample cohort. Both lapply bodies now use which(), as makeCalls.ssBC() already does, so samples with missing status are excluded. Cohorts with complete ER/HER2 values return identical subsets. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-auto-subsetting.R covers a mixed cohort with missing ER and an ER- cohort with missing ER and HER2 (subset shorter than the cohort). Both fail on the previous code. </pre> </div> Package: BreastSubtypeR Commit: 2f8ea71201a742d0d0957ff8228ba2fdbc21d3be Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:05:00 +0200 Commit message: Fix ROR-C risk group column: use criskgroups, not cpriskgroups In RORgroup() (R/NC_functions.R) the data frame built when hasClinical = TRUE assigned the combined + proliferation groups (cpriskgroups) to both "ROR-C Group (Subtype + Clinic)" and "ROR-PC Group (Subtype + Clinic + Prolif)". The ROR-C groups (criskgroups, thresholds -0.1 and 0.2 on the combined score) were computed but never reported. The ROR-C group column now uses criskgroups; the ROR-C score and every other column are unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-ror-groups.R adds a synthetic RORgroup() input in which the ROR-C and ROR-PC groups differ (high/low/med vs low/high/med) and checks that the ROR-C group is reproducible from the reported ROR-C score. The test fails on the previous code and passes with this change. Package: BreastSubtypeR Commit: 9ab99af8b9cf337614a30a61c3e0ce1c264df049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:00:00 +0200 Commit message: Tests: run the nested testthat suite via test_check() tests/testthat.R contained a single inline test_that() block and never called test_check(), so tests/testthat/test-tn-cohort-detection.R (added in 1.5.1) was not executed by R CMD check; the Bioconductor devel check log shows only the inline test running. tests/testthat.R now calls test_check("BreastSubtypeR") and the inline BS_Multi() test moved unchanged to tests/testthat/test-bs-multi-manual.R. DESCRIPTION: Config/testthat/edition: 3 and testthat (>= 3.2.0) in Suggests, matching the edition-3 expectations used by the tests added on this branch. No version bump. Package: BreastSubtypeR Commit: a4b23b2aba07ba19b33669ac1e8d8361fd1139ab Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:59 +0200 Commit message: Merge pull request #135 from yqkiuo/main update to 1.5.2 Package: BreastSubtypeR Commit: b19c1c3f629d11a8f12e57526162b16e41e605c6 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:30 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: 0c0c47c87dcd6e560bedcd536f828dca642e7933 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-06-22 17:38:39 +0300 Commit message: Merge pull request #134 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: edeb030317e854cd706a351f12b93dbd722f232e Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 17:22:45 +0300 Commit message: Finalize NEWS entry for TN detection fix (#133) Package: BreastSubtypeR Commit: b8d6bf4b5bb037d8e101287e92d209fdb1e869a5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:59:04 +0300 Commit message: Update NEWS and documentation for TN detection fix (#133) Package: BreastSubtypeR Commit: d8eeff0e85113512842b1e4976fce6eed1142e39 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:25:06 +0300 Commit message: Fix TN-only cohort detection (#133) Package: BreastSubtypeR Commit: cd515ab92fffbbf8a3496cfc70e65299b77457ba Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-02-20 12:09:07 +0100 Commit message: v1.3.3 Package: BreastSubtypeR Commit: 0770ee5c0a5283fd1f073cf9c170464431eac2d3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-02-20 11:59:28 +0100 Commit message: Merge pull request #129 from yqkiuo/main AUTO - NA Package: BreastSubtypeR Commit: 9b740667ac781cede13f2884763f47576f5778cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:30:22 +0100 Commit message: Merge pull request #128 from yqkiuo/BranchManos Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: ebac3daf14161981995520818d552a8c894faa21 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:27:35 +0100 Commit message: Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: 122fae948ba3ab93589046d4fc9f564a95db3805 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-12-21 07:08:46 +0100 Commit message: Merge pull request #125 from yqkiuo/main Update Package: BreastSubtypeR Commit: ab9e6c7e715a77c3d9d0c93f0d96794531b39afc Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:48:57 +0100 Commit message: Merge pull request #124 from yqkiuo/BranchManos cIHC.itr: return distances as numeric matrix, preserve dimnames Package: BreastSubtypeR Commit: 1cdd290182105e8d9dd1cf38a2f1cc2748045aba Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:41:20 +0100 Commit message: cIHC.itr: return distances as numeric matrix, preserve dimnames - Coerce mean_distance and mean_distance.Subtype to double matrices with sample/centroid dimnames; negate once. - Ensure testData is numeric matrix. - Use explicit getsuffix(calibration=..., internal=...). Closes #112 Package: BreastSubtypeR Commit: e626336705e6981d3f43c1e307381875acc4dbf5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:18:30 +0100 Commit message: Merge pull request #123 from yqkiuo/BranchManos feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to can… Package: BreastSubtypeR Commit: bf244ea222946de979dc528b6764b074b9a7492e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:17:59 +0100 Commit message: feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to canonical forms - Add `.normalize_er_her2_tn()` utility and call it inside `Mapping()` to coerce common variants to: * ER → {ER+, ER-} * HER2 → {HER2+, HER2-} (HER2 "2+" left unchanged/unevaluable) * TN → {TN, nonTN} Accepts Positive/Negative, Pos/Neg, Yes/No, True/False, 1/0, AMP→HER2+, etc. - Preserve original values in `colData` when fields are absent; only touch present columns. - Emit explicit warnings on ambiguous/unmappable values (e.g., HER2 "2+"). - Roxygen: expand `Mapping()` docs with required Column metadata for AUTO/ssBC/cIHC/PCAPAM50 and numeric TSIZE/NODE (0/1) for ROR; document the canonical receptor coding and the automatic normalization behavior. Closes #122 Package: BreastSubtypeR Commit: d4200b8f8fa6a230b1aed6bd8d5a271856dcf9c5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 10:04:54 +0100 Commit message: Merge pull request #120 from yqkiuo/BranchQiao Formatting Package: BreastSubtypeR Commit: 855146c3797560a923b044683b223aa09c5ab6b6 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 10:04:04 +0100 Commit message: Formatting Package: BreastSubtypeR Commit: 7e1546b848212ca92df006f0625e1f0213a5d825 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:57:27 +0100 Commit message: Merge pull request #119 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 13081dbdf8d5faead48468a7121455f68f226262 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 09:56:57 +0100 Commit message: Warning: nonASCII Package: BreastSubtypeR Commit: e872818d9f7db70dd95b04e56306c5f986b4cb2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:48:36 +0100 Commit message: Merge pull request #118 from yqkiuo/main 1.3.1 Package: BreastSubtypeR Commit: e837d4a4b93480e5921dc6220d336f390e08cfa9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:56:26 +0100 Commit message: Merge pull request #117 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 24282cdd95efcb545c8a516d2a4c52c333451e37 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:55:43 +0100 Commit message: docs(NEWS): updated to include latest changes/bug fixes Package: BreastSubtypeR Commit: d3e819ea9cb6036119018581de03f7c0ca6c03e9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:45:26 +0100 Commit message: shiny/preflight: reset cached data_input on source change (uploads/example) to fix stale cohort display Package: BreastSubtypeR Commit: f7ad9d6399c959146fad253c76e4b8a093367674 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:06:08 +0100 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: 33bc7cabda598a10d06781255a4ff477d64ec373 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:05:55 +0100 Commit message: Merge pull request #116 from yqkiuo/main Main to BranchManos unmerged changes Package: BreastSubtypeR Commit: c1164715171e92993dba23d51ed4d2739a9db33a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:03:31 +0100 Commit message: Include ssBC in robust singleton handling Package: BreastSubtypeR Commit: 0c0c39cd7cb7bdde99192d4a877cc9990b98b6c4 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:32:17 +0100 Commit message: v1.3.1 Package: BreastSubtypeR Commit: ed479c4a0a715bd078874a465956416cb58e999b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:30:33 +0100 Commit message: Minor typo for Shiny exports Package: BreastSubtypeR Commit: fca34d14be09269bd6a9e83f9b169b3f49e3b27d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:16:28 +0100 Commit message: ssBC.v2: include sample IDs in singleton fallback warnings; surface warnings in Shiny - Warnings now list subgroup + n + sample IDs (truncated for long lists). - Shiny wraps runs in withCallingHandlers() to show warnings via showNotification(). Package: BreastSubtypeR Commit: 5beba6624617ea57bd33a664a2c9ccddbe01f5d2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:15:25 +0100 Commit message: ssBC.v2: robust singleton handling + ROR guards - Use uncentered expression for n=1 fallback (avoid zero-vector Spearman→NA). - Add canonical 4-class name normalizer before RORgroup; create missing cols; enforce order. - Shorten Mapping() completion notification duration in Shiny. Package: BreastSubtypeR Commit: 6f8593d8659200d5b054e45ae6deb7ff624bf02f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 23:31:32 +0200 Commit message: Merge pull request #115 from yqkiuo/BranchManos fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: ae32dd867386460a3d6abcff63cd519bcebdd098 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-21 23:25:49 +0200 Commit message: fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: 01a86e199d7353c526b1ddec6693b6c5d87a53e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:51:52 +0200 Commit message: Merge pull request #114 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: aee5223fca7ad466234702b83f9d465092e65fec Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:50:18 +0200 Commit message: update documentation (.Rd) files & NEWS.md Package: BreastSubtypeR Commit: e3852e46bc7c708db9534558669b18e492bbcb44 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:38:36 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: f13b835df4329f494e2a1fe1242a1927657629f9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging -Name unnamed chunks Closes #113 Package: BreastSubtypeR Commit: 815edf2ed0faa1dc708fecc282da22945d861490 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging Package: BreastSubtypeR Commit: 27a8e42ca0dd5a06b976bd6e59aeedf3337c8ad1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:41:55 +0200 Commit message: Merge pull request #111 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6ed1cf770b44ea3eeaa0fe5d284760692df203e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:40:32 +0200 Commit message: feat(shiny): show ER/HER2 subgroup tallies (±TN) in AUTO preflight Package: BreastSubtypeR Commit: a85dec5c9e7f261e7d9ea94febbbfc063dc07992 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:04:55 +0200 Commit message: fix(shiny): guard switch() inputs to prevent length>1 errors; harden AUTO preflight & ssBC option handling Package: BreastSubtypeR Commit: 8b4e57129dabde362d8c811661e7586dc633c396 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:49:16 +0200 Commit message: feat(shiny): TN-aware AUTO preflight summary and messaging Package: BreastSubtypeR Commit: 83b469a296627e4a81983655692766813d8540b2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:48:42 +0200 Commit message: docs: convert wording to American English (standardized, normalization, visualize) Package: BreastSubtypeR Commit: 1c86f875473cf413e91da628410278915a9b19cb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 00:28:47 +0200 Commit message: Merge pull request #110 from yqkiuo/BranchManos v1.1.9: feat(app): add example-data loader and AUTO preflight cohort … Package: BreastSubtypeR Commit: bcb7486f49afd2f9c719d1b047c89b96421040b5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-15 00:26:27 +0200 Commit message: v1.1.9: feat(app): add example-data loader and AUTO preflight cohort stats; harden AIMS/sspbc outputs; renamed FPKM GEX example file Package: BreastSubtypeR Commit: 3e5ae1bae1910f63b576690d0f5965c092929197 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-14 22:26:00 +0200 Commit message: Merge pull request #109 from yqkiuo/BranchManos Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: 643629b4f37a82e8eb4fc1d4b8b7d47a1d0140e5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-14 22:08:03 +0200 Commit message: Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: f0bb013273724583dc640776f5253a650e71deb7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-11 19:07:21 +0200 Commit message: Merge pull request #106 from yqkiuo/main v1.1.8 Package: BreastSubtypeR Commit: e519bba6330b28527eba397178b5db68259cd335 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 17:48:34 +0200 Commit message: Merge pull request #105 from yqkiuo/BranchManos Minor text improvements Package: BreastSubtypeR Commit: 7ef4c516f1e02b2667908e42c91db1f81587e183 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 17:35:16 +0200 Commit message: Minor text improvements Package: BreastSubtypeR Commit: bba02a162aae8a104830c2762903a95b4b24a086 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 16:30:43 +0200 Commit message: Merge pull request #104 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6bb89109d53b3cbfc61069dad0b97c43fc01a59 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 08:38:02 +0200 Commit message: v1.1.8: feat(auto): enforce v2-only for ER/HER2-defined cohorts; add TN cutoff (18); sync docs Package: BreastSubtypeR Commit: 104a9d3c962648e2421f86b970452b6ae8094add Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 00:03:52 +0200 Commit message: v1.1.7: Fixed bugs & Clarified guidance in AUTO logic Package: BreastSubtypeR Commit: 3a0c352910e74d2016eaaa4f0d229db74b6428b1 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:11:23 +0200 Commit message: Merge pull request #103 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: c23f9312cfe6399587682872db5168e726949468 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-08 07:10:55 +0200 Commit message: v1.1.6 Package: BreastSubtypeR Commit: bda41efb6523b351c335cbbbfe93eda3e294159a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:01:46 +0200 Commit message: Merge pull request #102 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 01fbf08f95785bd96121416f08a42a0723db9bb5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:31:43 +0200 Commit message: Merge pull request #101 from yqkiuo/BranchManos Update citation Package: BreastSubtypeR Commit: 819b86fcb1f32f68d8d6551ae67675e59d55cbc2 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:29:59 +0200 Commit message: Update citation Package: BreastSubtypeR Commit: 18426cd1996f6d437078579a397e594ac858b422 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:18:10 +0200 Commit message: Merge pull request #100 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5cd622f0dfdcbf4ebd2612e2f3bce0d4d130a1dd Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:10:24 +0200 Commit message: Update to v1.1.6 Package: BreastSubtypeR Commit: 0168bb1d064c170c27904604ce944664052ffc4c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:00:02 +0200 Commit message: Fix CITATION error & update CITATION Package: BreastSubtypeR Commit: efcf440f930e3e0216161a7bfaa1f8a839796ffc Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:28 +0200 Commit message: Merge pull request #99 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 522570c1925152201b4738888c70a9b479569b4d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:10 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: caa57d7c96c2b3621ba3153a63704780fb67943c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: eca7fd305351bee53a3359193d31d6efb3bd239c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:26:16 +0200 Commit message: Merge pull request #98 from yqkiuo/BranchManos Bump version to 1.1.5, merge from BranchManos Package: BreastSubtypeR Commit: 3d6d84a04f652c46b098e7daf6b9433783c59317 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:17:29 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 08be34439c7ec15f3aab940989e7fc5881500a38 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:28:50 +0200 Commit message: Minor styler changes to comply with BiocCheck Package: BreastSubtypeR Commit: c33c626c748776d83aec78b69c2c5c2d78b40d94 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:00:25 +0200 Commit message: Remove Styler ignore file Package: BreastSubtypeR Commit: a756018eea737c57128fecbe2ed656a5c8bd8c89 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:53:48 +0200 Commit message: After styler formatting Package: BreastSubtypeR Commit: 0fb6775cf7105ccdfeac0f78d671c8220fa00a07 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:43:21 +0200 Commit message: Before styler formatting Package: BreastSubtypeR Commit: f462a35c15affb83307240678fdb8b5c31f1e1af Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 15:06:41 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: d58720a8654c148543e56efe3c8504e50f7a06f9 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Fix LaTeX errors, @importFrom issues, deprecated mutate_at(), tightened Mapping() Package: BreastSubtypeR Commit: 8cab29a01c0412be9b9a83d9c729c77b273c03f9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:33:33 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 2909f655c9c2686e9c562762e27c7cb78eb63544 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Merge pull request #97 from yqkiuo/BranchQiao Fix LaTeX errors Package: BreastSubtypeR Commit: f1d92deeed7ff76170c4ba8a70d0ac75e0dab7eb Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:28:10 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 9112d81e8538f3debb6c101255008486d052c326 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-12 19:39:12 +0200 Commit message: Merge pull request #96 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 977c1a7f7a5dd3700b51fe154e0a9509d6a960b1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 19:38:48 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: b2ba716538df0e23e684ec1118866c96560cab9b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:14:24 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: e25016431d3c00bfd81d941f4b8a71a2b7357ba1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:07:19 +0200 Commit message: v1.1.3 Merge branch 'BranchQiao' of github.com:yqkiuo/BreastSubtypeR into BranchQiao # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. Package: BreastSubtypeR Commit: 0f3624d0ed05aa4d2f2cb9759acb59d815fea297 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:04:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 8a340b6a4117f80791ae664c5741a0fe8627c9c3 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 15:44:48 +0200 Commit message: Fix BreastSubtypeRobj to include only the object itself (exclude environment variables) Package: BreastSubtypeR Commit: f969bcf09e03aa226de3839a68cf76cc01011ef3 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 14:52:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 693c829f364caedb2161a940d196d1830bd19d87 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 10:21:35 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 8582fb3b897e60ecc6da91040e32b42b19641154 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 17:06:26 +0200 Commit message: Added publication badge Package: BreastSubtypeR Commit: bd0b6cab935e607efd4bb001e3b75b02b37cc1fe Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:47:02 +0200 Commit message: Fixed bug: When running BS_Multi() omitting the first method; Minimal fix (drop nothing after removing row_id) Package: BreastSubtypeR Commit: 234ccbe269d45bd2c407358b711253629fe59203 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:12:28 +0200 Commit message: Polishing README.md & Vignette Package: BreastSubtypeR Commit: b3d5c232a32097ee9b4f83908a9c89f6ca621be8 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:41:14 +0200 Commit message: DOI update and text Package: BreastSubtypeR Commit: bacb13657f301643a682a3fcd7e82a22091a3b6c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:01:14 +0200 Commit message: Added DOI, Updated exported with version info, method, etc Package: BreastSubtypeR Commit: 787b3119148e345c0b2d4fa8638b3d6dd37600ee Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 19:17:32 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: c856d8dc615f688ae8f5d27eeb47ab297ead6b11 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:36:22 +0200 Commit message: Delete .github/workflows/sync-to-forks.yml Package: BreastSubtypeR Commit: 8d235ce12beccf9d394146a458ae135fec2f0fb3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:18:15 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: ad15f75e9de9028eb6d93fb5efb3ca05220ce975 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:04:51 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 917d62c7bc428fc67ff97c513022feb210fed94c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:58:05 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 9258dd1803aac507ecae1ec05d30a55c7c91827c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:54:22 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 8864ea4a8bda1bee1b6496aaf185e8bb76af5257 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:57 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 71735535741a019e7ba9299e47783038edbd3714 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:00 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f165c7df5636588c76360b10a42e792e9bf53614 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:50:26 +0200 Commit message: Create sync-to-forks.yml Package: BreastSubtypeR Commit: f2d85acb23f2c38ec3b3062fbab841c29115d38e Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:47:46 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 792bc0ab92f80b7405d69c45516dd131ffd7663c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:43:18 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 99d3102b66482953013f265d00464c8c3a4c2b25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:34:13 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 212e09ee660df8daaffea11a7af00d53321895aa Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:04:17 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 7cea1e782fedda5fef57f559c77dc39db8aceb9d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:56:40 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f33f344a6b0d06d3de393a783a23383e4ef5cac4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: adccaf9e7d8ce2b6234a1960e93e5d1543d98e09 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:31:34 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: a9e9e80f2f1063aae332963e474ea2f5804487b7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:27:58 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 4151dfa20943c89acdd55c5e1dec18a03da01e2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:14:01 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 1ab513bde94a41e4ab34856ca5e4f5ba5a6413e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 15:59:19 +0200 Commit message: Create sync-to-org.yml Package: BreastSubtypeR Commit: f9f0ea202177840660c02d39e203f67d4003e2cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:09:58 +0200 Commit message: Added description for new example dataset (TCGABRCAobj), updated the BreastSubtypeRobj with the 3 new medians info, tiny text improvements Package: BreastSubtypeR Commit: 056545172113202bb55a0ea0c2918851096fa0f2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:05:10 +0200 Commit message: Created a new example dataset (TCGABRCAobj) from TCGA-BRCA with Raw Counts, and similar results as OSLO2EMIT0obj Package: BreastSubtypeR Commit: 6de103db09589a53624341851237a8f547684ceb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:02:19 +0200 Commit message: Updated BreastSubtypeRobj with 3 more published medians Package: BreastSubtypeR Commit: 6acd15688f6e60db4e1f2ef151c103e865ce5663 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:00:19 +0200 Commit message: Guard docalibration, Improve External calibration, UX, and minor text improvements Package: BreastSubtypeR Commit: 8f7e3790ac94fead82f77e6564d87c542fcf5097 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 11:11:22 +0200 Commit message: Fixed error in BS_Multi() in AUTO Mode, when ssBC has <50 PAM50 genes: Add safe row-aligning cbind helper, made RORgroup() tolerant to missing ESR1/ERBB2 rows, and made BS_Multi() assemble results by PatientID Package: BreastSubtypeR Commit: 06bd9bce269ca12b4ca9f052f3d81cd730212a68 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 21:20:25 +0200 Commit message: Fixed the issue with pre-loading third-party libraries before initializing the Shiny app, Updated Help files Package: BreastSubtypeR Commit: ee560564150a7a5f11c00e8750583438a6c084e6 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:55 +0200 Commit message: Updated NEWS.md with major changes Package: BreastSubtypeR Commit: abd132463b65390c813f04ea50c530fd4b058507 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:18 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 74b20b933030517c45e68826a469dd88d79aa0b9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:24:07 +0200 Commit message: Added a TCGA-BRCA subset, with clinical & annotation data, for testing the RawCounts normalization pipeline Package: BreastSubtypeR Commit: d4fedc4c9b2a241b2652e563c2300d423f787287 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:21:08 +0200 Commit message: iBreastSubtypeR: UX polish, AUTO explainer, export refactor, AIMS constraint & bug fixes Package: BreastSubtypeR Commit: fb7c21f7ebc4f50be7610c8c0a023036f1559358 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 13:24:32 +0200 Commit message: Include three pre-computed Medians (external) as an option to Shiny App Package: BreastSubtypeR Commit: d1a90080950c9b5ddcad737979d072bdc177e038 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 11:34:43 +0200 Commit message: ssBC fixes: No crashes when < 50 PAM50 genes, No accidental subtype calls when a sample’s distance row is all-NA, Won't error when a subgroup has zero samples, qCtr won't produce NaN from zero range Package: BreastSubtypeR Commit: 10644b50e4721efe7b0d9f65445d30e1fdcf5a26 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 10:05:57 +0200 Commit message: Add our reference to Mapping() & BS_Multi() Package: BreastSubtypeR Commit: 5ea0dd73f932fbdd278f4e299de7270698d855c1 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 23:10:17 +0200 Commit message: New preflight for AUTO to prevent errors, new customizations, included new polished text for PAM50 to guide users, and more Package: BreastSubtypeR Commit: 3b08eed750427d72842bec852ff85c2446138cbe Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 13:21:06 +0200 Commit message: Fix issue when HER2 missing and user runs AUTO Package: BreastSubtypeR Commit: 16b805c817e0b7e3883b1aa7defd6da04f6a57f4 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:20:14 +0200 Commit message: Included a Prelight check for ER/HER2/Tn status availability in Clinical data BEFORE Running subtyping, avoiding App crashing due to missing values Package: BreastSubtypeR Commit: f003e4ecbfadb6a2a293ff39d838581dea5a0086 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:01:32 +0200 Commit message: Synchronized changes in BreastSubtypeR_methods.R and NC_functions.R, Created a theme to match the logo, made things unified, text improvements Package: BreastSubtypeR Commit: a66b4796231c8054f2093c6795ca4e67f2cb04de Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 10:08:20 +0200 Commit message: Parker original when calibration=None, or external calibration returns error: Fixed by Making NA equivalent to "medianCtr" (sync eith Parker et al.), and -1 to No calibration. Also, avoid requiring PatientID for BS_parker() when hasClinical = FALSE, included extra controls for hasClinical in all NC functions, polished help text, corrected typos (also tried to correct the 2nd error for ssBC, when < 50 genes, but will work more on this and come back with another Commit) Package: BreastSubtypeR Commit: 53ca58ec99d200f998a8be6896bab45f47d789e3 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-05 19:36:25 +0200 Commit message: Major changes: Multi method with AUTO mode added, Description text for each method with Refs added, Subtype 4-class selection Package: BreastSubtypeR Commit: bdf3bf291b59939171d85ff61f895b2ffc222b8d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:18:47 +0200 Commit message: Fix UI so the drop down menus are easier to select Package: BreastSubtypeR Commit: c0ed93ab5eed4a965f478a0dcac17355f8f91501 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:01:42 +0200 Commit message: Changed HasClinical with a Tick box, included many controls to check whether TSIZE, NODE are available, added different help functions for GEX and Annotation, improved text, and more Package: BreastSubtypeR Commit: 277869bea9c0c7d2747370cc657b2e87cb4e7dd2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 14:59:23 +0200 Commit message: Replaced the T -> TSIZE Package: BreastSubtypeR Commit: fd063a60aa8db3651975e89237ddb398d62c1100 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:28:48 +0200 Commit message: Minor edit Package: BreastSubtypeR Commit: 31e6bbfa2c897aa87caa09254cd2d4d2074b790f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:25:40 +0200 Commit message: Renamed folder to Shinny->Sniny, renamed data files with clear names Package: BreastSubtypeR Commit: 5ef9dd73efdccab438ee51f1ea0441ac565ca984 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:20:19 +0200 Commit message: Fix server.R bug Package: BreastSubtypeR Commit: c4c205e993f8791683fddf05392533aadded4b75 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-04 11:49:00 +0200 Commit message: refine shiny Package: BreastSubtypeR Commit: 304cb68143558163b4dd070c2498631f62a650e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-04 10:40:17 +0200 Commit message: Merge pull request #95 from yqkiuo/main Merge pull request #94 from yqkiuo/BranchQiao Package: BreastSubtypeR Commit: 6cbc1cb1b18907119b3414e3c0dafec607480a99 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:27:20 +0200 Commit message: Merge pull request #94 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 298458b861686b4ed9bfa17c070e5ffea513f3dd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-02 08:27:00 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: a50d8d4c3bea22f65836df6d099b269da685d8c2 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:25:43 +0200 Commit message: Merge pull request #93 from yqkiuo/main v1.1.2 Package: BreastSubtypeR Commit: 65b18fd8734f90e579fff40e53bbc51799b2c4ad Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:28 +0200 Commit message: Merge pull request #92 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5d09b44a5785c08a10d3d652d2a01db94678a1de Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:21 +0200 Commit message: Merge branch 'main' into BranchManos Package: BreastSubtypeR Commit: 8f4056fc16de285798c18e8c36e5399e5cd1fd23 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-01 10:18:12 +0200 Commit message: Merge pull request #91 from yqkiuo/BranchQiao v1.2.2 Package: BreastSubtypeR Commit: e11ffcd934d71dd5ee42c3816cabf93b997e6c64 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-01 10:17:53 +0200 Commit message: v1.2.2 Package: BreastSubtypeR Commit: 0969e8fa4d71d310d1d2f58c788af7a94566de25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-31 22:18:46 +0200 Commit message: Merge pull request #90 from yqkiuo/BranchQiao v1.1.2 Package: BreastSubtypeR Commit: c575280eed4e562e90ba6b9b7a6675353e532725 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-31 22:18:25 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: 031beb8e23f96e6f4894f56b550dd49d0c2a729b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-29 16:04:28 +0200 Commit message: Updated code to include separate cut-offs for ERpos & ERneg, as well as separate cut-offs ER(pos/neg)/HER2 (independent of HER2 status) based on the above cut-offfs. Note: The combined cut-offs will be released in the next submission Package: BreastSubtypeR Commit: 93ba44156f95a90bb74440d472157107e5ef0908 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 20:13:37 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: efee177e7f94d079d424ad79467615a63ce71698 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 2c6cfcacdc3550df0916ecb54833275bf2b9f04f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: d0154df0200108179568a150e1487e592a34e20a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 6a0be72275efbb8b9828b8765834d1ce97521134 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 3cf5afd43c31eeec90045902e6a082d82013bbf7 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: e91120bb63753900c47f80206b0662aef090c98a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: c09d132b8993a81ad16143b2ddbd5fb6b6f36f8b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 18:32:39 +0200 Commit message: Updated NEWS.md, BreastSubtypeR_methods.R, and minor updates to Utilities.R and data_doc.R Package: BreastSubtypeR Commit: 10f36184b66a9a0703d4296c9311b5ed1fc03e23 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 15:16:50 +0200 Commit message: Shiny app normalization clarification Package: BreastSubtypeR Commit: 24740ca0d3f45e43e674d247778b8e003871361c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:57:22 +0200 Commit message: Replaced the adaptive filtering as it was producing a reduced gene list for NC-based methods. Instead I introduce the calculation of UQ in the positively expressed subset and apply those calculcated factors to the full matrix. Package: BreastSubtypeR Commit: 347114047eeba2318371d4245043ae1d3b6bce86 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:34:21 +0200 Commit message: Include adaptive gene filtering so UQ normalization can work under real data Package: BreastSubtypeR Commit: f3bd9cdae36176a3857de89fac0c794bd8df369b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 16:29:18 +0200 Commit message: RawCounts test code include & help files updated Package: BreastSubtypeR Commit: c248d0fe615e9d6e3f4401bb6658908341de9208 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 16:07:29 +0200 Commit message: Shiny app: added descripted text Package: BreastSubtypeR Commit: 52bea350827dc0fba939551f50149d60acb3887b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 15:12:56 +0200 Commit message: Updated text in overview files Package: BreastSubtypeR Commit: 5b87399978a5d1cca09a82d5249a2b8863a553ea Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 15:10:09 +0200 Commit message: CITATION added Package: BreastSubtypeR Commit: e8fcac0bcab82793b586f5ffc8c930a0002ac609 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-21 11:29:40 +0200 Commit message: Merge pull request #89 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 0c75bf90f3070408ec5a156edf84b9c0bc70250b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:29:14 +0200 Commit message: update new features Package: BreastSubtypeR Commit: a99a93e94a90d6a715d64daedbe2e1f886f87917 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:27:58 +0200 Commit message: update new features Package: BreastSubtypeR Commit: c9f28c19c39695ad8a84ee4aa929c352be00e229 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 18:11:51 +0200 Commit message: Merge pull request #88 from yqkiuo/BranchQiao Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: e4a62355017220fe89ec8ea09376a0a56060de7c Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 18:11:26 +0200 Commit message: Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: 1993ab3e50725d01e8980a00eeaec8f0b0b766c4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:48:10 +0200 Commit message: Merge pull request #87 from yqkiuo/BranchQiao 1.1.1 Package: BreastSubtypeR Commit: 5d928ed37d8d0f47dd0392057846c43dc12e3dea Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:47:44 +0200 Commit message: 1.1.1 Package: BreastSubtypeR Commit: 52faaf9d7980c6d36524bcabbdcffe1f0fb92a0a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:39:51 +0200 Commit message: Merge pull request #86 from yqkiuo/BranchQiao 1.0.1 Package: BreastSubtypeR Commit: 35eef13e343edd2f9c6a1c26d780c97f470ac6c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:38:55 +0200 Commit message: 1.0.1 Package: BreastSubtypeR Commit: 6abaf3b4ae3d1772babec19c83d49c04728daa06 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-27 09:49:16 +0200 Commit message: Merge pull request #85 from yqkiuo/BranchQiao general update Package: BreastSubtypeR Commit: 453e9aac8dc81b86987e53e60659f2c97f6ba403 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-27 09:48:42 +0200 Commit message: general update Package: BreastSubtypeR Commit: 226607c2ae42706346a1e8911d1f2f82a5ca1490 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 19:12:11 +0200 Commit message: Merge pull request #84 from yqkiuo/BranchQiao v1.1.1 Package: BreastSubtypeR Commit: d773d4401e93ec12006f4e79122cbee8247d80d7 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 19:02:45 +0200 Commit message: v1.1.1 Package: BreastSubtypeR Commit: e74e86a2cfdf6daf92ed180095d27619cd45cd54 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:44:06 +0200 Commit message: Merge pull request #83 from yqkiuo/BranchQiao Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: fd30082d86b34d3ced41b7a7c385e01448c19794 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:41:43 +0200 Commit message: Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: 74145000a4ce350ca0e787fe5c459b79318b3edb Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:25:01 +0200 Commit message: Merge pull request #82 from yqkiuo/BranchQiao Bug fixes and minor improvements Package: BreastSubtypeR Commit: 1a5cb6636acfbd2ad1fc7c290bfba875dd2b22b0 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:24:35 +0200 Commit message: Bug fixes and minor improvements Package: BreastSubtypeR Commit: 4a895b8a8a149e0199b85eeaa19b6769dd8382df Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:27:17 +0200 Commit message: Merge pull request #81 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 4a03138457415f0164139373ee34038bd07ad300 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:21:40 +0200 Commit message: Update DESCRIPTION Package: BreastSubtypeR Commit: 856c6f8f91de5339988cf4c315bcaf96247f37d5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 10:39:20 +0200 Commit message: general update Package: BreastSubtypeR Commit: e35db8756a5fa3f30bf4addbeacd58145589e16b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:18:47 +0200 Commit message: general update Package: BreastSubtypeR Commit: 2e60c2222d3e9fdf48d3262ba087b447a95119a9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:03:00 +0200 Commit message: general update Package: BreastSubtypeR Commit: 7cfcfe95b2761178d17cc2af122f61883e7dc666 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:50:06 +0200 Commit message: update general Package: BreastSubtypeR Commit: b30131f2c073711d4b42e38af49bef1849da20c5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:48:53 +0200 Commit message: Update RawCounts para Package: BreastSubtypeR Commit: 6fa4d83d00b30727be9b1d4fd3798015fad0442a Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:32:10 +0200 Commit message: debug ROR Package: BreastSubtypeR Commit: ba045196fcd4a3bff148b3497a82f3f87d6bb324 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:31:55 +0200 Commit message: refine "-1" in parker.original Package: BreastSubtypeR Commit: b5e6254539fd38e41109056b2ddff7d36e0f9c19 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:15:41 +0200 Commit message: refine "-1" in parker.orignal Package: BreastSubtypeR Commit: bc7d097164cb411bfc4b40d5513073ae1bac35d8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:39 +0200 Commit message: 0.00.0 Package: BreastSubtypeR Commit: 5d966c161e4cdae464dd16d48421f6d5a4e26461 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:30 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 81f77832a0d7f8f5b8b70403616fe165ff96862d Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:08 +0200 Commit message: debug data type Package: BreastSubtypeR Commit: 8471668b9b9b43c3e27a87faa458488a8fba7f05 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:56 +0200 Commit message: debug BS_Multi Package: BreastSubtypeR Commit: 01fa8b576ca237667ed8a792477638cd4b023dbd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:34 +0200 Commit message: clear author Package: BreastSubtypeR Commit: a86f573778ed992a3d2dbb698b4c9c00a15619c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:20 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 00d2b9c5d71c6830e845dcddcb810b9640666207 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:33:01 +0200 Commit message: debug AUTO Package: BreastSubtypeR Commit: 8b3f7c2ef2d45cf772511a7290ba0a31baa43b62 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:32:46 +0200 Commit message: debug bad PCAPAM50 Package: BreastSubtypeR Commit: c70f4c9b0d64da1940659ae9a826d8221be05a32 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 09:32:30 +0200 Commit message: debug PCAPAM50 </div> </div>
Suggest org.Dr.eg.db, needed for danRer10 and danRer11 gene annotations Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Build basicgenes and cpgs per genome in the full tests Building every gene annotation type for every genome ran out of memory in an 8 GB Docker VM. Only the gene model and CpG sources differ between genomes, so test those per genome, and the other gene annotation types once for hg19. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Overhaul tests for testthat 3 and fix plot_categorical() with no fill Move to testthat 3rd edition, and rename the test files to test-.R since they no longer depend on file order. Shared data comes from helper-fixtures.R. Custom annotations use unique cache names, fixing tests that passed only because an earlier test had cached the entry they checked. Assertions compare values, e.g. expect_named() and expect_setequal(), instead of expect_equal(all(...), TRUE). Plot tests now build the plots with ggplot_build(). This found that plot_categorical() with the default fill = NULL failed when drawn; fix it, and map the All bar to a column so it isn't dropped without fill. Restore the build tests: small downloads run whenever online, and full builds for every genome run with ANNOTATR_FULL_TESTS=true, which docker/check.sh now sets, along with a persistent download cache. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> </pre> </div> Package: annotatr Commit: 50820a27a6907b9117c4abcb13f85f63b662e2dd Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 20:21:42 -0600 Commit message: Merge pull request #69 from rcavalcante/deprecate-randomize Deprecate randomize_regions() in favor of a background comparison Package: annotatr Commit: 09af749e4addbdd4602a8d4866b3b64bccb137d4 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 20:16:06 -0600 Commit message: Deprecate randomize_regions() in favor of a background comparison Regions placed uniformly at random across the genome are a poor null model: real regions come from a much narrower set of locations, so most data look enriched in genic and CpG annotations. Deprecate randomize_regions() and point to annotating a background of the regions the data could have come from, or regioneR::permTest() and regioneR::resampleRegions(). summarize_annotations(), plot_annotation(), and plot_categorical() now label annotated_random as "Background" instead of "Random Regions". The examples, tests, and vignette compare DM regions to all tested regions. Also fix the allow.overlaps documentation, which controls whether random regions overlap each other, not the input regions. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: ab795d19f14a4c80116f8cd5b8c3011bf7ca9215 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 20:07:14 -0600 Commit message: Merge pull request #68 from rcavalcante/docker-check Add Docker-based Bioconductor devel check Package: annotatr Commit: bb5c6c454ec3a9e29d7810976372e2339e39e0ef Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:18:57 -0600 Commit message: Add Docker-based Bioconductor devel check docker/check.sh runs R CMD build, R CMD check, and BiocCheck on the committed HEAD in a Bioconductor devel image with annotatr's dependencies preinstalled. Dependencies added since the image was built are installed at check time. Use --rebuild to refresh the image. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: ec750310fa1cb27af75186f72efb400e9c6ffb42 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 19:45:17 -0600 Commit message: Merge pull request #67 from rcavalcante/lncrna-gencode Fix hg38/mm10 lncRNA annotations by downloading from GENCODE Package: annotatr Commit: ea699780298650a09d66c8eff0c3d61ce22985b3 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:39:26 -0600 Commit message: Fix hg38/mm10 lncRNA annotations by downloading from GENCODE AnnotationHub removed its GENCODE resources, including AH75123 (hg38) and AH49550 (mm10), on 2026-04-28, so hg38_lncrna_gencode and mm10_lncrna_gencode failed. Download the same GENCODE releases directly over HTTPS, and move hg19 from FTP to HTTPS. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 0d593dc6eabebb817c27162c1003b90e1764c722 Author: Raymond Cavalcante <626455+rcavalcante@users.noreply.github.com> Date: 2026-09-24 19:36:20 -0600 Commit message: Merge pull request #66 from rcavalcante/oviariramb2 Add support for sheep (ARS-UI_Ramb_v2.0) as 'oviariramb2'. Gene annotations come from the Ensembl 113 EnsDb in AnnotationHub (AH119381), so tx_id and gene_id are Ensembl IDs. CpG islands come from the UCSC GenArk assembly hub. Sequences use UCSC-style names (chr1, ..., chrUn_*). Package: annotatr Commit: 86641326dc4047c9762fd9878876840fd5024d66 Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 19:17:58 -0600 Commit message: Version bump Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: annotatr Commit: 9781edf27897d6c77bd3f2e4b09ab5827f4af05a Author: Raymond Cavalcante <rcavalca@umich.edu> Date: 2026-09-24 18:57:30 -0600 Commit message: Add sheep (ARS-UI_Ramb_v2.0) as builtin genome oviariramb2 Sheep has no TxDb.* or org.*.eg.db packages, so gene annotations are built from the Ensembl 113 EnsDb in AnnotationHub (AH119381), with Ensembl tx_id/gene_id and symbols from the EnsDb. CpG islands, chromosome sizes, and chromosome aliases come from the UCSC GenArk assembly hub, and sequences are renamed to UCSC-style names. Genomes like this are registered in GENARK in R/utils.R. The TxDb code path is unchanged; hg19 gene annotations are identical to devel. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Package: methodical Commit: b39d98d2d4ac504cbd6f80a62b999406f694e993 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-25 02:16:59 +0100 Commit message: Merged changes Package: methodical Commit: 20761f4370f86ba9ee7211e4b47c6b3c63a607e4 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-25 00:50:46 +0100 Commit message: Updated liftover function Package: methodical Commit: 02ddeb7f0e3a2c852b0adcff0211e492dc0cdf3c Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-22 20:12:54 +0100 Commit message: update Package: methodical Commit: a39fa2dd4b3c1a417085c4a09ec882b3bc738522 Author: Richard Heery <richardheery@gmail.com> Date: 2026-08-27 17:25:10 +0100 Commit message: update Package: methodical Commit: ffc716b54e4118b1ced24b811211a8788e304a92 Author: Richard Heery <richardheery@gmail.com> Date: 2026-05-01 15:20:44 +0100 Commit message: Readded vignettes Package: methodical Commit: 464c57e15c8f97f697d8ce9373316805f6e73be1 Author: A Wokaty <andres.wokaty@sph.cuny.edu> Date: 2026-04-28 09:02:10 -0400 Commit message: bump x.y.z version to odd y following creation of RELEASE_3_23 branch Package: methodical Commit: 4215fb6e084e162ff4dd4201b1d4420d9c2533db Author: A Wokaty <andres.wokaty@sph.cuny.edu> Date: 2026-04-28 09:02:10 -0400 Commit message: bump x.y.z version to even y prior to creation of RELEASE_3_23 branch Package: methodical Commit: d169b576deecb57d9477aabf9196922e04e885ea Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-27 17:22:40 +0100 Commit message: Final commit for 3.23 Package: methodical Commit: 81883848e66b52382f58d48cd4ee465be8189db3 Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-24 22:47:39 +0100 Commit message: Fixed vignettes Package: methodical Commit: a4d3e6da701f57033dfd6ca9feba64d3c1c11a6a Author: Richard Heery <richardheery@gmail.com> Date: 2026-04-27 21:38:18 +0100 Commit message: Final commit for devel Package: lcmsPlot Commit: f451123907b59cd6a330688b933ff3fd6c2bd25e Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 22:11:26 +0100 Commit message: feat(features): name XChromatograms features from row names Package: RiboDiPA Commit: cf0c36801194370381bd3ceb90f5b2594e1247a1 Author: Dr. Ji-Ping Wang <jzwang@northwestern.edu> Date: 2026-09-24 20:46:05 +0000 Commit message: Fix vignette build error: convert Bioconductor objects via as.data.frame() before as.data.table() Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01LiK5WUAPmNmkHCv3HPRNog Package: lcmsPlot Commit: 18f10a9c7dfe282c08aa33c53c23566a192a7a6b Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 20:46:18 +0100 Commit message: feat(features): name manual features from row names or a feature_id column Package: scRNAseqApp Commit: 9421c5d26e1bf497251c6ccfb6526e9f612852c4 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-24 15:27:00 -0400 Commit message: Update the gene table only when file changed. Package: leapR Commit: 28136ae57197bd5fa892860b5017d5c9f1f0bb2c Author: Sara JC Gosline <sara.gosline@pnnl.gov> Date: 2026-09-24 10:42:52 -0700 Commit message: updated Package: geneslator Commit: b62f543f5874c5167105c705e32d15f0da8d4181 Author: Giovanni Micale <gmgmicky@gmail.com> Date: 2026-09-24 19:11:07 +0200 Commit message: Updated README and vignettes Package: DropletUtils Commit: ba4152de3596abef3bd69f9ce441aec8ea4c912e Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-25 02:56:55 +1000 Commit message: Set SVT leaves to NULL for empty columns when loading MatrixMarket data. (#133) Mostly backports of the updated C++ code and associated tests from crio. Package: DropletUtils Commit: ea9a299b36c52a71f305d612a97d6a69a20e25d0 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-24 18:21:09 +1000 Commit message: Merge remote-tracking branch 'upstream/devel' into devel Package: DropletUtils Commit: b423c0fafe7271b173317b407a8538bbbcbede5c Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-07-29 23:53:07 +1000 Commit message: Shorter chunk size for sparse data and indices for easier streaming. Package: SparseArray Commit: 9a0e93056f05879a15057e3d597d0102068f09bb Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-24 09:04:25 -0700 Commit message: some clarification about SVT leaf representation Package: lcmsPlot Commit: 14a5af5c83db317bc0d44e2b32ba8acfb54ab66f Author: Ossama Edbali <ossedb@gmail.com> Date: 2026-09-24 16:23:45 +0100 Commit message: feat(features): use featureDefinitions rownames as feature identifiers lcmsPlot derived its own xcms::groupnames-style MT labels from mzmed/rtmed, discarding the row names featureDefinitions() already carries. Feature identifiers now come from those row names, so renaming the rows is enough to get meaningful labels onto a plot. Identifiers matching no feature are now reported with a warning naming them, instead of being dropped silently into an empty plot. </pre> </div> Package: scRNAseqApp Commit: eb1f132e925ec26574be9a7055b51b67cf60b2cf Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-24 11:17:02 -0400 Commit message: Remove the duplicated notification for search. Package: rhdf5 Commit: 1c6ed01eaf8682004f647a15a200df1d0f55b0f6 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:21:40 +0200 Commit message: Fix duplicated logo Package: rhdf5 Commit: cab7d0212538b900883c3c6a80f27710cd80ebc5 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:03:23 +0200 Commit message: Add link to de.NBI survey Package: Rarr Commit: 56ddfff1ac32f46151b215a015cbc00b5d77744e Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:16:34 +0200 Commit message: Add deNBI funding acknowledgement and survey in README Package: Rarr Commit: accfb8f20be9b7fefe76e1b35a531704bcc8960b Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 11:06:37 +0200 Commit message: Use vectorized .store_check_exist() call Package: Rarr Commit: cbf89cd3891e3e0cdfeb474aaf153d1324b43d96 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 11:05:56 +0200 Commit message: Define is_structured once Package: Rarr Commit: 87389fada7676ae09ce5bfd3a3a4e74ba3708836 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 10:47:50 +0200 Commit message: Register bfloat routine Package: biomaRt Commit: 3e1a0768933f6c3e00895e02119e4f6e36050dac Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:05:20 +0200 Commit message: Add link to de.NBI survey Package: ISAnalytics Commit: 6e03f52a7925332d38562e8c2501425e92f89184 Author: francescogazzo <francesco.gazzo@gmail.com> Date: 2026-09-24 12:19:37 +0200 Commit message: Update collision filtering and bump devel to 1.23.2 Package: distinct Commit: 7ec08672fd2177c33c85779a82ab12deb8232802 Author: Simone Tiberi <simone.tiberi@unibo.it> Date: 2026-09-24 11:57:02 +0200 Commit message: T_obs added in results Package: distinct Commit: e749b22cf8c3c8eb925d3a293b916b7c11e75605 Author: Simone Tiberi <simone.tiberi@unibo.it> Date: 2026-09-24 11:49:37 +0200 Commit message: bug fixed in distinct_test Package: MsBackendMetaboLights Commit: 1b126b45bede3db584a54168617397078cc5c789 Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com> Date: 2026-09-24 11:52:26 +0200 Commit message: Merge pull request #26 from rformassspectrometry/jomain Add random sleep breaks to reduce failures on build systems Package: MsBackendMetaboLights Commit: c28ee3bc500c3e2a3764932bae457431cac07563 Author: Johannes Rainer <johannes.rainer@gmail.com> Date: 2026-09-24 08:45:39 +0200 Commit message: Add random sleep breaks to reduce failures on build systems - Adding/changing to random sleep times aiming at reducing the recurrent failures on the Bioconductor build system (most likely due to rate limitation from MetaboLights). Package: cellNexus Commit: 67fa18ce068ae3e0fe84da1f942a6d9a1138e052 Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 14:44:48 +1000 Commit message: Merge pull request #159 from myushen/master fix website examples Package: cellNexus Commit: 3ab2cd31f7d4a7acc40758abeed48bc0f3d8435c Author: myushen <mengyuan.shen@outlook.com> Date: 2026-09-24 14:25:14 +1000 Commit message: fix website examples Package: cellNexus Commit: 4719fb49b937acd11c9f898275920555e094c65d Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 13:37:28 +1000 Commit message: Merge pull request #153 from MangiolaLaboratory/copilot/rename-join-census-table Soft-deprecate `join_census_table()` in favor of `get_census_metadata()` Package: cellNexus Commit: 8b217f783900d3107ab0d07c0d9b57083a1e6c77 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-09-24 11:54:08 +1000 Commit message: unit test Package: cellNexus Commit: 3e4d038b291bc9ba79f306456e63fa4660958d47 Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 10:44:58 +1000 Commit message: Merge branch 'master' into copilot/rename-join-census-table Package: cellNexus Commit: 9aca6c192558b021c1c41b9071564d8daf4d7814 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-08-27 12:12:50 +1000 Commit message: soft deprecate since 0.99.27 Package: cellNexus Commit: cd885c844de21fea70d10ee653fc9c95386b8bd5 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-08-27 12:08:50 +1000 Commit message: Merge remote-tracking branch 'origin/master' into rename-join-census-table merge from origin Package: cellNexus Commit: 13ffb5d261f878cacd79484700b35b9a964cef67 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:33:16 +0000 Commit message: Trim redundant mock assertion Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: abf37b553b5800c09ee3e9deb65ee9d5246d9ab4 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:32:37 +0000 Commit message: Verify Census helper mock before wrapper call Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: a4bf9cc52cf658c48d4f00fdfbdd55ec094f4484 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:32:04 +0000 Commit message: Exercise deprecated table argument compatibility Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: 4b46e68aebf2b38ce850298cc145bdf52c84d14f Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:31:37 +0000 Commit message: Correct Census deprecation test assertions Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: 1515648f80a96e03452c82ac5e602057710f512e Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:31:02 +0000 Commit message: Stabilize deprecation warning test Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: d2fd0cfdaad895c2e60be674d50076ad04cecf24 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:30:23 +0000 Commit message: Soft-deprecate Census join helper Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: e7ae2c78928ba1b3bbb6f575e117365976743d72 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:27:22 +0000 Commit message: Initial plan Package: mia Commit: 416de1c5a6b73b70f42571f8a3d36d0294dcb770 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-24 07:54:25 +0300 Commit message: Update documents and namespace Package: clusterProfiler Commit: 33b36f13f3729b099a8d6fc20694831b7a5c62d9 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 12:48:46 +0800 Commit message: fixed r check Package: LRDE Commit: 710586499a483617f94c2d665b87a03be62d6531 Author: Ziyang Liu <jacobleo773@gmail.com> Date: 2026-09-23 18:45:18 -0700 Commit message: Improve numerical stability and bump version to 1.1.2 Package: DOSE Commit: 5846d72fe047f1de66d506a21c117d400e4a3ef8 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:21:11 +0800 Commit message: fixed r check Package: DOSE Commit: 9011c8c053e345cdca45bf1edb93fe66b7f80417 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:14 +0800 Commit message: gseDisease() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family. Package: ReactomePA Commit: e295d309811933101f2e808814212d3244f5c6aa Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:10:04 +0800 Commit message: update docs Package: ReactomePA Commit: 586975c51fadc162d78418ff1132eddcb009b157 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:13 +0800 Commit message: gsePathway() exposes eps and forwards extra arguments, #47 gsePathway() was the only GSEA wrapper in the family missing both eps and ..., so eps could not be controlled and additional enrichit::gsea_gson() arguments could not be passed through. Both are now supported, matching clusterProfiler::gseKEGG(). Package: ReactomePA Commit: 396a55c38c765045b0309c6935b663dd334e7c3d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:03:02 +0800 Commit message: ReactomePA 1.99.2: seed argument and a faster prepareReactomeNetwork() - gsePathway() and nsePathway() expose an explicit seed parameter for reproducible GSEA results, aligned with enrichit::gsea_gson(). - prepareReactomeNetwork() no longer round-trips through graphite::convertIdentifiers()/pathwayGraph() per pathway; it builds a single UNIPROT->Entrez map up front and converts edges with vectorized lookups, keeping mclapply() parallelization over pathways. Output is unchanged (same nodes and edge values; node ordering may differ). Default cores is now 1 instead of detectCores(). Package: ReactomePA Commit: a9a8627182db7226655362793f6b6c22c25e8d7b Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-08-15 18:42:41 +0800 Commit message: parallelize prepareReactomeNetwork pathway conversion via mclapply The one-time Reactome network build converts ~2700 pathways serially in R (convertIdentifiers/pathwayGraph/graph_from_graphnel per pathway). The conversions are independent, so the loop now runs over mclapply() with a new 'cores' argument (default getOption('mc.cores', detectCores())); mclapply falls back to serial on Windows and preserves input order, so the resulting edge set - and hence the cached network - is unchanged. Measured on the GSE53757 demo: serial build ~35-41 min; parallel build 614 s at 16 cores and 655 s at 56 cores; output byte-identical to the serial baseline. Scaling saturates at ~4-5 effective cores because the graphite identifier conversion is hash-lookup-bound. Package: ReactomePA Commit: 13cb4b3cbc4616e214d63ee59a3e42bba48b0a4c Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-07-09 15:24:15 +0800 Commit message: nsea Package: ReactomePA Commit: 4edeca90aedb3afdaa29b838323bbdabad62c391 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-04-29 12:24:13 +0800 Commit message: update bioc version Package: meshes Commit: 5732c93b839f7f820eb4501e3cff468737bfa71a Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:09:48 +0800 Commit message: bump version Package: meshes Commit: e7498dc7737b09bffacef28a72d666693e7be51d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:14 +0800 Commit message: gseMeSH() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family. Package: meshes Commit: 01c764a9285d4c77e77ff630885b8a79077cff10 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:03:02 +0800 Commit message: expose a seed argument on gseMeSH(), meshes 1.39.2 Forward an explicit seed to enrichit::gsea_gson() so GSEA runs are reproducible, and apply pvalueCutoff to both pvalue and p.adjust inside the enrichit engine (requires enrichit >= 0.2.2). Package: GOSemSim Commit: 769cd22f90eec52f67039121c265462c701680ad Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 08:58:26 +0800 Commit message: update docs Package: GOSemSim Commit: ca626082247cbb24fb95b5098558b71b0592e2be Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 12:55:48 +0800 Commit message: computeIC: take the term universe from GO.db, not the shipped gotbl table computeIC() decided which terms to score from the `gotbl` table shipped in data/: goids <- unique(godata[godata$Ontology == ont, "go_id"]) That table was last rebuilt in 2021-07, so every term GO.db has added since then was given no IC at all, and the IC-based methods returned NA for it even though its descendants carry annotations and its IC is computable. This is issue #33, and the reporter's diagnosis ("a conflict between the pre-calculated gotbl.rda and the local version of GO.db") was right. Measured against the current GO.db / org.Hs.eg.db, the number of annotated terms that can actually be scored: ontology annotated before now gained BP 11293 11126 11293 +167 CC 1832 1787 1832 +45 MF 4777 4410 4777 +367 and nothing loses an IC. The missing terms also biased every other IC, because they were counted in the `sum(gocount)` denominator but could never contribute to an ancestor's descendant sum. Terms finite under both universes agree for 92-95% of entries with a mean absolute difference of 0.003-0.011; about 0.3% were overestimated by more than 0.5, all of them in the "too specific" direction, which is what the mechanism predicts. The universe is now names(getAncestors(ont)) -- exactly the terms of that ontology in the installed GO.db, root included, and already cached by onto_relation() -- unioned with the annotated terms, so a term the local annotation package still uses keeps its IC even if GO.db has retired it. The same root cause also affects the `gotbl` that the Wang method walks, where a term newer than the table scores 0 instead of NA. That is left for a separate change because fixing it means either regenerating the shipped data or building the relation table at runtime. test-ICMethods.R now asserts that every annotated term gets a finite IC. Package: GOSemSim Commit: 32be2e18cb86a9ef84f796e174a39a1ac7658513 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 12:32:22 +0800 Commit message: cache ontology mappings, and load Rcpp so the compiled IC methods work Two independent defects, found while fixing TCSS. getAncestors(), getParents() and getOffsprings() each rebuilt their whole mapping on every call -- AnnotationDbi::as.list(GOBPANCESTOR) costs about half a second -- while callers only ever pick out one or two terms with `[[ID]]`. A single geneSim() call rebuilt the same mapping hundreds of times. The mappings are derived from a source that is already cached (GO.db is static, load_onto() caches the OntDb), so they are now cached per ontology rather than per term. A 5x5 termSim on previously unseen terms drops from 2.5 s to 0.5 s, geneSim from 5.6 s to 0.6 s cold and 0.12 s warm, with byte-identical results. The cache holds about 85 MB for BP and 110 MB for all nine mappings. Separately, Rcpp was listed in LinkingTo only, so loading GOSemSim never loaded the Rcpp namespace. The wrapper generated by compileAttributes() instantiates Rcpp::RNGScope, which resolves enterRNGScope through R_GetCCallable("Rcpp", ...), so every Resnik, Lin, Jiang and Rel call failed with "function 'enterRNGScope' not provided by package 'Rcpp'" unless the user happened to attach Rcpp first. importFrom(Rcpp, evalCpp) was dropped in ea7b2028 (2016) and is restored here. No test reached the compiled code and the vignette only mentions those methods in prose, which is why this went unnoticed for so long; test-ICMethods.R now covers all four methods on three ontologies. The ontology cache is also covered: test-GO.R checks that each mapping is cached under the ontology and is identical to what GO.db holds. Package: GOSemSim Commit: 50c6bd241416e703074e5e8e2839cf2cafe7133e Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 17:17:24 +0800 Commit message: correct the scope of the TCSS degeneracy fix The previous commit described the degeneracy as "a cluster with a single member", but calc_maxIC() indexes `all <- IC[cluster]; all <- all[is.finite(all)]`, so the real condition is "exactly one member carrying a finite IC". A cluster with several members where all but one have infinite IC is equally degenerate, and the old `length(all) == 0` guard did not cover it. Re-measured with the correct criterion (swapping calc_maxIC in and out of the namespace in one process so both versions see identical input): - the set of clusters whose ICA changes equals the set with exactly one finite-IC member, at every cutoff and ontology tested (BP 1/2/3.5/4/5/8, MF 3.5, CC 3.2) -- so the change is confined to the degenerate clusters; - the defect was not BP-only. 300 random pairs, % scoring exactly 1: BP 99.3% -> 0.0%, MF 27.3% -> 0.0%, CC 98.7% -> 0.0%; - the counts are larger than the single-member count suggested: BP has 1 degenerate cluster at cutoff 3.5 but 5 at cutoff 4 and 1141 at cutoff 5; MF has 3 and CC has 3, and the CC set includes the CC root GO:0005575. Fix the NEWS wording and the code comment to match, and make the regression test assert on the finite-IC criterion rather than on cluster size. Package: GOSemSim Commit: 2df9985c372e931e89994d25fe84f483b50c01fe Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 16:49:30 +0800 Commit message: fix TCSS similarity collapsing to 1 for nearly every term pair A cluster with a single member has no internal spread, so normalising it by its own maximum IC made its ICA identically 1 regardless of how general or how specific that term was. GO:0008150, the root of BP, is such a cluster and is a common ancestor of every BP pair, so `max(sim_value)` in tcssMethod_internal() returned 1 for 99.7% of random BP pairs and `mgeneSim(measure = "TCSS")` was an all-ones matrix. Fall back to the global maximum IC for single-member clusters. The collapse is not specific to the root: scanning cutoffs shows GO:0050896 and GO:0046337 also become single-member clusters for BP, and GO:0052745 does for MF, so special-casing the root would only have papered over one instance. After the change, 300 random BP pairs give min 0.0004 / median 0.0234 / max 0.5296 with 0% equal to 1, and ica[["GO:0008150"]] drops from 1 to 0.000414 (= IC[root] / global max IC). Add a regression test and bump to 2.39.3. Package: GOSemSim Commit: 34c4ae3b85f10b9107ca6feffbd6e6eb0a0206db Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 12:17:51 +0800 Commit message: fix TCSS for terms belonging to multiple clusters GO is a DAG, so a term can have several meta-term ancestors and `tcssdata$clusid[[term]]` is then a vector rather than a scalar. Indexing `ica` with `[[` then attempts recursive indexing, which raises "subscript out of bounds" (or "recursive indexing failed at level 2" depending on which element is hit first) and aborts any TCSS calculation for the whole ontology. Subset the list of clusters with `[` instead. This restores the behaviour already present in the Bioconductor release (2.38.3); the devel implementation had regressed. Adds a regression test covering a term that sits in more than one cluster. Package: clusterProfiler Commit: a38e9201b8ee6ad6f64fc1a5bf691421efc9d928 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 04:39:17 +0800 Commit message: enrichMKEGG()/gseMKEGG() accept a GSON, #623 enrichKEGG() and gseKEGG() take either a species code or a GSON object, but the module wrappers only took a species code, so there was no offline route for module enrichment at all -- even though the download errors now tell users to build a local database. Passing a GSON raised an unrelated error from the organism mapper instead. Both now mirror the KEGG wrappers, including the "organism should be a species name or a GSON object" message. A GSON reports its own keytype, so @keytype is taken from it; the species path keeps returning "UNKNOWN" exactly as before. Also documents the GSON option on the KEGG `organism` parameter, which had never been mentioned for enrichKEGG()/gseKEGG() either. Package: clusterProfiler Commit: 285885443b912177daec101c606664b33b41cc37 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 04:21:19 +0800 Commit message: enrichGO(): restrict the annotation by evidence code, #160 Enrichment used every annotation in the OrgDb, including electronically inferred ones, so there was no way to avoid circular reasoning when the gene sets themselves came from in-silico evidence (dropping IEP for co-expression clusters) or to keep only curated annotations (dropping IEA). enrichGO() now takes `evidence`, appended last so positional callers are unaffected and threaded through both recursive paths. The filtered annotation is built by go_annotation_by_evidence() from a gene-centred select() of GOALL/EVIDENCEALL/ONTOLOGYALL, because the evidence code is a property of the gene-annotation pair and the previous term-centred mapIds() could not see it. Two semantics worth stating, both documented: the background changes with the annotation, so a filtered result is not a subset of the unfiltered one; and a filtered annotation is never cached, since the cache key is (organism, ont, keytype) only and reusing it either way would answer with the wrong annotation. A regression test pins the cache isolation down. Package: clusterProfiler Commit: fa71a3ef739a1ef44e695e69823126c94c703bdb Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 02:33:01 +0800 Commit message: fix: enrichGO() survives an unidentifiable OrgDb organism, #232 The cached-GO-data check compared the cached organism against get_organism(OrgDb) inside a bare if(). get_organism() returns NA for an OrgDb it cannot identify -- an AnnotationHub OrgDb, for instance -- and `if (NA && ...)` aborts the call with "missing value where TRUE/FALSE needed", which names nothing about organisms or caches. It bites on the second enrichGO() call in a session, because the first one populates the cache. The check is now go_cache_usable(), where every comparison goes through isTRUE() so an unidentifiable organism means "not cached" and the annotation is rebuilt. Extracting it also makes the cache-hit logic unit-testable without an OrgDb. Package: clusterProfiler Commit: a39c2f63d533e20d6c4d03fd3a35b18a418dd08e Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 02:14:56 +0800 Commit message: fix: Gff2GeneTable() reads Ensembl-style GFF3, #193 The function only looked for an NCBI/RefSeq `GeneID=` attribute. On an Ensembl GFF3 (which writes `gene_id=`) every extracted key was NA, and merging two all-NA key columns is a cartesian product: on the reporter's cat genome that is ~1.3M x 40k rows, which R refuses with "negative length vectors are not allowed". At small sizes the same bug passes silently, because unique() collapses the duplicated NA rows into a plausible-looking table of NA ids. Field names are now detected from the file: `GeneID` or `gene_id` for the identifier, and `gene`, `Name` or `gene_name` for the symbol. Detection requires an exact attribute key, because getGffAttribution()'s heuristic fallback also looks inside values and would otherwise return the identifier out of `ID=gene:ENSG...` when asked for `gene`. A file with neither identifier style stops with a message saying what is expected instead of merging on all-NA keys. Package: clusterProfiler Commit: 41dd01bb5c7a078bd19397131f06fd3db2d59bfc Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 01:38:26 +0800 Commit message: add_go_level(): expose the GO level of each enriched term, #793 GO enrichment results carried the term, its ontology and its statistics, but not how deep the term sits in the hierarchy, so users who wanted to keep a band of levels had to reconstruct GO depth themselves. go_level_map() now returns the GO id -> level map (1 = ontology root) built by breadth-first traversal of the GO.db CHILDREN graph; getGOLevel() is rewritten on top of it with identical output (verified against a pre-change baseline for BP/CC/MF at levels 1-6), and add_go_level() appends a `level` column to an enrichResult/gseaResult/compareClusterResult. The level is taken from the ontology each term belongs to, so ont = "ALL" results are labelled term by term. gofilter() and dropGO() had no test coverage; the new test file locks their keep/drop-by-level behaviour down. Package: clusterProfiler Commit: c117200bb63575df335911dcd478aa164dda528d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 23:52:42 +0800 Commit message: simplify() infers the GO ontology for enricher() results too, #369 The enrichResult method required x@ontology to be BP/MF/CC/GOALL, so an enricher() run over a GO collection (MSigDB C5 GO, a custom TERM2GENE built from GO annotations) had to have the slot assigned by hand before simplify() would accept it. The ontology is now inferred from the GO IDs exactly as for gseaResult (#753), and non-GO gene sets are still refused with a message saying so. Package: clusterProfiler Commit: e930b50044bf8bb4fb883ea940a631aceb57ff18 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 23:21:11 +0800 Commit message: simplify() a GSEA result whose gene sets are GO terms, #753 simplify() reduces redundancy with GO semantic similarity, so it needs the ontology of the terms. It only accepted x@setType in BP/MF/CC/GOALL, which rejected a GSEA run over a GO gene-set collection (MSigDB C5, a gson GO file, a TERM2GENE built from GO annotations) because @setType then holds the collection name. The ontology is now inferred from the GO IDs, with results spanning several ontologies simplified as GOALL; non-GO gene sets are still refused, with a message that says so. Package: clusterProfiler Commit: dc94b240c1a42333f111338f46fb3633df2271be Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 22:46:23 +0800 Commit message: warn when compareCluster() is given a non-character universe, #654 compareCluster() wraps each per-cluster call in suppressMessages(), which swallowed the underlying enrichment function's "`universe` is not in character and will be ignored" message. A numeric universe therefore looked accepted while silently having no effect. The guard is now raised once in compareCluster() itself, where it cannot be suppressed, with a regression test for both the non-character (warns) and character (stays quiet) cases. Package: clusterProfiler Commit: 61236b6fa01a7d6474152ed7043639596dae48d1 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:10 +0800 Commit message: gsePC() and gseWP() expose an eps argument Both wrappers now declare eps = 1e-10 and forward it through GSEA() to enrichit::gsea_gson(), matching GSEA(), gseGO(), gseKEGG() and gseMKEGG(), which already exposed it. Package: clusterProfiler Commit: 58559c7a5a9babe970d3a3dad5e9708efc42f70c Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 18:54:09 +0800 Commit message: fix enrichKEGG(organism='cpd') and report KEGG download failures clearly, #828 - gson_cpd(): use the 'compound' KEGG REST endpoint. KEGG retired /link/cpd/pathway, which now answers HTTP 400, so enrichKEGG(organism='cpd') and gseKEGG(organism='cpd') failed with an obscure download error. - kegg_rest(): report the failure where it happens, telling an unreachable network apart from an HTTP error status and from an empty response. These used to surface much later as an opaque error. - download.KEGG.Path() / download.KEGG.Module(): replace the is.null() guard, which could never fire because kegg_rest() never returns NULL, and stop with an actionable message when the downloaded annotation is empty or when the gene/pathway table shares no ID with the pathway-name table. Previously an empty annotation was returned silently and surfaced downstream as a misleading "No gene can be mapped", #146, #378, #561, #646. Package: SAIGEgds Commit: 29da3dd06bce9321bc520c75353e1c695057e0df Author: Xiuwen Zheng <zhengxwen@gmail.com> Date: 2026-09-23 19:12:31 -0500 Commit message: update vignettes Package: MSstatsBioNet Commit: 409e9d4503aa239c3c619270333853289d37d080 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-23 16:57:12 -0400 Commit message: feat(filterSubnetworkByContext): adjust filterSubnetworkByContext to exclude key words (#111) Package: scRNAseqApp Commit: e8a48756927b63b7b69b59294f8c81232e689203 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:44:42 -0400 Commit message: fix the wrong number when calculate phyper. Package: scRNAseqApp Commit: 758edbb8626a1d38afe3c8d58678b43f325195e0 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:40:08 -0400 Commit message: fix a issue for if no hyper pval available. Package: scRNAseqApp Commit: 78ef7925d099f040cfa9b1638934fb49d4adfc91 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:29:19 -0400 Commit message: using promise process to update the gene table. Package: scRNAseqApp Commit: b4e729e4d87012189f26cfd746a09ebc9a04d6db Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 10:24:03 -0400 Commit message: import phyper from stats. Package: scRNAseqApp Commit: 4d94c7a0270315c3aea67c41287313c86ffb5655 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 10:15:42 -0400 Commit message: add phyper pval for co-expression. Package: dmGsea Commit: 3b9c68c53791e27f0abc9e95a8f4e0c050b7d75a Author: xuz1 <xuz@niehs.nih.gov> Date: 2026-09-23 13:54:34 -0400 Commit message: bugfix Signed-off-by: xuz1 <xuz@niehs.nih.gov> Package: decemedip Commit: 3de0b135bed2595498482c4d13078d0bd65c313e Author: nshen7 <shenning1997@gmail.com> Date: 2026-09-22 20:54:10 -0700 Commit message: Fix Stan old array syntax for stanc3 (BioC 3.23 build failure) Package: quantMSImageR Commit: 9aaed9e03b28ef01d3b1c05dc834288f2d00753c Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:46 +0200 Commit message: Version 0.99.8 Pieces of one tissue, regions of interest, and the report arranged by level. matrixStats leaves Imports: it was declared but called nowhere, so every user installed a package the code never used. Package: quantMSImageR Commit: 25eacbf10d0f5075ad89ee2884a76103bdb23a65 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:34 +0200 Commit message: Document the regions work The vignette says what regions are for -- a transition that marks a tissue type, or a toxicity study where the regions are drawn high and low in the toxicant and the endogenous species compared between them, within one animal rather than across a group. It also describes the by-level report, and how to see a palette before choosing it. AGENTS.md is gitignored: agent scratch notes, not part of the package. Package: quantMSImageR Commit: d37c8c4b93a96e7f51343144cda5a5c17dcc519b Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:34 +0200 Commit message: Arrange the report by level, and correlate at one level only Sections 2, 3 and 4 are each drawn by sample and then by region, so the two are read the same way rather than the regions living in a tab of their own. The region masks take a section before the ion images, which move down a number. "auto" judges the heatmap encoding per view, on the rows that view actually has. A study without regions is unchanged, headings included: a level heading only appears when there is a second level to tell it from. Correlation names one level -- 'sample', 'roi', False or auto -- and only ever computes that one. It is the slowest section in the report, and a region holds a fraction of a sample's pixels, so auto correlates within the regions when a study has them and is off otherwise. True still means 'sample'. roi: unit is per sample or per region, not both: a comparison has a single unit, and two views of the same numbers invite reading whichever looks better. compare: keeps "both", where the two arrangements are different contrasts rather than the same one twice. Each box-plot panel carries its own key, and colours: region sets the region palette (any package palette, or a grDevices qualitative one), kept distinct from the groups'. Package: quantMSImageR Commit: bfa6a46540be7a5e08f37ded27d10a504d244d59 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:19 +0200 Commit message: Score each region against itself in contributionHm() too The region heatmap could only be drawn per feature, because contributionHm() had no notion of a block. That made "auto" pick the wrong panel wherever a study has few samples and many regions: one animal per group takes the per-sample encoding by sample, but by region its rows are sample x region, so a group can have six or seven of them -- exactly the case the contribution encoding exists for. It now takes sample_block, and inside a block both the z-score and the group mean are computed against that block alone. The hue is therefore "how this group's airways sit among all the airways", not "airways differ from parenchyma", which is what a panel scored across regions would mostly report. A feature flat within a block cannot be scored there and is drawn in na_col, even where it varies across the section. Package: quantMSImageR Commit: b18abc94cf8fc51323b0836eccf9b684dd9758b9 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:50:33 +0200 Commit message: Fix the region tests and the vignette's feature lookup The row-split assertions read @row_order_list, which a Heatmap only fills in when it is drawn -- it is empty on the object, so the expectations compared against nothing. The split a heatmap will use is in @matrix_param$row_split, which is what they now check: the block test asserts a, a, b, b against groups that deliberately alternate, so passing it means the rows really were split by region rather than by group. The vignette indexed a feature by name, but spectra() returns a matrix with no dimnames, so it takes the row number instead. Package: quantMSImageR Commit: 0ff2ab13a672a37c90034e11545dc2e36e994da3 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:39:14 +0200 Commit message: Document pieces and regions; regenerate the example sections The vignette gains a section on pieces of one tissue, one on labelling regions, and a worked example on the bundled sections: the label table, the region maps and a box plot with one point per section per region rather than per pixel. The YAML section documents the samples forms, including pieces, and what each roi: option can be set to. The example sections are regenerated with the regions the vignette and runExample() now show. Seeds are unchanged and the region code draws no random numbers, so the intensities are identical. AGENTS.md is build-ignored, and the micro sign in stitchAcquisitions() is written as a \u00b5 escape: R CMD check requires ASCII source. Package: quantMSImageR Commit: a623d0241889b76e05f8b5d49aa2f121348d953b Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:54 +0200 Commit message: Carry regions through a study and into the report A study picks regions up on its own: generateTxtImages() attaches roi_label and roi_id from each acquisition's roi_labels.csv, matched on (x, y) like the tissue mask, and they survive panel binding and stitching. Regions numbered within a piece are renumbered across the stitched sample, so two airway_01s become two airways. The YAML gains a roi: block -- enabled (auto), include_unassigned, compare, unit, heatmap -- and pieces: for a tissue acquired in several passes, each piece normalised and SNR-filtered against its own background before being joined. The report gains a regions tab: maps, box plots by compare and unit, an ROI_summary sheet, and a heatmap with one row per sample and region. That heatmap z-scores each region against itself (quantileHm's new sample_block), since scoring across regions would mostly report that airways and parenchyma differ, which is not the question being asked. The map is repeated above the ion images, where it says which blob is which. quantileHm() also no longer loses its sample names when a study holds a feature with no variance: the unscoreable column returned an unnamed vector, and apply() drops the names for the whole matrix when one result's differ. output: colocalisation: gains auto, off whenever a sample merges several acquisitions -- most pixel pairs would then cross acquisitions. Package: quantMSImageR Commit: 9311401b6304a67f07b4b1fa3cf4bbcde84b66b7 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:39 +0200 Commit message: Add labelROIs() for regions within the tissue Run after selectTissuePixels(): it shows the ion image of a chosen transition across tissue pixels only, then loops draw -> name -> "add another". Several regions can share a label, since a section holds many airways, and each is numbered as it is drawn (airway_01, airway_02, ...) so it keeps its own identity while the label is what a study compares. Regions are saved per acquisition as roi_labels.csv beside the tissue mask, which is never touched, and copy_to writes the same file to the other panels over the same area. Re-running adds to them; overwrite = TRUE keeps the old file as a dated backup. The feature picker is shared with selectTissuePixels() rather than copied, and the bundled example sections gain two "a" and two "b" regions each so the downstream half can be shown without a drawing device. The regions differ because of where they sit on the existing intensity gradient; no value was adjusted to make them. Also splits the given names in Authors@R, so the citation reads "Smith MJ" rather than "Smith M". Package: quantMSImageR Commit: 52f47f09842bf4eecb4e8e7d214c84ec7d87a532 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:27 +0200 Commit message: Place pieces of one tissue by stage position A tissue too large for one acquisition is imaged in pieces, and those pieces are one sample: kept apart they count twice in every group summary, and because they agree with each other they look like a reproducible effect. readMRM() numbered each acquisition's pixels from its own first pixel and threw the stage coordinates away, so every piece started at (1, 1) and stitchAcquisitions() could only report that they overlapped. Its documentation claimed Waters coordinates were absolute, which stopped being true the moment readMRM() re-based them. readMRM() now keeps x_stage and y_stage (mm) alongside the grid indices, and stitchAcquisitions() places each piece where the stage recorded it: above, below or beside, in any order, gaps left empty. Pieces must share a pixel size; each is moved to the nearest position on a common grid and the largest shift is reported. Overlap is still an error rather than an average. Objects without stage positions keep their own coordinates and say how to get them. combineMSIs() fills a pData column that only some objects carry with NA, since stage positions and region labels are legitimately absent from some samples. Package: rhdf5 Commit: c72d938a7bd397d148e623a7c0f12e6b3865de1b Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 16:41:00 +0200 Commit message: Bump version Package: rhdf5 Commit: fe55afb12dd1583d7f6f58e236e3d85872da3e1f Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:40:28 +0200 Commit message: Document .matrix() methods removal Package: rhdf5 Commit: f1ad6e28ba024bdcfeede3cb1b3b89f92bb081e5 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:38:30 +0200 Commit message: Remove .matrix() methods and let them auto dispatch to array method Package: rhdf5 Commit: dc8ef2bbced3bfc17f95b284fb0b2981d20427f4 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:22:12 +0200 Commit message: Document on.exit change in NEWS Package: rhdf5 Commit: 2b34f2d0097aaf547999b5be0deeef35031694e8 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:20:32 +0200 Commit message: Use on.exit() more consistently to close Package: rhdf5 Commit: bbfebbf34a184471451df03fab4dfa74a29f1dd9 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:08:44 +0200 Commit message: Mention dead code removal in NEWS Package: rhdf5 Commit: aa7669dbe22003b61182dc3cd266b948ae055ad0 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:07:58 +0200 Commit message: Remove dead code in h5writeAttribute.array() Package: rhdf5 Commit: d1f0dc156114f8494ced58811c01fe1f092b1648 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:57:43 +0200 Commit message: Fix incorrect copy/pasted error messages Package: rhdf5 Commit: 81d91768bd5bc3a86b9c720a1a3c1681ad0851ae Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:43:10 +0200 Commit message: Remove extra call to H5loadConstants() Package: rhdf5 Commit: e28ea4ec812cfd7c63e15101b401a3aa12fac5f1 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:23:01 +0200 Commit message: Ensure .Call() always includes PACKAGE Package: rhdf5 Commit: 4f18f262fed53b25edbbd5db47138059a6a7a6cb Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:16:45 +0200 Commit message: Mention h5set_extent() fixes in NEWS Package: rhdf5 Commit: 98c8a7581553b43f8aa62575958b0a595394bb84 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:16:16 +0200 Commit message: Fix h5set_extent issue with dataset handle Package: GSVA Commit: 545a96a07fba745d24b021cde157b570597a7109 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 16:34:55 +0200 Commit message: Remove dependence on BiocSingular Package: aracne.networks Commit: d000659130672ee12ffa5a287616ffe16c334eb2 Author: federicogiorgi <federico.giorgi@gmail.com> Date: 2026-09-23 15:51:57 +0200 Commit message: Point to the Zenodo record 22918956 Fill in the Zenodo record (doi:10.5281/zenodo.22918956) hosting the networks and document the CC BY-NC-ND 4.0 license of the data files. Package: aracne.networks Commit: d768d15947c70f95dc353c4e3a21da480ffccdc3 Author: federicogiorgi <federico.giorgi@gmail.com> Date: 2026-09-23 14:47:27 +0200 Commit message: Move the networks to Zenodo The regulon data sets are no longer bundled in the package: they are hosted on Zenodo and retrieved with the new getRegulon() function, which caches them locally with BiocFileCache and verifies their MD5 checksums. listRegulons() lists the available networks. This brings the package size well below the 100 MB limit of the new build system. - documentation of the 25 networks merged into ?regulons - vignette converted to R Markdown - added unit tests - Authors@R replaces Author/Maintainer Package: GSVA Commit: 87cd4d7cdcae92c251c9b53c7f759c38b4ab1ed4 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 15:31:13 +0200 Commit message: Bump version Package: GSVA Commit: 9c1eb50150a6aaee271512838ad8739b3bb130fe Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 15:22:44 +0200 Commit message: Merge pull request #276 from rcastelo/275-average-method Average method for enrichment scores calculation Package: GSVA Commit: 9e68f27aaa3d02a7d4c28792365b50d35dc1b5aa Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 14:50:43 +0200 Commit message: Replace checkIdentical() for checkEqualsNumeric() to allow C unit tests pass across different platforms Package: GSVA Commit: 5f21614dc2ee103338d887a39e119f4fbbbf90d9 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 12:29:14 +0200 Commit message: Added C implementation of the average method, and its corresponding unit tests. For performance issues, genes within genesets are internally ordered after mapped to features, this required regenerating regression test for PLAGE since SVD flipped sign in values due to the different input order Package: GSVA Commit: 87cfe5db164c95b66710094c215285fbf17995a6 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:46:28 +0200 Commit message: Merge branch 'devel' into 275-average-method Package: GSVA Commit: cc12f1d01a63d0123a48e3fb3d576c61a5f6a14d Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 14:42:36 +0200 Commit message: Fixed namespace issues and unit tests Package: GSVA Commit: 6881306e155fe38933ff8cf6d3ec9be94b9b382d Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 12:16:49 +0200 Commit message: Add unit tests for CLR and average method Package: GSVA Commit: 730ce29c9eb3a6d8b94c1c327d96451241681fd5 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-21 17:07:11 +0200 Commit message: Added first version of the average method for calculating enrichment scores Package: fenr Commit: 78a5a1207281ef37881d399f562be49f4a4af6d2 Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 13:02:11 +0100 Commit message: Merge branch 'main' of https://github.com/bartongroup/fenr Package: fenr Commit: 83a93c2fe6a5bb8748799c1f369153a651713bea Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 13:00:33 +0100 Commit message: Reverting some changes Package: fenr Commit: 0274549e7ba96519bf153ae6736593f62e5f666a Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 12:01:32 +0100 Commit message: Version 1.11.3 Package: vsn Commit: cdb80675e45236c2f57a2b41d4f98f4f2d6814b2 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:27:07 +0200 Commit message: Bump version Package: vsn Commit: b5d9c153c5300b3209bd0bcef2285b4386731398 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:26:58 +0200 Commit message: Mention README and pkgdown site in NEWS Package: vsn Commit: fb67d77e139bbf2d24f020fcc99a770650124cb1 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:25:59 +0200 Commit message: Set up pkgdown Package: vsn Commit: 4e31e610b6c6afccfe348d107f05e277101f01be Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:25:04 +0200 Commit message: Add minimal README with deNBI survey Package: sesame Commit: 2acabdce8fbdd4fb9675db1fd76d60d05792be04 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 22:06:41 -0400 Commit message: 1.31.5: fix readControls column naming; qualityMask takes a custom mask readControls() built the control data.frame positionally: colnames(ctl) <- c('G','R','col','type') over a frame whose signal matrix has four columns, so Color_Channel and Type were cbind-ed past the end of that name vector and arrived unnamed, while `type` silently took a signal column. Downstream, controls(sdf)$Type was a vector of integers, so negControls()'s grep("negative", ...) matched nothing and detectionPnegEcdf() failed in ecdf() with "'x' must have 1 or more non-missing values" on EPIC and HM450 -- the platforms whose controls arrive through readControls() rather than as SigDF rows. The columns are now named explicitly. This was found from the C side, where it had been mistaken for an annotation divergence for two days. With it fixed, detectionPnegEcdf agrees between the two implementations at max|diff| = 0.00e+00 on EPICv2, MSA, EPIC and HM450. qualityMask() gains `platform` and `mask`, so a custom or combined-array mask can be passed in directly instead of being bolted on with addMask() after the fact -- the case that comes up for arrays built from two manifests. README: the two implementations are named and versioned. The R package is SeSAMe v1 and stays on the 1.x series; the C command line is SeSAMe2 on 2.x. They are parallel, not sequential. The conda line also said `sesame-cli`, which has not been the package name since 0.4. R CMD check: Status OK, vignettes built and re-run. Package: mia Commit: 859de8cd0be1bdd40982b6cd189141c84cb359cd Author: Giulio Benedetti <giuliobene2000@gmail.com> Date: 2026-09-23 14:27:37 +0800 Commit message: Clarify study subjects in ADHD microbiota profiles (#828) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: mia Commit: 751d24e22c26aaccc6ec7be1ece37540fc2eab37 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-23 08:57:53 +0300 Commit message: Add Rdpack references (#797) Signed-off-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: mia Commit: 3c4fd9e80ecf788464a2726cf15e64cbd0aeede2 Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Date: 2026-09-22 11:27:29 +0300 Commit message: Convert MAE to TreeSE and back (#810) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Package: OMA Commit: 1ff85f15276db0d08c8305d788808bc3d713d066 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-23 13:07:47 +0300 Commit message: Simplify importing Package: OMA Commit: f19c0abb3874a6386f4693912c59f010dc5ec331 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-22 15:05:08 +0300 Commit message: Fix rendering Package: OMA Commit: 1d6f339fb23ebbdd1a58d089605f547fb76413d1 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-22 14:31:13 +0300 Commit message: Fix rendering, update support forum address Package: OMA Commit: 3f130bdb5a124835ec56391806571a9a6954963e Author: jagadeesh <2400040120@kluniversity.in> Date: 2026-09-18 16:37:10 +0530 Commit message: docs: Add comprehensive Rarefaction section to transformation chapter (#825) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Co-authored-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <tvborm@utu.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 1a65548fafa7a1d699b74cabccff2cb6b8b74f3f Author: Rasmus Hindström <56149499+raivo-otus@users.noreply.github.com> Date: 2026-09-18 09:20:36 +0300 Commit message: docs/clarity improvement to mia::summarizeDominance (#852) Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Co-authored-by: TuomasBorman <TuomasBorman@users.noreply.github.com> Package: OMA Commit: bcf4b79324d7db13573f7d75f1921324f098bf37 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:11:59 +0000 Commit message: feat(ci): add whitespace stripping to style workflow (#864) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: be708a734fe6980f7fdb08cd7d29c0bf68d85d47 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:06:30 +0000 Commit message: fix(community_similarity): use official vegan docs (#872) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: d51543f698e697431a375bb5ee52ea224490b2a1 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:03:41 +0000 Commit message: feat(ci): add dependabot (#865) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 79c94b838aca89ac79e9544310302b5528c9a0b8 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 05:57:47 +0000 Commit message: bump(deps): actions/cache@v4 to v6 (#874) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 4e1978be84a4efc4813759e6f1a2d6aa262ba265 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-18 08:52:51 +0300 Commit message: Use scaled fitted values for DMM drivers (#881) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 7bd2fc8e6da903e0640182842001f3fd42f5a210 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-17 15:48:42 +0300 Commit message: Clarify exercise instructions across the book (#886) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 7ad1b506261f780a42bc9ffa0655f10f91047bb3 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-17 15:33:57 +0300 Commit message: Add tree visualization reference (#889) Package: OMA Commit: 0e655914be48d7af2242a012deeb8354ec31f033 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-08-08 19:29:22 +0300 Commit message: Suppress cheatsheet startup messages (#878) Package: beachmat Commit: 7fe7dc234ea2fe69bf8f4c711525428539033652 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 15:32:49 +1000 Commit message: Switch to DelayedNoOp to support all alabaster.matrix no-op subclasses. This saves us having to list all of the individual subclasses. Package: alabaster.matrix Commit: ff91f9ff04b310f74232613787d6abe1411769aa Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 14:54:50 +1000 Commit message: Introduce a no-op base class to catch all of our weird seeds. In particular, packages like beachmat don't have to add a specialization for each of the no-ops subclasses, they can just check for the DelayedNoOp class. Package: alabaster.matrix Commit: 998568738d4d76e3073b732c24eaf2a9d79f650a Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 14:26:07 +1000 Commit message: Implement ToBeRealizedArray class for fine control of delayed operations. Package: SparseArray Commit: fab50cb7a6f6b1c5735dd1f19b05b94e04503dcf Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:57:43 -0700 Commit message: some edits to SparseArray-abind.Rd Package: DelayedArray Commit: ef3f02a7227a0e6a07736601081925f2fccb43a9 Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:26:39 -0700 Commit message: requires S4Arrays >= 1.13.1 Package: DelayedArray Commit: 28a0ba92ed413f575dd5839324e9892eb8f840c2 Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:02:40 -0700 Commit message: DelayedArray 0.39.7: Add abind() method for DelayedArray objects Also: - Remove the rbind(), cbind() and bindROWS() methods defined for DelayedArray objects. These methods are now replaced by more generic methods defined in the S4Arrays package for Array objects that are all based on abind(). - Add coercion from array/matrix to DelayedArray/DelayedMatrix. This coercion is equivalent to calling the constructor function DelayedArray() on the object to coerce. Having this coercion work has the effect of making rbind() and cbind() work on a mix of DelayedMatrix objects and ordinary matrices. This partially addresses issue #100. Package: scDiagnostics Commit: bee3ff588074c8e26c3b15b12610f23b7c19acdc Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 21:24:22 -0400 Commit message: Silence scran deprecation warnings and tolerate missing Suggests, bump to 1.7.15 Two failures on the first run against Bioconductor 3.24 / R 4.6: R CMD check reported significant warnings in the examples on all three platforms. scran 1.41 deprecates its HVG helpers in favour of scrapper, so every modelGeneVar()/getTopHVGs() call - including the fitTrendVar() that modelGeneVar() calls internally - now signals a deprecatedWarning, and rcmdcheck runs with error_on = "warning". Add an internal muffleDeprecation() that muffles only the deprecatedWarning class, leaving genuine warnings alone, and wrap the six calls in processPCA(), detectAnomaly() and calculateReconstructionError() with it. The three examples that call scran::getTopHVGs() directly wrap it in suppressWarnings() instead, with a comment saying why. This is a stopgap: the HVG selection needs to move to scrapper before scran makes these functions defunct. The macOS job additionally failed with "Packages suggested but not available: 'scRNAseq', 'celldex'". Neither is used by anything that runs during the check - they appear in documentation prose and inst/script - and both currently fail their own Bioconductor 3.24 builds, so set _R_CHECK_FORCE_SUGGESTS_=false rather than fail this package's check over them. Package: scDiagnostics Commit: 964640ff9a5c7728f24141ce53575c0840966fd8 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 20:38:25 -0400 Commit message: Target Bioconductor devel 3.24 / R 4.6 in CI, bump to 1.7.14 The matrix was pinned to Bioconductor 3.22 / R 4.5, two release cycles behind: 3.23 is the current release and 3.24 is devel, which is what the Bioconductor build system checks this branch against. Point all three jobs at 3.24 / R 4.6 (the pairing BiocManager's version map requires), swap the Linux container for bioconductor/bioconductor_docker:devel, and move the RSPM mirror from jammy to noble to match that image's Ubuntu 24.04 base. Also refresh the cache keys and the check-results artifact name, which still referenced RELEASE_3_22/3_19; the new keys additionally force a cold cache so no 3.22-era binaries are restored. Package: knowYourCG Commit: 9a7cce4c69f010992c7694da610eab786d07b443 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 18:58:22 -0400 Commit message: Point users at KnowYourCG v2, and fix three dead links This package is KnowYourCG v1 and stays on the 1.x series. The C implementation is KnowYourCG v2, binary `kycg`, and nothing here said so. Framed as succession, not as a wind-down, and that distinction is the point. An earlier draft of this put "This package is in maintenance; active development continues in kycg" into DESCRIPTION -- the field that renders on the Bioconductor landing page. This package sits on an open Core Team deprecation watch (#4, "Bioconductor failure and risk of deprecation"), so publishing that it is in maintenance would have handed them the justification. A neutral pointer says the same true thing without inviting it: the project is not declining, it is on its second implementation. Three places, because they reach different readers. DESCRIPTION is the only one an installing user sees, rendered on the landing page. The README is for GitHub visitors. Sequencing.Rmd names v2 where a reader is most likely to want it -- that vignette's workflow is what v2 does natively over YAME stores. The URL is in angle brackets, the same convention the DOI in that sentence already uses; a bare URL is what R CMD check objects to. Each says plainly that the two are parallel implementations rather than an upgrade path: one is an R package, the other a command-line tool, and there is no upgrading from one to the other. Separately, three dead links. `R CMD check --as-cran` runs a URL liveness check that a plain check skips entirely, and it found Sequencing.Rmd linking to https://zhou-lab.github.io/YAME/docs/summarize.html (twice) and .../docs/pack_unpack.html -- both 404. YAME's documentation is a single page now and those paths no longer exist, so all three point at https://zhou-lab.github.io/YAME/ instead. Package: scDiagnostics Commit: 89c6ed709d444d28439a7c791cb151b11faca8fb Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 19:54:35 -0400 Commit message: Make BiocCheck's deprecation check resilient to bioconductor.org outages, bump to 1.7.13 BiocCheck's first check downloads checkResults//bioc-LATEST/ meat-index.dcf for both the release and devel branches, and a failed download is a hard error ("HTTP 504 Gateway Timeout" -> bfcadd() failed -> "not all 'rnames' found or unique"), which took down the Linux and macOS jobs even though the package itself was fine. Pre-populate BiocCheck's own BiocFileCache with up to three attempts before running BiocCheck, and only if bioconductor.org is still unreachable pass `no-check-deprecated` so that one check is skipped instead of failing the whole build. </pre> </div> Package: scDiagnostics Commit: 816fa92698fa534abefc3cc0f75df2319b8f11f6 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 17:32:41 -0400 Commit message: Disable public RSPM on macOS/Windows to fix root cause, bump to 1.7.12 The libomp install in the previous commit didn't fix stringdist's identical dlopen failure - same byte-for-byte error, meaning the install had no effect. Searched prior reports of this exact failure (tidymodels/tune#1199, Genentech/rdborrow#73/#74): the real cause is that r-lib/actions/setup-r configures Posit Package Manager (P3M) as the default macOS repo, and P3M's macOS arm64 binaries are compiled with OpenMP enabled. This runner can't resolve those OpenMP symbols at runtime (SIP strips DYLD_* for protected binaries, so even a correctly installed libomp isn't reliably picked up) - CRAN's own macOS binaries are built without OpenMP and never hit this. Set use-public-rspm: false on the "Setup R from r-lib" step so macOS (and Windows, already passing, no expected impact) resolve packages from CRAN directly instead of P3M, which should fix this for any OpenMP-linked package in the dependency tree - not just the three (RhpcBLASctl, isotree, stringdist) hit so far - rather than continuing to patch them one at a time. Left the earlier source-install and libomp workarounds in place; they're harmless if this makes them redundant, and there's no upside to stripping proven/plausible fixes before confirming this one actually resolves it on CI. Package: scDiagnostics Commit: 3aba0f79435c543deb4c129e486f16e5e92c6ba4 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 16:59:49 -0400 Commit message: Install CRAN's official libomp on macOS CI, bump to 1.7.11 The last two fixes patched RhpcBLASctl and isotree individually, but BiocCheck::BiocCheck() now hits the identical failure via one of its own dependencies (stringdist): unable to load shared object '.../stringdist.so': dlopen(...): symbol not found in flat namespace '___kmpc_barrier' Patching each OpenMP-linked CRAN package one at a time as it's reached doesn't scale - the actual root cause is that this GitHub Actions macOS runner is simply missing the libomp build that CRAN's macOS binaries are compiled against (documented at https://mac.r-project.org/openmp/; Homebrew's libomp installs to a different path and doesn't fix this). Installing it there via the official recipe should let CRAN's normal (faster) binaries load correctly for any OpenMP-using package, not just the two already patched. Left the RhpcBLASctl/isotree source-install workarounds in place since they're already confirmed working - no reason to touch proven fixes while chasing this. Package: scDiagnostics Commit: 58cf3022aee073ef86bf0e5695fe41dd4a701ec9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:24:46 -0400 Commit message: Also force isotree from source on macOS CI, bump to 1.7.10 RhpcBLASctl fixed the first macOS OpenMP dlopen failure, but the same issue exists one layer up: isotree's own CRAN macOS binary (isotree.so) fails to dlopen with "symbol not found in flat namespace '___kmpc_barrier'" - a Clang/LLVM OpenMP runtime symbol, same root cause (CRAN's macOS binary built with OpenMP support that isn't resolvable on this runner), just a different dependency in the chain. Applied the identical source-install workaround to isotree. Package: scDiagnostics Commit: 7809c44d4bc5e698aeb4d67f24e79535cfe513c9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:00:00 -0400 Commit message: Force RhpcBLASctl from source on macOS CI, bump to 1.7.9 Ubuntu and Windows now pass under the Bioc 3.22/R 4.5 bump (previous two commits), confirming those fixes. macOS still fails, but differently and on all 4 vignettes uniformly this time: Error: .onLoad failed in loadNamespace() for 'RhpcBLASctl' dlopen(.../RhpcBLASctl.so, ...): symbol not found in flat namespace '_omp_get_max_threads' RhpcBLASctl is a hard Import of isotree (detectAnomaly() calls isotree::isolation.forest()), so its namespace loads unconditionally. CRAN's macOS binary for RhpcBLASctl references an OpenMP runtime symbol that isn't resolvable on this GitHub Actions macOS runner - a known class of issue for R packages built with OpenMP support on macOS. Building from source instead compiles without OpenMP (Apple clang has no -fopenmp by default), so the resulting library never references that symbol. Added alongside the existing Matrix/irlba source-install workaround in the same step, which addresses the same kind of macOS binary incompatibility. Package: scDiagnostics Commit: 3386bcb54d27441922472dd08b49d1b1d786bb37 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 12:06:16 -0400 Commit message: Anchor SingleCellExperiment/SpatialExperiment Rd links, bump to 1.7.8 R CMD check now fails with error_on = "warning" on the Bioc 3.22/R 4.5 CI (bumped in the previous commit): "checking Rd cross-references" reports a genuine broken link (merfish_reference_data.Rd's \linkS4class{SpatialExperiment} doesn't resolve) plus 36 files whose \linkS4class{SingleCellExperiment}/{SpatialExperiment} links are missing package anchors - both promote the check from NOTE to WARNING under the newer toolchain. \linkS4class{} was reintroduced repo-wide by a September 17 commit ("docs: use \linkS4class{} for SingleCellExperiment roxygen links", for brevity) after an earlier commit had already fixed this exact issue with explicit \link[pkg:target]{text} anchors. Restoring that anchored form and re-running roxygen2 to regenerate man/ resolves it; verified with a full local R CMD check matching the CI invocation (0 errors, 0 warnings, 1 unrelated pre-existing note). Package: scDiagnostics Commit: b520b294d72834042d23e6c4c887c6c194847544 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 10:33:30 -0400 Commit message: Bump CI to Bioconductor 3.22/R 4.5 to fix vignette build failure COVIDCaseStudy.Rmd was failing to build on CI (macOS/Windows) with "unable to find required package 'Seqinfo'" inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause: covid_reference_data/covid_query_data were generated on current Bioconductor (3.22), where the Seqinfo class was split out into its own standalone package. check-bioc.yml was still pinned to the two-year-old Bioconductor 3.19/R 4.4, whose GenomeInfoDb predates that split and whose repos don't contain a 'Seqinfo' package at all, so the class tag baked into the serialized data can't be resolved. Two earlier attempts (adding set.seed() to rule out RNG state, then patching a subset of the shipped .rda files) missed this because neither addressed the actual CI environment being out of date. Bumped the workflow's matrix (r/bioc versions, container image, cache keys) to 4.5/3.22, matching the environment covid_reference_data was actually generated on; verified locally that a full R CMD build (fresh install + vignette rebuild) succeeds under this Bioc/R pairing. Package: scDiagnostics Commit: 02de5cdca9c45682ebceab3b3f7d6231d8cb8054 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:40:12 -0400 Commit message: Handle reference cell types with too few cells or absent from query detectAnomaly() previously assumed every reference cell type had at least 2 cells (to fit an isolation forest) and, when a query dataset was provided, implicitly assumed every reference cell type also had matching query cells. Neither is guaranteed: - A reference cell type with fewer than 2 cells can't fit an isolation forest; now skipped with a warning instead of erroring. - A reference cell type entirely absent from the query is a normal outcome (e.g. after subsetting/filtering the query), not an error; now reported with an empty query score vector instead of failing in predict(). Also fixes a latent bug where a cell-type subset reducing to exactly 1 row would silently drop to a vector (missing drop = FALSE), which would have broken the isolation forest input shape. Adds tests covering both edge cases. Package: scDiagnostics Commit: b0fc15de1e279c3a6e2d44c12837dd3667d35743 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:36:38 -0400 Commit message: Fix stale Seqinfo class tag causing vignette build failure, bump to 1.7.6 COVIDCaseStudy.Rmd failed to build on CI with: Error in .requirePackage(): unable to find required package 'Seqinfo' triggered inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause, confirmed via verbose updateObject() output: covid_reference_data's internal Seqinfo class was tagged with its old home package ("GenomeInfoDb", from before Seqinfo was split into its own standalone Bioconductor package), so a sufficiently new Bioconductor tries to auto-migrate it on load - and that migration path apparently isn't reliably available in a fresh CI environment. Fix: call updateObject() on serialized objects at data-generation time so the bundled .rda ships with the current internal representation baked in, rather than deferring to a lazy per-load migration. Applied to the new COVIDData.R/MERFISHData.R scripts (whose source data came from an external, older serialization), and audited/fixed the same latent issue in the pre-existing reference_data/query_data/qc_data (which had the identical stale tag despite already shipping in the package) and their generation scripts, so this doesn't resurface on a future regeneration or Bioconductor version bump. zeisel_/covid_/ merfish_ vignette datasets were already correctly tagged and are byte-identical after regeneration. Package: scDiagnostics Commit: 44dd05d3749412c865e5446d44a4520bd24df370 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:13:03 -0400 Commit message: Fix non-deterministic vignette failure and bump to 1.7.5 COVIDCaseStudy.Rmd and MERFISHCaseStudy.Rmd called detectAnomaly()/ calculateGeneShifts() (which use isotree::isolation.forest(), a randomized algorithm) without ever calling set.seed(), unlike the other two vignettes. This is the most likely cause of the CI vignette re-build failure on COVIDCaseStudy.Rmd after pushing 1.7.4 - a build without a seed picks up whatever RNG state the session happens to be in, which can land on the isolation forest / gene-shift edge cases seen elsewhere in this codebase. Verified against 15 different seeds plus a full local R CMD build (fresh install + vignette rebuild, not just devtools::load_all()) with no failures. Bumps to 1.7.5 rather than re-pushing 1.7.4, since 1.7.4 already has a recorded (failed) build on Bioconductor/GitHub. Package: MSstatsBioNet Commit: 0b9e21718beccbc1fb3847792481f8bda11b7ef5 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 18:27:25 -0400 Commit message: feat(decomposeSubnetworkIntoHierarchicalTopics): Enable NMF hierarchical decomposition (#110) Package: knowYourCG Commit: 5dbb3d5b4f6dcb4f6f54e4db6859b760358c9344 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 17:15:02 -0400 Commit message: Stop reaching the network when the vignettes and examples are built Three build-time downloads, all of the same two Zenodo files, none of them needed to show that the package works. The vignette one was failing outright. Sequencing.Rmd's QUICK START fetched mm10_f3_10cells.cg -- 11.4 MB, which takes ~101 s at the throughput a build host is likely to get. R's download.file() gives up at getOption("timeout"), 60 s by default, so the transfer truncated mid-file and the vignette errored. Measured twice here: it stopped at 6.0 MB and at 7.2 MB, both almost exactly 60 s of transfer, and completed only with timeout raised to 600. Raising the timeout would have kept a network dependency the package does not need. The sequencing workflow is superseded by the kycg command-line tool, which does this analysis natively over YAME .cg stores and fetches its own knowledgebases, so the chunk is now shown rather than run, with a line saying so and pointing there. The two examples had the same files behind a guard that does not guard. \donttest IS executed by the Bioconductor builders; only \dontrun is not. In bedToCg() the download.file() sat outside the guard entirely, so it ran on every check while only the bedToCg() call was skipped -- the whole example is now \dontrun. In testEnrichment() the guard was in the right place but was \donttest, now \dontrun; its offline part, which uses the sesameData cache, still runs. Both edited in the roxygen source and regenerated, so document() cannot revert them. Neither example has run lately: checksrc has been skipped for as long as buildsrc has been red, so these would have fired the moment the vignette fix made checksrc reachable again. BiocCheck NOTEs \dontrun in favour of \donttest. That NOTE is accepted here: \donttest does not keep the builders off the network, which is the point. visualization.Rmd still reads a small RDS over the network and is left alone -- it builds reliably and is not part of this failure. Package: knowYourCG Commit: 0a4ce5469ac8b4fbb9801a4af583639b65a36b4d Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 16:23:15 -0400 Commit message: Array.Rmd: use the base pipe, not the borrowed magrittr one buildsrc has failed on every builder in both release and devel with Quitting from Array.Rmd:218-233 [ky8, run-test-single] Error in `results %>% dplyr::filter(overlap > 10) %>% head`: ! could not find function "%>%" The vignette never attached the pipe. It worked anyway because library(sesameData) pulls ExperimentHub -> AnnotationHub -> BiocFileCache -> dbplyr, and dbplyr re-exports `%>%`, so the vignette was borrowing the operator from a package four levels down its own dependency chain and never named. When that chain stopped attaching dbplyr, the vignette broke without having changed. knowYourCG imports `%>%` via importFrom(magrittr) but does not export it, so library(knowYourCG) was never what made it resolve. DESCRIPTION has Depends: R (>= 4.4.0), so `|>` is available unconditionally and removes the dependency rather than renaming it; `%>% head` becomes `|> head()` since the base pipe needs a call. R/preparePlotDF.R keeps `%>%` -- package code has the import, only vignettes were ever exposed. Verified under R 4.6.0: all three rewrites return identical() results to the magrittr forms, the base pipe resolves with nothing attached, and Array.Rmd renders to completion. Fixes the buildsrc half of #4. Package: gDRutils Commit: a62ecdc187c6b4b726415cb33500813dfbbb0d10 Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 22:34:53 +0200 Commit message: Merge pull request #201 from gdrplatform/GDR-3612 refactor: read the constant-fit xc50 threshold from fit configuration Package: gDRutils Commit: 441d33fe8d5ca07d23f4dcbee9f59274a5f4f14f Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-22 21:17:54 +0200 Commit message: fix: read the fit configuration when the fitting layer is entered directly Package: gDRutils Commit: 11524511fd588673802ec057e728b96c9b089b0d Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 12:07:38 +0200 Commit message: Merge branch 'main' into GDR-3612 Package: gDRutils Commit: afa97f88532cc8d0539c9df9b2d5170b0e7f4f0c Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:50:27 +0200 Commit message: docs: flag that fit_curves still hardcodes the xc50 threshold Package: gDRutils Commit: f450b02a0beaa9ae1f8cec3fd09151e2f2fe5a98 Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:49:21 +0200 Commit message: Merge remote-tracking branch 'origin/GDR-3606' into GDR-3612 # Conflicts: # DESCRIPTION # NEWS.md Package: gDRutils Commit: b5e352cf6c88d1a7cb33ca89c106b55896cb1cbc Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 13:27:47 +0200 Commit message: refactor: read the constant-fit xc50 threshold from fit configuration The response level deciding whether a constant fit reports +Inf or -Inf was hardcoded at 0.5 in two functions. It is now one entry per normalization type in the fit_config block, alongside the priors and asymptote bounds. Numerically inert: every type keeps 0.5, which is what the code did before. The point is that the value becomes visible and decidable - for RV it means 50% viability and for GR it is the GR50 convention, but NGR is a bare ratio of slopes that is legitimately negative, where the threshold has no established meaning. Package: methodical Commit: 2ce1f224115807008cf8e4056bff3346c161cbe2 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-22 20:12:54 +0100 Commit message: update Package: MSstatsBioNet Commit: d6f02da47b7e915ef0c30923538cf7d516341aa2 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 14:43:07 -0400 Commit message: fix(pubmed): Reduce runtime for fetching pubmed abstracts (#109) Package: GSVA Commit: d2828ae6a4645e089dc931494a2b0f239850ae7b Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:45:59 +0200 Commit message: Switch a couple of install() calls in C for the corresponding more performant internal Rf_*() calls Package: alabaster.matrix Commit: 7cd81656f826538908e71cea03dbed7e42544cb8 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:53:29 +1000 Commit message: Mention all of the weird DelayedArrays that we support in the ANY method. Also move the LowRankMatrix code out of the ANY method for clarity. Also bump version and date for a new release. Package: alabaster.matrix Commit: 1d4b149bd9a329ea35a5033dc0318f6292f275ee Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:38:20 +1000 Commit message: Use a more precise R type hint for residual matrix objects. Also move ResidualMatrix code out of the ANY method for easier reading. Package: alabaster.matrix Commit: 1a17e99c4a5e64b68688da152c20434d3ae965bb Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:21:07 +1000 Commit message: Support scrapper::LogNormalizedMatrixSeed in storeDelayedObject. Package: MSstatsBioNet Commit: c6cb932731a5f1f1a743daed884638f2c14afd57 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:38 -0400 Commit message: Bump package version from 1.5.2 to 1.5.3 Package: MSstatsBioNet Commit: 57f2c7b2d94664d93f76a16b82cc5a5b7cff2ae9 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:10 -0400 Commit message: fix(proteinGroups): Adjust annotateProteinInfoFromIndra to handle protein groups (#108) Package: BreastSubtypeR Commit: 9aad28d9baa37a3a2acc3e040c72bc2fea5bced8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-09-22 20:24:05 +0800 Commit message: Merge upstream/devel, Updated Package: BreastSubtypeR Commit: f44f9d18a7ff9c1446d57cc8515dc427e98e0a4b Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:06:15 +0800 Commit message: Merge pull request #139 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 9e4904ff65cfc1320229f841b55402e08e0390fe Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:00:13 +0800 Commit message: Merge pull request #138 from yqkiuo/main New updates Package: BreastSubtypeR Commit: 252f893b32c10da768540ab3df667f3c6ef34419 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 12:56:55 +0800 Commit message: Merge pull request #136 from yqkiuo/maintenance/public-package-fixes-20260918 Maintenance fixes for 1.5.2: AUTO routing, ROR-C column, Shiny launcher and preflight, Mapping and documentation Package: BreastSubtypeR Commit: f9ca808290b0dfe73e62cff242e28cc301f69238 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-21 10:30:49 +0000 Commit message: Track .Rbuildignore and exclude the .github directory from the build R CMD check reported "hidden files and directories: .github" because the workflow directory reached the source tarball. .Rbuildignore was listed in .gitignore and therefore never shipped with the repository; it is now tracked, with the same content the Ensemble branch already carries, so the built package excludes .github, RStudio files, Rplots.pdf, doc, Meta and MANIFEST.txt. No R code changes. Package: BreastSubtypeR Commit: f3e3be4738438524e605ca70781d8ac359af9ca8 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-19 13:24:35 +0000 Commit message: Bump version to 1.5.2 and title the release notes DESCRIPTION 1.5.1 -> 1.5.2 for the Bioconductor devel submission of the maintenance fixes. The NEWS block collected under "Unreleased" becomes the 1.5.2 entry. One clause is added to the AUTO subsetting bullet: the supplementary pseudocode of the published paper records the strict comparison in the subsetting step while using ">=" for method selection, so readers comparing the package against the paper know that the package now applies ">=" in both and reproduces its shipped example. Package: BreastSubtypeR Commit: 1826b4a6941c152837ef57effbb3c23fdf9751a0 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:57:20 +0000 Commit message: Docs: keep the maintenance track free of unreleased-feature references The entropy change of the previous commits described the new NA behaviour by comparison with an unreleased voting feature, in the internal help text of get_entropy(), in the comment heading test-entropy.R and in the NEWS bullet. The maintenance branch is the public package: its sources, tests and NEWS must not name work that has not been released. The wording now states the behaviour on its own terms. No code, test assertion or behaviour changes. Package: BreastSubtypeR Commit: 252961fa606750b2c17e82363ee0e5ac4ac08d20 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:50:50 +0000 Commit message: Tests: do not let the equivocal HER2 case emit an unhandled warning The AUTO routing test feeds an equivocal "2+" HER2 code to check that a non-evaluable value is treated like a missing one. Builds that flag ambiguous HER2 codes warn on that input, which leaves an unhandled warning in the suite. The call is wrapped; the routing verdict it asserts is unchanged. Package: BreastSubtypeR Commit: 1931c45909ab5e0a56327d3024afd0331468caa5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:37:24 +0000 Commit message: AUTO: decide the HER2+ cohort from the HER2 column alone The HER2+ branch of get_methods() was entered when at least one evaluable HER2 value existed and the joint ER/HER2 counts held no HER2-negative sample. Those counts are computed with na.rm = TRUE, so a HER2-negative sample whose ER value was missing never reached them: one such sample left the cohort classified as HER2+, while an otherwise identical sample with a recorded ER value ended the classification. Whether a HER2-negative tumor counts must not depend on whether its ER status happens to be known. The branch now requires at least one evaluable HER2 value and every evaluable HER2 value to be HER2+. Values outside {HER2+, HER2-} are not evaluable; this covers missing values and the equivocal "2+" code that .normalize_er_her2_tn() deliberately leaves unchanged. Such samples neither create nor remove a HER2+ cohort, and AUTO now reports how many of them took no part in the decision, because a single unannotated sample used to be able to change the routing silently. Cohorts with complete HER2 information are routed exactly as before. The packaged OSLO2-EMIT0 example has no missing ER or HER2 value (ER+ 84, ER- 18, HER2+ 8, HER2- 94), so no shipped example or regression fixture changes. The test that pinned the previous behaviour (her2_pos_na_er) is replaced by a block asserting that both routes now agree, and a block asserting the new message. The NEWS bullet for the unreleased HER2+ change is consolidated into a single statement of the final rule rather than two successive refinements of the same unreleased behaviour. README and vignette state the rule. Package: BreastSubtypeR Commit: 14445c18179fdb40310ea13069f72cc6b5c59a60 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 18:20:00 +0200 Commit message: Entropy: report NA when no method returned a call get_entropy() computes the raw Shannon entropy of a per-sample row of method calls. table() drops missing values, so a row in which every executed method returned NA produced -sum(numeric(0)), that is 0, which on this scale reads as unanimous agreement. Such a row has no call distribution and therefore no entropy; it is now reported as NA. Rows with at least one call are unchanged, including the degenerate one-call case, whose entropy of 0 is the correct value for the observed distribution. The definition of the statistic - raw, unnormalized Shannon entropy in bits - is untouched, and no normalized variant is introduced. The change aligns the legacy path with the ENSEMBLE diagnostics, where raw_vote_entropy is already NA_real_ when valid_voter_count is zero. Exposure is narrow: every AUTO panel includes AIMS and sspbc, which are single-sample predictors and call essentially every sample, so an all-NA row cannot arise in AUTO. It arises in manual runs of nearest-centroid-only method sets (for example methods = c("ssBC", "ssBC.v2")), where a sample whose ER or ER/HER2 status is unknown gets no call from any executed method. The packaged OSLO2-EMIT0 example is unaffected: every tumor there has 7 or 8 calls, and its stored entropy column is reproduced exactly by the new function (asserted by a test). Side effect worth noting: Vis_Multi() orders rows by the entropy column and order() places NA last, so a sample with no calls now sorts to the end of the plot instead of appearing among the unanimous samples. The entropy column of res_subtypes is documented in ?BS_Multi for the first time, including that it is computed over the contributing methods only, so a low value from few contributing methods reflects few available calls rather than strong agreement. tests/testthat/test-entropy.R covers the NA cases, the unchanged values for rows with calls, reproduction of the packaged entropy column, and a manual two-method run in which four samples receive no call. Package: BreastSubtypeR Commit: 3668d9c93adb99e148dc577e8a82b0d556adb249 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 17:30:00 +0200 Commit message: PCAPAM50: exclude samples with unknown ER from the IHC-guided steps BS_PCAPAM50() builds the IHC column from the ER status with case_when(..., .default = NA), so a sample whose ER is missing or not coded "ER+"/"ER-" has no label. makeCalls.PC1ihc() expressed ER-negativity as !grepl("^L", IHC), which returns TRUE for NA, so those samples were counted as ER-negative in the PC1 axis check, in the misclassification-minimizing cutoff search and in the ER-balanced gene-centering set. The bias is one-directional and grows with the fraction of unknown ER. A new internal helper, .ihc_status(), classifies each label as "luminal", "nonluminal" or NA (missing or empty), and the three steps now use explicit luminal / non-luminal masks. Samples without an evaluable label take no part in estimating the cutoff or the centering set, a message reports how many were excluded, and they are still classified and returned. As a side effect the label test is now applied consistently: the mask is computed once, after trimming and upper-casing, instead of being evaluated before the upper-casing step in one place and after it in another. This is not a deviation from the published algorithm. The reference implementation (Raj-Kumar et al., CRAN package PCAPAM50 1.0.4, R/functions_PCA-PAM50.R lines 336, 355-356, 385-386) uses the same !grepl("^L", IHC) construct, but its IHC column is a user-supplied clinical subtype (LA, LB1, LB2, Her2+, TN) that the package never leaves missing; the vignette states that ER-positive subtypes start with "L" and all others are ER-negative. The NA category exists only because BreastSubtypeR derives the column itself. The change also removes an internal inconsistency: BS_cIHC() and BS_cIHC.itr() already exclude unknown ER from their ER groups via which(df.cln$ER == ...). Measured on the packaged OSLO2-EMIT0 input (R 4.3.3 sandbox), setting the first k ER values to NA and comparing calls before and after the change: k = 0 and k = 6 leave every call unchanged, k = 18 changes 2 of 102 calls, k = 30 changes 6 of 102. Cohorts with complete ER are unaffected, and the packaged example still reproduces its stored PCAPAM50 column. The help page of BS_PCAPAM50() gains a @details paragraph stating the exclusion, the message, that such samples are still classified, and the reference implementation's assumption of a complete IHC column. tests/testthat/test-pcapam50-unknown-er.R covers the helper, the unchanged complete-ER output against the packaged fixture, the message, and that unknown-ER samples still receive calls. Package: BreastSubtypeR Commit: 83ad6b3fa93553ba75cb3c641fb7a58070173806 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:10:00 +0200 Commit message: README/vignette: state the size gating of the ER/HER2-defined AUTO rule The AUTO bullet "ER/HER2-defined cohorts: ssBC.v2 only + SSP" read as an unconditional rule. In the code it applies only when the ER group reaches its minimum (15 for ER+, 18 for ER-) and the HER2 subgroup reaches its minimum (8 for ER+, 9 for ER-); smaller cohorts run AIMS and sspbc only. The bullet now says so, and a second bullet documents the handling of cohorts without any evaluable HER2 value (ER-based rules instead of the HER2+ branch). ASCII hyphens replace the typographic minus signs in the edited lines. Package: BreastSubtypeR Commit: 38aa1cc5cb833d260c5d5f82401a8ee528bd7fc1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:05:00 +0200 Commit message: Docs: Mapping "mean"/"median" collapse duplicate probes, as in the PAM50 code The Mapping() help (and the internal domapping() roxygen) described method = "mean" and "median" as keeping "the probe with the highest mean/median expression". duplicate_genes() computes the per-sample mean or median across all probes of a gene, i.e. it collapses the probes rather than selecting one; "iqr", "stdev" and "max" select one probe, and "max" selects by largest row sum, not by "highest expression value". Checked against the original PAM50 bioclassifier code (bioclassifier_R/subtypePrediction_functions.R, collapseIDs(), and the example parameter file): "mean" and "median" average the duplicate probes per sample there too, "iqr" and "stdev" select the probe with the highest IQR / SD, and no "max" method exists. BreastSubtypeR therefore reproduces Parker's behaviour; only its documentation was wrong. Author decision (2026-09-18): fix the documentation. The parameter text in R/BreastSubtypeR_methods.R, R/Utilities.R and man/Mapping.Rd now describes the averaging, credits collapseIDs() and marks "max" as a package addition. No code or mapped values changed. Package: BreastSubtypeR Commit: ba02d862d5e1c9cdbb43e23a1f8506faaed46946 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:00:00 +0200 Commit message: AUTO: include subgroups exactly at their minimum in the ssBC/ssBC.v2 subsets Method selection in get_methods() accepts a subgroup when its size is at least the minimum (15 for ER+, 18 for ER-, 8 and 9 for the HER2 subgroups), but the sample subsets handed to BS_Multi() for ssBC and ssBC.v2 were built with a strict ">". A subgroup of exactly the minimum size was therefore selected for the method and then excluded from its input, and its samples came back NA while the AUTO messages reported the method as running. The packaged OSLO2-EMIT0 example is such a case: 84 ER+ and 18 ER- tumors, so the cohort is classified as mixed and ssBC is selected, but the 18 ER- tumors were dropped from the ssBC input. Executed in a sandbox (R 4.3.3) on this branch: with the published strict comparison a fresh BS_Multi(methods = "AUTO") run yields ssBC = NA for those 18 tumors and does NOT reproduce the packaged frozen result OSLO2EMIT0obj$res (which carries ssBC calls for all 102 tumors); with ">=" the fresh run reproduces the stored result exactly, entropy included. The stored data object is therefore left unchanged; the fix restores agreement between the code and the shipped example. tests/testthat/test-auto-fixture-regression.R asserts the reproduction and that no ER- tumor is left without an ssBC call; tests/testthat/test-auto-subsetting.R adds exact-minimum subgroup cases and the OSLO2-EMIT0 colData. Package: BreastSubtypeR Commit: 13ea06daee8af82ab42c32cfceb38b43aecff9e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:55:00 +0200 Commit message: AUTO: require an evaluable HER2 value before calling a cohort HER2+ get_methods() entered the HER2+ branch whenever n_ERposHER2neg == 0 && n_ERnegHER2neg == 0. Both counts are also zero when HER2 is entirely missing or coded with unrecognized values, so such cohorts were classified as "small HER2+" and received AIMS and sspbc only (example: 60 ER+ / 40 ER- with HER2 all NA). The branch condition now also requires at least one evaluable HER2 value (HER2+ or HER2-). Cohorts without HER2 information fall through to the ER-based rules: a mixed ER cohort gets the mixed panel (ssBC.v2 then returns NA for every sample, which BS_ssBC() handles without error), an ER+-only cohort reaches the announced AIMS/sspbc fallback because its HER2 subgroups are empty. Cohorts with any evaluable HER2 value are routed exactly as before, including the existing treatment of HER2- samples whose ER is missing (excluded from the subgroup counts, as the AUTO message states). No effect on the packaged OSLO2-EMIT0 example. Author decision (2026-09-18): HER2+ branch only with evaluable HER2. tests/testthat/test-auto-routing.R covers the size-gated ER/HER2-defined cohorts and the cohorts without HER2 information. Package: BreastSubtypeR Commit: 94c6d57580acf6c6b77287f8e3968628ffeb2b84 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:50:00 +0200 Commit message: cIHC, cIHC.itr, PCAPAM50: clear error when an ER group is empty On a cohort with a single ER group (for example every sample ER+), makeCalls_ihc() and makeCalls.PC1ihc() failed with "undefined columns selected" and makeCalls_ihc.iterative() with "arguments imply differing number of rows: 0, 102", all from the median computation on an empty balanced set. The methods cannot balance by ER status without both groups. A small helper, .check_er_groups(), now stops with the group counts and a pointer to the cohort-aware modes in makeCalls_ihc() and makeCalls_ihc.iterative(). makeCalls.PC1ihc() checks the luminal / non-luminal IHC classes before the PC1 cutoff search and the balanced set after it, and makeCalls.v1PAM() checks its LumA / Basal groups. Cohorts with both groups take the same path as before (the OSLO2-EMIT0 cIHC calls are unchanged). Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-er-balancing-errors.R covers the three methods. Package: BreastSubtypeR Commit: 3894f47377e42f6c2f18cf8d7e04ecd0e38f7b16 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:45:00 +0200 Commit message: Docs: describe the actual return values of the NC methods; cIHC.itr ratio BS_PCAPAM50() and BS_ssBC() documented "a character vector of intrinsic subtype predictions", BS_cIHC() "a data.frame", and BS_cIHC.itr() a list with elements subtypes / confidence / ER_balance that do not exist. All four return a list: BS.all (PatientID, BS and, with Subtype = TRUE, BS.Subtype), score.ROR (correlations, calls, confidence, ESR1/ERBB2 expression, ROR-S/ROR-P and, with hasClinical = TRUE, ROR-C/ROR-PC scores and groups), the medians used for centering (mdns; mdns.fl for PCAPAM50; absent for cIHC.itr) and outList; BS_cIHC.itr() additionally returns BS.itr.keep and, with Subtype = TRUE, BS.itr.keep.Subtype. Verified on the packaged OSLO2-EMIT0 input. BS_cIHC.itr(ratio): makeCalls_ihc.iterative() swaps the larger ER group into the sampled position before drawing ceiling(ratio * n_smaller) samples from it, so the ratio applies to the larger group relative to the smaller one, not to ER+/ER- as such. The parameter text now says so, and the alphabetical tie-break used by get_consensus_subtype() for the consensus call is stated in the return value. roxygen comments and the corresponding man/*.Rd files were edited in parallel (no roxygen2 run, to avoid unrelated regeneration changes). Present in Bioconductor release 1.4.0 and devel 1.5.1. No code changes. Package: BreastSubtypeR Commit: abace8828bc01fa6ff7e1a70d6a9c1e28505cc74 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:40:00 +0200 Commit message: Shiny: cohort preflight requires both ER and HER2 columns .summarize_cohort() in inst/ShinyBreastSubtypeR/server.R returned ok = TRUE for kind "ER" (HER2 absent), kind "HER2" (ER absent) and for a valid TN column without ER/HER2. get_methods() stops in all three cases ("The 'AUTO' mode requires both 'ER' and 'HER2' columns in the 'pheno' dataframe"), which the app surfaced only as "Prediction failed" after the user pressed Run. The column summary is unchanged (now .summarize_cohort_columns()); .summarize_cohort() wraps it and sets ok = FALSE with the message "Cohort-aware analysis requires both 'ER' and 'HER2' columns; missing: ..." when either column is absent. Kind and statistics are still reported. tests/testthat/test-shiny-preflight.R covers the column combinations. Package: BreastSubtypeR Commit: 36e4de779bf6677fde472e81f613cf3f49799476 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:35:00 +0200 Commit message: iBreastSubtypeR: load app dependency namespaces correctly The launcher's .attach_if() helper called requireNamespace(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE). requireNamespace() has no such arguments, so the call failed with "unused arguments"; the failure was swallowed and FALSE returned, and nothing was loaded. The comment claimed the packages were attached to the search path, which requireNamespace() never does. The app still worked because ui.R/server.R use qualified calls and shiny::runApp() attaches shiny itself. The helper is now a package-internal function, .load_app_dependencies(), that checks installation, loads each namespace with requireNamespace(p, quietly = TRUE) and stops with a clear message when a package is missing or cannot be loaded. The tidyverse option uses the same helper. The exported signature and documentation are unchanged. tests/testthat/test-shiny-launcher.R covers the missing package error and the successful load. Package: BreastSubtypeR Commit: 6deac1db8d57cfbaee4e104edb9af6f160a9c536 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:30:00 +0200 Commit message: BS_Multi: report the error text when PCAPAM50 fails The tryCatch() around BS_PCAPAM50() in BS_Multi() warned "PCAPAM50 failed in this iteration: " and dropped the condition message, so users could not see why the method failed. The warning now appends conditionMessage(e) (with call. = FALSE). Behaviour is otherwise unchanged: the method's column is filled with NA. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-bs-multi-messages.R mocks a failing BS_PCAPAM50() and checks the warning text and the NA column. Package: BreastSubtypeR Commit: ff23703e8cb347524ad8fe1897d25d6514fd4049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:25:00 +0200 Commit message: Normalize factor phenodata like character; fix the FPKM imputation guard .normalize_er_her2_tn() used nested ifelse() calls whose fallback was the original column. For a factor column the fallback is the integer code, so unmatched levels came back as strings such as "3" instead of "Unknown". Mapping() converts colData factors to character before calling the helper, but BS_Multi() and get_methods() normalize the phenotype table directly, so a hand-built data_input with factor ER/HER2/TN columns was normalized differently from the same table with character columns. The helper now works on as.character() copies of the three columns; the coercion warnings compare character values, so canonical factor input no longer triggers them. Character input is unchanged. domapping(): the second imputation guard tested anyNA(x) after x had already been imputed, so counts.fpkm was never imputed. It now tests anyNA(counts.fpkm). In practice edgeR rejects NA counts earlier, so this is a logic correction with no expected effect on existing analyses. Both present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-phenodata-normalization.R compares factor and character input for the helper and for a full AUTO decision. Package: BreastSubtypeR Commit: 5deb60ce12da9448df97aa5079c0f312ad12cc6a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:20:00 +0200 Commit message: Mapping: keep matrix dimensions for single-sample input duplicate_genes() indexed x[names(entrezid), ] without drop = FALSE and rebuilt the collapsed matrix with mapply(SIMPLIFY = TRUE) followed by apply(x, 1, unlist), which requires a matrix. For a one-sample SummarizedExperiment the subset became a vector and Mapping() failed with "dim(X) must have a positive length". prepare_nc_matrix() and the probe filter in domapping() had the same drop issue. The collapse now builds the gene-by-sample matrix explicitly (lapply + rbind with dimnames from the split and the sample names), and the three subsets use drop = FALSE. For multi-sample input the returned values and dimnames are identical to the previous implementation for "mean", "median", "max", "stdev" and "iqr" (checked on random data with duplicated Entrez IDs and an NA value); the OSLO2-EMIT0 mapping of one sample equals the corresponding column of the full mapping. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: d6c6c20c4004d988e79c522ee4f1625dd0ad39fb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:15:00 +0200 Commit message: AUTO: announce the fallback to AIMS and sspbc instead of falling back silently The safety net at the end of get_methods() set methods to c("AIMS", "sspbc") without any message. It is reached by ER+-only or ER--only cohorts whose HER2 subgroups are all below their thresholds, typically because many HER2 values are missing (example: 17 ER+ samples with HER2+ 5, HER2- 6, missing 6). Users saw only the two SSP methods run, with no indication why the ssBC variants were not selected. The fallback now emits a .msg() (respecting the BreastSubtypeR.verbose option) naming the reason. Method selection is unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: a9f0de975795df873663f9cab6207455cb3b2d15 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:10:00 +0200 Commit message: AUTO: drop samples with missing ER/HER2 from the ssBC/ssBC.v2 subsets get_methods() built the AUTO-mode sample subsets with rownames(pheno)[pheno$ER == subtype] and the ER/HER2 analogue. A missing ER or HER2 value evaluates to NA in the comparison, so the subsets contained NA "sample names". BS_Multi() then either failed when it subset the SummarizedExperiment ([,j] index out of bounds: NA) or, when the NA-padded vector was at least as long as the cohort, treated it as "run on all samples" and skipped the intended subsetting. Example on 1.5.3: 50 ER+ / 45 ER- / 5 NA gives a 105-element subset with 10 NA entries for a 100-sample cohort. Both lapply bodies now use which(), as makeCalls.ssBC() already does, so samples with missing status are excluded. Cohorts with complete ER/HER2 values return identical subsets. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-auto-subsetting.R covers a mixed cohort with missing ER and an ER- cohort with missing ER and HER2 (subset shorter than the cohort). Both fail on the previous code. </pre> </div> Package: BreastSubtypeR Commit: 2f8ea71201a742d0d0957ff8228ba2fdbc21d3be Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:05:00 +0200 Commit message: Fix ROR-C risk group column: use criskgroups, not cpriskgroups In RORgroup() (R/NC_functions.R) the data frame built when hasClinical = TRUE assigned the combined + proliferation groups (cpriskgroups) to both "ROR-C Group (Subtype + Clinic)" and "ROR-PC Group (Subtype + Clinic + Prolif)". The ROR-C groups (criskgroups, thresholds -0.1 and 0.2 on the combined score) were computed but never reported. The ROR-C group column now uses criskgroups; the ROR-C score and every other column are unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-ror-groups.R adds a synthetic RORgroup() input in which the ROR-C and ROR-PC groups differ (high/low/med vs low/high/med) and checks that the ROR-C group is reproducible from the reported ROR-C score. The test fails on the previous code and passes with this change. Package: BreastSubtypeR Commit: 9ab99af8b9cf337614a30a61c3e0ce1c264df049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:00:00 +0200 Commit message: Tests: run the nested testthat suite via test_check() tests/testthat.R contained a single inline test_that() block and never called test_check(), so tests/testthat/test-tn-cohort-detection.R (added in 1.5.1) was not executed by R CMD check; the Bioconductor devel check log shows only the inline test running. tests/testthat.R now calls test_check("BreastSubtypeR") and the inline BS_Multi() test moved unchanged to tests/testthat/test-bs-multi-manual.R. DESCRIPTION: Config/testthat/edition: 3 and testthat (>= 3.2.0) in Suggests, matching the edition-3 expectations used by the tests added on this branch. No version bump. Package: BreastSubtypeR Commit: a4b23b2aba07ba19b33669ac1e8d8361fd1139ab Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:59 +0200 Commit message: Merge pull request #135 from yqkiuo/main update to 1.5.2 Package: BreastSubtypeR Commit: b19c1c3f629d11a8f12e57526162b16e41e605c6 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:30 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: 0c0c47c87dcd6e560bedcd536f828dca642e7933 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-06-22 17:38:39 +0300 Commit message: Merge pull request #134 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: edeb030317e854cd706a351f12b93dbd722f232e Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 17:22:45 +0300 Commit message: Finalize NEWS entry for TN detection fix (#133) Package: BreastSubtypeR Commit: b8d6bf4b5bb037d8e101287e92d209fdb1e869a5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:59:04 +0300 Commit message: Update NEWS and documentation for TN detection fix (#133) Package: BreastSubtypeR Commit: d8eeff0e85113512842b1e4976fce6eed1142e39 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:25:06 +0300 Commit message: Fix TN-only cohort detection (#133) Package: BreastSubtypeR Commit: cd515ab92fffbbf8a3496cfc70e65299b77457ba Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-02-20 12:09:07 +0100 Commit message: v1.3.3 Package: BreastSubtypeR Commit: 0770ee5c0a5283fd1f073cf9c170464431eac2d3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-02-20 11:59:28 +0100 Commit message: Merge pull request #129 from yqkiuo/main AUTO - NA Package: BreastSubtypeR Commit: 9b740667ac781cede13f2884763f47576f5778cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:30:22 +0100 Commit message: Merge pull request #128 from yqkiuo/BranchManos Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: ebac3daf14161981995520818d552a8c894faa21 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:27:35 +0100 Commit message: Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: 122fae948ba3ab93589046d4fc9f564a95db3805 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-12-21 07:08:46 +0100 Commit message: Merge pull request #125 from yqkiuo/main Update Package: BreastSubtypeR Commit: ab9e6c7e715a77c3d9d0c93f0d96794531b39afc Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:48:57 +0100 Commit message: Merge pull request #124 from yqkiuo/BranchManos cIHC.itr: return distances as numeric matrix, preserve dimnames Package: BreastSubtypeR Commit: 1cdd290182105e8d9dd1cf38a2f1cc2748045aba Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:41:20 +0100 Commit message: cIHC.itr: return distances as numeric matrix, preserve dimnames - Coerce mean_distance and mean_distance.Subtype to double matrices with sample/centroid dimnames; negate once. - Ensure testData is numeric matrix. - Use explicit getsuffix(calibration=..., internal=...). Closes #112 Package: BreastSubtypeR Commit: e626336705e6981d3f43c1e307381875acc4dbf5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:18:30 +0100 Commit message: Merge pull request #123 from yqkiuo/BranchManos feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to can… Package: BreastSubtypeR Commit: bf244ea222946de979dc528b6764b074b9a7492e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:17:59 +0100 Commit message: feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to canonical forms - Add `.normalize_er_her2_tn()` utility and call it inside `Mapping()` to coerce common variants to: * ER → {ER+, ER-} * HER2 → {HER2+, HER2-} (HER2 "2+" left unchanged/unevaluable) * TN → {TN, nonTN} Accepts Positive/Negative, Pos/Neg, Yes/No, True/False, 1/0, AMP→HER2+, etc. - Preserve original values in `colData` when fields are absent; only touch present columns. - Emit explicit warnings on ambiguous/unmappable values (e.g., HER2 "2+"). - Roxygen: expand `Mapping()` docs with required Column metadata for AUTO/ssBC/cIHC/PCAPAM50 and numeric TSIZE/NODE (0/1) for ROR; document the canonical receptor coding and the automatic normalization behavior. Closes #122 Package: BreastSubtypeR Commit: d4200b8f8fa6a230b1aed6bd8d5a271856dcf9c5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 10:04:54 +0100 Commit message: Merge pull request #120 from yqkiuo/BranchQiao Formatting Package: BreastSubtypeR Commit: 855146c3797560a923b044683b223aa09c5ab6b6 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 10:04:04 +0100 Commit message: Formatting Package: BreastSubtypeR Commit: 7e1546b848212ca92df006f0625e1f0213a5d825 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:57:27 +0100 Commit message: Merge pull request #119 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 13081dbdf8d5faead48468a7121455f68f226262 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 09:56:57 +0100 Commit message: Warning: nonASCII Package: BreastSubtypeR Commit: e872818d9f7db70dd95b04e56306c5f986b4cb2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:48:36 +0100 Commit message: Merge pull request #118 from yqkiuo/main 1.3.1 Package: BreastSubtypeR Commit: e837d4a4b93480e5921dc6220d336f390e08cfa9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:56:26 +0100 Commit message: Merge pull request #117 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 24282cdd95efcb545c8a516d2a4c52c333451e37 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:55:43 +0100 Commit message: docs(NEWS): updated to include latest changes/bug fixes Package: BreastSubtypeR Commit: d3e819ea9cb6036119018581de03f7c0ca6c03e9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:45:26 +0100 Commit message: shiny/preflight: reset cached data_input on source change (uploads/example) to fix stale cohort display Package: BreastSubtypeR Commit: f7ad9d6399c959146fad253c76e4b8a093367674 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:06:08 +0100 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: 33bc7cabda598a10d06781255a4ff477d64ec373 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:05:55 +0100 Commit message: Merge pull request #116 from yqkiuo/main Main to BranchManos unmerged changes Package: BreastSubtypeR Commit: c1164715171e92993dba23d51ed4d2739a9db33a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:03:31 +0100 Commit message: Include ssBC in robust singleton handling Package: BreastSubtypeR Commit: 0c0c39cd7cb7bdde99192d4a877cc9990b98b6c4 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:32:17 +0100 Commit message: v1.3.1 Package: BreastSubtypeR Commit: ed479c4a0a715bd078874a465956416cb58e999b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:30:33 +0100 Commit message: Minor typo for Shiny exports Package: BreastSubtypeR Commit: fca34d14be09269bd6a9e83f9b169b3f49e3b27d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:16:28 +0100 Commit message: ssBC.v2: include sample IDs in singleton fallback warnings; surface warnings in Shiny - Warnings now list subgroup + n + sample IDs (truncated for long lists). - Shiny wraps runs in withCallingHandlers() to show warnings via showNotification(). Package: BreastSubtypeR Commit: 5beba6624617ea57bd33a664a2c9ccddbe01f5d2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:15:25 +0100 Commit message: ssBC.v2: robust singleton handling + ROR guards - Use uncentered expression for n=1 fallback (avoid zero-vector Spearman→NA). - Add canonical 4-class name normalizer before RORgroup; create missing cols; enforce order. - Shorten Mapping() completion notification duration in Shiny. Package: BreastSubtypeR Commit: 6f8593d8659200d5b054e45ae6deb7ff624bf02f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 23:31:32 +0200 Commit message: Merge pull request #115 from yqkiuo/BranchManos fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: ae32dd867386460a3d6abcff63cd519bcebdd098 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-21 23:25:49 +0200 Commit message: fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: 01a86e199d7353c526b1ddec6693b6c5d87a53e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:51:52 +0200 Commit message: Merge pull request #114 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: aee5223fca7ad466234702b83f9d465092e65fec Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:50:18 +0200 Commit message: update documentation (.Rd) files & NEWS.md Package: BreastSubtypeR Commit: e3852e46bc7c708db9534558669b18e492bbcb44 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:38:36 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: f13b835df4329f494e2a1fe1242a1927657629f9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging -Name unnamed chunks Closes #113 Package: BreastSubtypeR Commit: 815edf2ed0faa1dc708fecc282da22945d861490 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging Package: BreastSubtypeR Commit: 27a8e42ca0dd5a06b976bd6e59aeedf3337c8ad1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:41:55 +0200 Commit message: Merge pull request #111 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6ed1cf770b44ea3eeaa0fe5d284760692df203e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:40:32 +0200 Commit message: feat(shiny): show ER/HER2 subgroup tallies (±TN) in AUTO preflight Package: BreastSubtypeR Commit: a85dec5c9e7f261e7d9ea94febbbfc063dc07992 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:04:55 +0200 Commit message: fix(shiny): guard switch() inputs to prevent length>1 errors; harden AUTO preflight & ssBC option handling Package: BreastSubtypeR Commit: 8b4e57129dabde362d8c811661e7586dc633c396 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:49:16 +0200 Commit message: feat(shiny): TN-aware AUTO preflight summary and messaging Package: BreastSubtypeR Commit: 83b469a296627e4a81983655692766813d8540b2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:48:42 +0200 Commit message: docs: convert wording to American English (standardized, normalization, visualize) Package: BreastSubtypeR Commit: 1c86f875473cf413e91da628410278915a9b19cb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 00:28:47 +0200 Commit message: Merge pull request #110 from yqkiuo/BranchManos v1.1.9: feat(app): add example-data loader and AUTO preflight cohort … Package: BreastSubtypeR Commit: bcb7486f49afd2f9c719d1b047c89b96421040b5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-15 00:26:27 +0200 Commit message: v1.1.9: feat(app): add example-data loader and AUTO preflight cohort stats; harden AIMS/sspbc outputs; renamed FPKM GEX example file Package: BreastSubtypeR Commit: 3e5ae1bae1910f63b576690d0f5965c092929197 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-14 22:26:00 +0200 Commit message: Merge pull request #109 from yqkiuo/BranchManos Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: 643629b4f37a82e8eb4fc1d4b8b7d47a1d0140e5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-14 22:08:03 +0200 Commit message: Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: f0bb013273724583dc640776f5253a650e71deb7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-11 19:07:21 +0200 Commit message: Merge pull request #106 from yqkiuo/main v1.1.8 Package: BreastSubtypeR Commit: e519bba6330b28527eba397178b5db68259cd335 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 17:48:34 +0200 Commit message: Merge pull request #105 from yqkiuo/BranchManos Minor text improvements Package: BreastSubtypeR Commit: 7ef4c516f1e02b2667908e42c91db1f81587e183 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 17:35:16 +0200 Commit message: Minor text improvements Package: BreastSubtypeR Commit: bba02a162aae8a104830c2762903a95b4b24a086 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 16:30:43 +0200 Commit message: Merge pull request #104 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6bb89109d53b3cbfc61069dad0b97c43fc01a59 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 08:38:02 +0200 Commit message: v1.1.8: feat(auto): enforce v2-only for ER/HER2-defined cohorts; add TN cutoff (18); sync docs Package: BreastSubtypeR Commit: 104a9d3c962648e2421f86b970452b6ae8094add Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 00:03:52 +0200 Commit message: v1.1.7: Fixed bugs & Clarified guidance in AUTO logic Package: BreastSubtypeR Commit: 3a0c352910e74d2016eaaa4f0d229db74b6428b1 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:11:23 +0200 Commit message: Merge pull request #103 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: c23f9312cfe6399587682872db5168e726949468 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-08 07:10:55 +0200 Commit message: v1.1.6 Package: BreastSubtypeR Commit: bda41efb6523b351c335cbbbfe93eda3e294159a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:01:46 +0200 Commit message: Merge pull request #102 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 01fbf08f95785bd96121416f08a42a0723db9bb5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:31:43 +0200 Commit message: Merge pull request #101 from yqkiuo/BranchManos Update citation Package: BreastSubtypeR Commit: 819b86fcb1f32f68d8d6551ae67675e59d55cbc2 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:29:59 +0200 Commit message: Update citation Package: BreastSubtypeR Commit: 18426cd1996f6d437078579a397e594ac858b422 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:18:10 +0200 Commit message: Merge pull request #100 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5cd622f0dfdcbf4ebd2612e2f3bce0d4d130a1dd Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:10:24 +0200 Commit message: Update to v1.1.6 Package: BreastSubtypeR Commit: 0168bb1d064c170c27904604ce944664052ffc4c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:00:02 +0200 Commit message: Fix CITATION error & update CITATION Package: BreastSubtypeR Commit: efcf440f930e3e0216161a7bfaa1f8a839796ffc Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:28 +0200 Commit message: Merge pull request #99 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 522570c1925152201b4738888c70a9b479569b4d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:10 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: caa57d7c96c2b3621ba3153a63704780fb67943c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: eca7fd305351bee53a3359193d31d6efb3bd239c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:26:16 +0200 Commit message: Merge pull request #98 from yqkiuo/BranchManos Bump version to 1.1.5, merge from BranchManos Package: BreastSubtypeR Commit: 3d6d84a04f652c46b098e7daf6b9433783c59317 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:17:29 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 08be34439c7ec15f3aab940989e7fc5881500a38 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:28:50 +0200 Commit message: Minor styler changes to comply with BiocCheck Package: BreastSubtypeR Commit: c33c626c748776d83aec78b69c2c5c2d78b40d94 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:00:25 +0200 Commit message: Remove Styler ignore file Package: BreastSubtypeR Commit: a756018eea737c57128fecbe2ed656a5c8bd8c89 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:53:48 +0200 Commit message: After styler formatting Package: BreastSubtypeR Commit: 0fb6775cf7105ccdfeac0f78d671c8220fa00a07 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:43:21 +0200 Commit message: Before styler formatting Package: BreastSubtypeR Commit: f462a35c15affb83307240678fdb8b5c31f1e1af Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 15:06:41 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: d58720a8654c148543e56efe3c8504e50f7a06f9 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Fix LaTeX errors, @importFrom issues, deprecated mutate_at(), tightened Mapping() Package: BreastSubtypeR Commit: 8cab29a01c0412be9b9a83d9c729c77b273c03f9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:33:33 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 2909f655c9c2686e9c562762e27c7cb78eb63544 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Merge pull request #97 from yqkiuo/BranchQiao Fix LaTeX errors Package: BreastSubtypeR Commit: f1d92deeed7ff76170c4ba8a70d0ac75e0dab7eb Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:28:10 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 9112d81e8538f3debb6c101255008486d052c326 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-12 19:39:12 +0200 Commit message: Merge pull request #96 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 977c1a7f7a5dd3700b51fe154e0a9509d6a960b1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 19:38:48 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: b2ba716538df0e23e684ec1118866c96560cab9b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:14:24 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: e25016431d3c00bfd81d941f4b8a71a2b7357ba1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:07:19 +0200 Commit message: v1.1.3 Merge branch 'BranchQiao' of github.com:yqkiuo/BreastSubtypeR into BranchQiao # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. Package: BreastSubtypeR Commit: 0f3624d0ed05aa4d2f2cb9759acb59d815fea297 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:04:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 8a340b6a4117f80791ae664c5741a0fe8627c9c3 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 15:44:48 +0200 Commit message: Fix BreastSubtypeRobj to include only the object itself (exclude environment variables) Package: BreastSubtypeR Commit: f969bcf09e03aa226de3839a68cf76cc01011ef3 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 14:52:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 693c829f364caedb2161a940d196d1830bd19d87 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 10:21:35 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 8582fb3b897e60ecc6da91040e32b42b19641154 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 17:06:26 +0200 Commit message: Added publication badge Package: BreastSubtypeR Commit: bd0b6cab935e607efd4bb001e3b75b02b37cc1fe Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:47:02 +0200 Commit message: Fixed bug: When running BS_Multi() omitting the first method; Minimal fix (drop nothing after removing row_id) Package: BreastSubtypeR Commit: 234ccbe269d45bd2c407358b711253629fe59203 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:12:28 +0200 Commit message: Polishing README.md & Vignette Package: BreastSubtypeR Commit: b3d5c232a32097ee9b4f83908a9c89f6ca621be8 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:41:14 +0200 Commit message: DOI update and text Package: BreastSubtypeR Commit: bacb13657f301643a682a3fcd7e82a22091a3b6c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:01:14 +0200 Commit message: Added DOI, Updated exported with version info, method, etc Package: BreastSubtypeR Commit: 787b3119148e345c0b2d4fa8638b3d6dd37600ee Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 19:17:32 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: c856d8dc615f688ae8f5d27eeb47ab297ead6b11 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:36:22 +0200 Commit message: Delete .github/workflows/sync-to-forks.yml Package: BreastSubtypeR Commit: 8d235ce12beccf9d394146a458ae135fec2f0fb3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:18:15 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: ad15f75e9de9028eb6d93fb5efb3ca05220ce975 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:04:51 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 917d62c7bc428fc67ff97c513022feb210fed94c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:58:05 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 9258dd1803aac507ecae1ec05d30a55c7c91827c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:54:22 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 8864ea4a8bda1bee1b6496aaf185e8bb76af5257 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:57 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 71735535741a019e7ba9299e47783038edbd3714 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:00 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f165c7df5636588c76360b10a42e792e9bf53614 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:50:26 +0200 Commit message: Create sync-to-forks.yml Package: BreastSubtypeR Commit: f2d85acb23f2c38ec3b3062fbab841c29115d38e Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:47:46 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 792bc0ab92f80b7405d69c45516dd131ffd7663c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:43:18 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 99d3102b66482953013f265d00464c8c3a4c2b25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:34:13 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 212e09ee660df8daaffea11a7af00d53321895aa Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:04:17 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 7cea1e782fedda5fef57f559c77dc39db8aceb9d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:56:40 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f33f344a6b0d06d3de393a783a23383e4ef5cac4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: adccaf9e7d8ce2b6234a1960e93e5d1543d98e09 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:31:34 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: a9e9e80f2f1063aae332963e474ea2f5804487b7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:27:58 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 4151dfa20943c89acdd55c5e1dec18a03da01e2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:14:01 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 1ab513bde94a41e4ab34856ca5e4f5ba5a6413e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 15:59:19 +0200 Commit message: Create sync-to-org.yml Package: BreastSubtypeR Commit: f9f0ea202177840660c02d39e203f67d4003e2cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:09:58 +0200 Commit message: Added description for new example dataset (TCGABRCAobj), updated the BreastSubtypeRobj with the 3 new medians info, tiny text improvements Package: BreastSubtypeR Commit: 056545172113202bb55a0ea0c2918851096fa0f2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:05:10 +0200 Commit message: Created a new example dataset (TCGABRCAobj) from TCGA-BRCA with Raw Counts, and similar results as OSLO2EMIT0obj Package: BreastSubtypeR Commit: 6de103db09589a53624341851237a8f547684ceb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:02:19 +0200 Commit message: Updated BreastSubtypeRobj with 3 more published medians Package: BreastSubtypeR Commit: 6acd15688f6e60db4e1f2ef151c103e865ce5663 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:00:19 +0200 Commit message: Guard docalibration, Improve External calibration, UX, and minor text improvements Package: BreastSubtypeR Commit: 8f7e3790ac94fead82f77e6564d87c542fcf5097 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 11:11:22 +0200 Commit message: Fixed error in BS_Multi() in AUTO Mode, when ssBC has <50 PAM50 genes: Add safe row-aligning cbind helper, made RORgroup() tolerant to missing ESR1/ERBB2 rows, and made BS_Multi() assemble results by PatientID Package: BreastSubtypeR Commit: 06bd9bce269ca12b4ca9f052f3d81cd730212a68 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 21:20:25 +0200 Commit message: Fixed the issue with pre-loading third-party libraries before initializing the Shiny app, Updated Help files Package: BreastSubtypeR Commit: ee560564150a7a5f11c00e8750583438a6c084e6 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:55 +0200 Commit message: Updated NEWS.md with major changes Package: BreastSubtypeR Commit: abd132463b65390c813f04ea50c530fd4b058507 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:18 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 74b20b933030517c45e68826a469dd88d79aa0b9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:24:07 +0200 Commit message: Added a TCGA-BRCA subset, with clinical & annotation data, for testing the RawCounts normalization pipeline Package: BreastSubtypeR Commit: d4fedc4c9b2a241b2652e563c2300d423f787287 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:21:08 +0200 Commit message: iBreastSubtypeR: UX polish, AUTO explainer, export refactor, AIMS constraint & bug fixes Package: BreastSubtypeR Commit: fb7c21f7ebc4f50be7610c8c0a023036f1559358 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 13:24:32 +0200 Commit message: Include three pre-computed Medians (external) as an option to Shiny App Package: BreastSubtypeR Commit: d1a90080950c9b5ddcad737979d072bdc177e038 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 11:34:43 +0200 Commit message: ssBC fixes: No crashes when < 50 PAM50 genes, No accidental subtype calls when a sample’s distance row is all-NA, Won't error when a subgroup has zero samples, qCtr won't produce NaN from zero range Package: BreastSubtypeR Commit: 10644b50e4721efe7b0d9f65445d30e1fdcf5a26 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 10:05:57 +0200 Commit message: Add our reference to Mapping() & BS_Multi() Package: BreastSubtypeR Commit: 5ea0dd73f932fbdd278f4e299de7270698d855c1 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 23:10:17 +0200 Commit message: New preflight for AUTO to prevent errors, new customizations, included new polished text for PAM50 to guide users, and more Package: BreastSubtypeR Commit: 3b08eed750427d72842bec852ff85c2446138cbe Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 13:21:06 +0200 Commit message: Fix issue when HER2 missing and user runs AUTO Package: BreastSubtypeR Commit: 16b805c817e0b7e3883b1aa7defd6da04f6a57f4 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:20:14 +0200 Commit message: Included a Prelight check for ER/HER2/Tn status availability in Clinical data BEFORE Running subtyping, avoiding App crashing due to missing values Package: BreastSubtypeR Commit: f003e4ecbfadb6a2a293ff39d838581dea5a0086 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:01:32 +0200 Commit message: Synchronized changes in BreastSubtypeR_methods.R and NC_functions.R, Created a theme to match the logo, made things unified, text improvements Package: BreastSubtypeR Commit: a66b4796231c8054f2093c6795ca4e67f2cb04de Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 10:08:20 +0200 Commit message: Parker original when calibration=None, or external calibration returns error: Fixed by Making NA equivalent to "medianCtr" (sync eith Parker et al.), and -1 to No calibration. Also, avoid requiring PatientID for BS_parker() when hasClinical = FALSE, included extra controls for hasClinical in all NC functions, polished help text, corrected typos (also tried to correct the 2nd error for ssBC, when < 50 genes, but will work more on this and come back with another Commit) Package: BreastSubtypeR Commit: 53ca58ec99d200f998a8be6896bab45f47d789e3 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-05 19:36:25 +0200 Commit message: Major changes: Multi method with AUTO mode added, Description text for each method with Refs added, Subtype 4-class selection Package: BreastSubtypeR Commit: bdf3bf291b59939171d85ff61f895b2ffc222b8d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:18:47 +0200 Commit message: Fix UI so the drop down menus are easier to select Package: BreastSubtypeR Commit: c0ed93ab5eed4a965f478a0dcac17355f8f91501 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:01:42 +0200 Commit message: Changed HasClinical with a Tick box, included many controls to check whether TSIZE, NODE are available, added different help functions for GEX and Annotation, improved text, and more Package: BreastSubtypeR Commit: 277869bea9c0c7d2747370cc657b2e87cb4e7dd2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 14:59:23 +0200 Commit message: Replaced the T -> TSIZE Package: BreastSubtypeR Commit: fd063a60aa8db3651975e89237ddb398d62c1100 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:28:48 +0200 Commit message: Minor edit Package: BreastSubtypeR Commit: 31e6bbfa2c897aa87caa09254cd2d4d2074b790f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:25:40 +0200 Commit message: Renamed folder to Shinny->Sniny, renamed data files with clear names Package: BreastSubtypeR Commit: 5ef9dd73efdccab438ee51f1ea0441ac565ca984 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:20:19 +0200 Commit message: Fix server.R bug Package: BreastSubtypeR Commit: c4c205e993f8791683fddf05392533aadded4b75 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-04 11:49:00 +0200 Commit message: refine shiny Package: BreastSubtypeR Commit: 304cb68143558163b4dd070c2498631f62a650e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-04 10:40:17 +0200 Commit message: Merge pull request #95 from yqkiuo/main Merge pull request #94 from yqkiuo/BranchQiao Package: BreastSubtypeR Commit: 6cbc1cb1b18907119b3414e3c0dafec607480a99 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:27:20 +0200 Commit message: Merge pull request #94 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 298458b861686b4ed9bfa17c070e5ffea513f3dd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-02 08:27:00 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: a50d8d4c3bea22f65836df6d099b269da685d8c2 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:25:43 +0200 Commit message: Merge pull request #93 from yqkiuo/main v1.1.2 Package: BreastSubtypeR Commit: 65b18fd8734f90e579fff40e53bbc51799b2c4ad Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:28 +0200 Commit message: Merge pull request #92 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5d09b44a5785c08a10d3d652d2a01db94678a1de Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:21 +0200 Commit message: Merge branch 'main' into BranchManos Package: BreastSubtypeR Commit: 8f4056fc16de285798c18e8c36e5399e5cd1fd23 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-01 10:18:12 +0200 Commit message: Merge pull request #91 from yqkiuo/BranchQiao v1.2.2 Package: BreastSubtypeR Commit: e11ffcd934d71dd5ee42c3816cabf93b997e6c64 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-01 10:17:53 +0200 Commit message: v1.2.2 Package: BreastSubtypeR Commit: 0969e8fa4d71d310d1d2f58c788af7a94566de25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-31 22:18:46 +0200 Commit message: Merge pull request #90 from yqkiuo/BranchQiao v1.1.2 Package: BreastSubtypeR Commit: c575280eed4e562e90ba6b9b7a6675353e532725 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-31 22:18:25 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: 031beb8e23f96e6f4894f56b550dd49d0c2a729b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-29 16:04:28 +0200 Commit message: Updated code to include separate cut-offs for ERpos & ERneg, as well as separate cut-offs ER(pos/neg)/HER2 (independent of HER2 status) based on the above cut-offfs. Note: The combined cut-offs will be released in the next submission Package: BreastSubtypeR Commit: 93ba44156f95a90bb74440d472157107e5ef0908 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 20:13:37 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: efee177e7f94d079d424ad79467615a63ce71698 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 2c6cfcacdc3550df0916ecb54833275bf2b9f04f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: d0154df0200108179568a150e1487e592a34e20a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 6a0be72275efbb8b9828b8765834d1ce97521134 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 3cf5afd43c31eeec90045902e6a082d82013bbf7 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: e91120bb63753900c47f80206b0662aef090c98a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: c09d132b8993a81ad16143b2ddbd5fb6b6f36f8b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 18:32:39 +0200 Commit message: Updated NEWS.md, BreastSubtypeR_methods.R, and minor updates to Utilities.R and data_doc.R Package: BreastSubtypeR Commit: 10f36184b66a9a0703d4296c9311b5ed1fc03e23 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 15:16:50 +0200 Commit message: Shiny app normalization clarification Package: BreastSubtypeR Commit: 24740ca0d3f45e43e674d247778b8e003871361c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:57:22 +0200 Commit message: Replaced the adaptive filtering as it was producing a reduced gene list for NC-based methods. Instead I introduce the calculation of UQ in the positively expressed subset and apply those calculcated factors to the full matrix. Package: BreastSubtypeR Commit: 347114047eeba2318371d4245043ae1d3b6bce86 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:34:21 +0200 Commit message: Include adaptive gene filtering so UQ normalization can work under real data Package: BreastSubtypeR Commit: f3bd9cdae36176a3857de89fac0c794bd8df369b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 16:29:18 +0200 Commit message: RawCounts test code include & help files updated Package: BreastSubtypeR Commit: c248d0fe615e9d6e3f4401bb6658908341de9208 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 16:07:29 +0200 Commit message: Shiny app: added descripted text Package: BreastSubtypeR Commit: 52bea350827dc0fba939551f50149d60acb3887b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 15:12:56 +0200 Commit message: Updated text in overview files Package: BreastSubtypeR Commit: 5b87399978a5d1cca09a82d5249a2b8863a553ea Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 15:10:09 +0200 Commit message: CITATION added Package: BreastSubtypeR Commit: e8fcac0bcab82793b586f5ffc8c930a0002ac609 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-21 11:29:40 +0200 Commit message: Merge pull request #89 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 0c75bf90f3070408ec5a156edf84b9c0bc70250b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:29:14 +0200 Commit message: update new features Package: BreastSubtypeR Commit: a99a93e94a90d6a715d64daedbe2e1f886f87917 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:27:58 +0200 Commit message: update new features Package: BreastSubtypeR Commit: c9f28c19c39695ad8a84ee4aa929c352be00e229 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 18:11:51 +0200 Commit message: Merge pull request #88 from yqkiuo/BranchQiao Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: e4a62355017220fe89ec8ea09376a0a56060de7c Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 18:11:26 +0200 Commit message: Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: 1993ab3e50725d01e8980a00eeaec8f0b0b766c4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:48:10 +0200 Commit message: Merge pull request #87 from yqkiuo/BranchQiao 1.1.1 Package: BreastSubtypeR Commit: 5d928ed37d8d0f47dd0392057846c43dc12e3dea Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:47:44 +0200 Commit message: 1.1.1 Package: BreastSubtypeR Commit: 52faaf9d7980c6d36524bcabbdcffe1f0fb92a0a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:39:51 +0200 Commit message: Merge pull request #86 from yqkiuo/BranchQiao 1.0.1 Package: BreastSubtypeR Commit: 35eef13e343edd2f9c6a1c26d780c97f470ac6c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:38:55 +0200 Commit message: 1.0.1 Package: BreastSubtypeR Commit: 6abaf3b4ae3d1772babec19c83d49c04728daa06 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-27 09:49:16 +0200 Commit message: Merge pull request #85 from yqkiuo/BranchQiao general update Package: BreastSubtypeR Commit: 453e9aac8dc81b86987e53e60659f2c97f6ba403 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-27 09:48:42 +0200 Commit message: general update Package: BreastSubtypeR Commit: 226607c2ae42706346a1e8911d1f2f82a5ca1490 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 19:12:11 +0200 Commit message: Merge pull request #84 from yqkiuo/BranchQiao v1.1.1 Package: BreastSubtypeR Commit: d773d4401e93ec12006f4e79122cbee8247d80d7 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 19:02:45 +0200 Commit message: v1.1.1 Package: BreastSubtypeR Commit: e74e86a2cfdf6daf92ed180095d27619cd45cd54 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:44:06 +0200 Commit message: Merge pull request #83 from yqkiuo/BranchQiao Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: fd30082d86b34d3ced41b7a7c385e01448c19794 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:41:43 +0200 Commit message: Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: 74145000a4ce350ca0e787fe5c459b79318b3edb Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:25:01 +0200 Commit message: Merge pull request #82 from yqkiuo/BranchQiao Bug fixes and minor improvements Package: BreastSubtypeR Commit: 1a5cb6636acfbd2ad1fc7c290bfba875dd2b22b0 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:24:35 +0200 Commit message: Bug fixes and minor improvements Package: BreastSubtypeR Commit: 4a895b8a8a149e0199b85eeaa19b6769dd8382df Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:27:17 +0200 Commit message: Merge pull request #81 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 4a03138457415f0164139373ee34038bd07ad300 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:21:40 +0200 Commit message: Update DESCRIPTION Package: BreastSubtypeR Commit: 856c6f8f91de5339988cf4c315bcaf96247f37d5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 10:39:20 +0200 Commit message: general update Package: BreastSubtypeR Commit: e35db8756a5fa3f30bf4addbeacd58145589e16b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:18:47 +0200 Commit message: general update Package: BreastSubtypeR Commit: 2e60c2222d3e9fdf48d3262ba087b447a95119a9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:03:00 +0200 Commit message: general update Package: BreastSubtypeR Commit: 7cfcfe95b2761178d17cc2af122f61883e7dc666 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:50:06 +0200 Commit message: update general Package: BreastSubtypeR Commit: b30131f2c073711d4b42e38af49bef1849da20c5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:48:53 +0200 Commit message: Update RawCounts para Package: BreastSubtypeR Commit: 6fa4d83d00b30727be9b1d4fd3798015fad0442a Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:32:10 +0200 Commit message: debug ROR Package: BreastSubtypeR Commit: ba045196fcd4a3bff148b3497a82f3f87d6bb324 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:31:55 +0200 Commit message: refine "-1" in parker.original Package: BreastSubtypeR Commit: b5e6254539fd38e41109056b2ddff7d36e0f9c19 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:15:41 +0200 Commit message: refine "-1" in parker.orignal Package: BreastSubtypeR Commit: bc7d097164cb411bfc4b40d5513073ae1bac35d8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:39 +0200 Commit message: 0.00.0 Package: BreastSubtypeR Commit: 5d966c161e4cdae464dd16d48421f6d5a4e26461 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:30 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 81f77832a0d7f8f5b8b70403616fe165ff96862d Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:08 +0200 Commit message: debug data type Package: BreastSubtypeR Commit: 8471668b9b9b43c3e27a87faa458488a8fba7f05 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:56 +0200 Commit message: debug BS_Multi Package: BreastSubtypeR Commit: 01fa8b576ca237667ed8a792477638cd4b023dbd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:34 +0200 Commit message: clear author Package: BreastSubtypeR Commit: a86f573778ed992a3d2dbb698b4c9c00a15619c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:20 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 00d2b9c5d71c6830e845dcddcb810b9640666207 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:33:01 +0200 Commit message: debug AUTO Package: BreastSubtypeR Commit: 8b3f7c2ef2d45cf772511a7290ba0a31baa43b62 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:32:46 +0200 Commit message: debug bad PCAPAM50 Package: BreastSubtypeR Commit: c70f4c9b0d64da1940659ae9a826d8221be05a32 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 09:32:30 +0200 Commit message: debug PCAPAM50 </div> </div>
Merge pull request #69 from rcavalcante/deprecate-randomize Deprecate randomize_regions() in favor of a background comparison
Deprecate randomize_regions() in favor of a background comparison Regions placed uniformly at random across the genome are a poor null model: real regions come from a much narrower set of locations, so most data look enriched in genic and CpG annotations. Deprecate randomize_regions() and point to annotating a background of the regions the data could have come from, or regioneR::permTest() and regioneR::resampleRegions(). summarize_annotations(), plot_annotation(), and plot_categorical() now label annotated_random as "Background" instead of "Random Regions". The examples, tests, and vignette compare DM regions to all tested regions. Also fix the allow.overlaps documentation, which controls whether random regions overlap each other, not the input regions. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Merge pull request #68 from rcavalcante/docker-check Add Docker-based Bioconductor devel check
Add Docker-based Bioconductor devel check docker/check.sh runs R CMD build, R CMD check, and BiocCheck on the committed HEAD in a Bioconductor devel image with annotatr's dependencies preinstalled. Dependencies added since the image was built are installed at check time. Use --rebuild to refresh the image. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Merge pull request #67 from rcavalcante/lncrna-gencode Fix hg38/mm10 lncRNA annotations by downloading from GENCODE
Fix hg38/mm10 lncRNA annotations by downloading from GENCODE AnnotationHub removed its GENCODE resources, including AH75123 (hg38) and AH49550 (mm10), on 2026-04-28, so hg38_lncrna_gencode and mm10_lncrna_gencode failed. Download the same GENCODE releases directly over HTTPS, and move hg19 from FTP to HTTPS. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Merge pull request #66 from rcavalcante/oviariramb2 Add support for sheep (ARS-UI_Ramb_v2.0) as 'oviariramb2'. Gene annotations come from the Ensembl 113 EnsDb in AnnotationHub (AH119381), so tx_id and gene_id are Ensembl IDs. CpG islands come from the UCSC GenArk assembly hub. Sequences use UCSC-style names (chr1, ..., chrUn_*).
Version bump Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Add sheep (ARS-UI_Ramb_v2.0) as builtin genome oviariramb2 Sheep has no TxDb.* or org.*.eg.db packages, so gene annotations are built from the Ensembl 113 EnsDb in AnnotationHub (AH119381), with Ensembl tx_id/gene_id and symbols from the EnsDb. CpG islands, chromosome sizes, and chromosome aliases come from the UCSC GenArk assembly hub, and sequences are renamed to UCSC-style names. Genomes like this are registered in GENARK in R/utils.R. The TxDb code path is unchanged; hg19 gene annotations are identical to devel. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Merged changes
Updated liftover function
Readded vignettes
bump x.y.z version to odd y following creation of RELEASE_3_23 branch
bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
Final commit for 3.23
Fixed vignettes
Final commit for devel
feat(features): name XChromatograms features from row names
Fix vignette build error: convert Bioconductor objects via as.data.frame() before as.data.table() Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01LiK5WUAPmNmkHCv3HPRNog
feat(features): name manual features from row names or a feature_id column
Update the gene table only when file changed.
updated
Updated README and vignettes
Set SVT leaves to NULL for empty columns when loading MatrixMarket data. (#133) Mostly backports of the updated C++ code and associated tests from crio.
Merge remote-tracking branch 'upstream/devel' into devel
Shorter chunk size for sparse data and indices for easier streaming.
some clarification about SVT leaf representation
feat(features): use featureDefinitions rownames as feature identifiers lcmsPlot derived its own xcms::groupnames-style MT labels from mzmed/rtmed, discarding the row names featureDefinitions() already carries. Feature identifiers now come from those row names, so renaming the rows is enough to get meaningful labels onto a plot. Identifiers matching no feature are now reported with a warning naming them, instead of being dropped silently into an empty plot. </pre> </div> Package: scRNAseqApp Commit: eb1f132e925ec26574be9a7055b51b67cf60b2cf Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-24 11:17:02 -0400 Commit message: Remove the duplicated notification for search. Package: rhdf5 Commit: 1c6ed01eaf8682004f647a15a200df1d0f55b0f6 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:21:40 +0200 Commit message: Fix duplicated logo Package: rhdf5 Commit: cab7d0212538b900883c3c6a80f27710cd80ebc5 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:03:23 +0200 Commit message: Add link to de.NBI survey Package: Rarr Commit: 56ddfff1ac32f46151b215a015cbc00b5d77744e Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:16:34 +0200 Commit message: Add deNBI funding acknowledgement and survey in README Package: Rarr Commit: accfb8f20be9b7fefe76e1b35a531704bcc8960b Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 11:06:37 +0200 Commit message: Use vectorized .store_check_exist() call Package: Rarr Commit: cbf89cd3891e3e0cdfeb474aaf153d1324b43d96 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 11:05:56 +0200 Commit message: Define is_structured once Package: Rarr Commit: 87389fada7676ae09ce5bfd3a3a4e74ba3708836 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 10:47:50 +0200 Commit message: Register bfloat routine Package: biomaRt Commit: 3e1a0768933f6c3e00895e02119e4f6e36050dac Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-24 15:05:20 +0200 Commit message: Add link to de.NBI survey Package: ISAnalytics Commit: 6e03f52a7925332d38562e8c2501425e92f89184 Author: francescogazzo <francesco.gazzo@gmail.com> Date: 2026-09-24 12:19:37 +0200 Commit message: Update collision filtering and bump devel to 1.23.2 Package: distinct Commit: 7ec08672fd2177c33c85779a82ab12deb8232802 Author: Simone Tiberi <simone.tiberi@unibo.it> Date: 2026-09-24 11:57:02 +0200 Commit message: T_obs added in results Package: distinct Commit: e749b22cf8c3c8eb925d3a293b916b7c11e75605 Author: Simone Tiberi <simone.tiberi@unibo.it> Date: 2026-09-24 11:49:37 +0200 Commit message: bug fixed in distinct_test Package: MsBackendMetaboLights Commit: 1b126b45bede3db584a54168617397078cc5c789 Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com> Date: 2026-09-24 11:52:26 +0200 Commit message: Merge pull request #26 from rformassspectrometry/jomain Add random sleep breaks to reduce failures on build systems Package: MsBackendMetaboLights Commit: c28ee3bc500c3e2a3764932bae457431cac07563 Author: Johannes Rainer <johannes.rainer@gmail.com> Date: 2026-09-24 08:45:39 +0200 Commit message: Add random sleep breaks to reduce failures on build systems - Adding/changing to random sleep times aiming at reducing the recurrent failures on the Bioconductor build system (most likely due to rate limitation from MetaboLights). Package: cellNexus Commit: 67fa18ce068ae3e0fe84da1f942a6d9a1138e052 Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 14:44:48 +1000 Commit message: Merge pull request #159 from myushen/master fix website examples Package: cellNexus Commit: 3ab2cd31f7d4a7acc40758abeed48bc0f3d8435c Author: myushen <mengyuan.shen@outlook.com> Date: 2026-09-24 14:25:14 +1000 Commit message: fix website examples Package: cellNexus Commit: 4719fb49b937acd11c9f898275920555e094c65d Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 13:37:28 +1000 Commit message: Merge pull request #153 from MangiolaLaboratory/copilot/rename-join-census-table Soft-deprecate `join_census_table()` in favor of `get_census_metadata()` Package: cellNexus Commit: 8b217f783900d3107ab0d07c0d9b57083a1e6c77 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-09-24 11:54:08 +1000 Commit message: unit test Package: cellNexus Commit: 3e4d038b291bc9ba79f306456e63fa4660958d47 Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com> Date: 2026-09-24 10:44:58 +1000 Commit message: Merge branch 'master' into copilot/rename-join-census-table Package: cellNexus Commit: 9aca6c192558b021c1c41b9071564d8daf4d7814 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-08-27 12:12:50 +1000 Commit message: soft deprecate since 0.99.27 Package: cellNexus Commit: cd885c844de21fea70d10ee653fc9c95386b8bd5 Author: myushen <mengyuan.shen@outlook.com> Date: 2026-08-27 12:08:50 +1000 Commit message: Merge remote-tracking branch 'origin/master' into rename-join-census-table merge from origin Package: cellNexus Commit: 13ffb5d261f878cacd79484700b35b9a964cef67 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:33:16 +0000 Commit message: Trim redundant mock assertion Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: abf37b553b5800c09ee3e9deb65ee9d5246d9ab4 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:32:37 +0000 Commit message: Verify Census helper mock before wrapper call Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: a4bf9cc52cf658c48d4f00fdfbdd55ec094f4484 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:32:04 +0000 Commit message: Exercise deprecated table argument compatibility Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: 4b46e68aebf2b38ce850298cc145bdf52c84d14f Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:31:37 +0000 Commit message: Correct Census deprecation test assertions Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: 1515648f80a96e03452c82ac5e602057710f512e Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:31:02 +0000 Commit message: Stabilize deprecation warning test Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: d2fd0cfdaad895c2e60be674d50076ad04cecf24 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:30:23 +0000 Commit message: Soft-deprecate Census join helper Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com> Package: cellNexus Commit: e7ae2c78928ba1b3bbb6f575e117365976743d72 Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Date: 2026-08-19 02:27:22 +0000 Commit message: Initial plan Package: mia Commit: 416de1c5a6b73b70f42571f8a3d36d0294dcb770 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-24 07:54:25 +0300 Commit message: Update documents and namespace Package: clusterProfiler Commit: 33b36f13f3729b099a8d6fc20694831b7a5c62d9 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 12:48:46 +0800 Commit message: fixed r check Package: LRDE Commit: 710586499a483617f94c2d665b87a03be62d6531 Author: Ziyang Liu <jacobleo773@gmail.com> Date: 2026-09-23 18:45:18 -0700 Commit message: Improve numerical stability and bump version to 1.1.2 Package: DOSE Commit: 5846d72fe047f1de66d506a21c117d400e4a3ef8 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:21:11 +0800 Commit message: fixed r check Package: DOSE Commit: 9011c8c053e345cdca45bf1edb93fe66b7f80417 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:14 +0800 Commit message: gseDisease() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family. Package: ReactomePA Commit: e295d309811933101f2e808814212d3244f5c6aa Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:10:04 +0800 Commit message: update docs Package: ReactomePA Commit: 586975c51fadc162d78418ff1132eddcb009b157 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:13 +0800 Commit message: gsePathway() exposes eps and forwards extra arguments, #47 gsePathway() was the only GSEA wrapper in the family missing both eps and ..., so eps could not be controlled and additional enrichit::gsea_gson() arguments could not be passed through. Both are now supported, matching clusterProfiler::gseKEGG(). Package: ReactomePA Commit: 396a55c38c765045b0309c6935b663dd334e7c3d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:03:02 +0800 Commit message: ReactomePA 1.99.2: seed argument and a faster prepareReactomeNetwork() - gsePathway() and nsePathway() expose an explicit seed parameter for reproducible GSEA results, aligned with enrichit::gsea_gson(). - prepareReactomeNetwork() no longer round-trips through graphite::convertIdentifiers()/pathwayGraph() per pathway; it builds a single UNIPROT->Entrez map up front and converts edges with vectorized lookups, keeping mclapply() parallelization over pathways. Output is unchanged (same nodes and edge values; node ordering may differ). Default cores is now 1 instead of detectCores(). Package: ReactomePA Commit: a9a8627182db7226655362793f6b6c22c25e8d7b Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-08-15 18:42:41 +0800 Commit message: parallelize prepareReactomeNetwork pathway conversion via mclapply The one-time Reactome network build converts ~2700 pathways serially in R (convertIdentifiers/pathwayGraph/graph_from_graphnel per pathway). The conversions are independent, so the loop now runs over mclapply() with a new 'cores' argument (default getOption('mc.cores', detectCores())); mclapply falls back to serial on Windows and preserves input order, so the resulting edge set - and hence the cached network - is unchanged. Measured on the GSE53757 demo: serial build ~35-41 min; parallel build 614 s at 16 cores and 655 s at 56 cores; output byte-identical to the serial baseline. Scaling saturates at ~4-5 effective cores because the graphite identifier conversion is hash-lookup-bound. Package: ReactomePA Commit: 13cb4b3cbc4616e214d63ee59a3e42bba48b0a4c Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-07-09 15:24:15 +0800 Commit message: nsea Package: ReactomePA Commit: 4edeca90aedb3afdaa29b838323bbdabad62c391 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-04-29 12:24:13 +0800 Commit message: update bioc version Package: meshes Commit: 5732c93b839f7f820eb4501e3cff468737bfa71a Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 09:09:48 +0800 Commit message: bump version Package: meshes Commit: e7498dc7737b09bffacef28a72d666693e7be51d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:14 +0800 Commit message: gseMeSH() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family. Package: meshes Commit: 01c764a9285d4c77e77ff630885b8a79077cff10 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:03:02 +0800 Commit message: expose a seed argument on gseMeSH(), meshes 1.39.2 Forward an explicit seed to enrichit::gsea_gson() so GSEA runs are reproducible, and apply pvalueCutoff to both pvalue and p.adjust inside the enrichit engine (requires enrichit >= 0.2.2). Package: GOSemSim Commit: 769cd22f90eec52f67039121c265462c701680ad Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-24 08:58:26 +0800 Commit message: update docs Package: GOSemSim Commit: ca626082247cbb24fb95b5098558b71b0592e2be Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 12:55:48 +0800 Commit message: computeIC: take the term universe from GO.db, not the shipped gotbl table computeIC() decided which terms to score from the `gotbl` table shipped in data/: goids <- unique(godata[godata$Ontology == ont, "go_id"]) That table was last rebuilt in 2021-07, so every term GO.db has added since then was given no IC at all, and the IC-based methods returned NA for it even though its descendants carry annotations and its IC is computable. This is issue #33, and the reporter's diagnosis ("a conflict between the pre-calculated gotbl.rda and the local version of GO.db") was right. Measured against the current GO.db / org.Hs.eg.db, the number of annotated terms that can actually be scored: ontology annotated before now gained BP 11293 11126 11293 +167 CC 1832 1787 1832 +45 MF 4777 4410 4777 +367 and nothing loses an IC. The missing terms also biased every other IC, because they were counted in the `sum(gocount)` denominator but could never contribute to an ancestor's descendant sum. Terms finite under both universes agree for 92-95% of entries with a mean absolute difference of 0.003-0.011; about 0.3% were overestimated by more than 0.5, all of them in the "too specific" direction, which is what the mechanism predicts. The universe is now names(getAncestors(ont)) -- exactly the terms of that ontology in the installed GO.db, root included, and already cached by onto_relation() -- unioned with the annotated terms, so a term the local annotation package still uses keeps its IC even if GO.db has retired it. The same root cause also affects the `gotbl` that the Wang method walks, where a term newer than the table scores 0 instead of NA. That is left for a separate change because fixing it means either regenerating the shipped data or building the relation table at runtime. test-ICMethods.R now asserts that every annotated term gets a finite IC. Package: GOSemSim Commit: 32be2e18cb86a9ef84f796e174a39a1ac7658513 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 12:32:22 +0800 Commit message: cache ontology mappings, and load Rcpp so the compiled IC methods work Two independent defects, found while fixing TCSS. getAncestors(), getParents() and getOffsprings() each rebuilt their whole mapping on every call -- AnnotationDbi::as.list(GOBPANCESTOR) costs about half a second -- while callers only ever pick out one or two terms with `[[ID]]`. A single geneSim() call rebuilt the same mapping hundreds of times. The mappings are derived from a source that is already cached (GO.db is static, load_onto() caches the OntDb), so they are now cached per ontology rather than per term. A 5x5 termSim on previously unseen terms drops from 2.5 s to 0.5 s, geneSim from 5.6 s to 0.6 s cold and 0.12 s warm, with byte-identical results. The cache holds about 85 MB for BP and 110 MB for all nine mappings. Separately, Rcpp was listed in LinkingTo only, so loading GOSemSim never loaded the Rcpp namespace. The wrapper generated by compileAttributes() instantiates Rcpp::RNGScope, which resolves enterRNGScope through R_GetCCallable("Rcpp", ...), so every Resnik, Lin, Jiang and Rel call failed with "function 'enterRNGScope' not provided by package 'Rcpp'" unless the user happened to attach Rcpp first. importFrom(Rcpp, evalCpp) was dropped in ea7b2028 (2016) and is restored here. No test reached the compiled code and the vignette only mentions those methods in prose, which is why this went unnoticed for so long; test-ICMethods.R now covers all four methods on three ontologies. The ontology cache is also covered: test-GO.R checks that each mapping is cached under the ontology and is identical to what GO.db holds. Package: GOSemSim Commit: 50c6bd241416e703074e5e8e2839cf2cafe7133e Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 17:17:24 +0800 Commit message: correct the scope of the TCSS degeneracy fix The previous commit described the degeneracy as "a cluster with a single member", but calc_maxIC() indexes `all <- IC[cluster]; all <- all[is.finite(all)]`, so the real condition is "exactly one member carrying a finite IC". A cluster with several members where all but one have infinite IC is equally degenerate, and the old `length(all) == 0` guard did not cover it. Re-measured with the correct criterion (swapping calc_maxIC in and out of the namespace in one process so both versions see identical input): - the set of clusters whose ICA changes equals the set with exactly one finite-IC member, at every cutoff and ontology tested (BP 1/2/3.5/4/5/8, MF 3.5, CC 3.2) -- so the change is confined to the degenerate clusters; - the defect was not BP-only. 300 random pairs, % scoring exactly 1: BP 99.3% -> 0.0%, MF 27.3% -> 0.0%, CC 98.7% -> 0.0%; - the counts are larger than the single-member count suggested: BP has 1 degenerate cluster at cutoff 3.5 but 5 at cutoff 4 and 1141 at cutoff 5; MF has 3 and CC has 3, and the CC set includes the CC root GO:0005575. Fix the NEWS wording and the code comment to match, and make the regression test assert on the finite-IC criterion rather than on cluster size. Package: GOSemSim Commit: 2df9985c372e931e89994d25fe84f483b50c01fe Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 16:49:30 +0800 Commit message: fix TCSS similarity collapsing to 1 for nearly every term pair A cluster with a single member has no internal spread, so normalising it by its own maximum IC made its ICA identically 1 regardless of how general or how specific that term was. GO:0008150, the root of BP, is such a cluster and is a common ancestor of every BP pair, so `max(sim_value)` in tcssMethod_internal() returned 1 for 99.7% of random BP pairs and `mgeneSim(measure = "TCSS")` was an all-ones matrix. Fall back to the global maximum IC for single-member clusters. The collapse is not specific to the root: scanning cutoffs shows GO:0050896 and GO:0046337 also become single-member clusters for BP, and GO:0052745 does for MF, so special-casing the root would only have papered over one instance. After the change, 300 random BP pairs give min 0.0004 / median 0.0234 / max 0.5296 with 0% equal to 1, and ica[["GO:0008150"]] drops from 1 to 0.000414 (= IC[root] / global max IC). Add a regression test and bump to 2.39.3. Package: GOSemSim Commit: 34c4ae3b85f10b9107ca6feffbd6e6eb0a0206db Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-21 12:17:51 +0800 Commit message: fix TCSS for terms belonging to multiple clusters GO is a DAG, so a term can have several meta-term ancestors and `tcssdata$clusid[[term]]` is then a vector rather than a scalar. Indexing `ica` with `[[` then attempts recursive indexing, which raises "subscript out of bounds" (or "recursive indexing failed at level 2" depending on which element is hit first) and aborts any TCSS calculation for the whole ontology. Subset the list of clusters with `[` instead. This restores the behaviour already present in the Bioconductor release (2.38.3); the devel implementation had regressed. Adds a regression test covering a term that sits in more than one cluster. Package: clusterProfiler Commit: a38e9201b8ee6ad6f64fc1a5bf691421efc9d928 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 04:39:17 +0800 Commit message: enrichMKEGG()/gseMKEGG() accept a GSON, #623 enrichKEGG() and gseKEGG() take either a species code or a GSON object, but the module wrappers only took a species code, so there was no offline route for module enrichment at all -- even though the download errors now tell users to build a local database. Passing a GSON raised an unrelated error from the organism mapper instead. Both now mirror the KEGG wrappers, including the "organism should be a species name or a GSON object" message. A GSON reports its own keytype, so @keytype is taken from it; the species path keeps returning "UNKNOWN" exactly as before. Also documents the GSON option on the KEGG `organism` parameter, which had never been mentioned for enrichKEGG()/gseKEGG() either. Package: clusterProfiler Commit: 285885443b912177daec101c606664b33b41cc37 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 04:21:19 +0800 Commit message: enrichGO(): restrict the annotation by evidence code, #160 Enrichment used every annotation in the OrgDb, including electronically inferred ones, so there was no way to avoid circular reasoning when the gene sets themselves came from in-silico evidence (dropping IEP for co-expression clusters) or to keep only curated annotations (dropping IEA). enrichGO() now takes `evidence`, appended last so positional callers are unaffected and threaded through both recursive paths. The filtered annotation is built by go_annotation_by_evidence() from a gene-centred select() of GOALL/EVIDENCEALL/ONTOLOGYALL, because the evidence code is a property of the gene-annotation pair and the previous term-centred mapIds() could not see it. Two semantics worth stating, both documented: the background changes with the annotation, so a filtered result is not a subset of the unfiltered one; and a filtered annotation is never cached, since the cache key is (organism, ont, keytype) only and reusing it either way would answer with the wrong annotation. A regression test pins the cache isolation down. Package: clusterProfiler Commit: fa71a3ef739a1ef44e695e69823126c94c703bdb Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 02:33:01 +0800 Commit message: fix: enrichGO() survives an unidentifiable OrgDb organism, #232 The cached-GO-data check compared the cached organism against get_organism(OrgDb) inside a bare if(). get_organism() returns NA for an OrgDb it cannot identify -- an AnnotationHub OrgDb, for instance -- and `if (NA && ...)` aborts the call with "missing value where TRUE/FALSE needed", which names nothing about organisms or caches. It bites on the second enrichGO() call in a session, because the first one populates the cache. The check is now go_cache_usable(), where every comparison goes through isTRUE() so an unidentifiable organism means "not cached" and the annotation is rebuilt. Extracting it also makes the cache-hit logic unit-testable without an OrgDb. Package: clusterProfiler Commit: a39c2f63d533e20d6c4d03fd3a35b18a418dd08e Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 02:14:56 +0800 Commit message: fix: Gff2GeneTable() reads Ensembl-style GFF3, #193 The function only looked for an NCBI/RefSeq `GeneID=` attribute. On an Ensembl GFF3 (which writes `gene_id=`) every extracted key was NA, and merging two all-NA key columns is a cartesian product: on the reporter's cat genome that is ~1.3M x 40k rows, which R refuses with "negative length vectors are not allowed". At small sizes the same bug passes silently, because unique() collapses the duplicated NA rows into a plausible-looking table of NA ids. Field names are now detected from the file: `GeneID` or `gene_id` for the identifier, and `gene`, `Name` or `gene_name` for the symbol. Detection requires an exact attribute key, because getGffAttribution()'s heuristic fallback also looks inside values and would otherwise return the identifier out of `ID=gene:ENSG...` when asked for `gene`. A file with neither identifier style stops with a message saying what is expected instead of merging on all-NA keys. Package: clusterProfiler Commit: 41dd01bb5c7a078bd19397131f06fd3db2d59bfc Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-23 01:38:26 +0800 Commit message: add_go_level(): expose the GO level of each enriched term, #793 GO enrichment results carried the term, its ontology and its statistics, but not how deep the term sits in the hierarchy, so users who wanted to keep a band of levels had to reconstruct GO depth themselves. go_level_map() now returns the GO id -> level map (1 = ontology root) built by breadth-first traversal of the GO.db CHILDREN graph; getGOLevel() is rewritten on top of it with identical output (verified against a pre-change baseline for BP/CC/MF at levels 1-6), and add_go_level() appends a `level` column to an enrichResult/gseaResult/compareClusterResult. The level is taken from the ontology each term belongs to, so ont = "ALL" results are labelled term by term. gofilter() and dropGO() had no test coverage; the new test file locks their keep/drop-by-level behaviour down. Package: clusterProfiler Commit: c117200bb63575df335911dcd478aa164dda528d Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 23:52:42 +0800 Commit message: simplify() infers the GO ontology for enricher() results too, #369 The enrichResult method required x@ontology to be BP/MF/CC/GOALL, so an enricher() run over a GO collection (MSigDB C5 GO, a custom TERM2GENE built from GO annotations) had to have the slot assigned by hand before simplify() would accept it. The ontology is now inferred from the GO IDs exactly as for gseaResult (#753), and non-GO gene sets are still refused with a message saying so. Package: clusterProfiler Commit: e930b50044bf8bb4fb883ea940a631aceb57ff18 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 23:21:11 +0800 Commit message: simplify() a GSEA result whose gene sets are GO terms, #753 simplify() reduces redundancy with GO semantic similarity, so it needs the ontology of the terms. It only accepted x@setType in BP/MF/CC/GOALL, which rejected a GSEA run over a GO gene-set collection (MSigDB C5, a gson GO file, a TERM2GENE built from GO annotations) because @setType then holds the collection name. The ontology is now inferred from the GO IDs, with results spanning several ontologies simplified as GOALL; non-GO gene sets are still refused, with a message that says so. Package: clusterProfiler Commit: dc94b240c1a42333f111338f46fb3633df2271be Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 22:46:23 +0800 Commit message: warn when compareCluster() is given a non-character universe, #654 compareCluster() wraps each per-cluster call in suppressMessages(), which swallowed the underlying enrichment function's "`universe` is not in character and will be ignored" message. A numeric universe therefore looked accepted while silently having no effect. The guard is now raised once in compareCluster() itself, where it cannot be suppressed, with a regression test for both the non-character (warns) and character (stays quiet) cases. Package: clusterProfiler Commit: 61236b6fa01a7d6474152ed7043639596dae48d1 Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 21:17:10 +0800 Commit message: gsePC() and gseWP() expose an eps argument Both wrappers now declare eps = 1e-10 and forward it through GSEA() to enrichit::gsea_gson(), matching GSEA(), gseGO(), gseKEGG() and gseMKEGG(), which already exposed it. Package: clusterProfiler Commit: 58559c7a5a9babe970d3a3dad5e9708efc42f70c Author: Guangchuang Yu <guangchuangyu@gmail.com> Date: 2026-09-22 18:54:09 +0800 Commit message: fix enrichKEGG(organism='cpd') and report KEGG download failures clearly, #828 - gson_cpd(): use the 'compound' KEGG REST endpoint. KEGG retired /link/cpd/pathway, which now answers HTTP 400, so enrichKEGG(organism='cpd') and gseKEGG(organism='cpd') failed with an obscure download error. - kegg_rest(): report the failure where it happens, telling an unreachable network apart from an HTTP error status and from an empty response. These used to surface much later as an opaque error. - download.KEGG.Path() / download.KEGG.Module(): replace the is.null() guard, which could never fire because kegg_rest() never returns NULL, and stop with an actionable message when the downloaded annotation is empty or when the gene/pathway table shares no ID with the pathway-name table. Previously an empty annotation was returned silently and surfaced downstream as a misleading "No gene can be mapped", #146, #378, #561, #646. Package: SAIGEgds Commit: 29da3dd06bce9321bc520c75353e1c695057e0df Author: Xiuwen Zheng <zhengxwen@gmail.com> Date: 2026-09-23 19:12:31 -0500 Commit message: update vignettes Package: MSstatsBioNet Commit: 409e9d4503aa239c3c619270333853289d37d080 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-23 16:57:12 -0400 Commit message: feat(filterSubnetworkByContext): adjust filterSubnetworkByContext to exclude key words (#111) Package: scRNAseqApp Commit: e8a48756927b63b7b69b59294f8c81232e689203 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:44:42 -0400 Commit message: fix the wrong number when calculate phyper. Package: scRNAseqApp Commit: 758edbb8626a1d38afe3c8d58678b43f325195e0 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:40:08 -0400 Commit message: fix a issue for if no hyper pval available. Package: scRNAseqApp Commit: 78ef7925d099f040cfa9b1638934fb49d4adfc91 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 14:29:19 -0400 Commit message: using promise process to update the gene table. Package: scRNAseqApp Commit: b4e729e4d87012189f26cfd746a09ebc9a04d6db Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 10:24:03 -0400 Commit message: import phyper from stats. Package: scRNAseqApp Commit: 4d94c7a0270315c3aea67c41287313c86ffb5655 Author: Jianhong Ou <jianhong.ou@gmail.com> Date: 2026-09-23 10:15:42 -0400 Commit message: add phyper pval for co-expression. Package: dmGsea Commit: 3b9c68c53791e27f0abc9e95a8f4e0c050b7d75a Author: xuz1 <xuz@niehs.nih.gov> Date: 2026-09-23 13:54:34 -0400 Commit message: bugfix Signed-off-by: xuz1 <xuz@niehs.nih.gov> Package: decemedip Commit: 3de0b135bed2595498482c4d13078d0bd65c313e Author: nshen7 <shenning1997@gmail.com> Date: 2026-09-22 20:54:10 -0700 Commit message: Fix Stan old array syntax for stanc3 (BioC 3.23 build failure) Package: quantMSImageR Commit: 9aaed9e03b28ef01d3b1c05dc834288f2d00753c Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:46 +0200 Commit message: Version 0.99.8 Pieces of one tissue, regions of interest, and the report arranged by level. matrixStats leaves Imports: it was declared but called nowhere, so every user installed a package the code never used. Package: quantMSImageR Commit: 25eacbf10d0f5075ad89ee2884a76103bdb23a65 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:34 +0200 Commit message: Document the regions work The vignette says what regions are for -- a transition that marks a tissue type, or a toxicity study where the regions are drawn high and low in the toxicant and the endogenous species compared between them, within one animal rather than across a group. It also describes the by-level report, and how to see a palette before choosing it. AGENTS.md is gitignored: agent scratch notes, not part of the package. Package: quantMSImageR Commit: d37c8c4b93a96e7f51343144cda5a5c17dcc519b Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:34 +0200 Commit message: Arrange the report by level, and correlate at one level only Sections 2, 3 and 4 are each drawn by sample and then by region, so the two are read the same way rather than the regions living in a tab of their own. The region masks take a section before the ion images, which move down a number. "auto" judges the heatmap encoding per view, on the rows that view actually has. A study without regions is unchanged, headings included: a level heading only appears when there is a second level to tell it from. Correlation names one level -- 'sample', 'roi', False or auto -- and only ever computes that one. It is the slowest section in the report, and a region holds a fraction of a sample's pixels, so auto correlates within the regions when a study has them and is off otherwise. True still means 'sample'. roi: unit is per sample or per region, not both: a comparison has a single unit, and two views of the same numbers invite reading whichever looks better. compare: keeps "both", where the two arrangements are different contrasts rather than the same one twice. Each box-plot panel carries its own key, and colours: region sets the region palette (any package palette, or a grDevices qualitative one), kept distinct from the groups'. Package: quantMSImageR Commit: bfa6a46540be7a5e08f37ded27d10a504d244d59 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 19:36:19 +0200 Commit message: Score each region against itself in contributionHm() too The region heatmap could only be drawn per feature, because contributionHm() had no notion of a block. That made "auto" pick the wrong panel wherever a study has few samples and many regions: one animal per group takes the per-sample encoding by sample, but by region its rows are sample x region, so a group can have six or seven of them -- exactly the case the contribution encoding exists for. It now takes sample_block, and inside a block both the z-score and the group mean are computed against that block alone. The hue is therefore "how this group's airways sit among all the airways", not "airways differ from parenchyma", which is what a panel scored across regions would mostly report. A feature flat within a block cannot be scored there and is drawn in na_col, even where it varies across the section. Package: quantMSImageR Commit: b18abc94cf8fc51323b0836eccf9b684dd9758b9 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:50:33 +0200 Commit message: Fix the region tests and the vignette's feature lookup The row-split assertions read @row_order_list, which a Heatmap only fills in when it is drawn -- it is empty on the object, so the expectations compared against nothing. The split a heatmap will use is in @matrix_param$row_split, which is what they now check: the block test asserts a, a, b, b against groups that deliberately alternate, so passing it means the rows really were split by region rather than by group. The vignette indexed a feature by name, but spectra() returns a matrix with no dimnames, so it takes the row number instead. Package: quantMSImageR Commit: 0ff2ab13a672a37c90034e11545dc2e36e994da3 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:39:14 +0200 Commit message: Document pieces and regions; regenerate the example sections The vignette gains a section on pieces of one tissue, one on labelling regions, and a worked example on the bundled sections: the label table, the region maps and a box plot with one point per section per region rather than per pixel. The YAML section documents the samples forms, including pieces, and what each roi: option can be set to. The example sections are regenerated with the regions the vignette and runExample() now show. Seeds are unchanged and the region code draws no random numbers, so the intensities are identical. AGENTS.md is build-ignored, and the micro sign in stitchAcquisitions() is written as a \u00b5 escape: R CMD check requires ASCII source. Package: quantMSImageR Commit: a623d0241889b76e05f8b5d49aa2f121348d953b Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:54 +0200 Commit message: Carry regions through a study and into the report A study picks regions up on its own: generateTxtImages() attaches roi_label and roi_id from each acquisition's roi_labels.csv, matched on (x, y) like the tissue mask, and they survive panel binding and stitching. Regions numbered within a piece are renumbered across the stitched sample, so two airway_01s become two airways. The YAML gains a roi: block -- enabled (auto), include_unassigned, compare, unit, heatmap -- and pieces: for a tissue acquired in several passes, each piece normalised and SNR-filtered against its own background before being joined. The report gains a regions tab: maps, box plots by compare and unit, an ROI_summary sheet, and a heatmap with one row per sample and region. That heatmap z-scores each region against itself (quantileHm's new sample_block), since scoring across regions would mostly report that airways and parenchyma differ, which is not the question being asked. The map is repeated above the ion images, where it says which blob is which. quantileHm() also no longer loses its sample names when a study holds a feature with no variance: the unscoreable column returned an unnamed vector, and apply() drops the names for the whole matrix when one result's differ. output: colocalisation: gains auto, off whenever a sample merges several acquisitions -- most pixel pairs would then cross acquisitions. Package: quantMSImageR Commit: 9311401b6304a67f07b4b1fa3cf4bbcde84b66b7 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:39 +0200 Commit message: Add labelROIs() for regions within the tissue Run after selectTissuePixels(): it shows the ion image of a chosen transition across tissue pixels only, then loops draw -> name -> "add another". Several regions can share a label, since a section holds many airways, and each is numbered as it is drawn (airway_01, airway_02, ...) so it keeps its own identity while the label is what a study compares. Regions are saved per acquisition as roi_labels.csv beside the tissue mask, which is never touched, and copy_to writes the same file to the other panels over the same area. Re-running adds to them; overwrite = TRUE keeps the old file as a dated backup. The feature picker is shared with selectTissuePixels() rather than copied, and the bundled example sections gain two "a" and two "b" regions each so the downstream half can be shown without a drawing device. The regions differ because of where they sit on the existing intensity gradient; no value was adjusted to make them. Also splits the given names in Authors@R, so the citation reads "Smith MJ" rather than "Smith M". Package: quantMSImageR Commit: 52f47f09842bf4eecb4e8e7d214c84ec7d87a532 Author: Matthew Smith <matthew.smith@ki.se> Date: 2026-09-23 11:38:27 +0200 Commit message: Place pieces of one tissue by stage position A tissue too large for one acquisition is imaged in pieces, and those pieces are one sample: kept apart they count twice in every group summary, and because they agree with each other they look like a reproducible effect. readMRM() numbered each acquisition's pixels from its own first pixel and threw the stage coordinates away, so every piece started at (1, 1) and stitchAcquisitions() could only report that they overlapped. Its documentation claimed Waters coordinates were absolute, which stopped being true the moment readMRM() re-based them. readMRM() now keeps x_stage and y_stage (mm) alongside the grid indices, and stitchAcquisitions() places each piece where the stage recorded it: above, below or beside, in any order, gaps left empty. Pieces must share a pixel size; each is moved to the nearest position on a common grid and the largest shift is reported. Overlap is still an error rather than an average. Objects without stage positions keep their own coordinates and say how to get them. combineMSIs() fills a pData column that only some objects carry with NA, since stage positions and region labels are legitimately absent from some samples. Package: rhdf5 Commit: c72d938a7bd397d148e623a7c0f12e6b3865de1b Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 16:41:00 +0200 Commit message: Bump version Package: rhdf5 Commit: fe55afb12dd1583d7f6f58e236e3d85872da3e1f Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:40:28 +0200 Commit message: Document .matrix() methods removal Package: rhdf5 Commit: f1ad6e28ba024bdcfeede3cb1b3b89f92bb081e5 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:38:30 +0200 Commit message: Remove .matrix() methods and let them auto dispatch to array method Package: rhdf5 Commit: dc8ef2bbced3bfc17f95b284fb0b2981d20427f4 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:22:12 +0200 Commit message: Document on.exit change in NEWS Package: rhdf5 Commit: 2b34f2d0097aaf547999b5be0deeef35031694e8 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:20:32 +0200 Commit message: Use on.exit() more consistently to close Package: rhdf5 Commit: bbfebbf34a184471451df03fab4dfa74a29f1dd9 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:08:44 +0200 Commit message: Mention dead code removal in NEWS Package: rhdf5 Commit: aa7669dbe22003b61182dc3cd266b948ae055ad0 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 15:07:58 +0200 Commit message: Remove dead code in h5writeAttribute.array() Package: rhdf5 Commit: d1f0dc156114f8494ced58811c01fe1f092b1648 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:57:43 +0200 Commit message: Fix incorrect copy/pasted error messages Package: rhdf5 Commit: 81d91768bd5bc3a86b9c720a1a3c1681ad0851ae Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:43:10 +0200 Commit message: Remove extra call to H5loadConstants() Package: rhdf5 Commit: e28ea4ec812cfd7c63e15101b401a3aa12fac5f1 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:23:01 +0200 Commit message: Ensure .Call() always includes PACKAGE Package: rhdf5 Commit: 4f18f262fed53b25edbbd5db47138059a6a7a6cb Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:16:45 +0200 Commit message: Mention h5set_extent() fixes in NEWS Package: rhdf5 Commit: 98c8a7581553b43f8aa62575958b0a595394bb84 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 14:16:16 +0200 Commit message: Fix h5set_extent issue with dataset handle Package: GSVA Commit: 545a96a07fba745d24b021cde157b570597a7109 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 16:34:55 +0200 Commit message: Remove dependence on BiocSingular Package: aracne.networks Commit: d000659130672ee12ffa5a287616ffe16c334eb2 Author: federicogiorgi <federico.giorgi@gmail.com> Date: 2026-09-23 15:51:57 +0200 Commit message: Point to the Zenodo record 22918956 Fill in the Zenodo record (doi:10.5281/zenodo.22918956) hosting the networks and document the CC BY-NC-ND 4.0 license of the data files. Package: aracne.networks Commit: d768d15947c70f95dc353c4e3a21da480ffccdc3 Author: federicogiorgi <federico.giorgi@gmail.com> Date: 2026-09-23 14:47:27 +0200 Commit message: Move the networks to Zenodo The regulon data sets are no longer bundled in the package: they are hosted on Zenodo and retrieved with the new getRegulon() function, which caches them locally with BiocFileCache and verifies their MD5 checksums. listRegulons() lists the available networks. This brings the package size well below the 100 MB limit of the new build system. - documentation of the 25 networks merged into ?regulons - vignette converted to R Markdown - added unit tests - Authors@R replaces Author/Maintainer Package: GSVA Commit: 87cd4d7cdcae92c251c9b53c7f759c38b4ab1ed4 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 15:31:13 +0200 Commit message: Bump version Package: GSVA Commit: 9c1eb50150a6aaee271512838ad8739b3bb130fe Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 15:22:44 +0200 Commit message: Merge pull request #276 from rcastelo/275-average-method Average method for enrichment scores calculation Package: GSVA Commit: 9e68f27aaa3d02a7d4c28792365b50d35dc1b5aa Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 14:50:43 +0200 Commit message: Replace checkIdentical() for checkEqualsNumeric() to allow C unit tests pass across different platforms Package: GSVA Commit: 5f21614dc2ee103338d887a39e119f4fbbbf90d9 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-23 12:29:14 +0200 Commit message: Added C implementation of the average method, and its corresponding unit tests. For performance issues, genes within genesets are internally ordered after mapped to features, this required regenerating regression test for PLAGE since SVD flipped sign in values due to the different input order Package: GSVA Commit: 87cfe5db164c95b66710094c215285fbf17995a6 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:46:28 +0200 Commit message: Merge branch 'devel' into 275-average-method Package: GSVA Commit: cc12f1d01a63d0123a48e3fb3d576c61a5f6a14d Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 14:42:36 +0200 Commit message: Fixed namespace issues and unit tests Package: GSVA Commit: 6881306e155fe38933ff8cf6d3ec9be94b9b382d Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 12:16:49 +0200 Commit message: Add unit tests for CLR and average method Package: GSVA Commit: 730ce29c9eb3a6d8b94c1c327d96451241681fd5 Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-21 17:07:11 +0200 Commit message: Added first version of the average method for calculating enrichment scores Package: fenr Commit: 78a5a1207281ef37881d399f562be49f4a4af6d2 Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 13:02:11 +0100 Commit message: Merge branch 'main' of https://github.com/bartongroup/fenr Package: fenr Commit: 83a93c2fe6a5bb8748799c1f369153a651713bea Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 13:00:33 +0100 Commit message: Reverting some changes Package: fenr Commit: 0274549e7ba96519bf153ae6736593f62e5f666a Author: Marek Gierlinski <mgierlinski@dundee.ac.uk> Date: 2026-09-23 12:01:32 +0100 Commit message: Version 1.11.3 Package: vsn Commit: cdb80675e45236c2f57a2b41d4f98f4f2d6814b2 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:27:07 +0200 Commit message: Bump version Package: vsn Commit: b5d9c153c5300b3209bd0bcef2285b4386731398 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:26:58 +0200 Commit message: Mention README and pkgdown site in NEWS Package: vsn Commit: fb67d77e139bbf2d24f020fcc99a770650124cb1 Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:25:59 +0200 Commit message: Set up pkgdown Package: vsn Commit: 4e31e610b6c6afccfe348d107f05e277101f01be Author: Hugo Gruson <git@hugogruson.fr> Date: 2026-09-23 13:25:04 +0200 Commit message: Add minimal README with deNBI survey Package: sesame Commit: 2acabdce8fbdd4fb9675db1fd76d60d05792be04 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 22:06:41 -0400 Commit message: 1.31.5: fix readControls column naming; qualityMask takes a custom mask readControls() built the control data.frame positionally: colnames(ctl) <- c('G','R','col','type') over a frame whose signal matrix has four columns, so Color_Channel and Type were cbind-ed past the end of that name vector and arrived unnamed, while `type` silently took a signal column. Downstream, controls(sdf)$Type was a vector of integers, so negControls()'s grep("negative", ...) matched nothing and detectionPnegEcdf() failed in ecdf() with "'x' must have 1 or more non-missing values" on EPIC and HM450 -- the platforms whose controls arrive through readControls() rather than as SigDF rows. The columns are now named explicitly. This was found from the C side, where it had been mistaken for an annotation divergence for two days. With it fixed, detectionPnegEcdf agrees between the two implementations at max|diff| = 0.00e+00 on EPICv2, MSA, EPIC and HM450. qualityMask() gains `platform` and `mask`, so a custom or combined-array mask can be passed in directly instead of being bolted on with addMask() after the fact -- the case that comes up for arrays built from two manifests. README: the two implementations are named and versioned. The R package is SeSAMe v1 and stays on the 1.x series; the C command line is SeSAMe2 on 2.x. They are parallel, not sequential. The conda line also said `sesame-cli`, which has not been the package name since 0.4. R CMD check: Status OK, vignettes built and re-run. Package: mia Commit: 859de8cd0be1bdd40982b6cd189141c84cb359cd Author: Giulio Benedetti <giuliobene2000@gmail.com> Date: 2026-09-23 14:27:37 +0800 Commit message: Clarify study subjects in ADHD microbiota profiles (#828) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: mia Commit: 751d24e22c26aaccc6ec7be1ece37540fc2eab37 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-23 08:57:53 +0300 Commit message: Add Rdpack references (#797) Signed-off-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: mia Commit: 3c4fd9e80ecf788464a2726cf15e64cbd0aeede2 Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Date: 2026-09-22 11:27:29 +0300 Commit message: Convert MAE to TreeSE and back (#810) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Package: OMA Commit: 1ff85f15276db0d08c8305d788808bc3d713d066 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-23 13:07:47 +0300 Commit message: Simplify importing Package: OMA Commit: f19c0abb3874a6386f4693912c59f010dc5ec331 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-22 15:05:08 +0300 Commit message: Fix rendering Package: OMA Commit: 1d6f339fb23ebbdd1a58d089605f547fb76413d1 Author: Tuomas Borman <tvborm@utu.fi> Date: 2026-09-22 14:31:13 +0300 Commit message: Fix rendering, update support forum address Package: OMA Commit: 3f130bdb5a124835ec56391806571a9a6954963e Author: jagadeesh <2400040120@kluniversity.in> Date: 2026-09-18 16:37:10 +0530 Commit message: docs: Add comprehensive Rarefaction section to transformation chapter (#825) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Co-authored-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <tvborm@utu.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 1a65548fafa7a1d699b74cabccff2cb6b8b74f3f Author: Rasmus Hindström <56149499+raivo-otus@users.noreply.github.com> Date: 2026-09-18 09:20:36 +0300 Commit message: docs/clarity improvement to mia::summarizeDominance (#852) Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Co-authored-by: TuomasBorman <TuomasBorman@users.noreply.github.com> Package: OMA Commit: bcf4b79324d7db13573f7d75f1921324f098bf37 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:11:59 +0000 Commit message: feat(ci): add whitespace stripping to style workflow (#864) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: be708a734fe6980f7fdb08cd7d29c0bf68d85d47 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:06:30 +0000 Commit message: fix(community_similarity): use official vegan docs (#872) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: d51543f698e697431a375bb5ee52ea224490b2a1 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 06:03:41 +0000 Commit message: feat(ci): add dependabot (#865) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 79c94b838aca89ac79e9544310302b5528c9a0b8 Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> Date: 2026-09-18 05:57:47 +0000 Commit message: bump(deps): actions/cache@v4 to v6 (#874) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 4e1978be84a4efc4813759e6f1a2d6aa262ba265 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-18 08:52:51 +0300 Commit message: Use scaled fitted values for DMM drivers (#881) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 7bd2fc8e6da903e0640182842001f3fd42f5a210 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-17 15:48:42 +0300 Commit message: Clarify exercise instructions across the book (#886) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Package: OMA Commit: 7ad1b506261f780a42bc9ffa0655f10f91047bb3 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-09-17 15:33:57 +0300 Commit message: Add tree visualization reference (#889) Package: OMA Commit: 0e655914be48d7af2242a012deeb8354ec31f033 Author: Muluh <127390183+0xMuluh@users.noreply.github.com> Date: 2026-08-08 19:29:22 +0300 Commit message: Suppress cheatsheet startup messages (#878) Package: beachmat Commit: 7fe7dc234ea2fe69bf8f4c711525428539033652 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 15:32:49 +1000 Commit message: Switch to DelayedNoOp to support all alabaster.matrix no-op subclasses. This saves us having to list all of the individual subclasses. Package: alabaster.matrix Commit: ff91f9ff04b310f74232613787d6abe1411769aa Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 14:54:50 +1000 Commit message: Introduce a no-op base class to catch all of our weird seeds. In particular, packages like beachmat don't have to add a specialization for each of the no-ops subclasses, they can just check for the DelayedNoOp class. Package: alabaster.matrix Commit: 998568738d4d76e3073b732c24eaf2a9d79f650a Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 14:26:07 +1000 Commit message: Implement ToBeRealizedArray class for fine control of delayed operations. Package: SparseArray Commit: fab50cb7a6f6b1c5735dd1f19b05b94e04503dcf Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:57:43 -0700 Commit message: some edits to SparseArray-abind.Rd Package: DelayedArray Commit: ef3f02a7227a0e6a07736601081925f2fccb43a9 Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:26:39 -0700 Commit message: requires S4Arrays >= 1.13.1 Package: DelayedArray Commit: 28a0ba92ed413f575dd5839324e9892eb8f840c2 Author: Hervé Pagès <hpages.on.github@gmail.com> Date: 2026-09-22 19:02:40 -0700 Commit message: DelayedArray 0.39.7: Add abind() method for DelayedArray objects Also: - Remove the rbind(), cbind() and bindROWS() methods defined for DelayedArray objects. These methods are now replaced by more generic methods defined in the S4Arrays package for Array objects that are all based on abind(). - Add coercion from array/matrix to DelayedArray/DelayedMatrix. This coercion is equivalent to calling the constructor function DelayedArray() on the object to coerce. Having this coercion work has the effect of making rbind() and cbind() work on a mix of DelayedMatrix objects and ordinary matrices. This partially addresses issue #100. Package: scDiagnostics Commit: bee3ff588074c8e26c3b15b12610f23b7c19acdc Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 21:24:22 -0400 Commit message: Silence scran deprecation warnings and tolerate missing Suggests, bump to 1.7.15 Two failures on the first run against Bioconductor 3.24 / R 4.6: R CMD check reported significant warnings in the examples on all three platforms. scran 1.41 deprecates its HVG helpers in favour of scrapper, so every modelGeneVar()/getTopHVGs() call - including the fitTrendVar() that modelGeneVar() calls internally - now signals a deprecatedWarning, and rcmdcheck runs with error_on = "warning". Add an internal muffleDeprecation() that muffles only the deprecatedWarning class, leaving genuine warnings alone, and wrap the six calls in processPCA(), detectAnomaly() and calculateReconstructionError() with it. The three examples that call scran::getTopHVGs() directly wrap it in suppressWarnings() instead, with a comment saying why. This is a stopgap: the HVG selection needs to move to scrapper before scran makes these functions defunct. The macOS job additionally failed with "Packages suggested but not available: 'scRNAseq', 'celldex'". Neither is used by anything that runs during the check - they appear in documentation prose and inst/script - and both currently fail their own Bioconductor 3.24 builds, so set _R_CHECK_FORCE_SUGGESTS_=false rather than fail this package's check over them. Package: scDiagnostics Commit: 964640ff9a5c7728f24141ce53575c0840966fd8 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 20:38:25 -0400 Commit message: Target Bioconductor devel 3.24 / R 4.6 in CI, bump to 1.7.14 The matrix was pinned to Bioconductor 3.22 / R 4.5, two release cycles behind: 3.23 is the current release and 3.24 is devel, which is what the Bioconductor build system checks this branch against. Point all three jobs at 3.24 / R 4.6 (the pairing BiocManager's version map requires), swap the Linux container for bioconductor/bioconductor_docker:devel, and move the RSPM mirror from jammy to noble to match that image's Ubuntu 24.04 base. Also refresh the cache keys and the check-results artifact name, which still referenced RELEASE_3_22/3_19; the new keys additionally force a cold cache so no 3.22-era binaries are restored. Package: knowYourCG Commit: 9a7cce4c69f010992c7694da610eab786d07b443 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 18:58:22 -0400 Commit message: Point users at KnowYourCG v2, and fix three dead links This package is KnowYourCG v1 and stays on the 1.x series. The C implementation is KnowYourCG v2, binary `kycg`, and nothing here said so. Framed as succession, not as a wind-down, and that distinction is the point. An earlier draft of this put "This package is in maintenance; active development continues in kycg" into DESCRIPTION -- the field that renders on the Bioconductor landing page. This package sits on an open Core Team deprecation watch (#4, "Bioconductor failure and risk of deprecation"), so publishing that it is in maintenance would have handed them the justification. A neutral pointer says the same true thing without inviting it: the project is not declining, it is on its second implementation. Three places, because they reach different readers. DESCRIPTION is the only one an installing user sees, rendered on the landing page. The README is for GitHub visitors. Sequencing.Rmd names v2 where a reader is most likely to want it -- that vignette's workflow is what v2 does natively over YAME stores. The URL is in angle brackets, the same convention the DOI in that sentence already uses; a bare URL is what R CMD check objects to. Each says plainly that the two are parallel implementations rather than an upgrade path: one is an R package, the other a command-line tool, and there is no upgrading from one to the other. Separately, three dead links. `R CMD check --as-cran` runs a URL liveness check that a plain check skips entirely, and it found Sequencing.Rmd linking to https://zhou-lab.github.io/YAME/docs/summarize.html (twice) and .../docs/pack_unpack.html -- both 404. YAME's documentation is a single page now and those paths no longer exist, so all three point at https://zhou-lab.github.io/YAME/ instead. Package: scDiagnostics Commit: 89c6ed709d444d28439a7c791cb151b11faca8fb Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 19:54:35 -0400 Commit message: Make BiocCheck's deprecation check resilient to bioconductor.org outages, bump to 1.7.13 BiocCheck's first check downloads checkResults//bioc-LATEST/ meat-index.dcf for both the release and devel branches, and a failed download is a hard error ("HTTP 504 Gateway Timeout" -> bfcadd() failed -> "not all 'rnames' found or unique"), which took down the Linux and macOS jobs even though the package itself was fine. Pre-populate BiocCheck's own BiocFileCache with up to three attempts before running BiocCheck, and only if bioconductor.org is still unreachable pass `no-check-deprecated` so that one check is skipped instead of failing the whole build. </pre> </div> Package: scDiagnostics Commit: 816fa92698fa534abefc3cc0f75df2319b8f11f6 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 17:32:41 -0400 Commit message: Disable public RSPM on macOS/Windows to fix root cause, bump to 1.7.12 The libomp install in the previous commit didn't fix stringdist's identical dlopen failure - same byte-for-byte error, meaning the install had no effect. Searched prior reports of this exact failure (tidymodels/tune#1199, Genentech/rdborrow#73/#74): the real cause is that r-lib/actions/setup-r configures Posit Package Manager (P3M) as the default macOS repo, and P3M's macOS arm64 binaries are compiled with OpenMP enabled. This runner can't resolve those OpenMP symbols at runtime (SIP strips DYLD_* for protected binaries, so even a correctly installed libomp isn't reliably picked up) - CRAN's own macOS binaries are built without OpenMP and never hit this. Set use-public-rspm: false on the "Setup R from r-lib" step so macOS (and Windows, already passing, no expected impact) resolve packages from CRAN directly instead of P3M, which should fix this for any OpenMP-linked package in the dependency tree - not just the three (RhpcBLASctl, isotree, stringdist) hit so far - rather than continuing to patch them one at a time. Left the earlier source-install and libomp workarounds in place; they're harmless if this makes them redundant, and there's no upside to stripping proven/plausible fixes before confirming this one actually resolves it on CI. Package: scDiagnostics Commit: 3aba0f79435c543deb4c129e486f16e5e92c6ba4 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 16:59:49 -0400 Commit message: Install CRAN's official libomp on macOS CI, bump to 1.7.11 The last two fixes patched RhpcBLASctl and isotree individually, but BiocCheck::BiocCheck() now hits the identical failure via one of its own dependencies (stringdist): unable to load shared object '.../stringdist.so': dlopen(...): symbol not found in flat namespace '___kmpc_barrier' Patching each OpenMP-linked CRAN package one at a time as it's reached doesn't scale - the actual root cause is that this GitHub Actions macOS runner is simply missing the libomp build that CRAN's macOS binaries are compiled against (documented at https://mac.r-project.org/openmp/; Homebrew's libomp installs to a different path and doesn't fix this). Installing it there via the official recipe should let CRAN's normal (faster) binaries load correctly for any OpenMP-using package, not just the two already patched. Left the RhpcBLASctl/isotree source-install workarounds in place since they're already confirmed working - no reason to touch proven fixes while chasing this. Package: scDiagnostics Commit: 58cf3022aee073ef86bf0e5695fe41dd4a701ec9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:24:46 -0400 Commit message: Also force isotree from source on macOS CI, bump to 1.7.10 RhpcBLASctl fixed the first macOS OpenMP dlopen failure, but the same issue exists one layer up: isotree's own CRAN macOS binary (isotree.so) fails to dlopen with "symbol not found in flat namespace '___kmpc_barrier'" - a Clang/LLVM OpenMP runtime symbol, same root cause (CRAN's macOS binary built with OpenMP support that isn't resolvable on this runner), just a different dependency in the chain. Applied the identical source-install workaround to isotree. Package: scDiagnostics Commit: 7809c44d4bc5e698aeb4d67f24e79535cfe513c9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:00:00 -0400 Commit message: Force RhpcBLASctl from source on macOS CI, bump to 1.7.9 Ubuntu and Windows now pass under the Bioc 3.22/R 4.5 bump (previous two commits), confirming those fixes. macOS still fails, but differently and on all 4 vignettes uniformly this time: Error: .onLoad failed in loadNamespace() for 'RhpcBLASctl' dlopen(.../RhpcBLASctl.so, ...): symbol not found in flat namespace '_omp_get_max_threads' RhpcBLASctl is a hard Import of isotree (detectAnomaly() calls isotree::isolation.forest()), so its namespace loads unconditionally. CRAN's macOS binary for RhpcBLASctl references an OpenMP runtime symbol that isn't resolvable on this GitHub Actions macOS runner - a known class of issue for R packages built with OpenMP support on macOS. Building from source instead compiles without OpenMP (Apple clang has no -fopenmp by default), so the resulting library never references that symbol. Added alongside the existing Matrix/irlba source-install workaround in the same step, which addresses the same kind of macOS binary incompatibility. Package: scDiagnostics Commit: 3386bcb54d27441922472dd08b49d1b1d786bb37 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 12:06:16 -0400 Commit message: Anchor SingleCellExperiment/SpatialExperiment Rd links, bump to 1.7.8 R CMD check now fails with error_on = "warning" on the Bioc 3.22/R 4.5 CI (bumped in the previous commit): "checking Rd cross-references" reports a genuine broken link (merfish_reference_data.Rd's \linkS4class{SpatialExperiment} doesn't resolve) plus 36 files whose \linkS4class{SingleCellExperiment}/{SpatialExperiment} links are missing package anchors - both promote the check from NOTE to WARNING under the newer toolchain. \linkS4class{} was reintroduced repo-wide by a September 17 commit ("docs: use \linkS4class{} for SingleCellExperiment roxygen links", for brevity) after an earlier commit had already fixed this exact issue with explicit \link[pkg:target]{text} anchors. Restoring that anchored form and re-running roxygen2 to regenerate man/ resolves it; verified with a full local R CMD check matching the CI invocation (0 errors, 0 warnings, 1 unrelated pre-existing note). Package: scDiagnostics Commit: b520b294d72834042d23e6c4c887c6c194847544 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 10:33:30 -0400 Commit message: Bump CI to Bioconductor 3.22/R 4.5 to fix vignette build failure COVIDCaseStudy.Rmd was failing to build on CI (macOS/Windows) with "unable to find required package 'Seqinfo'" inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause: covid_reference_data/covid_query_data were generated on current Bioconductor (3.22), where the Seqinfo class was split out into its own standalone package. check-bioc.yml was still pinned to the two-year-old Bioconductor 3.19/R 4.4, whose GenomeInfoDb predates that split and whose repos don't contain a 'Seqinfo' package at all, so the class tag baked into the serialized data can't be resolved. Two earlier attempts (adding set.seed() to rule out RNG state, then patching a subset of the shipped .rda files) missed this because neither addressed the actual CI environment being out of date. Bumped the workflow's matrix (r/bioc versions, container image, cache keys) to 4.5/3.22, matching the environment covid_reference_data was actually generated on; verified locally that a full R CMD build (fresh install + vignette rebuild) succeeds under this Bioc/R pairing. Package: scDiagnostics Commit: 02de5cdca9c45682ebceab3b3f7d6231d8cb8054 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:40:12 -0400 Commit message: Handle reference cell types with too few cells or absent from query detectAnomaly() previously assumed every reference cell type had at least 2 cells (to fit an isolation forest) and, when a query dataset was provided, implicitly assumed every reference cell type also had matching query cells. Neither is guaranteed: - A reference cell type with fewer than 2 cells can't fit an isolation forest; now skipped with a warning instead of erroring. - A reference cell type entirely absent from the query is a normal outcome (e.g. after subsetting/filtering the query), not an error; now reported with an empty query score vector instead of failing in predict(). Also fixes a latent bug where a cell-type subset reducing to exactly 1 row would silently drop to a vector (missing drop = FALSE), which would have broken the isolation forest input shape. Adds tests covering both edge cases. Package: scDiagnostics Commit: b0fc15de1e279c3a6e2d44c12837dd3667d35743 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:36:38 -0400 Commit message: Fix stale Seqinfo class tag causing vignette build failure, bump to 1.7.6 COVIDCaseStudy.Rmd failed to build on CI with: Error in .requirePackage(): unable to find required package 'Seqinfo' triggered inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause, confirmed via verbose updateObject() output: covid_reference_data's internal Seqinfo class was tagged with its old home package ("GenomeInfoDb", from before Seqinfo was split into its own standalone Bioconductor package), so a sufficiently new Bioconductor tries to auto-migrate it on load - and that migration path apparently isn't reliably available in a fresh CI environment. Fix: call updateObject() on serialized objects at data-generation time so the bundled .rda ships with the current internal representation baked in, rather than deferring to a lazy per-load migration. Applied to the new COVIDData.R/MERFISHData.R scripts (whose source data came from an external, older serialization), and audited/fixed the same latent issue in the pre-existing reference_data/query_data/qc_data (which had the identical stale tag despite already shipping in the package) and their generation scripts, so this doesn't resurface on a future regeneration or Bioconductor version bump. zeisel_/covid_/ merfish_ vignette datasets were already correctly tagged and are byte-identical after regeneration. Package: scDiagnostics Commit: 44dd05d3749412c865e5446d44a4520bd24df370 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:13:03 -0400 Commit message: Fix non-deterministic vignette failure and bump to 1.7.5 COVIDCaseStudy.Rmd and MERFISHCaseStudy.Rmd called detectAnomaly()/ calculateGeneShifts() (which use isotree::isolation.forest(), a randomized algorithm) without ever calling set.seed(), unlike the other two vignettes. This is the most likely cause of the CI vignette re-build failure on COVIDCaseStudy.Rmd after pushing 1.7.4 - a build without a seed picks up whatever RNG state the session happens to be in, which can land on the isolation forest / gene-shift edge cases seen elsewhere in this codebase. Verified against 15 different seeds plus a full local R CMD build (fresh install + vignette rebuild, not just devtools::load_all()) with no failures. Bumps to 1.7.5 rather than re-pushing 1.7.4, since 1.7.4 already has a recorded (failed) build on Bioconductor/GitHub. Package: MSstatsBioNet Commit: 0b9e21718beccbc1fb3847792481f8bda11b7ef5 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 18:27:25 -0400 Commit message: feat(decomposeSubnetworkIntoHierarchicalTopics): Enable NMF hierarchical decomposition (#110) Package: knowYourCG Commit: 5dbb3d5b4f6dcb4f6f54e4db6859b760358c9344 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 17:15:02 -0400 Commit message: Stop reaching the network when the vignettes and examples are built Three build-time downloads, all of the same two Zenodo files, none of them needed to show that the package works. The vignette one was failing outright. Sequencing.Rmd's QUICK START fetched mm10_f3_10cells.cg -- 11.4 MB, which takes ~101 s at the throughput a build host is likely to get. R's download.file() gives up at getOption("timeout"), 60 s by default, so the transfer truncated mid-file and the vignette errored. Measured twice here: it stopped at 6.0 MB and at 7.2 MB, both almost exactly 60 s of transfer, and completed only with timeout raised to 600. Raising the timeout would have kept a network dependency the package does not need. The sequencing workflow is superseded by the kycg command-line tool, which does this analysis natively over YAME .cg stores and fetches its own knowledgebases, so the chunk is now shown rather than run, with a line saying so and pointing there. The two examples had the same files behind a guard that does not guard. \donttest IS executed by the Bioconductor builders; only \dontrun is not. In bedToCg() the download.file() sat outside the guard entirely, so it ran on every check while only the bedToCg() call was skipped -- the whole example is now \dontrun. In testEnrichment() the guard was in the right place but was \donttest, now \dontrun; its offline part, which uses the sesameData cache, still runs. Both edited in the roxygen source and regenerated, so document() cannot revert them. Neither example has run lately: checksrc has been skipped for as long as buildsrc has been red, so these would have fired the moment the vignette fix made checksrc reachable again. BiocCheck NOTEs \dontrun in favour of \donttest. That NOTE is accepted here: \donttest does not keep the builders off the network, which is the point. visualization.Rmd still reads a small RDS over the network and is left alone -- it builds reliably and is not part of this failure. Package: knowYourCG Commit: 0a4ce5469ac8b4fbb9801a4af583639b65a36b4d Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 16:23:15 -0400 Commit message: Array.Rmd: use the base pipe, not the borrowed magrittr one buildsrc has failed on every builder in both release and devel with Quitting from Array.Rmd:218-233 [ky8, run-test-single] Error in `results %>% dplyr::filter(overlap > 10) %>% head`: ! could not find function "%>%" The vignette never attached the pipe. It worked anyway because library(sesameData) pulls ExperimentHub -> AnnotationHub -> BiocFileCache -> dbplyr, and dbplyr re-exports `%>%`, so the vignette was borrowing the operator from a package four levels down its own dependency chain and never named. When that chain stopped attaching dbplyr, the vignette broke without having changed. knowYourCG imports `%>%` via importFrom(magrittr) but does not export it, so library(knowYourCG) was never what made it resolve. DESCRIPTION has Depends: R (>= 4.4.0), so `|>` is available unconditionally and removes the dependency rather than renaming it; `%>% head` becomes `|> head()` since the base pipe needs a call. R/preparePlotDF.R keeps `%>%` -- package code has the import, only vignettes were ever exposed. Verified under R 4.6.0: all three rewrites return identical() results to the magrittr forms, the base pipe resolves with nothing attached, and Array.Rmd renders to completion. Fixes the buildsrc half of #4. Package: gDRutils Commit: a62ecdc187c6b4b726415cb33500813dfbbb0d10 Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 22:34:53 +0200 Commit message: Merge pull request #201 from gdrplatform/GDR-3612 refactor: read the constant-fit xc50 threshold from fit configuration Package: gDRutils Commit: 441d33fe8d5ca07d23f4dcbee9f59274a5f4f14f Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-22 21:17:54 +0200 Commit message: fix: read the fit configuration when the fitting layer is entered directly Package: gDRutils Commit: 11524511fd588673802ec057e728b96c9b089b0d Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 12:07:38 +0200 Commit message: Merge branch 'main' into GDR-3612 Package: gDRutils Commit: afa97f88532cc8d0539c9df9b2d5170b0e7f4f0c Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:50:27 +0200 Commit message: docs: flag that fit_curves still hardcodes the xc50 threshold Package: gDRutils Commit: f450b02a0beaa9ae1f8cec3fd09151e2f2fe5a98 Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:49:21 +0200 Commit message: Merge remote-tracking branch 'origin/GDR-3606' into GDR-3612 # Conflicts: # DESCRIPTION # NEWS.md Package: gDRutils Commit: b5e352cf6c88d1a7cb33ca89c106b55896cb1cbc Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 13:27:47 +0200 Commit message: refactor: read the constant-fit xc50 threshold from fit configuration The response level deciding whether a constant fit reports +Inf or -Inf was hardcoded at 0.5 in two functions. It is now one entry per normalization type in the fit_config block, alongside the priors and asymptote bounds. Numerically inert: every type keeps 0.5, which is what the code did before. The point is that the value becomes visible and decidable - for RV it means 50% viability and for GR it is the GR50 convention, but NGR is a bare ratio of slopes that is legitimately negative, where the threshold has no established meaning. Package: methodical Commit: 2ce1f224115807008cf8e4056bff3346c161cbe2 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-22 20:12:54 +0100 Commit message: update Package: MSstatsBioNet Commit: d6f02da47b7e915ef0c30923538cf7d516341aa2 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 14:43:07 -0400 Commit message: fix(pubmed): Reduce runtime for fetching pubmed abstracts (#109) Package: GSVA Commit: d2828ae6a4645e089dc931494a2b0f239850ae7b Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:45:59 +0200 Commit message: Switch a couple of install() calls in C for the corresponding more performant internal Rf_*() calls Package: alabaster.matrix Commit: 7cd81656f826538908e71cea03dbed7e42544cb8 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:53:29 +1000 Commit message: Mention all of the weird DelayedArrays that we support in the ANY method. Also move the LowRankMatrix code out of the ANY method for clarity. Also bump version and date for a new release. Package: alabaster.matrix Commit: 1d4b149bd9a329ea35a5033dc0318f6292f275ee Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:38:20 +1000 Commit message: Use a more precise R type hint for residual matrix objects. Also move ResidualMatrix code out of the ANY method for easier reading. Package: alabaster.matrix Commit: 1a17e99c4a5e64b68688da152c20434d3ae965bb Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:21:07 +1000 Commit message: Support scrapper::LogNormalizedMatrixSeed in storeDelayedObject. Package: MSstatsBioNet Commit: c6cb932731a5f1f1a743daed884638f2c14afd57 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:38 -0400 Commit message: Bump package version from 1.5.2 to 1.5.3 Package: MSstatsBioNet Commit: 57f2c7b2d94664d93f76a16b82cc5a5b7cff2ae9 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:10 -0400 Commit message: fix(proteinGroups): Adjust annotateProteinInfoFromIndra to handle protein groups (#108) Package: BreastSubtypeR Commit: 9aad28d9baa37a3a2acc3e040c72bc2fea5bced8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-09-22 20:24:05 +0800 Commit message: Merge upstream/devel, Updated Package: BreastSubtypeR Commit: f44f9d18a7ff9c1446d57cc8515dc427e98e0a4b Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:06:15 +0800 Commit message: Merge pull request #139 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 9e4904ff65cfc1320229f841b55402e08e0390fe Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:00:13 +0800 Commit message: Merge pull request #138 from yqkiuo/main New updates Package: BreastSubtypeR Commit: 252f893b32c10da768540ab3df667f3c6ef34419 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 12:56:55 +0800 Commit message: Merge pull request #136 from yqkiuo/maintenance/public-package-fixes-20260918 Maintenance fixes for 1.5.2: AUTO routing, ROR-C column, Shiny launcher and preflight, Mapping and documentation Package: BreastSubtypeR Commit: f9ca808290b0dfe73e62cff242e28cc301f69238 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-21 10:30:49 +0000 Commit message: Track .Rbuildignore and exclude the .github directory from the build R CMD check reported "hidden files and directories: .github" because the workflow directory reached the source tarball. .Rbuildignore was listed in .gitignore and therefore never shipped with the repository; it is now tracked, with the same content the Ensemble branch already carries, so the built package excludes .github, RStudio files, Rplots.pdf, doc, Meta and MANIFEST.txt. No R code changes. Package: BreastSubtypeR Commit: f3e3be4738438524e605ca70781d8ac359af9ca8 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-19 13:24:35 +0000 Commit message: Bump version to 1.5.2 and title the release notes DESCRIPTION 1.5.1 -> 1.5.2 for the Bioconductor devel submission of the maintenance fixes. The NEWS block collected under "Unreleased" becomes the 1.5.2 entry. One clause is added to the AUTO subsetting bullet: the supplementary pseudocode of the published paper records the strict comparison in the subsetting step while using ">=" for method selection, so readers comparing the package against the paper know that the package now applies ">=" in both and reproduces its shipped example. Package: BreastSubtypeR Commit: 1826b4a6941c152837ef57effbb3c23fdf9751a0 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:57:20 +0000 Commit message: Docs: keep the maintenance track free of unreleased-feature references The entropy change of the previous commits described the new NA behaviour by comparison with an unreleased voting feature, in the internal help text of get_entropy(), in the comment heading test-entropy.R and in the NEWS bullet. The maintenance branch is the public package: its sources, tests and NEWS must not name work that has not been released. The wording now states the behaviour on its own terms. No code, test assertion or behaviour changes. Package: BreastSubtypeR Commit: 252961fa606750b2c17e82363ee0e5ac4ac08d20 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:50:50 +0000 Commit message: Tests: do not let the equivocal HER2 case emit an unhandled warning The AUTO routing test feeds an equivocal "2+" HER2 code to check that a non-evaluable value is treated like a missing one. Builds that flag ambiguous HER2 codes warn on that input, which leaves an unhandled warning in the suite. The call is wrapped; the routing verdict it asserts is unchanged. Package: BreastSubtypeR Commit: 1931c45909ab5e0a56327d3024afd0331468caa5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:37:24 +0000 Commit message: AUTO: decide the HER2+ cohort from the HER2 column alone The HER2+ branch of get_methods() was entered when at least one evaluable HER2 value existed and the joint ER/HER2 counts held no HER2-negative sample. Those counts are computed with na.rm = TRUE, so a HER2-negative sample whose ER value was missing never reached them: one such sample left the cohort classified as HER2+, while an otherwise identical sample with a recorded ER value ended the classification. Whether a HER2-negative tumor counts must not depend on whether its ER status happens to be known. The branch now requires at least one evaluable HER2 value and every evaluable HER2 value to be HER2+. Values outside {HER2+, HER2-} are not evaluable; this covers missing values and the equivocal "2+" code that .normalize_er_her2_tn() deliberately leaves unchanged. Such samples neither create nor remove a HER2+ cohort, and AUTO now reports how many of them took no part in the decision, because a single unannotated sample used to be able to change the routing silently. Cohorts with complete HER2 information are routed exactly as before. The packaged OSLO2-EMIT0 example has no missing ER or HER2 value (ER+ 84, ER- 18, HER2+ 8, HER2- 94), so no shipped example or regression fixture changes. The test that pinned the previous behaviour (her2_pos_na_er) is replaced by a block asserting that both routes now agree, and a block asserting the new message. The NEWS bullet for the unreleased HER2+ change is consolidated into a single statement of the final rule rather than two successive refinements of the same unreleased behaviour. README and vignette state the rule. Package: BreastSubtypeR Commit: 14445c18179fdb40310ea13069f72cc6b5c59a60 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 18:20:00 +0200 Commit message: Entropy: report NA when no method returned a call get_entropy() computes the raw Shannon entropy of a per-sample row of method calls. table() drops missing values, so a row in which every executed method returned NA produced -sum(numeric(0)), that is 0, which on this scale reads as unanimous agreement. Such a row has no call distribution and therefore no entropy; it is now reported as NA. Rows with at least one call are unchanged, including the degenerate one-call case, whose entropy of 0 is the correct value for the observed distribution. The definition of the statistic - raw, unnormalized Shannon entropy in bits - is untouched, and no normalized variant is introduced. The change aligns the legacy path with the ENSEMBLE diagnostics, where raw_vote_entropy is already NA_real_ when valid_voter_count is zero. Exposure is narrow: every AUTO panel includes AIMS and sspbc, which are single-sample predictors and call essentially every sample, so an all-NA row cannot arise in AUTO. It arises in manual runs of nearest-centroid-only method sets (for example methods = c("ssBC", "ssBC.v2")), where a sample whose ER or ER/HER2 status is unknown gets no call from any executed method. The packaged OSLO2-EMIT0 example is unaffected: every tumor there has 7 or 8 calls, and its stored entropy column is reproduced exactly by the new function (asserted by a test). Side effect worth noting: Vis_Multi() orders rows by the entropy column and order() places NA last, so a sample with no calls now sorts to the end of the plot instead of appearing among the unanimous samples. The entropy column of res_subtypes is documented in ?BS_Multi for the first time, including that it is computed over the contributing methods only, so a low value from few contributing methods reflects few available calls rather than strong agreement. tests/testthat/test-entropy.R covers the NA cases, the unchanged values for rows with calls, reproduction of the packaged entropy column, and a manual two-method run in which four samples receive no call. Package: BreastSubtypeR Commit: 3668d9c93adb99e148dc577e8a82b0d556adb249 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 17:30:00 +0200 Commit message: PCAPAM50: exclude samples with unknown ER from the IHC-guided steps BS_PCAPAM50() builds the IHC column from the ER status with case_when(..., .default = NA), so a sample whose ER is missing or not coded "ER+"/"ER-" has no label. makeCalls.PC1ihc() expressed ER-negativity as !grepl("^L", IHC), which returns TRUE for NA, so those samples were counted as ER-negative in the PC1 axis check, in the misclassification-minimizing cutoff search and in the ER-balanced gene-centering set. The bias is one-directional and grows with the fraction of unknown ER. A new internal helper, .ihc_status(), classifies each label as "luminal", "nonluminal" or NA (missing or empty), and the three steps now use explicit luminal / non-luminal masks. Samples without an evaluable label take no part in estimating the cutoff or the centering set, a message reports how many were excluded, and they are still classified and returned. As a side effect the label test is now applied consistently: the mask is computed once, after trimming and upper-casing, instead of being evaluated before the upper-casing step in one place and after it in another. This is not a deviation from the published algorithm. The reference implementation (Raj-Kumar et al., CRAN package PCAPAM50 1.0.4, R/functions_PCA-PAM50.R lines 336, 355-356, 385-386) uses the same !grepl("^L", IHC) construct, but its IHC column is a user-supplied clinical subtype (LA, LB1, LB2, Her2+, TN) that the package never leaves missing; the vignette states that ER-positive subtypes start with "L" and all others are ER-negative. The NA category exists only because BreastSubtypeR derives the column itself. The change also removes an internal inconsistency: BS_cIHC() and BS_cIHC.itr() already exclude unknown ER from their ER groups via which(df.cln$ER == ...). Measured on the packaged OSLO2-EMIT0 input (R 4.3.3 sandbox), setting the first k ER values to NA and comparing calls before and after the change: k = 0 and k = 6 leave every call unchanged, k = 18 changes 2 of 102 calls, k = 30 changes 6 of 102. Cohorts with complete ER are unaffected, and the packaged example still reproduces its stored PCAPAM50 column. The help page of BS_PCAPAM50() gains a @details paragraph stating the exclusion, the message, that such samples are still classified, and the reference implementation's assumption of a complete IHC column. tests/testthat/test-pcapam50-unknown-er.R covers the helper, the unchanged complete-ER output against the packaged fixture, the message, and that unknown-ER samples still receive calls. Package: BreastSubtypeR Commit: 83ad6b3fa93553ba75cb3c641fb7a58070173806 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:10:00 +0200 Commit message: README/vignette: state the size gating of the ER/HER2-defined AUTO rule The AUTO bullet "ER/HER2-defined cohorts: ssBC.v2 only + SSP" read as an unconditional rule. In the code it applies only when the ER group reaches its minimum (15 for ER+, 18 for ER-) and the HER2 subgroup reaches its minimum (8 for ER+, 9 for ER-); smaller cohorts run AIMS and sspbc only. The bullet now says so, and a second bullet documents the handling of cohorts without any evaluable HER2 value (ER-based rules instead of the HER2+ branch). ASCII hyphens replace the typographic minus signs in the edited lines. Package: BreastSubtypeR Commit: 38aa1cc5cb833d260c5d5f82401a8ee528bd7fc1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:05:00 +0200 Commit message: Docs: Mapping "mean"/"median" collapse duplicate probes, as in the PAM50 code The Mapping() help (and the internal domapping() roxygen) described method = "mean" and "median" as keeping "the probe with the highest mean/median expression". duplicate_genes() computes the per-sample mean or median across all probes of a gene, i.e. it collapses the probes rather than selecting one; "iqr", "stdev" and "max" select one probe, and "max" selects by largest row sum, not by "highest expression value". Checked against the original PAM50 bioclassifier code (bioclassifier_R/subtypePrediction_functions.R, collapseIDs(), and the example parameter file): "mean" and "median" average the duplicate probes per sample there too, "iqr" and "stdev" select the probe with the highest IQR / SD, and no "max" method exists. BreastSubtypeR therefore reproduces Parker's behaviour; only its documentation was wrong. Author decision (2026-09-18): fix the documentation. The parameter text in R/BreastSubtypeR_methods.R, R/Utilities.R and man/Mapping.Rd now describes the averaging, credits collapseIDs() and marks "max" as a package addition. No code or mapped values changed. Package: BreastSubtypeR Commit: ba02d862d5e1c9cdbb43e23a1f8506faaed46946 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:00:00 +0200 Commit message: AUTO: include subgroups exactly at their minimum in the ssBC/ssBC.v2 subsets Method selection in get_methods() accepts a subgroup when its size is at least the minimum (15 for ER+, 18 for ER-, 8 and 9 for the HER2 subgroups), but the sample subsets handed to BS_Multi() for ssBC and ssBC.v2 were built with a strict ">". A subgroup of exactly the minimum size was therefore selected for the method and then excluded from its input, and its samples came back NA while the AUTO messages reported the method as running. The packaged OSLO2-EMIT0 example is such a case: 84 ER+ and 18 ER- tumors, so the cohort is classified as mixed and ssBC is selected, but the 18 ER- tumors were dropped from the ssBC input. Executed in a sandbox (R 4.3.3) on this branch: with the published strict comparison a fresh BS_Multi(methods = "AUTO") run yields ssBC = NA for those 18 tumors and does NOT reproduce the packaged frozen result OSLO2EMIT0obj$res (which carries ssBC calls for all 102 tumors); with ">=" the fresh run reproduces the stored result exactly, entropy included. The stored data object is therefore left unchanged; the fix restores agreement between the code and the shipped example. tests/testthat/test-auto-fixture-regression.R asserts the reproduction and that no ER- tumor is left without an ssBC call; tests/testthat/test-auto-subsetting.R adds exact-minimum subgroup cases and the OSLO2-EMIT0 colData. Package: BreastSubtypeR Commit: 13ea06daee8af82ab42c32cfceb38b43aecff9e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:55:00 +0200 Commit message: AUTO: require an evaluable HER2 value before calling a cohort HER2+ get_methods() entered the HER2+ branch whenever n_ERposHER2neg == 0 && n_ERnegHER2neg == 0. Both counts are also zero when HER2 is entirely missing or coded with unrecognized values, so such cohorts were classified as "small HER2+" and received AIMS and sspbc only (example: 60 ER+ / 40 ER- with HER2 all NA). The branch condition now also requires at least one evaluable HER2 value (HER2+ or HER2-). Cohorts without HER2 information fall through to the ER-based rules: a mixed ER cohort gets the mixed panel (ssBC.v2 then returns NA for every sample, which BS_ssBC() handles without error), an ER+-only cohort reaches the announced AIMS/sspbc fallback because its HER2 subgroups are empty. Cohorts with any evaluable HER2 value are routed exactly as before, including the existing treatment of HER2- samples whose ER is missing (excluded from the subgroup counts, as the AUTO message states). No effect on the packaged OSLO2-EMIT0 example. Author decision (2026-09-18): HER2+ branch only with evaluable HER2. tests/testthat/test-auto-routing.R covers the size-gated ER/HER2-defined cohorts and the cohorts without HER2 information. Package: BreastSubtypeR Commit: 94c6d57580acf6c6b77287f8e3968628ffeb2b84 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:50:00 +0200 Commit message: cIHC, cIHC.itr, PCAPAM50: clear error when an ER group is empty On a cohort with a single ER group (for example every sample ER+), makeCalls_ihc() and makeCalls.PC1ihc() failed with "undefined columns selected" and makeCalls_ihc.iterative() with "arguments imply differing number of rows: 0, 102", all from the median computation on an empty balanced set. The methods cannot balance by ER status without both groups. A small helper, .check_er_groups(), now stops with the group counts and a pointer to the cohort-aware modes in makeCalls_ihc() and makeCalls_ihc.iterative(). makeCalls.PC1ihc() checks the luminal / non-luminal IHC classes before the PC1 cutoff search and the balanced set after it, and makeCalls.v1PAM() checks its LumA / Basal groups. Cohorts with both groups take the same path as before (the OSLO2-EMIT0 cIHC calls are unchanged). Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-er-balancing-errors.R covers the three methods. Package: BreastSubtypeR Commit: 3894f47377e42f6c2f18cf8d7e04ecd0e38f7b16 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:45:00 +0200 Commit message: Docs: describe the actual return values of the NC methods; cIHC.itr ratio BS_PCAPAM50() and BS_ssBC() documented "a character vector of intrinsic subtype predictions", BS_cIHC() "a data.frame", and BS_cIHC.itr() a list with elements subtypes / confidence / ER_balance that do not exist. All four return a list: BS.all (PatientID, BS and, with Subtype = TRUE, BS.Subtype), score.ROR (correlations, calls, confidence, ESR1/ERBB2 expression, ROR-S/ROR-P and, with hasClinical = TRUE, ROR-C/ROR-PC scores and groups), the medians used for centering (mdns; mdns.fl for PCAPAM50; absent for cIHC.itr) and outList; BS_cIHC.itr() additionally returns BS.itr.keep and, with Subtype = TRUE, BS.itr.keep.Subtype. Verified on the packaged OSLO2-EMIT0 input. BS_cIHC.itr(ratio): makeCalls_ihc.iterative() swaps the larger ER group into the sampled position before drawing ceiling(ratio * n_smaller) samples from it, so the ratio applies to the larger group relative to the smaller one, not to ER+/ER- as such. The parameter text now says so, and the alphabetical tie-break used by get_consensus_subtype() for the consensus call is stated in the return value. roxygen comments and the corresponding man/*.Rd files were edited in parallel (no roxygen2 run, to avoid unrelated regeneration changes). Present in Bioconductor release 1.4.0 and devel 1.5.1. No code changes. Package: BreastSubtypeR Commit: abace8828bc01fa6ff7e1a70d6a9c1e28505cc74 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:40:00 +0200 Commit message: Shiny: cohort preflight requires both ER and HER2 columns .summarize_cohort() in inst/ShinyBreastSubtypeR/server.R returned ok = TRUE for kind "ER" (HER2 absent), kind "HER2" (ER absent) and for a valid TN column without ER/HER2. get_methods() stops in all three cases ("The 'AUTO' mode requires both 'ER' and 'HER2' columns in the 'pheno' dataframe"), which the app surfaced only as "Prediction failed" after the user pressed Run. The column summary is unchanged (now .summarize_cohort_columns()); .summarize_cohort() wraps it and sets ok = FALSE with the message "Cohort-aware analysis requires both 'ER' and 'HER2' columns; missing: ..." when either column is absent. Kind and statistics are still reported. tests/testthat/test-shiny-preflight.R covers the column combinations. Package: BreastSubtypeR Commit: 36e4de779bf6677fde472e81f613cf3f49799476 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:35:00 +0200 Commit message: iBreastSubtypeR: load app dependency namespaces correctly The launcher's .attach_if() helper called requireNamespace(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE). requireNamespace() has no such arguments, so the call failed with "unused arguments"; the failure was swallowed and FALSE returned, and nothing was loaded. The comment claimed the packages were attached to the search path, which requireNamespace() never does. The app still worked because ui.R/server.R use qualified calls and shiny::runApp() attaches shiny itself. The helper is now a package-internal function, .load_app_dependencies(), that checks installation, loads each namespace with requireNamespace(p, quietly = TRUE) and stops with a clear message when a package is missing or cannot be loaded. The tidyverse option uses the same helper. The exported signature and documentation are unchanged. tests/testthat/test-shiny-launcher.R covers the missing package error and the successful load. Package: BreastSubtypeR Commit: 6deac1db8d57cfbaee4e104edb9af6f160a9c536 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:30:00 +0200 Commit message: BS_Multi: report the error text when PCAPAM50 fails The tryCatch() around BS_PCAPAM50() in BS_Multi() warned "PCAPAM50 failed in this iteration: " and dropped the condition message, so users could not see why the method failed. The warning now appends conditionMessage(e) (with call. = FALSE). Behaviour is otherwise unchanged: the method's column is filled with NA. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-bs-multi-messages.R mocks a failing BS_PCAPAM50() and checks the warning text and the NA column. Package: BreastSubtypeR Commit: ff23703e8cb347524ad8fe1897d25d6514fd4049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:25:00 +0200 Commit message: Normalize factor phenodata like character; fix the FPKM imputation guard .normalize_er_her2_tn() used nested ifelse() calls whose fallback was the original column. For a factor column the fallback is the integer code, so unmatched levels came back as strings such as "3" instead of "Unknown". Mapping() converts colData factors to character before calling the helper, but BS_Multi() and get_methods() normalize the phenotype table directly, so a hand-built data_input with factor ER/HER2/TN columns was normalized differently from the same table with character columns. The helper now works on as.character() copies of the three columns; the coercion warnings compare character values, so canonical factor input no longer triggers them. Character input is unchanged. domapping(): the second imputation guard tested anyNA(x) after x had already been imputed, so counts.fpkm was never imputed. It now tests anyNA(counts.fpkm). In practice edgeR rejects NA counts earlier, so this is a logic correction with no expected effect on existing analyses. Both present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-phenodata-normalization.R compares factor and character input for the helper and for a full AUTO decision. Package: BreastSubtypeR Commit: 5deb60ce12da9448df97aa5079c0f312ad12cc6a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:20:00 +0200 Commit message: Mapping: keep matrix dimensions for single-sample input duplicate_genes() indexed x[names(entrezid), ] without drop = FALSE and rebuilt the collapsed matrix with mapply(SIMPLIFY = TRUE) followed by apply(x, 1, unlist), which requires a matrix. For a one-sample SummarizedExperiment the subset became a vector and Mapping() failed with "dim(X) must have a positive length". prepare_nc_matrix() and the probe filter in domapping() had the same drop issue. The collapse now builds the gene-by-sample matrix explicitly (lapply + rbind with dimnames from the split and the sample names), and the three subsets use drop = FALSE. For multi-sample input the returned values and dimnames are identical to the previous implementation for "mean", "median", "max", "stdev" and "iqr" (checked on random data with duplicated Entrez IDs and an NA value); the OSLO2-EMIT0 mapping of one sample equals the corresponding column of the full mapping. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: d6c6c20c4004d988e79c522ee4f1625dd0ad39fb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:15:00 +0200 Commit message: AUTO: announce the fallback to AIMS and sspbc instead of falling back silently The safety net at the end of get_methods() set methods to c("AIMS", "sspbc") without any message. It is reached by ER+-only or ER--only cohorts whose HER2 subgroups are all below their thresholds, typically because many HER2 values are missing (example: 17 ER+ samples with HER2+ 5, HER2- 6, missing 6). Users saw only the two SSP methods run, with no indication why the ssBC variants were not selected. The fallback now emits a .msg() (respecting the BreastSubtypeR.verbose option) naming the reason. Method selection is unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: a9f0de975795df873663f9cab6207455cb3b2d15 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:10:00 +0200 Commit message: AUTO: drop samples with missing ER/HER2 from the ssBC/ssBC.v2 subsets get_methods() built the AUTO-mode sample subsets with rownames(pheno)[pheno$ER == subtype] and the ER/HER2 analogue. A missing ER or HER2 value evaluates to NA in the comparison, so the subsets contained NA "sample names". BS_Multi() then either failed when it subset the SummarizedExperiment ([,j] index out of bounds: NA) or, when the NA-padded vector was at least as long as the cohort, treated it as "run on all samples" and skipped the intended subsetting. Example on 1.5.3: 50 ER+ / 45 ER- / 5 NA gives a 105-element subset with 10 NA entries for a 100-sample cohort. Both lapply bodies now use which(), as makeCalls.ssBC() already does, so samples with missing status are excluded. Cohorts with complete ER/HER2 values return identical subsets. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-auto-subsetting.R covers a mixed cohort with missing ER and an ER- cohort with missing ER and HER2 (subset shorter than the cohort). Both fail on the previous code. </pre> </div> Package: BreastSubtypeR Commit: 2f8ea71201a742d0d0957ff8228ba2fdbc21d3be Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:05:00 +0200 Commit message: Fix ROR-C risk group column: use criskgroups, not cpriskgroups In RORgroup() (R/NC_functions.R) the data frame built when hasClinical = TRUE assigned the combined + proliferation groups (cpriskgroups) to both "ROR-C Group (Subtype + Clinic)" and "ROR-PC Group (Subtype + Clinic + Prolif)". The ROR-C groups (criskgroups, thresholds -0.1 and 0.2 on the combined score) were computed but never reported. The ROR-C group column now uses criskgroups; the ROR-C score and every other column are unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-ror-groups.R adds a synthetic RORgroup() input in which the ROR-C and ROR-PC groups differ (high/low/med vs low/high/med) and checks that the ROR-C group is reproducible from the reported ROR-C score. The test fails on the previous code and passes with this change. Package: BreastSubtypeR Commit: 9ab99af8b9cf337614a30a61c3e0ce1c264df049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:00:00 +0200 Commit message: Tests: run the nested testthat suite via test_check() tests/testthat.R contained a single inline test_that() block and never called test_check(), so tests/testthat/test-tn-cohort-detection.R (added in 1.5.1) was not executed by R CMD check; the Bioconductor devel check log shows only the inline test running. tests/testthat.R now calls test_check("BreastSubtypeR") and the inline BS_Multi() test moved unchanged to tests/testthat/test-bs-multi-manual.R. DESCRIPTION: Config/testthat/edition: 3 and testthat (>= 3.2.0) in Suggests, matching the edition-3 expectations used by the tests added on this branch. No version bump. Package: BreastSubtypeR Commit: a4b23b2aba07ba19b33669ac1e8d8361fd1139ab Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:59 +0200 Commit message: Merge pull request #135 from yqkiuo/main update to 1.5.2 Package: BreastSubtypeR Commit: b19c1c3f629d11a8f12e57526162b16e41e605c6 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:30 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: 0c0c47c87dcd6e560bedcd536f828dca642e7933 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-06-22 17:38:39 +0300 Commit message: Merge pull request #134 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: edeb030317e854cd706a351f12b93dbd722f232e Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 17:22:45 +0300 Commit message: Finalize NEWS entry for TN detection fix (#133) Package: BreastSubtypeR Commit: b8d6bf4b5bb037d8e101287e92d209fdb1e869a5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:59:04 +0300 Commit message: Update NEWS and documentation for TN detection fix (#133) Package: BreastSubtypeR Commit: d8eeff0e85113512842b1e4976fce6eed1142e39 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:25:06 +0300 Commit message: Fix TN-only cohort detection (#133) Package: BreastSubtypeR Commit: cd515ab92fffbbf8a3496cfc70e65299b77457ba Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-02-20 12:09:07 +0100 Commit message: v1.3.3 Package: BreastSubtypeR Commit: 0770ee5c0a5283fd1f073cf9c170464431eac2d3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-02-20 11:59:28 +0100 Commit message: Merge pull request #129 from yqkiuo/main AUTO - NA Package: BreastSubtypeR Commit: 9b740667ac781cede13f2884763f47576f5778cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:30:22 +0100 Commit message: Merge pull request #128 from yqkiuo/BranchManos Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: ebac3daf14161981995520818d552a8c894faa21 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:27:35 +0100 Commit message: Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: 122fae948ba3ab93589046d4fc9f564a95db3805 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-12-21 07:08:46 +0100 Commit message: Merge pull request #125 from yqkiuo/main Update Package: BreastSubtypeR Commit: ab9e6c7e715a77c3d9d0c93f0d96794531b39afc Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:48:57 +0100 Commit message: Merge pull request #124 from yqkiuo/BranchManos cIHC.itr: return distances as numeric matrix, preserve dimnames Package: BreastSubtypeR Commit: 1cdd290182105e8d9dd1cf38a2f1cc2748045aba Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:41:20 +0100 Commit message: cIHC.itr: return distances as numeric matrix, preserve dimnames - Coerce mean_distance and mean_distance.Subtype to double matrices with sample/centroid dimnames; negate once. - Ensure testData is numeric matrix. - Use explicit getsuffix(calibration=..., internal=...). Closes #112 Package: BreastSubtypeR Commit: e626336705e6981d3f43c1e307381875acc4dbf5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:18:30 +0100 Commit message: Merge pull request #123 from yqkiuo/BranchManos feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to can… Package: BreastSubtypeR Commit: bf244ea222946de979dc528b6764b074b9a7492e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:17:59 +0100 Commit message: feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to canonical forms - Add `.normalize_er_her2_tn()` utility and call it inside `Mapping()` to coerce common variants to: * ER → {ER+, ER-} * HER2 → {HER2+, HER2-} (HER2 "2+" left unchanged/unevaluable) * TN → {TN, nonTN} Accepts Positive/Negative, Pos/Neg, Yes/No, True/False, 1/0, AMP→HER2+, etc. - Preserve original values in `colData` when fields are absent; only touch present columns. - Emit explicit warnings on ambiguous/unmappable values (e.g., HER2 "2+"). - Roxygen: expand `Mapping()` docs with required Column metadata for AUTO/ssBC/cIHC/PCAPAM50 and numeric TSIZE/NODE (0/1) for ROR; document the canonical receptor coding and the automatic normalization behavior. Closes #122 Package: BreastSubtypeR Commit: d4200b8f8fa6a230b1aed6bd8d5a271856dcf9c5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 10:04:54 +0100 Commit message: Merge pull request #120 from yqkiuo/BranchQiao Formatting Package: BreastSubtypeR Commit: 855146c3797560a923b044683b223aa09c5ab6b6 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 10:04:04 +0100 Commit message: Formatting Package: BreastSubtypeR Commit: 7e1546b848212ca92df006f0625e1f0213a5d825 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:57:27 +0100 Commit message: Merge pull request #119 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 13081dbdf8d5faead48468a7121455f68f226262 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 09:56:57 +0100 Commit message: Warning: nonASCII Package: BreastSubtypeR Commit: e872818d9f7db70dd95b04e56306c5f986b4cb2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:48:36 +0100 Commit message: Merge pull request #118 from yqkiuo/main 1.3.1 Package: BreastSubtypeR Commit: e837d4a4b93480e5921dc6220d336f390e08cfa9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:56:26 +0100 Commit message: Merge pull request #117 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 24282cdd95efcb545c8a516d2a4c52c333451e37 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:55:43 +0100 Commit message: docs(NEWS): updated to include latest changes/bug fixes Package: BreastSubtypeR Commit: d3e819ea9cb6036119018581de03f7c0ca6c03e9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:45:26 +0100 Commit message: shiny/preflight: reset cached data_input on source change (uploads/example) to fix stale cohort display Package: BreastSubtypeR Commit: f7ad9d6399c959146fad253c76e4b8a093367674 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:06:08 +0100 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: 33bc7cabda598a10d06781255a4ff477d64ec373 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:05:55 +0100 Commit message: Merge pull request #116 from yqkiuo/main Main to BranchManos unmerged changes Package: BreastSubtypeR Commit: c1164715171e92993dba23d51ed4d2739a9db33a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:03:31 +0100 Commit message: Include ssBC in robust singleton handling Package: BreastSubtypeR Commit: 0c0c39cd7cb7bdde99192d4a877cc9990b98b6c4 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:32:17 +0100 Commit message: v1.3.1 Package: BreastSubtypeR Commit: ed479c4a0a715bd078874a465956416cb58e999b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:30:33 +0100 Commit message: Minor typo for Shiny exports Package: BreastSubtypeR Commit: fca34d14be09269bd6a9e83f9b169b3f49e3b27d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:16:28 +0100 Commit message: ssBC.v2: include sample IDs in singleton fallback warnings; surface warnings in Shiny - Warnings now list subgroup + n + sample IDs (truncated for long lists). - Shiny wraps runs in withCallingHandlers() to show warnings via showNotification(). Package: BreastSubtypeR Commit: 5beba6624617ea57bd33a664a2c9ccddbe01f5d2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:15:25 +0100 Commit message: ssBC.v2: robust singleton handling + ROR guards - Use uncentered expression for n=1 fallback (avoid zero-vector Spearman→NA). - Add canonical 4-class name normalizer before RORgroup; create missing cols; enforce order. - Shorten Mapping() completion notification duration in Shiny. Package: BreastSubtypeR Commit: 6f8593d8659200d5b054e45ae6deb7ff624bf02f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 23:31:32 +0200 Commit message: Merge pull request #115 from yqkiuo/BranchManos fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: ae32dd867386460a3d6abcff63cd519bcebdd098 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-21 23:25:49 +0200 Commit message: fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: 01a86e199d7353c526b1ddec6693b6c5d87a53e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:51:52 +0200 Commit message: Merge pull request #114 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: aee5223fca7ad466234702b83f9d465092e65fec Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:50:18 +0200 Commit message: update documentation (.Rd) files & NEWS.md Package: BreastSubtypeR Commit: e3852e46bc7c708db9534558669b18e492bbcb44 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:38:36 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: f13b835df4329f494e2a1fe1242a1927657629f9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging -Name unnamed chunks Closes #113 Package: BreastSubtypeR Commit: 815edf2ed0faa1dc708fecc282da22945d861490 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging Package: BreastSubtypeR Commit: 27a8e42ca0dd5a06b976bd6e59aeedf3337c8ad1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:41:55 +0200 Commit message: Merge pull request #111 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6ed1cf770b44ea3eeaa0fe5d284760692df203e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:40:32 +0200 Commit message: feat(shiny): show ER/HER2 subgroup tallies (±TN) in AUTO preflight Package: BreastSubtypeR Commit: a85dec5c9e7f261e7d9ea94febbbfc063dc07992 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:04:55 +0200 Commit message: fix(shiny): guard switch() inputs to prevent length>1 errors; harden AUTO preflight & ssBC option handling Package: BreastSubtypeR Commit: 8b4e57129dabde362d8c811661e7586dc633c396 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:49:16 +0200 Commit message: feat(shiny): TN-aware AUTO preflight summary and messaging Package: BreastSubtypeR Commit: 83b469a296627e4a81983655692766813d8540b2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:48:42 +0200 Commit message: docs: convert wording to American English (standardized, normalization, visualize) Package: BreastSubtypeR Commit: 1c86f875473cf413e91da628410278915a9b19cb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 00:28:47 +0200 Commit message: Merge pull request #110 from yqkiuo/BranchManos v1.1.9: feat(app): add example-data loader and AUTO preflight cohort … Package: BreastSubtypeR Commit: bcb7486f49afd2f9c719d1b047c89b96421040b5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-15 00:26:27 +0200 Commit message: v1.1.9: feat(app): add example-data loader and AUTO preflight cohort stats; harden AIMS/sspbc outputs; renamed FPKM GEX example file Package: BreastSubtypeR Commit: 3e5ae1bae1910f63b576690d0f5965c092929197 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-14 22:26:00 +0200 Commit message: Merge pull request #109 from yqkiuo/BranchManos Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: 643629b4f37a82e8eb4fc1d4b8b7d47a1d0140e5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-14 22:08:03 +0200 Commit message: Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: f0bb013273724583dc640776f5253a650e71deb7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-11 19:07:21 +0200 Commit message: Merge pull request #106 from yqkiuo/main v1.1.8 Package: BreastSubtypeR Commit: e519bba6330b28527eba397178b5db68259cd335 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 17:48:34 +0200 Commit message: Merge pull request #105 from yqkiuo/BranchManos Minor text improvements Package: BreastSubtypeR Commit: 7ef4c516f1e02b2667908e42c91db1f81587e183 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 17:35:16 +0200 Commit message: Minor text improvements Package: BreastSubtypeR Commit: bba02a162aae8a104830c2762903a95b4b24a086 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 16:30:43 +0200 Commit message: Merge pull request #104 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6bb89109d53b3cbfc61069dad0b97c43fc01a59 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 08:38:02 +0200 Commit message: v1.1.8: feat(auto): enforce v2-only for ER/HER2-defined cohorts; add TN cutoff (18); sync docs Package: BreastSubtypeR Commit: 104a9d3c962648e2421f86b970452b6ae8094add Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 00:03:52 +0200 Commit message: v1.1.7: Fixed bugs & Clarified guidance in AUTO logic Package: BreastSubtypeR Commit: 3a0c352910e74d2016eaaa4f0d229db74b6428b1 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:11:23 +0200 Commit message: Merge pull request #103 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: c23f9312cfe6399587682872db5168e726949468 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-08 07:10:55 +0200 Commit message: v1.1.6 Package: BreastSubtypeR Commit: bda41efb6523b351c335cbbbfe93eda3e294159a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:01:46 +0200 Commit message: Merge pull request #102 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 01fbf08f95785bd96121416f08a42a0723db9bb5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:31:43 +0200 Commit message: Merge pull request #101 from yqkiuo/BranchManos Update citation Package: BreastSubtypeR Commit: 819b86fcb1f32f68d8d6551ae67675e59d55cbc2 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:29:59 +0200 Commit message: Update citation Package: BreastSubtypeR Commit: 18426cd1996f6d437078579a397e594ac858b422 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:18:10 +0200 Commit message: Merge pull request #100 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5cd622f0dfdcbf4ebd2612e2f3bce0d4d130a1dd Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:10:24 +0200 Commit message: Update to v1.1.6 Package: BreastSubtypeR Commit: 0168bb1d064c170c27904604ce944664052ffc4c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:00:02 +0200 Commit message: Fix CITATION error & update CITATION Package: BreastSubtypeR Commit: efcf440f930e3e0216161a7bfaa1f8a839796ffc Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:28 +0200 Commit message: Merge pull request #99 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 522570c1925152201b4738888c70a9b479569b4d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:10 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: caa57d7c96c2b3621ba3153a63704780fb67943c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: eca7fd305351bee53a3359193d31d6efb3bd239c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:26:16 +0200 Commit message: Merge pull request #98 from yqkiuo/BranchManos Bump version to 1.1.5, merge from BranchManos Package: BreastSubtypeR Commit: 3d6d84a04f652c46b098e7daf6b9433783c59317 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:17:29 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 08be34439c7ec15f3aab940989e7fc5881500a38 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:28:50 +0200 Commit message: Minor styler changes to comply with BiocCheck Package: BreastSubtypeR Commit: c33c626c748776d83aec78b69c2c5c2d78b40d94 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:00:25 +0200 Commit message: Remove Styler ignore file Package: BreastSubtypeR Commit: a756018eea737c57128fecbe2ed656a5c8bd8c89 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:53:48 +0200 Commit message: After styler formatting Package: BreastSubtypeR Commit: 0fb6775cf7105ccdfeac0f78d671c8220fa00a07 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:43:21 +0200 Commit message: Before styler formatting Package: BreastSubtypeR Commit: f462a35c15affb83307240678fdb8b5c31f1e1af Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 15:06:41 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: d58720a8654c148543e56efe3c8504e50f7a06f9 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Fix LaTeX errors, @importFrom issues, deprecated mutate_at(), tightened Mapping() Package: BreastSubtypeR Commit: 8cab29a01c0412be9b9a83d9c729c77b273c03f9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:33:33 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 2909f655c9c2686e9c562762e27c7cb78eb63544 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Merge pull request #97 from yqkiuo/BranchQiao Fix LaTeX errors Package: BreastSubtypeR Commit: f1d92deeed7ff76170c4ba8a70d0ac75e0dab7eb Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:28:10 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 9112d81e8538f3debb6c101255008486d052c326 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-12 19:39:12 +0200 Commit message: Merge pull request #96 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 977c1a7f7a5dd3700b51fe154e0a9509d6a960b1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 19:38:48 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: b2ba716538df0e23e684ec1118866c96560cab9b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:14:24 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: e25016431d3c00bfd81d941f4b8a71a2b7357ba1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:07:19 +0200 Commit message: v1.1.3 Merge branch 'BranchQiao' of github.com:yqkiuo/BreastSubtypeR into BranchQiao # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. Package: BreastSubtypeR Commit: 0f3624d0ed05aa4d2f2cb9759acb59d815fea297 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:04:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 8a340b6a4117f80791ae664c5741a0fe8627c9c3 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 15:44:48 +0200 Commit message: Fix BreastSubtypeRobj to include only the object itself (exclude environment variables) Package: BreastSubtypeR Commit: f969bcf09e03aa226de3839a68cf76cc01011ef3 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 14:52:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 693c829f364caedb2161a940d196d1830bd19d87 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 10:21:35 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 8582fb3b897e60ecc6da91040e32b42b19641154 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 17:06:26 +0200 Commit message: Added publication badge Package: BreastSubtypeR Commit: bd0b6cab935e607efd4bb001e3b75b02b37cc1fe Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:47:02 +0200 Commit message: Fixed bug: When running BS_Multi() omitting the first method; Minimal fix (drop nothing after removing row_id) Package: BreastSubtypeR Commit: 234ccbe269d45bd2c407358b711253629fe59203 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:12:28 +0200 Commit message: Polishing README.md & Vignette Package: BreastSubtypeR Commit: b3d5c232a32097ee9b4f83908a9c89f6ca621be8 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:41:14 +0200 Commit message: DOI update and text Package: BreastSubtypeR Commit: bacb13657f301643a682a3fcd7e82a22091a3b6c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:01:14 +0200 Commit message: Added DOI, Updated exported with version info, method, etc Package: BreastSubtypeR Commit: 787b3119148e345c0b2d4fa8638b3d6dd37600ee Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 19:17:32 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: c856d8dc615f688ae8f5d27eeb47ab297ead6b11 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:36:22 +0200 Commit message: Delete .github/workflows/sync-to-forks.yml Package: BreastSubtypeR Commit: 8d235ce12beccf9d394146a458ae135fec2f0fb3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:18:15 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: ad15f75e9de9028eb6d93fb5efb3ca05220ce975 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:04:51 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 917d62c7bc428fc67ff97c513022feb210fed94c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:58:05 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 9258dd1803aac507ecae1ec05d30a55c7c91827c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:54:22 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 8864ea4a8bda1bee1b6496aaf185e8bb76af5257 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:57 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 71735535741a019e7ba9299e47783038edbd3714 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:00 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f165c7df5636588c76360b10a42e792e9bf53614 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:50:26 +0200 Commit message: Create sync-to-forks.yml Package: BreastSubtypeR Commit: f2d85acb23f2c38ec3b3062fbab841c29115d38e Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:47:46 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 792bc0ab92f80b7405d69c45516dd131ffd7663c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:43:18 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 99d3102b66482953013f265d00464c8c3a4c2b25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:34:13 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 212e09ee660df8daaffea11a7af00d53321895aa Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:04:17 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 7cea1e782fedda5fef57f559c77dc39db8aceb9d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:56:40 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f33f344a6b0d06d3de393a783a23383e4ef5cac4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: adccaf9e7d8ce2b6234a1960e93e5d1543d98e09 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:31:34 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: a9e9e80f2f1063aae332963e474ea2f5804487b7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:27:58 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 4151dfa20943c89acdd55c5e1dec18a03da01e2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:14:01 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 1ab513bde94a41e4ab34856ca5e4f5ba5a6413e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 15:59:19 +0200 Commit message: Create sync-to-org.yml Package: BreastSubtypeR Commit: f9f0ea202177840660c02d39e203f67d4003e2cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:09:58 +0200 Commit message: Added description for new example dataset (TCGABRCAobj), updated the BreastSubtypeRobj with the 3 new medians info, tiny text improvements Package: BreastSubtypeR Commit: 056545172113202bb55a0ea0c2918851096fa0f2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:05:10 +0200 Commit message: Created a new example dataset (TCGABRCAobj) from TCGA-BRCA with Raw Counts, and similar results as OSLO2EMIT0obj Package: BreastSubtypeR Commit: 6de103db09589a53624341851237a8f547684ceb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:02:19 +0200 Commit message: Updated BreastSubtypeRobj with 3 more published medians Package: BreastSubtypeR Commit: 6acd15688f6e60db4e1f2ef151c103e865ce5663 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:00:19 +0200 Commit message: Guard docalibration, Improve External calibration, UX, and minor text improvements Package: BreastSubtypeR Commit: 8f7e3790ac94fead82f77e6564d87c542fcf5097 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 11:11:22 +0200 Commit message: Fixed error in BS_Multi() in AUTO Mode, when ssBC has <50 PAM50 genes: Add safe row-aligning cbind helper, made RORgroup() tolerant to missing ESR1/ERBB2 rows, and made BS_Multi() assemble results by PatientID Package: BreastSubtypeR Commit: 06bd9bce269ca12b4ca9f052f3d81cd730212a68 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 21:20:25 +0200 Commit message: Fixed the issue with pre-loading third-party libraries before initializing the Shiny app, Updated Help files Package: BreastSubtypeR Commit: ee560564150a7a5f11c00e8750583438a6c084e6 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:55 +0200 Commit message: Updated NEWS.md with major changes Package: BreastSubtypeR Commit: abd132463b65390c813f04ea50c530fd4b058507 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:18 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 74b20b933030517c45e68826a469dd88d79aa0b9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:24:07 +0200 Commit message: Added a TCGA-BRCA subset, with clinical & annotation data, for testing the RawCounts normalization pipeline Package: BreastSubtypeR Commit: d4fedc4c9b2a241b2652e563c2300d423f787287 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:21:08 +0200 Commit message: iBreastSubtypeR: UX polish, AUTO explainer, export refactor, AIMS constraint & bug fixes Package: BreastSubtypeR Commit: fb7c21f7ebc4f50be7610c8c0a023036f1559358 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 13:24:32 +0200 Commit message: Include three pre-computed Medians (external) as an option to Shiny App Package: BreastSubtypeR Commit: d1a90080950c9b5ddcad737979d072bdc177e038 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 11:34:43 +0200 Commit message: ssBC fixes: No crashes when < 50 PAM50 genes, No accidental subtype calls when a sample’s distance row is all-NA, Won't error when a subgroup has zero samples, qCtr won't produce NaN from zero range Package: BreastSubtypeR Commit: 10644b50e4721efe7b0d9f65445d30e1fdcf5a26 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 10:05:57 +0200 Commit message: Add our reference to Mapping() & BS_Multi() Package: BreastSubtypeR Commit: 5ea0dd73f932fbdd278f4e299de7270698d855c1 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 23:10:17 +0200 Commit message: New preflight for AUTO to prevent errors, new customizations, included new polished text for PAM50 to guide users, and more Package: BreastSubtypeR Commit: 3b08eed750427d72842bec852ff85c2446138cbe Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 13:21:06 +0200 Commit message: Fix issue when HER2 missing and user runs AUTO Package: BreastSubtypeR Commit: 16b805c817e0b7e3883b1aa7defd6da04f6a57f4 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:20:14 +0200 Commit message: Included a Prelight check for ER/HER2/Tn status availability in Clinical data BEFORE Running subtyping, avoiding App crashing due to missing values Package: BreastSubtypeR Commit: f003e4ecbfadb6a2a293ff39d838581dea5a0086 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:01:32 +0200 Commit message: Synchronized changes in BreastSubtypeR_methods.R and NC_functions.R, Created a theme to match the logo, made things unified, text improvements Package: BreastSubtypeR Commit: a66b4796231c8054f2093c6795ca4e67f2cb04de Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 10:08:20 +0200 Commit message: Parker original when calibration=None, or external calibration returns error: Fixed by Making NA equivalent to "medianCtr" (sync eith Parker et al.), and -1 to No calibration. Also, avoid requiring PatientID for BS_parker() when hasClinical = FALSE, included extra controls for hasClinical in all NC functions, polished help text, corrected typos (also tried to correct the 2nd error for ssBC, when < 50 genes, but will work more on this and come back with another Commit) Package: BreastSubtypeR Commit: 53ca58ec99d200f998a8be6896bab45f47d789e3 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-05 19:36:25 +0200 Commit message: Major changes: Multi method with AUTO mode added, Description text for each method with Refs added, Subtype 4-class selection Package: BreastSubtypeR Commit: bdf3bf291b59939171d85ff61f895b2ffc222b8d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:18:47 +0200 Commit message: Fix UI so the drop down menus are easier to select Package: BreastSubtypeR Commit: c0ed93ab5eed4a965f478a0dcac17355f8f91501 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:01:42 +0200 Commit message: Changed HasClinical with a Tick box, included many controls to check whether TSIZE, NODE are available, added different help functions for GEX and Annotation, improved text, and more Package: BreastSubtypeR Commit: 277869bea9c0c7d2747370cc657b2e87cb4e7dd2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 14:59:23 +0200 Commit message: Replaced the T -> TSIZE Package: BreastSubtypeR Commit: fd063a60aa8db3651975e89237ddb398d62c1100 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:28:48 +0200 Commit message: Minor edit Package: BreastSubtypeR Commit: 31e6bbfa2c897aa87caa09254cd2d4d2074b790f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:25:40 +0200 Commit message: Renamed folder to Shinny->Sniny, renamed data files with clear names Package: BreastSubtypeR Commit: 5ef9dd73efdccab438ee51f1ea0441ac565ca984 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:20:19 +0200 Commit message: Fix server.R bug Package: BreastSubtypeR Commit: c4c205e993f8791683fddf05392533aadded4b75 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-04 11:49:00 +0200 Commit message: refine shiny Package: BreastSubtypeR Commit: 304cb68143558163b4dd070c2498631f62a650e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-04 10:40:17 +0200 Commit message: Merge pull request #95 from yqkiuo/main Merge pull request #94 from yqkiuo/BranchQiao Package: BreastSubtypeR Commit: 6cbc1cb1b18907119b3414e3c0dafec607480a99 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:27:20 +0200 Commit message: Merge pull request #94 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 298458b861686b4ed9bfa17c070e5ffea513f3dd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-02 08:27:00 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: a50d8d4c3bea22f65836df6d099b269da685d8c2 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:25:43 +0200 Commit message: Merge pull request #93 from yqkiuo/main v1.1.2 Package: BreastSubtypeR Commit: 65b18fd8734f90e579fff40e53bbc51799b2c4ad Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:28 +0200 Commit message: Merge pull request #92 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5d09b44a5785c08a10d3d652d2a01db94678a1de Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:21 +0200 Commit message: Merge branch 'main' into BranchManos Package: BreastSubtypeR Commit: 8f4056fc16de285798c18e8c36e5399e5cd1fd23 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-01 10:18:12 +0200 Commit message: Merge pull request #91 from yqkiuo/BranchQiao v1.2.2 Package: BreastSubtypeR Commit: e11ffcd934d71dd5ee42c3816cabf93b997e6c64 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-01 10:17:53 +0200 Commit message: v1.2.2 Package: BreastSubtypeR Commit: 0969e8fa4d71d310d1d2f58c788af7a94566de25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-31 22:18:46 +0200 Commit message: Merge pull request #90 from yqkiuo/BranchQiao v1.1.2 Package: BreastSubtypeR Commit: c575280eed4e562e90ba6b9b7a6675353e532725 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-31 22:18:25 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: 031beb8e23f96e6f4894f56b550dd49d0c2a729b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-29 16:04:28 +0200 Commit message: Updated code to include separate cut-offs for ERpos & ERneg, as well as separate cut-offs ER(pos/neg)/HER2 (independent of HER2 status) based on the above cut-offfs. Note: The combined cut-offs will be released in the next submission Package: BreastSubtypeR Commit: 93ba44156f95a90bb74440d472157107e5ef0908 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 20:13:37 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: efee177e7f94d079d424ad79467615a63ce71698 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 2c6cfcacdc3550df0916ecb54833275bf2b9f04f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: d0154df0200108179568a150e1487e592a34e20a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 6a0be72275efbb8b9828b8765834d1ce97521134 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 3cf5afd43c31eeec90045902e6a082d82013bbf7 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: e91120bb63753900c47f80206b0662aef090c98a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: c09d132b8993a81ad16143b2ddbd5fb6b6f36f8b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 18:32:39 +0200 Commit message: Updated NEWS.md, BreastSubtypeR_methods.R, and minor updates to Utilities.R and data_doc.R Package: BreastSubtypeR Commit: 10f36184b66a9a0703d4296c9311b5ed1fc03e23 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 15:16:50 +0200 Commit message: Shiny app normalization clarification Package: BreastSubtypeR Commit: 24740ca0d3f45e43e674d247778b8e003871361c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:57:22 +0200 Commit message: Replaced the adaptive filtering as it was producing a reduced gene list for NC-based methods. Instead I introduce the calculation of UQ in the positively expressed subset and apply those calculcated factors to the full matrix. Package: BreastSubtypeR Commit: 347114047eeba2318371d4245043ae1d3b6bce86 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:34:21 +0200 Commit message: Include adaptive gene filtering so UQ normalization can work under real data Package: BreastSubtypeR Commit: f3bd9cdae36176a3857de89fac0c794bd8df369b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 16:29:18 +0200 Commit message: RawCounts test code include & help files updated Package: BreastSubtypeR Commit: c248d0fe615e9d6e3f4401bb6658908341de9208 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 16:07:29 +0200 Commit message: Shiny app: added descripted text Package: BreastSubtypeR Commit: 52bea350827dc0fba939551f50149d60acb3887b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 15:12:56 +0200 Commit message: Updated text in overview files Package: BreastSubtypeR Commit: 5b87399978a5d1cca09a82d5249a2b8863a553ea Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 15:10:09 +0200 Commit message: CITATION added Package: BreastSubtypeR Commit: e8fcac0bcab82793b586f5ffc8c930a0002ac609 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-21 11:29:40 +0200 Commit message: Merge pull request #89 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 0c75bf90f3070408ec5a156edf84b9c0bc70250b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:29:14 +0200 Commit message: update new features Package: BreastSubtypeR Commit: a99a93e94a90d6a715d64daedbe2e1f886f87917 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:27:58 +0200 Commit message: update new features Package: BreastSubtypeR Commit: c9f28c19c39695ad8a84ee4aa929c352be00e229 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 18:11:51 +0200 Commit message: Merge pull request #88 from yqkiuo/BranchQiao Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: e4a62355017220fe89ec8ea09376a0a56060de7c Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 18:11:26 +0200 Commit message: Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: 1993ab3e50725d01e8980a00eeaec8f0b0b766c4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:48:10 +0200 Commit message: Merge pull request #87 from yqkiuo/BranchQiao 1.1.1 Package: BreastSubtypeR Commit: 5d928ed37d8d0f47dd0392057846c43dc12e3dea Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:47:44 +0200 Commit message: 1.1.1 Package: BreastSubtypeR Commit: 52faaf9d7980c6d36524bcabbdcffe1f0fb92a0a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:39:51 +0200 Commit message: Merge pull request #86 from yqkiuo/BranchQiao 1.0.1 Package: BreastSubtypeR Commit: 35eef13e343edd2f9c6a1c26d780c97f470ac6c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:38:55 +0200 Commit message: 1.0.1 Package: BreastSubtypeR Commit: 6abaf3b4ae3d1772babec19c83d49c04728daa06 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-27 09:49:16 +0200 Commit message: Merge pull request #85 from yqkiuo/BranchQiao general update Package: BreastSubtypeR Commit: 453e9aac8dc81b86987e53e60659f2c97f6ba403 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-27 09:48:42 +0200 Commit message: general update Package: BreastSubtypeR Commit: 226607c2ae42706346a1e8911d1f2f82a5ca1490 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 19:12:11 +0200 Commit message: Merge pull request #84 from yqkiuo/BranchQiao v1.1.1 Package: BreastSubtypeR Commit: d773d4401e93ec12006f4e79122cbee8247d80d7 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 19:02:45 +0200 Commit message: v1.1.1 Package: BreastSubtypeR Commit: e74e86a2cfdf6daf92ed180095d27619cd45cd54 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:44:06 +0200 Commit message: Merge pull request #83 from yqkiuo/BranchQiao Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: fd30082d86b34d3ced41b7a7c385e01448c19794 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:41:43 +0200 Commit message: Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: 74145000a4ce350ca0e787fe5c459b79318b3edb Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:25:01 +0200 Commit message: Merge pull request #82 from yqkiuo/BranchQiao Bug fixes and minor improvements Package: BreastSubtypeR Commit: 1a5cb6636acfbd2ad1fc7c290bfba875dd2b22b0 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:24:35 +0200 Commit message: Bug fixes and minor improvements Package: BreastSubtypeR Commit: 4a895b8a8a149e0199b85eeaa19b6769dd8382df Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:27:17 +0200 Commit message: Merge pull request #81 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 4a03138457415f0164139373ee34038bd07ad300 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:21:40 +0200 Commit message: Update DESCRIPTION Package: BreastSubtypeR Commit: 856c6f8f91de5339988cf4c315bcaf96247f37d5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 10:39:20 +0200 Commit message: general update Package: BreastSubtypeR Commit: e35db8756a5fa3f30bf4addbeacd58145589e16b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:18:47 +0200 Commit message: general update Package: BreastSubtypeR Commit: 2e60c2222d3e9fdf48d3262ba087b447a95119a9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:03:00 +0200 Commit message: general update Package: BreastSubtypeR Commit: 7cfcfe95b2761178d17cc2af122f61883e7dc666 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:50:06 +0200 Commit message: update general Package: BreastSubtypeR Commit: b30131f2c073711d4b42e38af49bef1849da20c5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:48:53 +0200 Commit message: Update RawCounts para Package: BreastSubtypeR Commit: 6fa4d83d00b30727be9b1d4fd3798015fad0442a Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:32:10 +0200 Commit message: debug ROR Package: BreastSubtypeR Commit: ba045196fcd4a3bff148b3497a82f3f87d6bb324 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:31:55 +0200 Commit message: refine "-1" in parker.original Package: BreastSubtypeR Commit: b5e6254539fd38e41109056b2ddff7d36e0f9c19 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:15:41 +0200 Commit message: refine "-1" in parker.orignal Package: BreastSubtypeR Commit: bc7d097164cb411bfc4b40d5513073ae1bac35d8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:39 +0200 Commit message: 0.00.0 Package: BreastSubtypeR Commit: 5d966c161e4cdae464dd16d48421f6d5a4e26461 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:30 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 81f77832a0d7f8f5b8b70403616fe165ff96862d Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:08 +0200 Commit message: debug data type Package: BreastSubtypeR Commit: 8471668b9b9b43c3e27a87faa458488a8fba7f05 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:56 +0200 Commit message: debug BS_Multi Package: BreastSubtypeR Commit: 01fa8b576ca237667ed8a792477638cd4b023dbd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:34 +0200 Commit message: clear author Package: BreastSubtypeR Commit: a86f573778ed992a3d2dbb698b4c9c00a15619c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:20 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 00d2b9c5d71c6830e845dcddcb810b9640666207 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:33:01 +0200 Commit message: debug AUTO Package: BreastSubtypeR Commit: 8b3f7c2ef2d45cf772511a7290ba0a31baa43b62 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:32:46 +0200 Commit message: debug bad PCAPAM50 Package: BreastSubtypeR Commit: c70f4c9b0d64da1940659ae9a826d8221be05a32 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 09:32:30 +0200 Commit message: debug PCAPAM50 </div> </div>
Remove the duplicated notification for search.
Fix duplicated logo
Add link to de.NBI survey
Add deNBI funding acknowledgement and survey in README
Use vectorized .store_check_exist() call
Define is_structured once
Register bfloat routine
Update collision filtering and bump devel to 1.23.2
T_obs added in results
bug fixed in distinct_test
Merge pull request #26 from rformassspectrometry/jomain Add random sleep breaks to reduce failures on build systems
Add random sleep breaks to reduce failures on build systems - Adding/changing to random sleep times aiming at reducing the recurrent failures on the Bioconductor build system (most likely due to rate limitation from MetaboLights).
Merge pull request #159 from myushen/master fix website examples
fix website examples
Merge pull request #153 from MangiolaLaboratory/copilot/rename-join-census-table Soft-deprecate `join_census_table()` in favor of `get_census_metadata()`
unit test
Merge branch 'master' into copilot/rename-join-census-table
soft deprecate since 0.99.27
Merge remote-tracking branch 'origin/master' into rename-join-census-table merge from origin
Trim redundant mock assertion Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Verify Census helper mock before wrapper call Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Exercise deprecated table argument compatibility Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Correct Census deprecation test assertions Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Stabilize deprecation warning test Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Soft-deprecate Census join helper Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Initial plan
Update documents and namespace
Improve numerical stability and bump version to 1.1.2
gseDisease() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family.
update docs
gsePathway() exposes eps and forwards extra arguments, #47 gsePathway() was the only GSEA wrapper in the family missing both eps and ..., so eps could not be controlled and additional enrichit::gsea_gson() arguments could not be passed through. Both are now supported, matching clusterProfiler::gseKEGG().
ReactomePA 1.99.2: seed argument and a faster prepareReactomeNetwork() - gsePathway() and nsePathway() expose an explicit seed parameter for reproducible GSEA results, aligned with enrichit::gsea_gson(). - prepareReactomeNetwork() no longer round-trips through graphite::convertIdentifiers()/pathwayGraph() per pathway; it builds a single UNIPROT->Entrez map up front and converts edges with vectorized lookups, keeping mclapply() parallelization over pathways. Output is unchanged (same nodes and edge values; node ordering may differ). Default cores is now 1 instead of detectCores().
parallelize prepareReactomeNetwork pathway conversion via mclapply The one-time Reactome network build converts ~2700 pathways serially in R (convertIdentifiers/pathwayGraph/graph_from_graphnel per pathway). The conversions are independent, so the loop now runs over mclapply() with a new 'cores' argument (default getOption('mc.cores', detectCores())); mclapply falls back to serial on Windows and preserves input order, so the resulting edge set - and hence the cached network - is unchanged. Measured on the GSE53757 demo: serial build ~35-41 min; parallel build 614 s at 16 cores and 655 s at 56 cores; output byte-identical to the serial baseline. Scaling saturates at ~4-5 effective cores because the graphite identifier conversion is hash-lookup-bound.
nsea
update bioc version
gseMeSH() exposes an eps argument Declare eps = 1e-10 and forward it to enrichit::gsea_gson(), matching the other GSEA wrappers in the family.
expose a seed argument on gseMeSH(), meshes 1.39.2 Forward an explicit seed to enrichit::gsea_gson() so GSEA runs are reproducible, and apply pvalueCutoff to both pvalue and p.adjust inside the enrichit engine (requires enrichit >= 0.2.2).
computeIC: take the term universe from GO.db, not the shipped gotbl table computeIC() decided which terms to score from the `gotbl` table shipped in data/: goids <- unique(godata[godata$Ontology == ont, "go_id"]) That table was last rebuilt in 2021-07, so every term GO.db has added since then was given no IC at all, and the IC-based methods returned NA for it even though its descendants carry annotations and its IC is computable. This is issue #33, and the reporter's diagnosis ("a conflict between the pre-calculated gotbl.rda and the local version of GO.db") was right. Measured against the current GO.db / org.Hs.eg.db, the number of annotated terms that can actually be scored: ontology annotated before now gained BP 11293 11126 11293 +167 CC 1832 1787 1832 +45 MF 4777 4410 4777 +367 and nothing loses an IC. The missing terms also biased every other IC, because they were counted in the `sum(gocount)` denominator but could never contribute to an ancestor's descendant sum. Terms finite under both universes agree for 92-95% of entries with a mean absolute difference of 0.003-0.011; about 0.3% were overestimated by more than 0.5, all of them in the "too specific" direction, which is what the mechanism predicts. The universe is now names(getAncestors(ont)) -- exactly the terms of that ontology in the installed GO.db, root included, and already cached by onto_relation() -- unioned with the annotated terms, so a term the local annotation package still uses keeps its IC even if GO.db has retired it. The same root cause also affects the `gotbl` that the Wang method walks, where a term newer than the table scores 0 instead of NA. That is left for a separate change because fixing it means either regenerating the shipped data or building the relation table at runtime. test-ICMethods.R now asserts that every annotated term gets a finite IC.
cache ontology mappings, and load Rcpp so the compiled IC methods work Two independent defects, found while fixing TCSS. getAncestors(), getParents() and getOffsprings() each rebuilt their whole mapping on every call -- AnnotationDbi::as.list(GOBPANCESTOR) costs about half a second -- while callers only ever pick out one or two terms with `[[ID]]`. A single geneSim() call rebuilt the same mapping hundreds of times. The mappings are derived from a source that is already cached (GO.db is static, load_onto() caches the OntDb), so they are now cached per ontology rather than per term. A 5x5 termSim on previously unseen terms drops from 2.5 s to 0.5 s, geneSim from 5.6 s to 0.6 s cold and 0.12 s warm, with byte-identical results. The cache holds about 85 MB for BP and 110 MB for all nine mappings. Separately, Rcpp was listed in LinkingTo only, so loading GOSemSim never loaded the Rcpp namespace. The wrapper generated by compileAttributes() instantiates Rcpp::RNGScope, which resolves enterRNGScope through R_GetCCallable("Rcpp", ...), so every Resnik, Lin, Jiang and Rel call failed with "function 'enterRNGScope' not provided by package 'Rcpp'" unless the user happened to attach Rcpp first. importFrom(Rcpp, evalCpp) was dropped in ea7b2028 (2016) and is restored here. No test reached the compiled code and the vignette only mentions those methods in prose, which is why this went unnoticed for so long; test-ICMethods.R now covers all four methods on three ontologies. The ontology cache is also covered: test-GO.R checks that each mapping is cached under the ontology and is identical to what GO.db holds.
correct the scope of the TCSS degeneracy fix The previous commit described the degeneracy as "a cluster with a single member", but calc_maxIC() indexes `all <- IC[cluster]; all <- all[is.finite(all)]`, so the real condition is "exactly one member carrying a finite IC". A cluster with several members where all but one have infinite IC is equally degenerate, and the old `length(all) == 0` guard did not cover it. Re-measured with the correct criterion (swapping calc_maxIC in and out of the namespace in one process so both versions see identical input): - the set of clusters whose ICA changes equals the set with exactly one finite-IC member, at every cutoff and ontology tested (BP 1/2/3.5/4/5/8, MF 3.5, CC 3.2) -- so the change is confined to the degenerate clusters; - the defect was not BP-only. 300 random pairs, % scoring exactly 1: BP 99.3% -> 0.0%, MF 27.3% -> 0.0%, CC 98.7% -> 0.0%; - the counts are larger than the single-member count suggested: BP has 1 degenerate cluster at cutoff 3.5 but 5 at cutoff 4 and 1141 at cutoff 5; MF has 3 and CC has 3, and the CC set includes the CC root GO:0005575. Fix the NEWS wording and the code comment to match, and make the regression test assert on the finite-IC criterion rather than on cluster size.
fix TCSS similarity collapsing to 1 for nearly every term pair A cluster with a single member has no internal spread, so normalising it by its own maximum IC made its ICA identically 1 regardless of how general or how specific that term was. GO:0008150, the root of BP, is such a cluster and is a common ancestor of every BP pair, so `max(sim_value)` in tcssMethod_internal() returned 1 for 99.7% of random BP pairs and `mgeneSim(measure = "TCSS")` was an all-ones matrix. Fall back to the global maximum IC for single-member clusters. The collapse is not specific to the root: scanning cutoffs shows GO:0050896 and GO:0046337 also become single-member clusters for BP, and GO:0052745 does for MF, so special-casing the root would only have papered over one instance. After the change, 300 random BP pairs give min 0.0004 / median 0.0234 / max 0.5296 with 0% equal to 1, and ica[["GO:0008150"]] drops from 1 to 0.000414 (= IC[root] / global max IC). Add a regression test and bump to 2.39.3.
fix TCSS for terms belonging to multiple clusters GO is a DAG, so a term can have several meta-term ancestors and `tcssdata$clusid[[term]]` is then a vector rather than a scalar. Indexing `ica` with `[[` then attempts recursive indexing, which raises "subscript out of bounds" (or "recursive indexing failed at level 2" depending on which element is hit first) and aborts any TCSS calculation for the whole ontology. Subset the list of clusters with `[` instead. This restores the behaviour already present in the Bioconductor release (2.38.3); the devel implementation had regressed. Adds a regression test covering a term that sits in more than one cluster.
enrichMKEGG()/gseMKEGG() accept a GSON, #623 enrichKEGG() and gseKEGG() take either a species code or a GSON object, but the module wrappers only took a species code, so there was no offline route for module enrichment at all -- even though the download errors now tell users to build a local database. Passing a GSON raised an unrelated error from the organism mapper instead. Both now mirror the KEGG wrappers, including the "organism should be a species name or a GSON object" message. A GSON reports its own keytype, so @keytype is taken from it; the species path keeps returning "UNKNOWN" exactly as before. Also documents the GSON option on the KEGG `organism` parameter, which had never been mentioned for enrichKEGG()/gseKEGG() either.
enrichGO(): restrict the annotation by evidence code, #160 Enrichment used every annotation in the OrgDb, including electronically inferred ones, so there was no way to avoid circular reasoning when the gene sets themselves came from in-silico evidence (dropping IEP for co-expression clusters) or to keep only curated annotations (dropping IEA). enrichGO() now takes `evidence`, appended last so positional callers are unaffected and threaded through both recursive paths. The filtered annotation is built by go_annotation_by_evidence() from a gene-centred select() of GOALL/EVIDENCEALL/ONTOLOGYALL, because the evidence code is a property of the gene-annotation pair and the previous term-centred mapIds() could not see it. Two semantics worth stating, both documented: the background changes with the annotation, so a filtered result is not a subset of the unfiltered one; and a filtered annotation is never cached, since the cache key is (organism, ont, keytype) only and reusing it either way would answer with the wrong annotation. A regression test pins the cache isolation down.
fix: enrichGO() survives an unidentifiable OrgDb organism, #232 The cached-GO-data check compared the cached organism against get_organism(OrgDb) inside a bare if(). get_organism() returns NA for an OrgDb it cannot identify -- an AnnotationHub OrgDb, for instance -- and `if (NA && ...)` aborts the call with "missing value where TRUE/FALSE needed", which names nothing about organisms or caches. It bites on the second enrichGO() call in a session, because the first one populates the cache. The check is now go_cache_usable(), where every comparison goes through isTRUE() so an unidentifiable organism means "not cached" and the annotation is rebuilt. Extracting it also makes the cache-hit logic unit-testable without an OrgDb.
fix: Gff2GeneTable() reads Ensembl-style GFF3, #193 The function only looked for an NCBI/RefSeq `GeneID=` attribute. On an Ensembl GFF3 (which writes `gene_id=`) every extracted key was NA, and merging two all-NA key columns is a cartesian product: on the reporter's cat genome that is ~1.3M x 40k rows, which R refuses with "negative length vectors are not allowed". At small sizes the same bug passes silently, because unique() collapses the duplicated NA rows into a plausible-looking table of NA ids. Field names are now detected from the file: `GeneID` or `gene_id` for the identifier, and `gene`, `Name` or `gene_name` for the symbol. Detection requires an exact attribute key, because getGffAttribution()'s heuristic fallback also looks inside values and would otherwise return the identifier out of `ID=gene:ENSG...` when asked for `gene`. A file with neither identifier style stops with a message saying what is expected instead of merging on all-NA keys.
add_go_level(): expose the GO level of each enriched term, #793 GO enrichment results carried the term, its ontology and its statistics, but not how deep the term sits in the hierarchy, so users who wanted to keep a band of levels had to reconstruct GO depth themselves. go_level_map() now returns the GO id -> level map (1 = ontology root) built by breadth-first traversal of the GO.db CHILDREN graph; getGOLevel() is rewritten on top of it with identical output (verified against a pre-change baseline for BP/CC/MF at levels 1-6), and add_go_level() appends a `level` column to an enrichResult/gseaResult/compareClusterResult. The level is taken from the ontology each term belongs to, so ont = "ALL" results are labelled term by term. gofilter() and dropGO() had no test coverage; the new test file locks their keep/drop-by-level behaviour down.
simplify() infers the GO ontology for enricher() results too, #369 The enrichResult method required x@ontology to be BP/MF/CC/GOALL, so an enricher() run over a GO collection (MSigDB C5 GO, a custom TERM2GENE built from GO annotations) had to have the slot assigned by hand before simplify() would accept it. The ontology is now inferred from the GO IDs exactly as for gseaResult (#753), and non-GO gene sets are still refused with a message saying so.
simplify() a GSEA result whose gene sets are GO terms, #753 simplify() reduces redundancy with GO semantic similarity, so it needs the ontology of the terms. It only accepted x@setType in BP/MF/CC/GOALL, which rejected a GSEA run over a GO gene-set collection (MSigDB C5, a gson GO file, a TERM2GENE built from GO annotations) because @setType then holds the collection name. The ontology is now inferred from the GO IDs, with results spanning several ontologies simplified as GOALL; non-GO gene sets are still refused, with a message that says so.
warn when compareCluster() is given a non-character universe, #654 compareCluster() wraps each per-cluster call in suppressMessages(), which swallowed the underlying enrichment function's "`universe` is not in character and will be ignored" message. A numeric universe therefore looked accepted while silently having no effect. The guard is now raised once in compareCluster() itself, where it cannot be suppressed, with a regression test for both the non-character (warns) and character (stays quiet) cases.
gsePC() and gseWP() expose an eps argument Both wrappers now declare eps = 1e-10 and forward it through GSEA() to enrichit::gsea_gson(), matching GSEA(), gseGO(), gseKEGG() and gseMKEGG(), which already exposed it.
fix enrichKEGG(organism='cpd') and report KEGG download failures clearly, #828 - gson_cpd(): use the 'compound' KEGG REST endpoint. KEGG retired /link/cpd/pathway, which now answers HTTP 400, so enrichKEGG(organism='cpd') and gseKEGG(organism='cpd') failed with an obscure download error. - kegg_rest(): report the failure where it happens, telling an unreachable network apart from an HTTP error status and from an empty response. These used to surface much later as an opaque error. - download.KEGG.Path() / download.KEGG.Module(): replace the is.null() guard, which could never fire because kegg_rest() never returns NULL, and stop with an actionable message when the downloaded annotation is empty or when the gene/pathway table shares no ID with the pathway-name table. Previously an empty annotation was returned silently and surfaced downstream as a misleading "No gene can be mapped", #146, #378, #561, #646.
update vignettes
feat(filterSubnetworkByContext): adjust filterSubnetworkByContext to exclude key words (#111)
fix the wrong number when calculate phyper.
fix a issue for if no hyper pval available.
using promise process to update the gene table.
import phyper from stats.
add phyper pval for co-expression.
bugfix Signed-off-by: xuz1 <xuz@niehs.nih.gov>
Fix Stan old array syntax for stanc3 (BioC 3.23 build failure)
Version 0.99.8 Pieces of one tissue, regions of interest, and the report arranged by level. matrixStats leaves Imports: it was declared but called nowhere, so every user installed a package the code never used.
Document the regions work The vignette says what regions are for -- a transition that marks a tissue type, or a toxicity study where the regions are drawn high and low in the toxicant and the endogenous species compared between them, within one animal rather than across a group. It also describes the by-level report, and how to see a palette before choosing it. AGENTS.md is gitignored: agent scratch notes, not part of the package.
Arrange the report by level, and correlate at one level only Sections 2, 3 and 4 are each drawn by sample and then by region, so the two are read the same way rather than the regions living in a tab of their own. The region masks take a section before the ion images, which move down a number. "auto" judges the heatmap encoding per view, on the rows that view actually has. A study without regions is unchanged, headings included: a level heading only appears when there is a second level to tell it from. Correlation names one level -- 'sample', 'roi', False or auto -- and only ever computes that one. It is the slowest section in the report, and a region holds a fraction of a sample's pixels, so auto correlates within the regions when a study has them and is off otherwise. True still means 'sample'. roi: unit is per sample or per region, not both: a comparison has a single unit, and two views of the same numbers invite reading whichever looks better. compare: keeps "both", where the two arrangements are different contrasts rather than the same one twice. Each box-plot panel carries its own key, and colours: region sets the region palette (any package palette, or a grDevices qualitative one), kept distinct from the groups'.
Score each region against itself in contributionHm() too The region heatmap could only be drawn per feature, because contributionHm() had no notion of a block. That made "auto" pick the wrong panel wherever a study has few samples and many regions: one animal per group takes the per-sample encoding by sample, but by region its rows are sample x region, so a group can have six or seven of them -- exactly the case the contribution encoding exists for. It now takes sample_block, and inside a block both the z-score and the group mean are computed against that block alone. The hue is therefore "how this group's airways sit among all the airways", not "airways differ from parenchyma", which is what a panel scored across regions would mostly report. A feature flat within a block cannot be scored there and is drawn in na_col, even where it varies across the section.
Fix the region tests and the vignette's feature lookup The row-split assertions read @row_order_list, which a Heatmap only fills in when it is drawn -- it is empty on the object, so the expectations compared against nothing. The split a heatmap will use is in @matrix_param$row_split, which is what they now check: the block test asserts a, a, b, b against groups that deliberately alternate, so passing it means the rows really were split by region rather than by group. The vignette indexed a feature by name, but spectra() returns a matrix with no dimnames, so it takes the row number instead.
Document pieces and regions; regenerate the example sections The vignette gains a section on pieces of one tissue, one on labelling regions, and a worked example on the bundled sections: the label table, the region maps and a box plot with one point per section per region rather than per pixel. The YAML section documents the samples forms, including pieces, and what each roi: option can be set to. The example sections are regenerated with the regions the vignette and runExample() now show. Seeds are unchanged and the region code draws no random numbers, so the intensities are identical. AGENTS.md is build-ignored, and the micro sign in stitchAcquisitions() is written as a \u00b5 escape: R CMD check requires ASCII source.
Carry regions through a study and into the report A study picks regions up on its own: generateTxtImages() attaches roi_label and roi_id from each acquisition's roi_labels.csv, matched on (x, y) like the tissue mask, and they survive panel binding and stitching. Regions numbered within a piece are renumbered across the stitched sample, so two airway_01s become two airways. The YAML gains a roi: block -- enabled (auto), include_unassigned, compare, unit, heatmap -- and pieces: for a tissue acquired in several passes, each piece normalised and SNR-filtered against its own background before being joined. The report gains a regions tab: maps, box plots by compare and unit, an ROI_summary sheet, and a heatmap with one row per sample and region. That heatmap z-scores each region against itself (quantileHm's new sample_block), since scoring across regions would mostly report that airways and parenchyma differ, which is not the question being asked. The map is repeated above the ion images, where it says which blob is which. quantileHm() also no longer loses its sample names when a study holds a feature with no variance: the unscoreable column returned an unnamed vector, and apply() drops the names for the whole matrix when one result's differ. output: colocalisation: gains auto, off whenever a sample merges several acquisitions -- most pixel pairs would then cross acquisitions.
Add labelROIs() for regions within the tissue Run after selectTissuePixels(): it shows the ion image of a chosen transition across tissue pixels only, then loops draw -> name -> "add another". Several regions can share a label, since a section holds many airways, and each is numbered as it is drawn (airway_01, airway_02, ...) so it keeps its own identity while the label is what a study compares. Regions are saved per acquisition as roi_labels.csv beside the tissue mask, which is never touched, and copy_to writes the same file to the other panels over the same area. Re-running adds to them; overwrite = TRUE keeps the old file as a dated backup. The feature picker is shared with selectTissuePixels() rather than copied, and the bundled example sections gain two "a" and two "b" regions each so the downstream half can be shown without a drawing device. The regions differ because of where they sit on the existing intensity gradient; no value was adjusted to make them. Also splits the given names in Authors@R, so the citation reads "Smith MJ" rather than "Smith M".
Place pieces of one tissue by stage position A tissue too large for one acquisition is imaged in pieces, and those pieces are one sample: kept apart they count twice in every group summary, and because they agree with each other they look like a reproducible effect. readMRM() numbered each acquisition's pixels from its own first pixel and threw the stage coordinates away, so every piece started at (1, 1) and stitchAcquisitions() could only report that they overlapped. Its documentation claimed Waters coordinates were absolute, which stopped being true the moment readMRM() re-based them. readMRM() now keeps x_stage and y_stage (mm) alongside the grid indices, and stitchAcquisitions() places each piece where the stage recorded it: above, below or beside, in any order, gaps left empty. Pieces must share a pixel size; each is moved to the nearest position on a common grid and the largest shift is reported. Overlap is still an error rather than an average. Objects without stage positions keep their own coordinates and say how to get them. combineMSIs() fills a pData column that only some objects carry with NA, since stage positions and region labels are legitimately absent from some samples.
Bump version
Document .matrix() methods removal
Remove .matrix() methods and let them auto dispatch to array method
Document on.exit change in NEWS
Use on.exit() more consistently to close
Mention dead code removal in NEWS
Remove dead code in h5writeAttribute.array()
Fix incorrect copy/pasted error messages
Remove extra call to H5loadConstants()
Ensure .Call() always includes PACKAGE
Mention h5set_extent() fixes in NEWS
Fix h5set_extent issue with dataset handle
Remove dependence on BiocSingular
Point to the Zenodo record 22918956 Fill in the Zenodo record (doi:10.5281/zenodo.22918956) hosting the networks and document the CC BY-NC-ND 4.0 license of the data files.
Move the networks to Zenodo The regulon data sets are no longer bundled in the package: they are hosted on Zenodo and retrieved with the new getRegulon() function, which caches them locally with BiocFileCache and verifies their MD5 checksums. listRegulons() lists the available networks. This brings the package size well below the 100 MB limit of the new build system. - documentation of the 25 networks merged into ?regulons - vignette converted to R Markdown - added unit tests - Authors@R replaces Author/Maintainer
Merge pull request #276 from rcastelo/275-average-method Average method for enrichment scores calculation
Replace checkIdentical() for checkEqualsNumeric() to allow C unit tests pass across different platforms
Added C implementation of the average method, and its corresponding unit tests. For performance issues, genes within genesets are internally ordered after mapped to features, this required regenerating regression test for PLAGE since SVD flipped sign in values due to the different input order
Merge branch 'devel' into 275-average-method
Fixed namespace issues and unit tests
Add unit tests for CLR and average method
Added first version of the average method for calculating enrichment scores
Merge branch 'main' of https://github.com/bartongroup/fenr
Reverting some changes
Version 1.11.3
Mention README and pkgdown site in NEWS
Set up pkgdown
Add minimal README with deNBI survey
1.31.5: fix readControls column naming; qualityMask takes a custom mask readControls() built the control data.frame positionally: colnames(ctl) <- c('G','R','col','type') over a frame whose signal matrix has four columns, so Color_Channel and Type were cbind-ed past the end of that name vector and arrived unnamed, while `type` silently took a signal column. Downstream, controls(sdf)$Type was a vector of integers, so negControls()'s grep("negative", ...) matched nothing and detectionPnegEcdf() failed in ecdf() with "'x' must have 1 or more non-missing values" on EPIC and HM450 -- the platforms whose controls arrive through readControls() rather than as SigDF rows. The columns are now named explicitly. This was found from the C side, where it had been mistaken for an annotation divergence for two days. With it fixed, detectionPnegEcdf agrees between the two implementations at max|diff| = 0.00e+00 on EPICv2, MSA, EPIC and HM450. qualityMask() gains `platform` and `mask`, so a custom or combined-array mask can be passed in directly instead of being bolted on with addMask() after the fact -- the case that comes up for arrays built from two manifests. README: the two implementations are named and versioned. The R package is SeSAMe v1 and stays on the 1.x series; the C command line is SeSAMe2 on 2.x. They are parallel, not sequential. The conda line also said `sesame-cli`, which has not been the package name since 0.4. R CMD check: Status OK, vignettes built and re-run.
Clarify study subjects in ADHD microbiota profiles (#828) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Add Rdpack references (#797) Signed-off-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Convert MAE to TreeSE and back (#810) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com>
Simplify importing
Fix rendering
Fix rendering, update support forum address
docs: Add comprehensive Rarefaction section to transformation chapter (#825) Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> Co-authored-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <tvborm@utu.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
docs/clarity improvement to mia::summarizeDominance (#852) Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Co-authored-by: TuomasBorman <TuomasBorman@users.noreply.github.com>
feat(ci): add whitespace stripping to style workflow (#864) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
fix(community_similarity): use official vegan docs (#872) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
feat(ci): add dependabot (#865) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
bump(deps): actions/cache@v4 to v6 (#874) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Use scaled fitted values for DMM drivers (#881) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Clarify exercise instructions across the book (#886) Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Add tree visualization reference (#889)
Suppress cheatsheet startup messages (#878)
Switch to DelayedNoOp to support all alabaster.matrix no-op subclasses. This saves us having to list all of the individual subclasses.
Introduce a no-op base class to catch all of our weird seeds. In particular, packages like beachmat don't have to add a specialization for each of the no-ops subclasses, they can just check for the DelayedNoOp class.
Implement ToBeRealizedArray class for fine control of delayed operations.
some edits to SparseArray-abind.Rd
requires S4Arrays >= 1.13.1
DelayedArray 0.39.7: Add abind() method for DelayedArray objects Also: - Remove the rbind(), cbind() and bindROWS() methods defined for DelayedArray objects. These methods are now replaced by more generic methods defined in the S4Arrays package for Array objects that are all based on abind(). - Add coercion from array/matrix to DelayedArray/DelayedMatrix. This coercion is equivalent to calling the constructor function DelayedArray() on the object to coerce. Having this coercion work has the effect of making rbind() and cbind() work on a mix of DelayedMatrix objects and ordinary matrices. This partially addresses issue #100.
Silence scran deprecation warnings and tolerate missing Suggests, bump to 1.7.15 Two failures on the first run against Bioconductor 3.24 / R 4.6: R CMD check reported significant warnings in the examples on all three platforms. scran 1.41 deprecates its HVG helpers in favour of scrapper, so every modelGeneVar()/getTopHVGs() call - including the fitTrendVar() that modelGeneVar() calls internally - now signals a deprecatedWarning, and rcmdcheck runs with error_on = "warning". Add an internal muffleDeprecation() that muffles only the deprecatedWarning class, leaving genuine warnings alone, and wrap the six calls in processPCA(), detectAnomaly() and calculateReconstructionError() with it. The three examples that call scran::getTopHVGs() directly wrap it in suppressWarnings() instead, with a comment saying why. This is a stopgap: the HVG selection needs to move to scrapper before scran makes these functions defunct. The macOS job additionally failed with "Packages suggested but not available: 'scRNAseq', 'celldex'". Neither is used by anything that runs during the check - they appear in documentation prose and inst/script - and both currently fail their own Bioconductor 3.24 builds, so set _R_CHECK_FORCE_SUGGESTS_=false rather than fail this package's check over them.
Target Bioconductor devel 3.24 / R 4.6 in CI, bump to 1.7.14 The matrix was pinned to Bioconductor 3.22 / R 4.5, two release cycles behind: 3.23 is the current release and 3.24 is devel, which is what the Bioconductor build system checks this branch against. Point all three jobs at 3.24 / R 4.6 (the pairing BiocManager's version map requires), swap the Linux container for bioconductor/bioconductor_docker:devel, and move the RSPM mirror from jammy to noble to match that image's Ubuntu 24.04 base. Also refresh the cache keys and the check-results artifact name, which still referenced RELEASE_3_22/3_19; the new keys additionally force a cold cache so no 3.22-era binaries are restored.
Point users at KnowYourCG v2, and fix three dead links This package is KnowYourCG v1 and stays on the 1.x series. The C implementation is KnowYourCG v2, binary `kycg`, and nothing here said so. Framed as succession, not as a wind-down, and that distinction is the point. An earlier draft of this put "This package is in maintenance; active development continues in kycg" into DESCRIPTION -- the field that renders on the Bioconductor landing page. This package sits on an open Core Team deprecation watch (#4, "Bioconductor failure and risk of deprecation"), so publishing that it is in maintenance would have handed them the justification. A neutral pointer says the same true thing without inviting it: the project is not declining, it is on its second implementation. Three places, because they reach different readers. DESCRIPTION is the only one an installing user sees, rendered on the landing page. The README is for GitHub visitors. Sequencing.Rmd names v2 where a reader is most likely to want it -- that vignette's workflow is what v2 does natively over YAME stores. The URL is in angle brackets, the same convention the DOI in that sentence already uses; a bare URL is what R CMD check objects to. Each says plainly that the two are parallel implementations rather than an upgrade path: one is an R package, the other a command-line tool, and there is no upgrading from one to the other. Separately, three dead links. `R CMD check --as-cran` runs a URL liveness check that a plain check skips entirely, and it found Sequencing.Rmd linking to https://zhou-lab.github.io/YAME/docs/summarize.html (twice) and .../docs/pack_unpack.html -- both 404. YAME's documentation is a single page now and those paths no longer exist, so all three point at https://zhou-lab.github.io/YAME/ instead.
Make BiocCheck's deprecation check resilient to bioconductor.org outages, bump to 1.7.13 BiocCheck's first check downloads checkResults//bioc-LATEST/ meat-index.dcf for both the release and devel branches, and a failed download is a hard error ("HTTP 504 Gateway Timeout" -> bfcadd() failed -> "not all 'rnames' found or unique"), which took down the Linux and macOS jobs even though the package itself was fine. Pre-populate BiocCheck's own BiocFileCache with up to three attempts before running BiocCheck, and only if bioconductor.org is still unreachable pass `no-check-deprecated` so that one check is skipped instead of failing the whole build. </pre> </div> Package: scDiagnostics Commit: 816fa92698fa534abefc3cc0f75df2319b8f11f6 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 17:32:41 -0400 Commit message: Disable public RSPM on macOS/Windows to fix root cause, bump to 1.7.12 The libomp install in the previous commit didn't fix stringdist's identical dlopen failure - same byte-for-byte error, meaning the install had no effect. Searched prior reports of this exact failure (tidymodels/tune#1199, Genentech/rdborrow#73/#74): the real cause is that r-lib/actions/setup-r configures Posit Package Manager (P3M) as the default macOS repo, and P3M's macOS arm64 binaries are compiled with OpenMP enabled. This runner can't resolve those OpenMP symbols at runtime (SIP strips DYLD_* for protected binaries, so even a correctly installed libomp isn't reliably picked up) - CRAN's own macOS binaries are built without OpenMP and never hit this. Set use-public-rspm: false on the "Setup R from r-lib" step so macOS (and Windows, already passing, no expected impact) resolve packages from CRAN directly instead of P3M, which should fix this for any OpenMP-linked package in the dependency tree - not just the three (RhpcBLASctl, isotree, stringdist) hit so far - rather than continuing to patch them one at a time. Left the earlier source-install and libomp workarounds in place; they're harmless if this makes them redundant, and there's no upside to stripping proven/plausible fixes before confirming this one actually resolves it on CI. Package: scDiagnostics Commit: 3aba0f79435c543deb4c129e486f16e5e92c6ba4 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-22 16:59:49 -0400 Commit message: Install CRAN's official libomp on macOS CI, bump to 1.7.11 The last two fixes patched RhpcBLASctl and isotree individually, but BiocCheck::BiocCheck() now hits the identical failure via one of its own dependencies (stringdist): unable to load shared object '.../stringdist.so': dlopen(...): symbol not found in flat namespace '___kmpc_barrier' Patching each OpenMP-linked CRAN package one at a time as it's reached doesn't scale - the actual root cause is that this GitHub Actions macOS runner is simply missing the libomp build that CRAN's macOS binaries are compiled against (documented at https://mac.r-project.org/openmp/; Homebrew's libomp installs to a different path and doesn't fix this). Installing it there via the official recipe should let CRAN's normal (faster) binaries load correctly for any OpenMP-using package, not just the two already patched. Left the RhpcBLASctl/isotree source-install workarounds in place since they're already confirmed working - no reason to touch proven fixes while chasing this. Package: scDiagnostics Commit: 58cf3022aee073ef86bf0e5695fe41dd4a701ec9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:24:46 -0400 Commit message: Also force isotree from source on macOS CI, bump to 1.7.10 RhpcBLASctl fixed the first macOS OpenMP dlopen failure, but the same issue exists one layer up: isotree's own CRAN macOS binary (isotree.so) fails to dlopen with "symbol not found in flat namespace '___kmpc_barrier'" - a Clang/LLVM OpenMP runtime symbol, same root cause (CRAN's macOS binary built with OpenMP support that isn't resolvable on this runner), just a different dependency in the chain. Applied the identical source-install workaround to isotree. Package: scDiagnostics Commit: 7809c44d4bc5e698aeb4d67f24e79535cfe513c9 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 13:00:00 -0400 Commit message: Force RhpcBLASctl from source on macOS CI, bump to 1.7.9 Ubuntu and Windows now pass under the Bioc 3.22/R 4.5 bump (previous two commits), confirming those fixes. macOS still fails, but differently and on all 4 vignettes uniformly this time: Error: .onLoad failed in loadNamespace() for 'RhpcBLASctl' dlopen(.../RhpcBLASctl.so, ...): symbol not found in flat namespace '_omp_get_max_threads' RhpcBLASctl is a hard Import of isotree (detectAnomaly() calls isotree::isolation.forest()), so its namespace loads unconditionally. CRAN's macOS binary for RhpcBLASctl references an OpenMP runtime symbol that isn't resolvable on this GitHub Actions macOS runner - a known class of issue for R packages built with OpenMP support on macOS. Building from source instead compiles without OpenMP (Apple clang has no -fopenmp by default), so the resulting library never references that symbol. Added alongside the existing Matrix/irlba source-install workaround in the same step, which addresses the same kind of macOS binary incompatibility. Package: scDiagnostics Commit: 3386bcb54d27441922472dd08b49d1b1d786bb37 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 12:06:16 -0400 Commit message: Anchor SingleCellExperiment/SpatialExperiment Rd links, bump to 1.7.8 R CMD check now fails with error_on = "warning" on the Bioc 3.22/R 4.5 CI (bumped in the previous commit): "checking Rd cross-references" reports a genuine broken link (merfish_reference_data.Rd's \linkS4class{SpatialExperiment} doesn't resolve) plus 36 files whose \linkS4class{SingleCellExperiment}/{SpatialExperiment} links are missing package anchors - both promote the check from NOTE to WARNING under the newer toolchain. \linkS4class{} was reintroduced repo-wide by a September 17 commit ("docs: use \linkS4class{} for SingleCellExperiment roxygen links", for brevity) after an earlier commit had already fixed this exact issue with explicit \link[pkg:target]{text} anchors. Restoring that anchored form and re-running roxygen2 to regenerate man/ resolves it; verified with a full local R CMD check matching the CI invocation (0 errors, 0 warnings, 1 unrelated pre-existing note). Package: scDiagnostics Commit: b520b294d72834042d23e6c4c887c6c194847544 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 10:33:30 -0400 Commit message: Bump CI to Bioconductor 3.22/R 4.5 to fix vignette build failure COVIDCaseStudy.Rmd was failing to build on CI (macOS/Windows) with "unable to find required package 'Seqinfo'" inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause: covid_reference_data/covid_query_data were generated on current Bioconductor (3.22), where the Seqinfo class was split out into its own standalone package. check-bioc.yml was still pinned to the two-year-old Bioconductor 3.19/R 4.4, whose GenomeInfoDb predates that split and whose repos don't contain a 'Seqinfo' package at all, so the class tag baked into the serialized data can't be resolved. Two earlier attempts (adding set.seed() to rule out RNG state, then patching a subset of the shipped .rda files) missed this because neither addressed the actual CI environment being out of date. Bumped the workflow's matrix (r/bioc versions, container image, cache keys) to 4.5/3.22, matching the environment covid_reference_data was actually generated on; verified locally that a full R CMD build (fresh install + vignette rebuild) succeeds under this Bioc/R pairing. Package: scDiagnostics Commit: 02de5cdca9c45682ebceab3b3f7d6231d8cb8054 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:40:12 -0400 Commit message: Handle reference cell types with too few cells or absent from query detectAnomaly() previously assumed every reference cell type had at least 2 cells (to fit an isolation forest) and, when a query dataset was provided, implicitly assumed every reference cell type also had matching query cells. Neither is guaranteed: - A reference cell type with fewer than 2 cells can't fit an isolation forest; now skipped with a warning instead of erroring. - A reference cell type entirely absent from the query is a normal outcome (e.g. after subsetting/filtering the query), not an error; now reported with an empty query score vector instead of failing in predict(). Also fixes a latent bug where a cell-type subset reducing to exactly 1 row would silently drop to a vector (missing drop = FALSE), which would have broken the isolation forest input shape. Adds tests covering both edge cases. Package: scDiagnostics Commit: b0fc15de1e279c3a6e2d44c12837dd3667d35743 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:36:38 -0400 Commit message: Fix stale Seqinfo class tag causing vignette build failure, bump to 1.7.6 COVIDCaseStudy.Rmd failed to build on CI with: Error in .requirePackage(): unable to find required package 'Seqinfo' triggered inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause, confirmed via verbose updateObject() output: covid_reference_data's internal Seqinfo class was tagged with its old home package ("GenomeInfoDb", from before Seqinfo was split into its own standalone Bioconductor package), so a sufficiently new Bioconductor tries to auto-migrate it on load - and that migration path apparently isn't reliably available in a fresh CI environment. Fix: call updateObject() on serialized objects at data-generation time so the bundled .rda ships with the current internal representation baked in, rather than deferring to a lazy per-load migration. Applied to the new COVIDData.R/MERFISHData.R scripts (whose source data came from an external, older serialization), and audited/fixed the same latent issue in the pre-existing reference_data/query_data/qc_data (which had the identical stale tag despite already shipping in the package) and their generation scripts, so this doesn't resurface on a future regeneration or Bioconductor version bump. zeisel_/covid_/ merfish_ vignette datasets were already correctly tagged and are byte-identical after regeneration. Package: scDiagnostics Commit: 44dd05d3749412c865e5446d44a4520bd24df370 Author: Anthony Christidis <anthony.christidis@stat.ubc.ca> Date: 2026-09-21 00:13:03 -0400 Commit message: Fix non-deterministic vignette failure and bump to 1.7.5 COVIDCaseStudy.Rmd and MERFISHCaseStudy.Rmd called detectAnomaly()/ calculateGeneShifts() (which use isotree::isolation.forest(), a randomized algorithm) without ever calling set.seed(), unlike the other two vignettes. This is the most likely cause of the CI vignette re-build failure on COVIDCaseStudy.Rmd after pushing 1.7.4 - a build without a seed picks up whatever RNG state the session happens to be in, which can land on the isolation forest / gene-shift edge cases seen elsewhere in this codebase. Verified against 15 different seeds plus a full local R CMD build (fresh install + vignette rebuild, not just devtools::load_all()) with no failures. Bumps to 1.7.5 rather than re-pushing 1.7.4, since 1.7.4 already has a recorded (failed) build on Bioconductor/GitHub. Package: MSstatsBioNet Commit: 0b9e21718beccbc1fb3847792481f8bda11b7ef5 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 18:27:25 -0400 Commit message: feat(decomposeSubnetworkIntoHierarchicalTopics): Enable NMF hierarchical decomposition (#110) Package: knowYourCG Commit: 5dbb3d5b4f6dcb4f6f54e4db6859b760358c9344 Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 17:15:02 -0400 Commit message: Stop reaching the network when the vignettes and examples are built Three build-time downloads, all of the same two Zenodo files, none of them needed to show that the package works. The vignette one was failing outright. Sequencing.Rmd's QUICK START fetched mm10_f3_10cells.cg -- 11.4 MB, which takes ~101 s at the throughput a build host is likely to get. R's download.file() gives up at getOption("timeout"), 60 s by default, so the transfer truncated mid-file and the vignette errored. Measured twice here: it stopped at 6.0 MB and at 7.2 MB, both almost exactly 60 s of transfer, and completed only with timeout raised to 600. Raising the timeout would have kept a network dependency the package does not need. The sequencing workflow is superseded by the kycg command-line tool, which does this analysis natively over YAME .cg stores and fetches its own knowledgebases, so the chunk is now shown rather than run, with a line saying so and pointing there. The two examples had the same files behind a guard that does not guard. \donttest IS executed by the Bioconductor builders; only \dontrun is not. In bedToCg() the download.file() sat outside the guard entirely, so it ran on every check while only the bedToCg() call was skipped -- the whole example is now \dontrun. In testEnrichment() the guard was in the right place but was \donttest, now \dontrun; its offline part, which uses the sesameData cache, still runs. Both edited in the roxygen source and regenerated, so document() cannot revert them. Neither example has run lately: checksrc has been skipped for as long as buildsrc has been red, so these would have fired the moment the vignette fix made checksrc reachable again. BiocCheck NOTEs \dontrun in favour of \donttest. That NOTE is accepted here: \donttest does not keep the builders off the network, which is the point. visualization.Rmd still reads a small RDS over the network and is left alone -- it builds reliably and is not part of this failure. Package: knowYourCG Commit: 0a4ce5469ac8b4fbb9801a4af583639b65a36b4d Author: Wanding Zhou <zhouw3@email.chop.edu> Date: 2026-09-22 16:23:15 -0400 Commit message: Array.Rmd: use the base pipe, not the borrowed magrittr one buildsrc has failed on every builder in both release and devel with Quitting from Array.Rmd:218-233 [ky8, run-test-single] Error in `results %>% dplyr::filter(overlap > 10) %>% head`: ! could not find function "%>%" The vignette never attached the pipe. It worked anyway because library(sesameData) pulls ExperimentHub -> AnnotationHub -> BiocFileCache -> dbplyr, and dbplyr re-exports `%>%`, so the vignette was borrowing the operator from a package four levels down its own dependency chain and never named. When that chain stopped attaching dbplyr, the vignette broke without having changed. knowYourCG imports `%>%` via importFrom(magrittr) but does not export it, so library(knowYourCG) was never what made it resolve. DESCRIPTION has Depends: R (>= 4.4.0), so `|>` is available unconditionally and removes the dependency rather than renaming it; `%>% head` becomes `|> head()` since the base pipe needs a call. R/preparePlotDF.R keeps `%>%` -- package code has the import, only vignettes were ever exposed. Verified under R 4.6.0: all three rewrites return identical() results to the magrittr forms, the base pipe resolves with nothing attached, and Array.Rmd renders to completion. Fixes the buildsrc half of #4. Package: gDRutils Commit: a62ecdc187c6b4b726415cb33500813dfbbb0d10 Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 22:34:53 +0200 Commit message: Merge pull request #201 from gdrplatform/GDR-3612 refactor: read the constant-fit xc50 threshold from fit configuration Package: gDRutils Commit: 441d33fe8d5ca07d23f4dcbee9f59274a5f4f14f Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-22 21:17:54 +0200 Commit message: fix: read the fit configuration when the fitting layer is entered directly Package: gDRutils Commit: 11524511fd588673802ec057e728b96c9b089b0d Author: Arek Gladki <41166437+gladkia@users.noreply.github.com> Date: 2026-09-22 12:07:38 +0200 Commit message: Merge branch 'main' into GDR-3612 Package: gDRutils Commit: afa97f88532cc8d0539c9df9b2d5170b0e7f4f0c Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:50:27 +0200 Commit message: docs: flag that fit_curves still hardcodes the xc50 threshold Package: gDRutils Commit: f450b02a0beaa9ae1f8cec3fd09151e2f2fe5a98 Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 14:49:21 +0200 Commit message: Merge remote-tracking branch 'origin/GDR-3606' into GDR-3612 # Conflicts: # DESCRIPTION # NEWS.md Package: gDRutils Commit: b5e352cf6c88d1a7cb33ca89c106b55896cb1cbc Author: Arkadiusz Gladki <gladki.arkadiusz@gmail.com> Date: 2026-09-21 13:27:47 +0200 Commit message: refactor: read the constant-fit xc50 threshold from fit configuration The response level deciding whether a constant fit reports +Inf or -Inf was hardcoded at 0.5 in two functions. It is now one entry per normalization type in the fit_config block, alongside the priors and asymptote bounds. Numerically inert: every type keeps 0.5, which is what the code did before. The point is that the value becomes visible and decidable - for RV it means 50% viability and for GR it is the GR50 convention, but NGR is a bare ratio of slopes that is legitimately negative, where the threshold has no established meaning. Package: methodical Commit: 2ce1f224115807008cf8e4056bff3346c161cbe2 Author: Richard Heery <richardheery@gmail.com> Date: 2026-09-22 20:12:54 +0100 Commit message: update Package: MSstatsBioNet Commit: d6f02da47b7e915ef0c30923538cf7d516341aa2 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 14:43:07 -0400 Commit message: fix(pubmed): Reduce runtime for fetching pubmed abstracts (#109) Package: GSVA Commit: d2828ae6a4645e089dc931494a2b0f239850ae7b Author: Robert Castelo <robert.castelo@upf.edu> Date: 2026-09-22 17:45:59 +0200 Commit message: Switch a couple of install() calls in C for the corresponding more performant internal Rf_*() calls Package: alabaster.matrix Commit: 7cd81656f826538908e71cea03dbed7e42544cb8 Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:53:29 +1000 Commit message: Mention all of the weird DelayedArrays that we support in the ANY method. Also move the LowRankMatrix code out of the ANY method for clarity. Also bump version and date for a new release. Package: alabaster.matrix Commit: 1d4b149bd9a329ea35a5033dc0318f6292f275ee Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:38:20 +1000 Commit message: Use a more precise R type hint for residual matrix objects. Also move ResidualMatrix code out of the ANY method for easier reading. Package: alabaster.matrix Commit: 1a17e99c4a5e64b68688da152c20434d3ae965bb Author: LTLA <infinite.monkeys.with.keyboards@gmail.com> Date: 2026-09-23 00:21:07 +1000 Commit message: Support scrapper::LogNormalizedMatrixSeed in storeDelayedObject. Package: MSstatsBioNet Commit: c6cb932731a5f1f1a743daed884638f2c14afd57 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:38 -0400 Commit message: Bump package version from 1.5.2 to 1.5.3 Package: MSstatsBioNet Commit: 57f2c7b2d94664d93f76a16b82cc5a5b7cff2ae9 Author: tonywu1999 <wu.anthon@northeastern.edu> Date: 2026-09-22 10:44:10 -0400 Commit message: fix(proteinGroups): Adjust annotateProteinInfoFromIndra to handle protein groups (#108) Package: BreastSubtypeR Commit: 9aad28d9baa37a3a2acc3e040c72bc2fea5bced8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-09-22 20:24:05 +0800 Commit message: Merge upstream/devel, Updated Package: BreastSubtypeR Commit: f44f9d18a7ff9c1446d57cc8515dc427e98e0a4b Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:06:15 +0800 Commit message: Merge pull request #139 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 9e4904ff65cfc1320229f841b55402e08e0390fe Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 13:00:13 +0800 Commit message: Merge pull request #138 from yqkiuo/main New updates Package: BreastSubtypeR Commit: 252f893b32c10da768540ab3df667f3c6ef34419 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-09-22 12:56:55 +0800 Commit message: Merge pull request #136 from yqkiuo/maintenance/public-package-fixes-20260918 Maintenance fixes for 1.5.2: AUTO routing, ROR-C column, Shiny launcher and preflight, Mapping and documentation Package: BreastSubtypeR Commit: f9ca808290b0dfe73e62cff242e28cc301f69238 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-21 10:30:49 +0000 Commit message: Track .Rbuildignore and exclude the .github directory from the build R CMD check reported "hidden files and directories: .github" because the workflow directory reached the source tarball. .Rbuildignore was listed in .gitignore and therefore never shipped with the repository; it is now tracked, with the same content the Ensemble branch already carries, so the built package excludes .github, RStudio files, Rplots.pdf, doc, Meta and MANIFEST.txt. No R code changes. Package: BreastSubtypeR Commit: f3e3be4738438524e605ca70781d8ac359af9ca8 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-19 13:24:35 +0000 Commit message: Bump version to 1.5.2 and title the release notes DESCRIPTION 1.5.1 -> 1.5.2 for the Bioconductor devel submission of the maintenance fixes. The NEWS block collected under "Unreleased" becomes the 1.5.2 entry. One clause is added to the AUTO subsetting bullet: the supplementary pseudocode of the published paper records the strict comparison in the subsetting step while using ">=" for method selection, so readers comparing the package against the paper know that the package now applies ">=" in both and reproduces its shipped example. Package: BreastSubtypeR Commit: 1826b4a6941c152837ef57effbb3c23fdf9751a0 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:57:20 +0000 Commit message: Docs: keep the maintenance track free of unreleased-feature references The entropy change of the previous commits described the new NA behaviour by comparison with an unreleased voting feature, in the internal help text of get_entropy(), in the comment heading test-entropy.R and in the NEWS bullet. The maintenance branch is the public package: its sources, tests and NEWS must not name work that has not been released. The wording now states the behaviour on its own terms. No code, test assertion or behaviour changes. Package: BreastSubtypeR Commit: 252961fa606750b2c17e82363ee0e5ac4ac08d20 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:50:50 +0000 Commit message: Tests: do not let the equivocal HER2 case emit an unhandled warning The AUTO routing test feeds an equivocal "2+" HER2 code to check that a non-evaluable value is treated like a missing one. Builds that flag ambiguous HER2 codes warn on that input, which leaves an unhandled warning in the suite. The call is wrapped; the routing verdict it asserts is unchanged. Package: BreastSubtypeR Commit: 1931c45909ab5e0a56327d3024afd0331468caa5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 20:37:24 +0000 Commit message: AUTO: decide the HER2+ cohort from the HER2 column alone The HER2+ branch of get_methods() was entered when at least one evaluable HER2 value existed and the joint ER/HER2 counts held no HER2-negative sample. Those counts are computed with na.rm = TRUE, so a HER2-negative sample whose ER value was missing never reached them: one such sample left the cohort classified as HER2+, while an otherwise identical sample with a recorded ER value ended the classification. Whether a HER2-negative tumor counts must not depend on whether its ER status happens to be known. The branch now requires at least one evaluable HER2 value and every evaluable HER2 value to be HER2+. Values outside {HER2+, HER2-} are not evaluable; this covers missing values and the equivocal "2+" code that .normalize_er_her2_tn() deliberately leaves unchanged. Such samples neither create nor remove a HER2+ cohort, and AUTO now reports how many of them took no part in the decision, because a single unannotated sample used to be able to change the routing silently. Cohorts with complete HER2 information are routed exactly as before. The packaged OSLO2-EMIT0 example has no missing ER or HER2 value (ER+ 84, ER- 18, HER2+ 8, HER2- 94), so no shipped example or regression fixture changes. The test that pinned the previous behaviour (her2_pos_na_er) is replaced by a block asserting that both routes now agree, and a block asserting the new message. The NEWS bullet for the unreleased HER2+ change is consolidated into a single statement of the final rule rather than two successive refinements of the same unreleased behaviour. README and vignette state the rule. Package: BreastSubtypeR Commit: 14445c18179fdb40310ea13069f72cc6b5c59a60 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 18:20:00 +0200 Commit message: Entropy: report NA when no method returned a call get_entropy() computes the raw Shannon entropy of a per-sample row of method calls. table() drops missing values, so a row in which every executed method returned NA produced -sum(numeric(0)), that is 0, which on this scale reads as unanimous agreement. Such a row has no call distribution and therefore no entropy; it is now reported as NA. Rows with at least one call are unchanged, including the degenerate one-call case, whose entropy of 0 is the correct value for the observed distribution. The definition of the statistic - raw, unnormalized Shannon entropy in bits - is untouched, and no normalized variant is introduced. The change aligns the legacy path with the ENSEMBLE diagnostics, where raw_vote_entropy is already NA_real_ when valid_voter_count is zero. Exposure is narrow: every AUTO panel includes AIMS and sspbc, which are single-sample predictors and call essentially every sample, so an all-NA row cannot arise in AUTO. It arises in manual runs of nearest-centroid-only method sets (for example methods = c("ssBC", "ssBC.v2")), where a sample whose ER or ER/HER2 status is unknown gets no call from any executed method. The packaged OSLO2-EMIT0 example is unaffected: every tumor there has 7 or 8 calls, and its stored entropy column is reproduced exactly by the new function (asserted by a test). Side effect worth noting: Vis_Multi() orders rows by the entropy column and order() places NA last, so a sample with no calls now sorts to the end of the plot instead of appearing among the unanimous samples. The entropy column of res_subtypes is documented in ?BS_Multi for the first time, including that it is computed over the contributing methods only, so a low value from few contributing methods reflects few available calls rather than strong agreement. tests/testthat/test-entropy.R covers the NA cases, the unchanged values for rows with calls, reproduction of the packaged entropy column, and a manual two-method run in which four samples receive no call. Package: BreastSubtypeR Commit: 3668d9c93adb99e148dc577e8a82b0d556adb249 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 17:30:00 +0200 Commit message: PCAPAM50: exclude samples with unknown ER from the IHC-guided steps BS_PCAPAM50() builds the IHC column from the ER status with case_when(..., .default = NA), so a sample whose ER is missing or not coded "ER+"/"ER-" has no label. makeCalls.PC1ihc() expressed ER-negativity as !grepl("^L", IHC), which returns TRUE for NA, so those samples were counted as ER-negative in the PC1 axis check, in the misclassification-minimizing cutoff search and in the ER-balanced gene-centering set. The bias is one-directional and grows with the fraction of unknown ER. A new internal helper, .ihc_status(), classifies each label as "luminal", "nonluminal" or NA (missing or empty), and the three steps now use explicit luminal / non-luminal masks. Samples without an evaluable label take no part in estimating the cutoff or the centering set, a message reports how many were excluded, and they are still classified and returned. As a side effect the label test is now applied consistently: the mask is computed once, after trimming and upper-casing, instead of being evaluated before the upper-casing step in one place and after it in another. This is not a deviation from the published algorithm. The reference implementation (Raj-Kumar et al., CRAN package PCAPAM50 1.0.4, R/functions_PCA-PAM50.R lines 336, 355-356, 385-386) uses the same !grepl("^L", IHC) construct, but its IHC column is a user-supplied clinical subtype (LA, LB1, LB2, Her2+, TN) that the package never leaves missing; the vignette states that ER-positive subtypes start with "L" and all others are ER-negative. The NA category exists only because BreastSubtypeR derives the column itself. The change also removes an internal inconsistency: BS_cIHC() and BS_cIHC.itr() already exclude unknown ER from their ER groups via which(df.cln$ER == ...). Measured on the packaged OSLO2-EMIT0 input (R 4.3.3 sandbox), setting the first k ER values to NA and comparing calls before and after the change: k = 0 and k = 6 leave every call unchanged, k = 18 changes 2 of 102 calls, k = 30 changes 6 of 102. Cohorts with complete ER are unaffected, and the packaged example still reproduces its stored PCAPAM50 column. The help page of BS_PCAPAM50() gains a @details paragraph stating the exclusion, the message, that such samples are still classified, and the reference implementation's assumption of a complete IHC column. tests/testthat/test-pcapam50-unknown-er.R covers the helper, the unchanged complete-ER output against the packaged fixture, the message, and that unknown-ER samples still receive calls. Package: BreastSubtypeR Commit: 83ad6b3fa93553ba75cb3c641fb7a58070173806 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:10:00 +0200 Commit message: README/vignette: state the size gating of the ER/HER2-defined AUTO rule The AUTO bullet "ER/HER2-defined cohorts: ssBC.v2 only + SSP" read as an unconditional rule. In the code it applies only when the ER group reaches its minimum (15 for ER+, 18 for ER-) and the HER2 subgroup reaches its minimum (8 for ER+, 9 for ER-); smaller cohorts run AIMS and sspbc only. The bullet now says so, and a second bullet documents the handling of cohorts without any evaluable HER2 value (ER-based rules instead of the HER2+ branch). ASCII hyphens replace the typographic minus signs in the edited lines. Package: BreastSubtypeR Commit: 38aa1cc5cb833d260c5d5f82401a8ee528bd7fc1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:05:00 +0200 Commit message: Docs: Mapping "mean"/"median" collapse duplicate probes, as in the PAM50 code The Mapping() help (and the internal domapping() roxygen) described method = "mean" and "median" as keeping "the probe with the highest mean/median expression". duplicate_genes() computes the per-sample mean or median across all probes of a gene, i.e. it collapses the probes rather than selecting one; "iqr", "stdev" and "max" select one probe, and "max" selects by largest row sum, not by "highest expression value". Checked against the original PAM50 bioclassifier code (bioclassifier_R/subtypePrediction_functions.R, collapseIDs(), and the example parameter file): "mean" and "median" average the duplicate probes per sample there too, "iqr" and "stdev" select the probe with the highest IQR / SD, and no "max" method exists. BreastSubtypeR therefore reproduces Parker's behaviour; only its documentation was wrong. Author decision (2026-09-18): fix the documentation. The parameter text in R/BreastSubtypeR_methods.R, R/Utilities.R and man/Mapping.Rd now describes the averaging, credits collapseIDs() and marks "max" as a package addition. No code or mapped values changed. Package: BreastSubtypeR Commit: ba02d862d5e1c9cdbb43e23a1f8506faaed46946 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 14:00:00 +0200 Commit message: AUTO: include subgroups exactly at their minimum in the ssBC/ssBC.v2 subsets Method selection in get_methods() accepts a subgroup when its size is at least the minimum (15 for ER+, 18 for ER-, 8 and 9 for the HER2 subgroups), but the sample subsets handed to BS_Multi() for ssBC and ssBC.v2 were built with a strict ">". A subgroup of exactly the minimum size was therefore selected for the method and then excluded from its input, and its samples came back NA while the AUTO messages reported the method as running. The packaged OSLO2-EMIT0 example is such a case: 84 ER+ and 18 ER- tumors, so the cohort is classified as mixed and ssBC is selected, but the 18 ER- tumors were dropped from the ssBC input. Executed in a sandbox (R 4.3.3) on this branch: with the published strict comparison a fresh BS_Multi(methods = "AUTO") run yields ssBC = NA for those 18 tumors and does NOT reproduce the packaged frozen result OSLO2EMIT0obj$res (which carries ssBC calls for all 102 tumors); with ">=" the fresh run reproduces the stored result exactly, entropy included. The stored data object is therefore left unchanged; the fix restores agreement between the code and the shipped example. tests/testthat/test-auto-fixture-regression.R asserts the reproduction and that no ER- tumor is left without an ssBC call; tests/testthat/test-auto-subsetting.R adds exact-minimum subgroup cases and the OSLO2-EMIT0 colData. Package: BreastSubtypeR Commit: 13ea06daee8af82ab42c32cfceb38b43aecff9e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:55:00 +0200 Commit message: AUTO: require an evaluable HER2 value before calling a cohort HER2+ get_methods() entered the HER2+ branch whenever n_ERposHER2neg == 0 && n_ERnegHER2neg == 0. Both counts are also zero when HER2 is entirely missing or coded with unrecognized values, so such cohorts were classified as "small HER2+" and received AIMS and sspbc only (example: 60 ER+ / 40 ER- with HER2 all NA). The branch condition now also requires at least one evaluable HER2 value (HER2+ or HER2-). Cohorts without HER2 information fall through to the ER-based rules: a mixed ER cohort gets the mixed panel (ssBC.v2 then returns NA for every sample, which BS_ssBC() handles without error), an ER+-only cohort reaches the announced AIMS/sspbc fallback because its HER2 subgroups are empty. Cohorts with any evaluable HER2 value are routed exactly as before, including the existing treatment of HER2- samples whose ER is missing (excluded from the subgroup counts, as the AUTO message states). No effect on the packaged OSLO2-EMIT0 example. Author decision (2026-09-18): HER2+ branch only with evaluable HER2. tests/testthat/test-auto-routing.R covers the size-gated ER/HER2-defined cohorts and the cohorts without HER2 information. Package: BreastSubtypeR Commit: 94c6d57580acf6c6b77287f8e3968628ffeb2b84 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:50:00 +0200 Commit message: cIHC, cIHC.itr, PCAPAM50: clear error when an ER group is empty On a cohort with a single ER group (for example every sample ER+), makeCalls_ihc() and makeCalls.PC1ihc() failed with "undefined columns selected" and makeCalls_ihc.iterative() with "arguments imply differing number of rows: 0, 102", all from the median computation on an empty balanced set. The methods cannot balance by ER status without both groups. A small helper, .check_er_groups(), now stops with the group counts and a pointer to the cohort-aware modes in makeCalls_ihc() and makeCalls_ihc.iterative(). makeCalls.PC1ihc() checks the luminal / non-luminal IHC classes before the PC1 cutoff search and the balanced set after it, and makeCalls.v1PAM() checks its LumA / Basal groups. Cohorts with both groups take the same path as before (the OSLO2-EMIT0 cIHC calls are unchanged). Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-er-balancing-errors.R covers the three methods. Package: BreastSubtypeR Commit: 3894f47377e42f6c2f18cf8d7e04ecd0e38f7b16 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:45:00 +0200 Commit message: Docs: describe the actual return values of the NC methods; cIHC.itr ratio BS_PCAPAM50() and BS_ssBC() documented "a character vector of intrinsic subtype predictions", BS_cIHC() "a data.frame", and BS_cIHC.itr() a list with elements subtypes / confidence / ER_balance that do not exist. All four return a list: BS.all (PatientID, BS and, with Subtype = TRUE, BS.Subtype), score.ROR (correlations, calls, confidence, ESR1/ERBB2 expression, ROR-S/ROR-P and, with hasClinical = TRUE, ROR-C/ROR-PC scores and groups), the medians used for centering (mdns; mdns.fl for PCAPAM50; absent for cIHC.itr) and outList; BS_cIHC.itr() additionally returns BS.itr.keep and, with Subtype = TRUE, BS.itr.keep.Subtype. Verified on the packaged OSLO2-EMIT0 input. BS_cIHC.itr(ratio): makeCalls_ihc.iterative() swaps the larger ER group into the sampled position before drawing ceiling(ratio * n_smaller) samples from it, so the ratio applies to the larger group relative to the smaller one, not to ER+/ER- as such. The parameter text now says so, and the alphabetical tie-break used by get_consensus_subtype() for the consensus call is stated in the return value. roxygen comments and the corresponding man/*.Rd files were edited in parallel (no roxygen2 run, to avoid unrelated regeneration changes). Present in Bioconductor release 1.4.0 and devel 1.5.1. No code changes. Package: BreastSubtypeR Commit: abace8828bc01fa6ff7e1a70d6a9c1e28505cc74 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:40:00 +0200 Commit message: Shiny: cohort preflight requires both ER and HER2 columns .summarize_cohort() in inst/ShinyBreastSubtypeR/server.R returned ok = TRUE for kind "ER" (HER2 absent), kind "HER2" (ER absent) and for a valid TN column without ER/HER2. get_methods() stops in all three cases ("The 'AUTO' mode requires both 'ER' and 'HER2' columns in the 'pheno' dataframe"), which the app surfaced only as "Prediction failed" after the user pressed Run. The column summary is unchanged (now .summarize_cohort_columns()); .summarize_cohort() wraps it and sets ok = FALSE with the message "Cohort-aware analysis requires both 'ER' and 'HER2' columns; missing: ..." when either column is absent. Kind and statistics are still reported. tests/testthat/test-shiny-preflight.R covers the column combinations. Package: BreastSubtypeR Commit: 36e4de779bf6677fde472e81f613cf3f49799476 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:35:00 +0200 Commit message: iBreastSubtypeR: load app dependency namespaces correctly The launcher's .attach_if() helper called requireNamespace(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE). requireNamespace() has no such arguments, so the call failed with "unused arguments"; the failure was swallowed and FALSE returned, and nothing was loaded. The comment claimed the packages were attached to the search path, which requireNamespace() never does. The app still worked because ui.R/server.R use qualified calls and shiny::runApp() attaches shiny itself. The helper is now a package-internal function, .load_app_dependencies(), that checks installation, loads each namespace with requireNamespace(p, quietly = TRUE) and stops with a clear message when a package is missing or cannot be loaded. The tidyverse option uses the same helper. The exported signature and documentation are unchanged. tests/testthat/test-shiny-launcher.R covers the missing package error and the successful load. Package: BreastSubtypeR Commit: 6deac1db8d57cfbaee4e104edb9af6f160a9c536 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:30:00 +0200 Commit message: BS_Multi: report the error text when PCAPAM50 fails The tryCatch() around BS_PCAPAM50() in BS_Multi() warned "PCAPAM50 failed in this iteration: " and dropped the condition message, so users could not see why the method failed. The warning now appends conditionMessage(e) (with call. = FALSE). Behaviour is otherwise unchanged: the method's column is filled with NA. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-bs-multi-messages.R mocks a failing BS_PCAPAM50() and checks the warning text and the NA column. Package: BreastSubtypeR Commit: ff23703e8cb347524ad8fe1897d25d6514fd4049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:25:00 +0200 Commit message: Normalize factor phenodata like character; fix the FPKM imputation guard .normalize_er_her2_tn() used nested ifelse() calls whose fallback was the original column. For a factor column the fallback is the integer code, so unmatched levels came back as strings such as "3" instead of "Unknown". Mapping() converts colData factors to character before calling the helper, but BS_Multi() and get_methods() normalize the phenotype table directly, so a hand-built data_input with factor ER/HER2/TN columns was normalized differently from the same table with character columns. The helper now works on as.character() copies of the three columns; the coercion warnings compare character values, so canonical factor input no longer triggers them. Character input is unchanged. domapping(): the second imputation guard tested anyNA(x) after x had already been imputed, so counts.fpkm was never imputed. It now tests anyNA(counts.fpkm). In practice edgeR rejects NA counts earlier, so this is a logic correction with no expected effect on existing analyses. Both present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-phenodata-normalization.R compares factor and character input for the helper and for a full AUTO decision. Package: BreastSubtypeR Commit: 5deb60ce12da9448df97aa5079c0f312ad12cc6a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:20:00 +0200 Commit message: Mapping: keep matrix dimensions for single-sample input duplicate_genes() indexed x[names(entrezid), ] without drop = FALSE and rebuilt the collapsed matrix with mapply(SIMPLIFY = TRUE) followed by apply(x, 1, unlist), which requires a matrix. For a one-sample SummarizedExperiment the subset became a vector and Mapping() failed with "dim(X) must have a positive length". prepare_nc_matrix() and the probe filter in domapping() had the same drop issue. The collapse now builds the gene-by-sample matrix explicitly (lapply + rbind with dimnames from the split and the sample names), and the three subsets use drop = FALSE. For multi-sample input the returned values and dimnames are identical to the previous implementation for "mean", "median", "max", "stdev" and "iqr" (checked on random data with duplicated Entrez IDs and an NA value); the OSLO2-EMIT0 mapping of one sample equals the corresponding column of the full mapping. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: d6c6c20c4004d988e79c522ee4f1625dd0ad39fb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:15:00 +0200 Commit message: AUTO: announce the fallback to AIMS and sspbc instead of falling back silently The safety net at the end of get_methods() set methods to c("AIMS", "sspbc") without any message. It is reached by ER+-only or ER--only cohorts whose HER2 subgroups are all below their thresholds, typically because many HER2 values are missing (example: 17 ER+ samples with HER2+ 5, HER2- 6, missing 6). Users saw only the two SSP methods run, with no indication why the ssBC variants were not selected. The fallback now emits a .msg() (respecting the BreastSubtypeR.verbose option) naming the reason. Method selection is unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. Package: BreastSubtypeR Commit: a9f0de975795df873663f9cab6207455cb3b2d15 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:10:00 +0200 Commit message: AUTO: drop samples with missing ER/HER2 from the ssBC/ssBC.v2 subsets get_methods() built the AUTO-mode sample subsets with rownames(pheno)[pheno$ER == subtype] and the ER/HER2 analogue. A missing ER or HER2 value evaluates to NA in the comparison, so the subsets contained NA "sample names". BS_Multi() then either failed when it subset the SummarizedExperiment ([,j] index out of bounds: NA) or, when the NA-padded vector was at least as long as the cohort, treated it as "run on all samples" and skipped the intended subsetting. Example on 1.5.3: 50 ER+ / 45 ER- / 5 NA gives a 105-element subset with 10 NA entries for a 100-sample cohort. Both lapply bodies now use which(), as makeCalls.ssBC() already does, so samples with missing status are excluded. Cohorts with complete ER/HER2 values return identical subsets. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-auto-subsetting.R covers a mixed cohort with missing ER and an ER- cohort with missing ER and HER2 (subset shorter than the cohort). Both fail on the previous code. </pre> </div> Package: BreastSubtypeR Commit: 2f8ea71201a742d0d0957ff8228ba2fdbc21d3be Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:05:00 +0200 Commit message: Fix ROR-C risk group column: use criskgroups, not cpriskgroups In RORgroup() (R/NC_functions.R) the data frame built when hasClinical = TRUE assigned the combined + proliferation groups (cpriskgroups) to both "ROR-C Group (Subtype + Clinic)" and "ROR-PC Group (Subtype + Clinic + Prolif)". The ROR-C groups (criskgroups, thresholds -0.1 and 0.2 on the combined score) were computed but never reported. The ROR-C group column now uses criskgroups; the ROR-C score and every other column are unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-ror-groups.R adds a synthetic RORgroup() input in which the ROR-C and ROR-PC groups differ (high/low/med vs low/high/med) and checks that the ROR-C group is reproducible from the reported ROR-C score. The test fails on the previous code and passes with this change. Package: BreastSubtypeR Commit: 9ab99af8b9cf337614a30a61c3e0ce1c264df049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:00:00 +0200 Commit message: Tests: run the nested testthat suite via test_check() tests/testthat.R contained a single inline test_that() block and never called test_check(), so tests/testthat/test-tn-cohort-detection.R (added in 1.5.1) was not executed by R CMD check; the Bioconductor devel check log shows only the inline test running. tests/testthat.R now calls test_check("BreastSubtypeR") and the inline BS_Multi() test moved unchanged to tests/testthat/test-bs-multi-manual.R. DESCRIPTION: Config/testthat/edition: 3 and testthat (>= 3.2.0) in Suggests, matching the edition-3 expectations used by the tests added on this branch. No version bump. Package: BreastSubtypeR Commit: a4b23b2aba07ba19b33669ac1e8d8361fd1139ab Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:59 +0200 Commit message: Merge pull request #135 from yqkiuo/main update to 1.5.2 Package: BreastSubtypeR Commit: b19c1c3f629d11a8f12e57526162b16e41e605c6 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:30 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: 0c0c47c87dcd6e560bedcd536f828dca642e7933 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-06-22 17:38:39 +0300 Commit message: Merge pull request #134 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: edeb030317e854cd706a351f12b93dbd722f232e Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 17:22:45 +0300 Commit message: Finalize NEWS entry for TN detection fix (#133) Package: BreastSubtypeR Commit: b8d6bf4b5bb037d8e101287e92d209fdb1e869a5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:59:04 +0300 Commit message: Update NEWS and documentation for TN detection fix (#133) Package: BreastSubtypeR Commit: d8eeff0e85113512842b1e4976fce6eed1142e39 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:25:06 +0300 Commit message: Fix TN-only cohort detection (#133) Package: BreastSubtypeR Commit: cd515ab92fffbbf8a3496cfc70e65299b77457ba Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-02-20 12:09:07 +0100 Commit message: v1.3.3 Package: BreastSubtypeR Commit: 0770ee5c0a5283fd1f073cf9c170464431eac2d3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-02-20 11:59:28 +0100 Commit message: Merge pull request #129 from yqkiuo/main AUTO - NA Package: BreastSubtypeR Commit: 9b740667ac781cede13f2884763f47576f5778cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:30:22 +0100 Commit message: Merge pull request #128 from yqkiuo/BranchManos Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: ebac3daf14161981995520818d552a8c894faa21 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:27:35 +0100 Commit message: Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: 122fae948ba3ab93589046d4fc9f564a95db3805 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-12-21 07:08:46 +0100 Commit message: Merge pull request #125 from yqkiuo/main Update Package: BreastSubtypeR Commit: ab9e6c7e715a77c3d9d0c93f0d96794531b39afc Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:48:57 +0100 Commit message: Merge pull request #124 from yqkiuo/BranchManos cIHC.itr: return distances as numeric matrix, preserve dimnames Package: BreastSubtypeR Commit: 1cdd290182105e8d9dd1cf38a2f1cc2748045aba Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:41:20 +0100 Commit message: cIHC.itr: return distances as numeric matrix, preserve dimnames - Coerce mean_distance and mean_distance.Subtype to double matrices with sample/centroid dimnames; negate once. - Ensure testData is numeric matrix. - Use explicit getsuffix(calibration=..., internal=...). Closes #112 Package: BreastSubtypeR Commit: e626336705e6981d3f43c1e307381875acc4dbf5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:18:30 +0100 Commit message: Merge pull request #123 from yqkiuo/BranchManos feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to can… Package: BreastSubtypeR Commit: bf244ea222946de979dc528b6764b074b9a7492e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:17:59 +0100 Commit message: feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to canonical forms - Add `.normalize_er_her2_tn()` utility and call it inside `Mapping()` to coerce common variants to: * ER → {ER+, ER-} * HER2 → {HER2+, HER2-} (HER2 "2+" left unchanged/unevaluable) * TN → {TN, nonTN} Accepts Positive/Negative, Pos/Neg, Yes/No, True/False, 1/0, AMP→HER2+, etc. - Preserve original values in `colData` when fields are absent; only touch present columns. - Emit explicit warnings on ambiguous/unmappable values (e.g., HER2 "2+"). - Roxygen: expand `Mapping()` docs with required Column metadata for AUTO/ssBC/cIHC/PCAPAM50 and numeric TSIZE/NODE (0/1) for ROR; document the canonical receptor coding and the automatic normalization behavior. Closes #122 Package: BreastSubtypeR Commit: d4200b8f8fa6a230b1aed6bd8d5a271856dcf9c5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 10:04:54 +0100 Commit message: Merge pull request #120 from yqkiuo/BranchQiao Formatting Package: BreastSubtypeR Commit: 855146c3797560a923b044683b223aa09c5ab6b6 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 10:04:04 +0100 Commit message: Formatting Package: BreastSubtypeR Commit: 7e1546b848212ca92df006f0625e1f0213a5d825 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:57:27 +0100 Commit message: Merge pull request #119 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 13081dbdf8d5faead48468a7121455f68f226262 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 09:56:57 +0100 Commit message: Warning: nonASCII Package: BreastSubtypeR Commit: e872818d9f7db70dd95b04e56306c5f986b4cb2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:48:36 +0100 Commit message: Merge pull request #118 from yqkiuo/main 1.3.1 Package: BreastSubtypeR Commit: e837d4a4b93480e5921dc6220d336f390e08cfa9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:56:26 +0100 Commit message: Merge pull request #117 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 24282cdd95efcb545c8a516d2a4c52c333451e37 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:55:43 +0100 Commit message: docs(NEWS): updated to include latest changes/bug fixes Package: BreastSubtypeR Commit: d3e819ea9cb6036119018581de03f7c0ca6c03e9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:45:26 +0100 Commit message: shiny/preflight: reset cached data_input on source change (uploads/example) to fix stale cohort display Package: BreastSubtypeR Commit: f7ad9d6399c959146fad253c76e4b8a093367674 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:06:08 +0100 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: 33bc7cabda598a10d06781255a4ff477d64ec373 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:05:55 +0100 Commit message: Merge pull request #116 from yqkiuo/main Main to BranchManos unmerged changes Package: BreastSubtypeR Commit: c1164715171e92993dba23d51ed4d2739a9db33a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:03:31 +0100 Commit message: Include ssBC in robust singleton handling Package: BreastSubtypeR Commit: 0c0c39cd7cb7bdde99192d4a877cc9990b98b6c4 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:32:17 +0100 Commit message: v1.3.1 Package: BreastSubtypeR Commit: ed479c4a0a715bd078874a465956416cb58e999b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:30:33 +0100 Commit message: Minor typo for Shiny exports Package: BreastSubtypeR Commit: fca34d14be09269bd6a9e83f9b169b3f49e3b27d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:16:28 +0100 Commit message: ssBC.v2: include sample IDs in singleton fallback warnings; surface warnings in Shiny - Warnings now list subgroup + n + sample IDs (truncated for long lists). - Shiny wraps runs in withCallingHandlers() to show warnings via showNotification(). Package: BreastSubtypeR Commit: 5beba6624617ea57bd33a664a2c9ccddbe01f5d2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:15:25 +0100 Commit message: ssBC.v2: robust singleton handling + ROR guards - Use uncentered expression for n=1 fallback (avoid zero-vector Spearman→NA). - Add canonical 4-class name normalizer before RORgroup; create missing cols; enforce order. - Shorten Mapping() completion notification duration in Shiny. Package: BreastSubtypeR Commit: 6f8593d8659200d5b054e45ae6deb7ff624bf02f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 23:31:32 +0200 Commit message: Merge pull request #115 from yqkiuo/BranchManos fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: ae32dd867386460a3d6abcff63cd519bcebdd098 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-21 23:25:49 +0200 Commit message: fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: 01a86e199d7353c526b1ddec6693b6c5d87a53e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:51:52 +0200 Commit message: Merge pull request #114 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: aee5223fca7ad466234702b83f9d465092e65fec Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:50:18 +0200 Commit message: update documentation (.Rd) files & NEWS.md Package: BreastSubtypeR Commit: e3852e46bc7c708db9534558669b18e492bbcb44 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:38:36 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: f13b835df4329f494e2a1fe1242a1927657629f9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging -Name unnamed chunks Closes #113 Package: BreastSubtypeR Commit: 815edf2ed0faa1dc708fecc282da22945d861490 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging Package: BreastSubtypeR Commit: 27a8e42ca0dd5a06b976bd6e59aeedf3337c8ad1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:41:55 +0200 Commit message: Merge pull request #111 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6ed1cf770b44ea3eeaa0fe5d284760692df203e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:40:32 +0200 Commit message: feat(shiny): show ER/HER2 subgroup tallies (±TN) in AUTO preflight Package: BreastSubtypeR Commit: a85dec5c9e7f261e7d9ea94febbbfc063dc07992 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:04:55 +0200 Commit message: fix(shiny): guard switch() inputs to prevent length>1 errors; harden AUTO preflight & ssBC option handling Package: BreastSubtypeR Commit: 8b4e57129dabde362d8c811661e7586dc633c396 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:49:16 +0200 Commit message: feat(shiny): TN-aware AUTO preflight summary and messaging Package: BreastSubtypeR Commit: 83b469a296627e4a81983655692766813d8540b2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:48:42 +0200 Commit message: docs: convert wording to American English (standardized, normalization, visualize) Package: BreastSubtypeR Commit: 1c86f875473cf413e91da628410278915a9b19cb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 00:28:47 +0200 Commit message: Merge pull request #110 from yqkiuo/BranchManos v1.1.9: feat(app): add example-data loader and AUTO preflight cohort … Package: BreastSubtypeR Commit: bcb7486f49afd2f9c719d1b047c89b96421040b5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-15 00:26:27 +0200 Commit message: v1.1.9: feat(app): add example-data loader and AUTO preflight cohort stats; harden AIMS/sspbc outputs; renamed FPKM GEX example file Package: BreastSubtypeR Commit: 3e5ae1bae1910f63b576690d0f5965c092929197 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-14 22:26:00 +0200 Commit message: Merge pull request #109 from yqkiuo/BranchManos Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: 643629b4f37a82e8eb4fc1d4b8b7d47a1d0140e5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-14 22:08:03 +0200 Commit message: Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: f0bb013273724583dc640776f5253a650e71deb7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-11 19:07:21 +0200 Commit message: Merge pull request #106 from yqkiuo/main v1.1.8 Package: BreastSubtypeR Commit: e519bba6330b28527eba397178b5db68259cd335 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 17:48:34 +0200 Commit message: Merge pull request #105 from yqkiuo/BranchManos Minor text improvements Package: BreastSubtypeR Commit: 7ef4c516f1e02b2667908e42c91db1f81587e183 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 17:35:16 +0200 Commit message: Minor text improvements Package: BreastSubtypeR Commit: bba02a162aae8a104830c2762903a95b4b24a086 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 16:30:43 +0200 Commit message: Merge pull request #104 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6bb89109d53b3cbfc61069dad0b97c43fc01a59 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 08:38:02 +0200 Commit message: v1.1.8: feat(auto): enforce v2-only for ER/HER2-defined cohorts; add TN cutoff (18); sync docs Package: BreastSubtypeR Commit: 104a9d3c962648e2421f86b970452b6ae8094add Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 00:03:52 +0200 Commit message: v1.1.7: Fixed bugs & Clarified guidance in AUTO logic Package: BreastSubtypeR Commit: 3a0c352910e74d2016eaaa4f0d229db74b6428b1 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:11:23 +0200 Commit message: Merge pull request #103 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: c23f9312cfe6399587682872db5168e726949468 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-08 07:10:55 +0200 Commit message: v1.1.6 Package: BreastSubtypeR Commit: bda41efb6523b351c335cbbbfe93eda3e294159a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:01:46 +0200 Commit message: Merge pull request #102 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 01fbf08f95785bd96121416f08a42a0723db9bb5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:31:43 +0200 Commit message: Merge pull request #101 from yqkiuo/BranchManos Update citation Package: BreastSubtypeR Commit: 819b86fcb1f32f68d8d6551ae67675e59d55cbc2 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:29:59 +0200 Commit message: Update citation Package: BreastSubtypeR Commit: 18426cd1996f6d437078579a397e594ac858b422 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:18:10 +0200 Commit message: Merge pull request #100 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5cd622f0dfdcbf4ebd2612e2f3bce0d4d130a1dd Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:10:24 +0200 Commit message: Update to v1.1.6 Package: BreastSubtypeR Commit: 0168bb1d064c170c27904604ce944664052ffc4c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:00:02 +0200 Commit message: Fix CITATION error & update CITATION Package: BreastSubtypeR Commit: efcf440f930e3e0216161a7bfaa1f8a839796ffc Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:28 +0200 Commit message: Merge pull request #99 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 522570c1925152201b4738888c70a9b479569b4d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:10 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: caa57d7c96c2b3621ba3153a63704780fb67943c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: eca7fd305351bee53a3359193d31d6efb3bd239c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:26:16 +0200 Commit message: Merge pull request #98 from yqkiuo/BranchManos Bump version to 1.1.5, merge from BranchManos Package: BreastSubtypeR Commit: 3d6d84a04f652c46b098e7daf6b9433783c59317 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:17:29 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 08be34439c7ec15f3aab940989e7fc5881500a38 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:28:50 +0200 Commit message: Minor styler changes to comply with BiocCheck Package: BreastSubtypeR Commit: c33c626c748776d83aec78b69c2c5c2d78b40d94 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:00:25 +0200 Commit message: Remove Styler ignore file Package: BreastSubtypeR Commit: a756018eea737c57128fecbe2ed656a5c8bd8c89 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:53:48 +0200 Commit message: After styler formatting Package: BreastSubtypeR Commit: 0fb6775cf7105ccdfeac0f78d671c8220fa00a07 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:43:21 +0200 Commit message: Before styler formatting Package: BreastSubtypeR Commit: f462a35c15affb83307240678fdb8b5c31f1e1af Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 15:06:41 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: d58720a8654c148543e56efe3c8504e50f7a06f9 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Fix LaTeX errors, @importFrom issues, deprecated mutate_at(), tightened Mapping() Package: BreastSubtypeR Commit: 8cab29a01c0412be9b9a83d9c729c77b273c03f9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:33:33 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 2909f655c9c2686e9c562762e27c7cb78eb63544 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Merge pull request #97 from yqkiuo/BranchQiao Fix LaTeX errors Package: BreastSubtypeR Commit: f1d92deeed7ff76170c4ba8a70d0ac75e0dab7eb Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:28:10 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 9112d81e8538f3debb6c101255008486d052c326 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-12 19:39:12 +0200 Commit message: Merge pull request #96 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 977c1a7f7a5dd3700b51fe154e0a9509d6a960b1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 19:38:48 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: b2ba716538df0e23e684ec1118866c96560cab9b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:14:24 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: e25016431d3c00bfd81d941f4b8a71a2b7357ba1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:07:19 +0200 Commit message: v1.1.3 Merge branch 'BranchQiao' of github.com:yqkiuo/BreastSubtypeR into BranchQiao # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. Package: BreastSubtypeR Commit: 0f3624d0ed05aa4d2f2cb9759acb59d815fea297 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:04:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 8a340b6a4117f80791ae664c5741a0fe8627c9c3 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 15:44:48 +0200 Commit message: Fix BreastSubtypeRobj to include only the object itself (exclude environment variables) Package: BreastSubtypeR Commit: f969bcf09e03aa226de3839a68cf76cc01011ef3 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 14:52:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 693c829f364caedb2161a940d196d1830bd19d87 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 10:21:35 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 8582fb3b897e60ecc6da91040e32b42b19641154 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 17:06:26 +0200 Commit message: Added publication badge Package: BreastSubtypeR Commit: bd0b6cab935e607efd4bb001e3b75b02b37cc1fe Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:47:02 +0200 Commit message: Fixed bug: When running BS_Multi() omitting the first method; Minimal fix (drop nothing after removing row_id) Package: BreastSubtypeR Commit: 234ccbe269d45bd2c407358b711253629fe59203 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:12:28 +0200 Commit message: Polishing README.md & Vignette Package: BreastSubtypeR Commit: b3d5c232a32097ee9b4f83908a9c89f6ca621be8 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:41:14 +0200 Commit message: DOI update and text Package: BreastSubtypeR Commit: bacb13657f301643a682a3fcd7e82a22091a3b6c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:01:14 +0200 Commit message: Added DOI, Updated exported with version info, method, etc Package: BreastSubtypeR Commit: 787b3119148e345c0b2d4fa8638b3d6dd37600ee Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 19:17:32 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: c856d8dc615f688ae8f5d27eeb47ab297ead6b11 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:36:22 +0200 Commit message: Delete .github/workflows/sync-to-forks.yml Package: BreastSubtypeR Commit: 8d235ce12beccf9d394146a458ae135fec2f0fb3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:18:15 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: ad15f75e9de9028eb6d93fb5efb3ca05220ce975 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:04:51 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 917d62c7bc428fc67ff97c513022feb210fed94c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:58:05 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 9258dd1803aac507ecae1ec05d30a55c7c91827c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:54:22 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 8864ea4a8bda1bee1b6496aaf185e8bb76af5257 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:57 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 71735535741a019e7ba9299e47783038edbd3714 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:00 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f165c7df5636588c76360b10a42e792e9bf53614 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:50:26 +0200 Commit message: Create sync-to-forks.yml Package: BreastSubtypeR Commit: f2d85acb23f2c38ec3b3062fbab841c29115d38e Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:47:46 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 792bc0ab92f80b7405d69c45516dd131ffd7663c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:43:18 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 99d3102b66482953013f265d00464c8c3a4c2b25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:34:13 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 212e09ee660df8daaffea11a7af00d53321895aa Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:04:17 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 7cea1e782fedda5fef57f559c77dc39db8aceb9d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:56:40 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f33f344a6b0d06d3de393a783a23383e4ef5cac4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: adccaf9e7d8ce2b6234a1960e93e5d1543d98e09 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:31:34 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: a9e9e80f2f1063aae332963e474ea2f5804487b7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:27:58 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 4151dfa20943c89acdd55c5e1dec18a03da01e2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:14:01 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 1ab513bde94a41e4ab34856ca5e4f5ba5a6413e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 15:59:19 +0200 Commit message: Create sync-to-org.yml Package: BreastSubtypeR Commit: f9f0ea202177840660c02d39e203f67d4003e2cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:09:58 +0200 Commit message: Added description for new example dataset (TCGABRCAobj), updated the BreastSubtypeRobj with the 3 new medians info, tiny text improvements Package: BreastSubtypeR Commit: 056545172113202bb55a0ea0c2918851096fa0f2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:05:10 +0200 Commit message: Created a new example dataset (TCGABRCAobj) from TCGA-BRCA with Raw Counts, and similar results as OSLO2EMIT0obj Package: BreastSubtypeR Commit: 6de103db09589a53624341851237a8f547684ceb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:02:19 +0200 Commit message: Updated BreastSubtypeRobj with 3 more published medians Package: BreastSubtypeR Commit: 6acd15688f6e60db4e1f2ef151c103e865ce5663 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:00:19 +0200 Commit message: Guard docalibration, Improve External calibration, UX, and minor text improvements Package: BreastSubtypeR Commit: 8f7e3790ac94fead82f77e6564d87c542fcf5097 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 11:11:22 +0200 Commit message: Fixed error in BS_Multi() in AUTO Mode, when ssBC has <50 PAM50 genes: Add safe row-aligning cbind helper, made RORgroup() tolerant to missing ESR1/ERBB2 rows, and made BS_Multi() assemble results by PatientID Package: BreastSubtypeR Commit: 06bd9bce269ca12b4ca9f052f3d81cd730212a68 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 21:20:25 +0200 Commit message: Fixed the issue with pre-loading third-party libraries before initializing the Shiny app, Updated Help files Package: BreastSubtypeR Commit: ee560564150a7a5f11c00e8750583438a6c084e6 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:55 +0200 Commit message: Updated NEWS.md with major changes Package: BreastSubtypeR Commit: abd132463b65390c813f04ea50c530fd4b058507 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:18 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 74b20b933030517c45e68826a469dd88d79aa0b9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:24:07 +0200 Commit message: Added a TCGA-BRCA subset, with clinical & annotation data, for testing the RawCounts normalization pipeline Package: BreastSubtypeR Commit: d4fedc4c9b2a241b2652e563c2300d423f787287 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:21:08 +0200 Commit message: iBreastSubtypeR: UX polish, AUTO explainer, export refactor, AIMS constraint & bug fixes Package: BreastSubtypeR Commit: fb7c21f7ebc4f50be7610c8c0a023036f1559358 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 13:24:32 +0200 Commit message: Include three pre-computed Medians (external) as an option to Shiny App Package: BreastSubtypeR Commit: d1a90080950c9b5ddcad737979d072bdc177e038 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 11:34:43 +0200 Commit message: ssBC fixes: No crashes when < 50 PAM50 genes, No accidental subtype calls when a sample’s distance row is all-NA, Won't error when a subgroup has zero samples, qCtr won't produce NaN from zero range Package: BreastSubtypeR Commit: 10644b50e4721efe7b0d9f65445d30e1fdcf5a26 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 10:05:57 +0200 Commit message: Add our reference to Mapping() & BS_Multi() Package: BreastSubtypeR Commit: 5ea0dd73f932fbdd278f4e299de7270698d855c1 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 23:10:17 +0200 Commit message: New preflight for AUTO to prevent errors, new customizations, included new polished text for PAM50 to guide users, and more Package: BreastSubtypeR Commit: 3b08eed750427d72842bec852ff85c2446138cbe Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 13:21:06 +0200 Commit message: Fix issue when HER2 missing and user runs AUTO Package: BreastSubtypeR Commit: 16b805c817e0b7e3883b1aa7defd6da04f6a57f4 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:20:14 +0200 Commit message: Included a Prelight check for ER/HER2/Tn status availability in Clinical data BEFORE Running subtyping, avoiding App crashing due to missing values Package: BreastSubtypeR Commit: f003e4ecbfadb6a2a293ff39d838581dea5a0086 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:01:32 +0200 Commit message: Synchronized changes in BreastSubtypeR_methods.R and NC_functions.R, Created a theme to match the logo, made things unified, text improvements Package: BreastSubtypeR Commit: a66b4796231c8054f2093c6795ca4e67f2cb04de Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 10:08:20 +0200 Commit message: Parker original when calibration=None, or external calibration returns error: Fixed by Making NA equivalent to "medianCtr" (sync eith Parker et al.), and -1 to No calibration. Also, avoid requiring PatientID for BS_parker() when hasClinical = FALSE, included extra controls for hasClinical in all NC functions, polished help text, corrected typos (also tried to correct the 2nd error for ssBC, when < 50 genes, but will work more on this and come back with another Commit) Package: BreastSubtypeR Commit: 53ca58ec99d200f998a8be6896bab45f47d789e3 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-05 19:36:25 +0200 Commit message: Major changes: Multi method with AUTO mode added, Description text for each method with Refs added, Subtype 4-class selection Package: BreastSubtypeR Commit: bdf3bf291b59939171d85ff61f895b2ffc222b8d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:18:47 +0200 Commit message: Fix UI so the drop down menus are easier to select Package: BreastSubtypeR Commit: c0ed93ab5eed4a965f478a0dcac17355f8f91501 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:01:42 +0200 Commit message: Changed HasClinical with a Tick box, included many controls to check whether TSIZE, NODE are available, added different help functions for GEX and Annotation, improved text, and more Package: BreastSubtypeR Commit: 277869bea9c0c7d2747370cc657b2e87cb4e7dd2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 14:59:23 +0200 Commit message: Replaced the T -> TSIZE Package: BreastSubtypeR Commit: fd063a60aa8db3651975e89237ddb398d62c1100 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:28:48 +0200 Commit message: Minor edit Package: BreastSubtypeR Commit: 31e6bbfa2c897aa87caa09254cd2d4d2074b790f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:25:40 +0200 Commit message: Renamed folder to Shinny->Sniny, renamed data files with clear names Package: BreastSubtypeR Commit: 5ef9dd73efdccab438ee51f1ea0441ac565ca984 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:20:19 +0200 Commit message: Fix server.R bug Package: BreastSubtypeR Commit: c4c205e993f8791683fddf05392533aadded4b75 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-04 11:49:00 +0200 Commit message: refine shiny Package: BreastSubtypeR Commit: 304cb68143558163b4dd070c2498631f62a650e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-04 10:40:17 +0200 Commit message: Merge pull request #95 from yqkiuo/main Merge pull request #94 from yqkiuo/BranchQiao Package: BreastSubtypeR Commit: 6cbc1cb1b18907119b3414e3c0dafec607480a99 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:27:20 +0200 Commit message: Merge pull request #94 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 298458b861686b4ed9bfa17c070e5ffea513f3dd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-02 08:27:00 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: a50d8d4c3bea22f65836df6d099b269da685d8c2 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:25:43 +0200 Commit message: Merge pull request #93 from yqkiuo/main v1.1.2 Package: BreastSubtypeR Commit: 65b18fd8734f90e579fff40e53bbc51799b2c4ad Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:28 +0200 Commit message: Merge pull request #92 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5d09b44a5785c08a10d3d652d2a01db94678a1de Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:21 +0200 Commit message: Merge branch 'main' into BranchManos Package: BreastSubtypeR Commit: 8f4056fc16de285798c18e8c36e5399e5cd1fd23 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-01 10:18:12 +0200 Commit message: Merge pull request #91 from yqkiuo/BranchQiao v1.2.2 Package: BreastSubtypeR Commit: e11ffcd934d71dd5ee42c3816cabf93b997e6c64 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-01 10:17:53 +0200 Commit message: v1.2.2 Package: BreastSubtypeR Commit: 0969e8fa4d71d310d1d2f58c788af7a94566de25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-31 22:18:46 +0200 Commit message: Merge pull request #90 from yqkiuo/BranchQiao v1.1.2 Package: BreastSubtypeR Commit: c575280eed4e562e90ba6b9b7a6675353e532725 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-31 22:18:25 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: 031beb8e23f96e6f4894f56b550dd49d0c2a729b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-29 16:04:28 +0200 Commit message: Updated code to include separate cut-offs for ERpos & ERneg, as well as separate cut-offs ER(pos/neg)/HER2 (independent of HER2 status) based on the above cut-offfs. Note: The combined cut-offs will be released in the next submission Package: BreastSubtypeR Commit: 93ba44156f95a90bb74440d472157107e5ef0908 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 20:13:37 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: efee177e7f94d079d424ad79467615a63ce71698 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 2c6cfcacdc3550df0916ecb54833275bf2b9f04f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: d0154df0200108179568a150e1487e592a34e20a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 6a0be72275efbb8b9828b8765834d1ce97521134 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 3cf5afd43c31eeec90045902e6a082d82013bbf7 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: e91120bb63753900c47f80206b0662aef090c98a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: c09d132b8993a81ad16143b2ddbd5fb6b6f36f8b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 18:32:39 +0200 Commit message: Updated NEWS.md, BreastSubtypeR_methods.R, and minor updates to Utilities.R and data_doc.R Package: BreastSubtypeR Commit: 10f36184b66a9a0703d4296c9311b5ed1fc03e23 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 15:16:50 +0200 Commit message: Shiny app normalization clarification Package: BreastSubtypeR Commit: 24740ca0d3f45e43e674d247778b8e003871361c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:57:22 +0200 Commit message: Replaced the adaptive filtering as it was producing a reduced gene list for NC-based methods. Instead I introduce the calculation of UQ in the positively expressed subset and apply those calculcated factors to the full matrix. 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<emmanouil.sifakis@ki.se> Date: 2025-08-27 15:10:09 +0200 Commit message: CITATION added Package: BreastSubtypeR Commit: e8fcac0bcab82793b586f5ffc8c930a0002ac609 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-21 11:29:40 +0200 Commit message: Merge pull request #89 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 0c75bf90f3070408ec5a156edf84b9c0bc70250b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:29:14 +0200 Commit message: update new features Package: BreastSubtypeR Commit: a99a93e94a90d6a715d64daedbe2e1f886f87917 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:27:58 +0200 Commit message: update new features Package: BreastSubtypeR Commit: c9f28c19c39695ad8a84ee4aa929c352be00e229 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 18:11:51 +0200 Commit message: Merge pull request #88 from yqkiuo/BranchQiao Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: e4a62355017220fe89ec8ea09376a0a56060de7c Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 18:11:26 +0200 Commit message: Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: 1993ab3e50725d01e8980a00eeaec8f0b0b766c4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:48:10 +0200 Commit message: Merge pull request #87 from yqkiuo/BranchQiao 1.1.1 Package: BreastSubtypeR Commit: 5d928ed37d8d0f47dd0392057846c43dc12e3dea Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:47:44 +0200 Commit message: 1.1.1 Package: BreastSubtypeR Commit: 52faaf9d7980c6d36524bcabbdcffe1f0fb92a0a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:39:51 +0200 Commit message: Merge pull request #86 from yqkiuo/BranchQiao 1.0.1 Package: BreastSubtypeR Commit: 35eef13e343edd2f9c6a1c26d780c97f470ac6c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:38:55 +0200 Commit message: 1.0.1 Package: BreastSubtypeR Commit: 6abaf3b4ae3d1772babec19c83d49c04728daa06 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-27 09:49:16 +0200 Commit message: Merge pull request #85 from yqkiuo/BranchQiao general update Package: BreastSubtypeR Commit: 453e9aac8dc81b86987e53e60659f2c97f6ba403 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-27 09:48:42 +0200 Commit message: general update Package: BreastSubtypeR Commit: 226607c2ae42706346a1e8911d1f2f82a5ca1490 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 19:12:11 +0200 Commit message: Merge pull request #84 from yqkiuo/BranchQiao v1.1.1 Package: BreastSubtypeR Commit: d773d4401e93ec12006f4e79122cbee8247d80d7 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 19:02:45 +0200 Commit message: v1.1.1 Package: BreastSubtypeR Commit: e74e86a2cfdf6daf92ed180095d27619cd45cd54 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:44:06 +0200 Commit message: Merge pull request #83 from yqkiuo/BranchQiao Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: fd30082d86b34d3ced41b7a7c385e01448c19794 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:41:43 +0200 Commit message: Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: 74145000a4ce350ca0e787fe5c459b79318b3edb Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:25:01 +0200 Commit message: Merge pull request #82 from yqkiuo/BranchQiao Bug fixes and minor improvements Package: BreastSubtypeR Commit: 1a5cb6636acfbd2ad1fc7c290bfba875dd2b22b0 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:24:35 +0200 Commit message: Bug fixes and minor improvements Package: BreastSubtypeR Commit: 4a895b8a8a149e0199b85eeaa19b6769dd8382df Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:27:17 +0200 Commit message: Merge pull request #81 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 4a03138457415f0164139373ee34038bd07ad300 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:21:40 +0200 Commit message: Update DESCRIPTION Package: BreastSubtypeR Commit: 856c6f8f91de5339988cf4c315bcaf96247f37d5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 10:39:20 +0200 Commit message: general update Package: BreastSubtypeR Commit: e35db8756a5fa3f30bf4addbeacd58145589e16b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:18:47 +0200 Commit message: general update Package: BreastSubtypeR Commit: 2e60c2222d3e9fdf48d3262ba087b447a95119a9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:03:00 +0200 Commit message: general update Package: BreastSubtypeR Commit: 7cfcfe95b2761178d17cc2af122f61883e7dc666 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:50:06 +0200 Commit message: update general Package: BreastSubtypeR Commit: b30131f2c073711d4b42e38af49bef1849da20c5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:48:53 +0200 Commit message: Update RawCounts para Package: BreastSubtypeR Commit: 6fa4d83d00b30727be9b1d4fd3798015fad0442a Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:32:10 +0200 Commit message: debug ROR Package: BreastSubtypeR Commit: ba045196fcd4a3bff148b3497a82f3f87d6bb324 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:31:55 +0200 Commit message: refine "-1" in parker.original Package: BreastSubtypeR Commit: b5e6254539fd38e41109056b2ddff7d36e0f9c19 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:15:41 +0200 Commit message: refine "-1" in parker.orignal Package: BreastSubtypeR Commit: bc7d097164cb411bfc4b40d5513073ae1bac35d8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:39 +0200 Commit message: 0.00.0 Package: BreastSubtypeR Commit: 5d966c161e4cdae464dd16d48421f6d5a4e26461 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:30 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 81f77832a0d7f8f5b8b70403616fe165ff96862d Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:08 +0200 Commit message: debug data type Package: BreastSubtypeR Commit: 8471668b9b9b43c3e27a87faa458488a8fba7f05 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:56 +0200 Commit message: debug BS_Multi Package: BreastSubtypeR Commit: 01fa8b576ca237667ed8a792477638cd4b023dbd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:34 +0200 Commit message: clear author Package: BreastSubtypeR Commit: a86f573778ed992a3d2dbb698b4c9c00a15619c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:20 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 00d2b9c5d71c6830e845dcddcb810b9640666207 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:33:01 +0200 Commit message: debug AUTO Package: BreastSubtypeR Commit: 8b3f7c2ef2d45cf772511a7290ba0a31baa43b62 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:32:46 +0200 Commit message: debug bad PCAPAM50 Package: BreastSubtypeR Commit: c70f4c9b0d64da1940659ae9a826d8221be05a32 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 09:32:30 +0200 Commit message: debug PCAPAM50 </div> </div>
Disable public RSPM on macOS/Windows to fix root cause, bump to 1.7.12 The libomp install in the previous commit didn't fix stringdist's identical dlopen failure - same byte-for-byte error, meaning the install had no effect. Searched prior reports of this exact failure (tidymodels/tune#1199, Genentech/rdborrow#73/#74): the real cause is that r-lib/actions/setup-r configures Posit Package Manager (P3M) as the default macOS repo, and P3M's macOS arm64 binaries are compiled with OpenMP enabled. This runner can't resolve those OpenMP symbols at runtime (SIP strips DYLD_* for protected binaries, so even a correctly installed libomp isn't reliably picked up) - CRAN's own macOS binaries are built without OpenMP and never hit this. Set use-public-rspm: false on the "Setup R from r-lib" step so macOS (and Windows, already passing, no expected impact) resolve packages from CRAN directly instead of P3M, which should fix this for any OpenMP-linked package in the dependency tree - not just the three (RhpcBLASctl, isotree, stringdist) hit so far - rather than continuing to patch them one at a time. Left the earlier source-install and libomp workarounds in place; they're harmless if this makes them redundant, and there's no upside to stripping proven/plausible fixes before confirming this one actually resolves it on CI.
Install CRAN's official libomp on macOS CI, bump to 1.7.11 The last two fixes patched RhpcBLASctl and isotree individually, but BiocCheck::BiocCheck() now hits the identical failure via one of its own dependencies (stringdist): unable to load shared object '.../stringdist.so': dlopen(...): symbol not found in flat namespace '___kmpc_barrier' Patching each OpenMP-linked CRAN package one at a time as it's reached doesn't scale - the actual root cause is that this GitHub Actions macOS runner is simply missing the libomp build that CRAN's macOS binaries are compiled against (documented at https://mac.r-project.org/openmp/; Homebrew's libomp installs to a different path and doesn't fix this). Installing it there via the official recipe should let CRAN's normal (faster) binaries load correctly for any OpenMP-using package, not just the two already patched. Left the RhpcBLASctl/isotree source-install workarounds in place since they're already confirmed working - no reason to touch proven fixes while chasing this.
Also force isotree from source on macOS CI, bump to 1.7.10 RhpcBLASctl fixed the first macOS OpenMP dlopen failure, but the same issue exists one layer up: isotree's own CRAN macOS binary (isotree.so) fails to dlopen with "symbol not found in flat namespace '___kmpc_barrier'" - a Clang/LLVM OpenMP runtime symbol, same root cause (CRAN's macOS binary built with OpenMP support that isn't resolvable on this runner), just a different dependency in the chain. Applied the identical source-install workaround to isotree.
Force RhpcBLASctl from source on macOS CI, bump to 1.7.9 Ubuntu and Windows now pass under the Bioc 3.22/R 4.5 bump (previous two commits), confirming those fixes. macOS still fails, but differently and on all 4 vignettes uniformly this time: Error: .onLoad failed in loadNamespace() for 'RhpcBLASctl' dlopen(.../RhpcBLASctl.so, ...): symbol not found in flat namespace '_omp_get_max_threads' RhpcBLASctl is a hard Import of isotree (detectAnomaly() calls isotree::isolation.forest()), so its namespace loads unconditionally. CRAN's macOS binary for RhpcBLASctl references an OpenMP runtime symbol that isn't resolvable on this GitHub Actions macOS runner - a known class of issue for R packages built with OpenMP support on macOS. Building from source instead compiles without OpenMP (Apple clang has no -fopenmp by default), so the resulting library never references that symbol. Added alongside the existing Matrix/irlba source-install workaround in the same step, which addresses the same kind of macOS binary incompatibility.
Anchor SingleCellExperiment/SpatialExperiment Rd links, bump to 1.7.8 R CMD check now fails with error_on = "warning" on the Bioc 3.22/R 4.5 CI (bumped in the previous commit): "checking Rd cross-references" reports a genuine broken link (merfish_reference_data.Rd's \linkS4class{SpatialExperiment} doesn't resolve) plus 36 files whose \linkS4class{SingleCellExperiment}/{SpatialExperiment} links are missing package anchors - both promote the check from NOTE to WARNING under the newer toolchain. \linkS4class{} was reintroduced repo-wide by a September 17 commit ("docs: use \linkS4class{} for SingleCellExperiment roxygen links", for brevity) after an earlier commit had already fixed this exact issue with explicit \link[pkg:target]{text} anchors. Restoring that anchored form and re-running roxygen2 to regenerate man/ resolves it; verified with a full local R CMD check matching the CI invocation (0 errors, 0 warnings, 1 unrelated pre-existing note).
Bump CI to Bioconductor 3.22/R 4.5 to fix vignette build failure COVIDCaseStudy.Rmd was failing to build on CI (macOS/Windows) with "unable to find required package 'Seqinfo'" inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause: covid_reference_data/covid_query_data were generated on current Bioconductor (3.22), where the Seqinfo class was split out into its own standalone package. check-bioc.yml was still pinned to the two-year-old Bioconductor 3.19/R 4.4, whose GenomeInfoDb predates that split and whose repos don't contain a 'Seqinfo' package at all, so the class tag baked into the serialized data can't be resolved. Two earlier attempts (adding set.seed() to rule out RNG state, then patching a subset of the shipped .rda files) missed this because neither addressed the actual CI environment being out of date. Bumped the workflow's matrix (r/bioc versions, container image, cache keys) to 4.5/3.22, matching the environment covid_reference_data was actually generated on; verified locally that a full R CMD build (fresh install + vignette rebuild) succeeds under this Bioc/R pairing.
Handle reference cell types with too few cells or absent from query detectAnomaly() previously assumed every reference cell type had at least 2 cells (to fit an isolation forest) and, when a query dataset was provided, implicitly assumed every reference cell type also had matching query cells. Neither is guaranteed: - A reference cell type with fewer than 2 cells can't fit an isolation forest; now skipped with a warning instead of erroring. - A reference cell type entirely absent from the query is a normal outcome (e.g. after subsetting/filtering the query), not an error; now reported with an empty query score vector instead of failing in predict(). Also fixes a latent bug where a cell-type subset reducing to exactly 1 row would silently drop to a vector (missing drop = FALSE), which would have broken the isolation forest input shape. Adds tests covering both edge cases.
Fix stale Seqinfo class tag causing vignette build failure, bump to 1.7.6 COVIDCaseStudy.Rmd failed to build on CI with: Error in .requirePackage(): unable to find required package 'Seqinfo' triggered inside SingleCellExperiment::reducedDims()'s lazy updateObject() machinery. Root cause, confirmed via verbose updateObject() output: covid_reference_data's internal Seqinfo class was tagged with its old home package ("GenomeInfoDb", from before Seqinfo was split into its own standalone Bioconductor package), so a sufficiently new Bioconductor tries to auto-migrate it on load - and that migration path apparently isn't reliably available in a fresh CI environment. Fix: call updateObject() on serialized objects at data-generation time so the bundled .rda ships with the current internal representation baked in, rather than deferring to a lazy per-load migration. Applied to the new COVIDData.R/MERFISHData.R scripts (whose source data came from an external, older serialization), and audited/fixed the same latent issue in the pre-existing reference_data/query_data/qc_data (which had the identical stale tag despite already shipping in the package) and their generation scripts, so this doesn't resurface on a future regeneration or Bioconductor version bump. zeisel_/covid_/ merfish_ vignette datasets were already correctly tagged and are byte-identical after regeneration.
Fix non-deterministic vignette failure and bump to 1.7.5 COVIDCaseStudy.Rmd and MERFISHCaseStudy.Rmd called detectAnomaly()/ calculateGeneShifts() (which use isotree::isolation.forest(), a randomized algorithm) without ever calling set.seed(), unlike the other two vignettes. This is the most likely cause of the CI vignette re-build failure on COVIDCaseStudy.Rmd after pushing 1.7.4 - a build without a seed picks up whatever RNG state the session happens to be in, which can land on the isolation forest / gene-shift edge cases seen elsewhere in this codebase. Verified against 15 different seeds plus a full local R CMD build (fresh install + vignette rebuild, not just devtools::load_all()) with no failures. Bumps to 1.7.5 rather than re-pushing 1.7.4, since 1.7.4 already has a recorded (failed) build on Bioconductor/GitHub.
feat(decomposeSubnetworkIntoHierarchicalTopics): Enable NMF hierarchical decomposition (#110)
Stop reaching the network when the vignettes and examples are built Three build-time downloads, all of the same two Zenodo files, none of them needed to show that the package works. The vignette one was failing outright. Sequencing.Rmd's QUICK START fetched mm10_f3_10cells.cg -- 11.4 MB, which takes ~101 s at the throughput a build host is likely to get. R's download.file() gives up at getOption("timeout"), 60 s by default, so the transfer truncated mid-file and the vignette errored. Measured twice here: it stopped at 6.0 MB and at 7.2 MB, both almost exactly 60 s of transfer, and completed only with timeout raised to 600. Raising the timeout would have kept a network dependency the package does not need. The sequencing workflow is superseded by the kycg command-line tool, which does this analysis natively over YAME .cg stores and fetches its own knowledgebases, so the chunk is now shown rather than run, with a line saying so and pointing there. The two examples had the same files behind a guard that does not guard. \donttest IS executed by the Bioconductor builders; only \dontrun is not. In bedToCg() the download.file() sat outside the guard entirely, so it ran on every check while only the bedToCg() call was skipped -- the whole example is now \dontrun. In testEnrichment() the guard was in the right place but was \donttest, now \dontrun; its offline part, which uses the sesameData cache, still runs. Both edited in the roxygen source and regenerated, so document() cannot revert them. Neither example has run lately: checksrc has been skipped for as long as buildsrc has been red, so these would have fired the moment the vignette fix made checksrc reachable again. BiocCheck NOTEs \dontrun in favour of \donttest. That NOTE is accepted here: \donttest does not keep the builders off the network, which is the point. visualization.Rmd still reads a small RDS over the network and is left alone -- it builds reliably and is not part of this failure.
Array.Rmd: use the base pipe, not the borrowed magrittr one buildsrc has failed on every builder in both release and devel with Quitting from Array.Rmd:218-233 [ky8, run-test-single] Error in `results %>% dplyr::filter(overlap > 10) %>% head`: ! could not find function "%>%" The vignette never attached the pipe. It worked anyway because library(sesameData) pulls ExperimentHub -> AnnotationHub -> BiocFileCache -> dbplyr, and dbplyr re-exports `%>%`, so the vignette was borrowing the operator from a package four levels down its own dependency chain and never named. When that chain stopped attaching dbplyr, the vignette broke without having changed. knowYourCG imports `%>%` via importFrom(magrittr) but does not export it, so library(knowYourCG) was never what made it resolve. DESCRIPTION has Depends: R (>= 4.4.0), so `|>` is available unconditionally and removes the dependency rather than renaming it; `%>% head` becomes `|> head()` since the base pipe needs a call. R/preparePlotDF.R keeps `%>%` -- package code has the import, only vignettes were ever exposed. Verified under R 4.6.0: all three rewrites return identical() results to the magrittr forms, the base pipe resolves with nothing attached, and Array.Rmd renders to completion. Fixes the buildsrc half of #4.
Merge pull request #201 from gdrplatform/GDR-3612 refactor: read the constant-fit xc50 threshold from fit configuration
fix: read the fit configuration when the fitting layer is entered directly
Merge branch 'main' into GDR-3612
docs: flag that fit_curves still hardcodes the xc50 threshold
Merge remote-tracking branch 'origin/GDR-3606' into GDR-3612 # Conflicts: # DESCRIPTION # NEWS.md
refactor: read the constant-fit xc50 threshold from fit configuration The response level deciding whether a constant fit reports +Inf or -Inf was hardcoded at 0.5 in two functions. It is now one entry per normalization type in the fit_config block, alongside the priors and asymptote bounds. Numerically inert: every type keeps 0.5, which is what the code did before. The point is that the value becomes visible and decidable - for RV it means 50% viability and for GR it is the GR50 convention, but NGR is a bare ratio of slopes that is legitimately negative, where the threshold has no established meaning.
fix(pubmed): Reduce runtime for fetching pubmed abstracts (#109)
Switch a couple of install() calls in C for the corresponding more performant internal Rf_*() calls
Mention all of the weird DelayedArrays that we support in the ANY method. Also move the LowRankMatrix code out of the ANY method for clarity. Also bump version and date for a new release.
Use a more precise R type hint for residual matrix objects. Also move ResidualMatrix code out of the ANY method for easier reading.
Support scrapper::LogNormalizedMatrixSeed in storeDelayedObject.
Bump package version from 1.5.2 to 1.5.3
fix(proteinGroups): Adjust annotateProteinInfoFromIndra to handle protein groups (#108)
Merge upstream/devel, Updated
Merge pull request #139 from yqkiuo/BranchQiao Branch qiao
Merge pull request #138 from yqkiuo/main New updates
Merge pull request #136 from yqkiuo/maintenance/public-package-fixes-20260918 Maintenance fixes for 1.5.2: AUTO routing, ROR-C column, Shiny launcher and preflight, Mapping and documentation
Track .Rbuildignore and exclude the .github directory from the build R CMD check reported "hidden files and directories: .github" because the workflow directory reached the source tarball. .Rbuildignore was listed in .gitignore and therefore never shipped with the repository; it is now tracked, with the same content the Ensemble branch already carries, so the built package excludes .github, RStudio files, Rplots.pdf, doc, Meta and MANIFEST.txt. No R code changes.
Bump version to 1.5.2 and title the release notes DESCRIPTION 1.5.1 -> 1.5.2 for the Bioconductor devel submission of the maintenance fixes. The NEWS block collected under "Unreleased" becomes the 1.5.2 entry. One clause is added to the AUTO subsetting bullet: the supplementary pseudocode of the published paper records the strict comparison in the subsetting step while using ">=" for method selection, so readers comparing the package against the paper know that the package now applies ">=" in both and reproduces its shipped example.
Docs: keep the maintenance track free of unreleased-feature references The entropy change of the previous commits described the new NA behaviour by comparison with an unreleased voting feature, in the internal help text of get_entropy(), in the comment heading test-entropy.R and in the NEWS bullet. The maintenance branch is the public package: its sources, tests and NEWS must not name work that has not been released. The wording now states the behaviour on its own terms. No code, test assertion or behaviour changes.
Tests: do not let the equivocal HER2 case emit an unhandled warning The AUTO routing test feeds an equivocal "2+" HER2 code to check that a non-evaluable value is treated like a missing one. Builds that flag ambiguous HER2 codes warn on that input, which leaves an unhandled warning in the suite. The call is wrapped; the routing verdict it asserts is unchanged.
AUTO: decide the HER2+ cohort from the HER2 column alone The HER2+ branch of get_methods() was entered when at least one evaluable HER2 value existed and the joint ER/HER2 counts held no HER2-negative sample. Those counts are computed with na.rm = TRUE, so a HER2-negative sample whose ER value was missing never reached them: one such sample left the cohort classified as HER2+, while an otherwise identical sample with a recorded ER value ended the classification. Whether a HER2-negative tumor counts must not depend on whether its ER status happens to be known. The branch now requires at least one evaluable HER2 value and every evaluable HER2 value to be HER2+. Values outside {HER2+, HER2-} are not evaluable; this covers missing values and the equivocal "2+" code that .normalize_er_her2_tn() deliberately leaves unchanged. Such samples neither create nor remove a HER2+ cohort, and AUTO now reports how many of them took no part in the decision, because a single unannotated sample used to be able to change the routing silently. Cohorts with complete HER2 information are routed exactly as before. The packaged OSLO2-EMIT0 example has no missing ER or HER2 value (ER+ 84, ER- 18, HER2+ 8, HER2- 94), so no shipped example or regression fixture changes. The test that pinned the previous behaviour (her2_pos_na_er) is replaced by a block asserting that both routes now agree, and a block asserting the new message. The NEWS bullet for the unreleased HER2+ change is consolidated into a single statement of the final rule rather than two successive refinements of the same unreleased behaviour. README and vignette state the rule.
Entropy: report NA when no method returned a call get_entropy() computes the raw Shannon entropy of a per-sample row of method calls. table() drops missing values, so a row in which every executed method returned NA produced -sum(numeric(0)), that is 0, which on this scale reads as unanimous agreement. Such a row has no call distribution and therefore no entropy; it is now reported as NA. Rows with at least one call are unchanged, including the degenerate one-call case, whose entropy of 0 is the correct value for the observed distribution. The definition of the statistic - raw, unnormalized Shannon entropy in bits - is untouched, and no normalized variant is introduced. The change aligns the legacy path with the ENSEMBLE diagnostics, where raw_vote_entropy is already NA_real_ when valid_voter_count is zero. Exposure is narrow: every AUTO panel includes AIMS and sspbc, which are single-sample predictors and call essentially every sample, so an all-NA row cannot arise in AUTO. It arises in manual runs of nearest-centroid-only method sets (for example methods = c("ssBC", "ssBC.v2")), where a sample whose ER or ER/HER2 status is unknown gets no call from any executed method. The packaged OSLO2-EMIT0 example is unaffected: every tumor there has 7 or 8 calls, and its stored entropy column is reproduced exactly by the new function (asserted by a test). Side effect worth noting: Vis_Multi() orders rows by the entropy column and order() places NA last, so a sample with no calls now sorts to the end of the plot instead of appearing among the unanimous samples. The entropy column of res_subtypes is documented in ?BS_Multi for the first time, including that it is computed over the contributing methods only, so a low value from few contributing methods reflects few available calls rather than strong agreement. tests/testthat/test-entropy.R covers the NA cases, the unchanged values for rows with calls, reproduction of the packaged entropy column, and a manual two-method run in which four samples receive no call.
PCAPAM50: exclude samples with unknown ER from the IHC-guided steps BS_PCAPAM50() builds the IHC column from the ER status with case_when(..., .default = NA), so a sample whose ER is missing or not coded "ER+"/"ER-" has no label. makeCalls.PC1ihc() expressed ER-negativity as !grepl("^L", IHC), which returns TRUE for NA, so those samples were counted as ER-negative in the PC1 axis check, in the misclassification-minimizing cutoff search and in the ER-balanced gene-centering set. The bias is one-directional and grows with the fraction of unknown ER. A new internal helper, .ihc_status(), classifies each label as "luminal", "nonluminal" or NA (missing or empty), and the three steps now use explicit luminal / non-luminal masks. Samples without an evaluable label take no part in estimating the cutoff or the centering set, a message reports how many were excluded, and they are still classified and returned. As a side effect the label test is now applied consistently: the mask is computed once, after trimming and upper-casing, instead of being evaluated before the upper-casing step in one place and after it in another. This is not a deviation from the published algorithm. The reference implementation (Raj-Kumar et al., CRAN package PCAPAM50 1.0.4, R/functions_PCA-PAM50.R lines 336, 355-356, 385-386) uses the same !grepl("^L", IHC) construct, but its IHC column is a user-supplied clinical subtype (LA, LB1, LB2, Her2+, TN) that the package never leaves missing; the vignette states that ER-positive subtypes start with "L" and all others are ER-negative. The NA category exists only because BreastSubtypeR derives the column itself. The change also removes an internal inconsistency: BS_cIHC() and BS_cIHC.itr() already exclude unknown ER from their ER groups via which(df.cln$ER == ...). Measured on the packaged OSLO2-EMIT0 input (R 4.3.3 sandbox), setting the first k ER values to NA and comparing calls before and after the change: k = 0 and k = 6 leave every call unchanged, k = 18 changes 2 of 102 calls, k = 30 changes 6 of 102. Cohorts with complete ER are unaffected, and the packaged example still reproduces its stored PCAPAM50 column. The help page of BS_PCAPAM50() gains a @details paragraph stating the exclusion, the message, that such samples are still classified, and the reference implementation's assumption of a complete IHC column. tests/testthat/test-pcapam50-unknown-er.R covers the helper, the unchanged complete-ER output against the packaged fixture, the message, and that unknown-ER samples still receive calls.
README/vignette: state the size gating of the ER/HER2-defined AUTO rule The AUTO bullet "ER/HER2-defined cohorts: ssBC.v2 only + SSP" read as an unconditional rule. In the code it applies only when the ER group reaches its minimum (15 for ER+, 18 for ER-) and the HER2 subgroup reaches its minimum (8 for ER+, 9 for ER-); smaller cohorts run AIMS and sspbc only. The bullet now says so, and a second bullet documents the handling of cohorts without any evaluable HER2 value (ER-based rules instead of the HER2+ branch). ASCII hyphens replace the typographic minus signs in the edited lines.
Docs: Mapping "mean"/"median" collapse duplicate probes, as in the PAM50 code The Mapping() help (and the internal domapping() roxygen) described method = "mean" and "median" as keeping "the probe with the highest mean/median expression". duplicate_genes() computes the per-sample mean or median across all probes of a gene, i.e. it collapses the probes rather than selecting one; "iqr", "stdev" and "max" select one probe, and "max" selects by largest row sum, not by "highest expression value". Checked against the original PAM50 bioclassifier code (bioclassifier_R/subtypePrediction_functions.R, collapseIDs(), and the example parameter file): "mean" and "median" average the duplicate probes per sample there too, "iqr" and "stdev" select the probe with the highest IQR / SD, and no "max" method exists. BreastSubtypeR therefore reproduces Parker's behaviour; only its documentation was wrong. Author decision (2026-09-18): fix the documentation. The parameter text in R/BreastSubtypeR_methods.R, R/Utilities.R and man/Mapping.Rd now describes the averaging, credits collapseIDs() and marks "max" as a package addition. No code or mapped values changed.
AUTO: include subgroups exactly at their minimum in the ssBC/ssBC.v2 subsets Method selection in get_methods() accepts a subgroup when its size is at least the minimum (15 for ER+, 18 for ER-, 8 and 9 for the HER2 subgroups), but the sample subsets handed to BS_Multi() for ssBC and ssBC.v2 were built with a strict ">". A subgroup of exactly the minimum size was therefore selected for the method and then excluded from its input, and its samples came back NA while the AUTO messages reported the method as running. The packaged OSLO2-EMIT0 example is such a case: 84 ER+ and 18 ER- tumors, so the cohort is classified as mixed and ssBC is selected, but the 18 ER- tumors were dropped from the ssBC input. Executed in a sandbox (R 4.3.3) on this branch: with the published strict comparison a fresh BS_Multi(methods = "AUTO") run yields ssBC = NA for those 18 tumors and does NOT reproduce the packaged frozen result OSLO2EMIT0obj$res (which carries ssBC calls for all 102 tumors); with ">=" the fresh run reproduces the stored result exactly, entropy included. The stored data object is therefore left unchanged; the fix restores agreement between the code and the shipped example. tests/testthat/test-auto-fixture-regression.R asserts the reproduction and that no ER- tumor is left without an ssBC call; tests/testthat/test-auto-subsetting.R adds exact-minimum subgroup cases and the OSLO2-EMIT0 colData.
AUTO: require an evaluable HER2 value before calling a cohort HER2+ get_methods() entered the HER2+ branch whenever n_ERposHER2neg == 0 && n_ERnegHER2neg == 0. Both counts are also zero when HER2 is entirely missing or coded with unrecognized values, so such cohorts were classified as "small HER2+" and received AIMS and sspbc only (example: 60 ER+ / 40 ER- with HER2 all NA). The branch condition now also requires at least one evaluable HER2 value (HER2+ or HER2-). Cohorts without HER2 information fall through to the ER-based rules: a mixed ER cohort gets the mixed panel (ssBC.v2 then returns NA for every sample, which BS_ssBC() handles without error), an ER+-only cohort reaches the announced AIMS/sspbc fallback because its HER2 subgroups are empty. Cohorts with any evaluable HER2 value are routed exactly as before, including the existing treatment of HER2- samples whose ER is missing (excluded from the subgroup counts, as the AUTO message states). No effect on the packaged OSLO2-EMIT0 example. Author decision (2026-09-18): HER2+ branch only with evaluable HER2. tests/testthat/test-auto-routing.R covers the size-gated ER/HER2-defined cohorts and the cohorts without HER2 information.
cIHC, cIHC.itr, PCAPAM50: clear error when an ER group is empty On a cohort with a single ER group (for example every sample ER+), makeCalls_ihc() and makeCalls.PC1ihc() failed with "undefined columns selected" and makeCalls_ihc.iterative() with "arguments imply differing number of rows: 0, 102", all from the median computation on an empty balanced set. The methods cannot balance by ER status without both groups. A small helper, .check_er_groups(), now stops with the group counts and a pointer to the cohort-aware modes in makeCalls_ihc() and makeCalls_ihc.iterative(). makeCalls.PC1ihc() checks the luminal / non-luminal IHC classes before the PC1 cutoff search and the balanced set after it, and makeCalls.v1PAM() checks its LumA / Basal groups. Cohorts with both groups take the same path as before (the OSLO2-EMIT0 cIHC calls are unchanged). Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-er-balancing-errors.R covers the three methods.
Docs: describe the actual return values of the NC methods; cIHC.itr ratio BS_PCAPAM50() and BS_ssBC() documented "a character vector of intrinsic subtype predictions", BS_cIHC() "a data.frame", and BS_cIHC.itr() a list with elements subtypes / confidence / ER_balance that do not exist. All four return a list: BS.all (PatientID, BS and, with Subtype = TRUE, BS.Subtype), score.ROR (correlations, calls, confidence, ESR1/ERBB2 expression, ROR-S/ROR-P and, with hasClinical = TRUE, ROR-C/ROR-PC scores and groups), the medians used for centering (mdns; mdns.fl for PCAPAM50; absent for cIHC.itr) and outList; BS_cIHC.itr() additionally returns BS.itr.keep and, with Subtype = TRUE, BS.itr.keep.Subtype. Verified on the packaged OSLO2-EMIT0 input. BS_cIHC.itr(ratio): makeCalls_ihc.iterative() swaps the larger ER group into the sampled position before drawing ceiling(ratio * n_smaller) samples from it, so the ratio applies to the larger group relative to the smaller one, not to ER+/ER- as such. The parameter text now says so, and the alphabetical tie-break used by get_consensus_subtype() for the consensus call is stated in the return value. roxygen comments and the corresponding man/*.Rd files were edited in parallel (no roxygen2 run, to avoid unrelated regeneration changes). Present in Bioconductor release 1.4.0 and devel 1.5.1. No code changes.
Shiny: cohort preflight requires both ER and HER2 columns .summarize_cohort() in inst/ShinyBreastSubtypeR/server.R returned ok = TRUE for kind "ER" (HER2 absent), kind "HER2" (ER absent) and for a valid TN column without ER/HER2. get_methods() stops in all three cases ("The 'AUTO' mode requires both 'ER' and 'HER2' columns in the 'pheno' dataframe"), which the app surfaced only as "Prediction failed" after the user pressed Run. The column summary is unchanged (now .summarize_cohort_columns()); .summarize_cohort() wraps it and sets ok = FALSE with the message "Cohort-aware analysis requires both 'ER' and 'HER2' columns; missing: ..." when either column is absent. Kind and statistics are still reported. tests/testthat/test-shiny-preflight.R covers the column combinations.
iBreastSubtypeR: load app dependency namespaces correctly The launcher's .attach_if() helper called requireNamespace(p, character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE). requireNamespace() has no such arguments, so the call failed with "unused arguments"; the failure was swallowed and FALSE returned, and nothing was loaded. The comment claimed the packages were attached to the search path, which requireNamespace() never does. The app still worked because ui.R/server.R use qualified calls and shiny::runApp() attaches shiny itself. The helper is now a package-internal function, .load_app_dependencies(), that checks installation, loads each namespace with requireNamespace(p, quietly = TRUE) and stops with a clear message when a package is missing or cannot be loaded. The tidyverse option uses the same helper. The exported signature and documentation are unchanged. tests/testthat/test-shiny-launcher.R covers the missing package error and the successful load.
BS_Multi: report the error text when PCAPAM50 fails The tryCatch() around BS_PCAPAM50() in BS_Multi() warned "PCAPAM50 failed in this iteration: " and dropped the condition message, so users could not see why the method failed. The warning now appends conditionMessage(e) (with call. = FALSE). Behaviour is otherwise unchanged: the method's column is filled with NA. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-bs-multi-messages.R mocks a failing BS_PCAPAM50() and checks the warning text and the NA column.
Normalize factor phenodata like character; fix the FPKM imputation guard .normalize_er_her2_tn() used nested ifelse() calls whose fallback was the original column. For a factor column the fallback is the integer code, so unmatched levels came back as strings such as "3" instead of "Unknown". Mapping() converts colData factors to character before calling the helper, but BS_Multi() and get_methods() normalize the phenotype table directly, so a hand-built data_input with factor ER/HER2/TN columns was normalized differently from the same table with character columns. The helper now works on as.character() copies of the three columns; the coercion warnings compare character values, so canonical factor input no longer triggers them. Character input is unchanged. domapping(): the second imputation guard tested anyNA(x) after x had already been imputed, so counts.fpkm was never imputed. It now tests anyNA(counts.fpkm). In practice edgeR rejects NA counts earlier, so this is a logic correction with no expected effect on existing analyses. Both present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-phenodata-normalization.R compares factor and character input for the helper and for a full AUTO decision.
Mapping: keep matrix dimensions for single-sample input duplicate_genes() indexed x[names(entrezid), ] without drop = FALSE and rebuilt the collapsed matrix with mapply(SIMPLIFY = TRUE) followed by apply(x, 1, unlist), which requires a matrix. For a one-sample SummarizedExperiment the subset became a vector and Mapping() failed with "dim(X) must have a positive length". prepare_nc_matrix() and the probe filter in domapping() had the same drop issue. The collapse now builds the gene-by-sample matrix explicitly (lapply + rbind with dimnames from the split and the sample names), and the three subsets use drop = FALSE. For multi-sample input the returned values and dimnames are identical to the previous implementation for "mean", "median", "max", "stdev" and "iqr" (checked on random data with duplicated Entrez IDs and an NA value); the OSLO2-EMIT0 mapping of one sample equals the corresponding column of the full mapping. Present in Bioconductor release 1.4.0 and devel 1.5.1.
AUTO: announce the fallback to AIMS and sspbc instead of falling back silently The safety net at the end of get_methods() set methods to c("AIMS", "sspbc") without any message. It is reached by ER+-only or ER--only cohorts whose HER2 subgroups are all below their thresholds, typically because many HER2 values are missing (example: 17 ER+ samples with HER2+ 5, HER2- 6, missing 6). Users saw only the two SSP methods run, with no indication why the ssBC variants were not selected. The fallback now emits a .msg() (respecting the BreastSubtypeR.verbose option) naming the reason. Method selection is unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1.
AUTO: drop samples with missing ER/HER2 from the ssBC/ssBC.v2 subsets get_methods() built the AUTO-mode sample subsets with rownames(pheno)[pheno$ER == subtype] and the ER/HER2 analogue. A missing ER or HER2 value evaluates to NA in the comparison, so the subsets contained NA "sample names". BS_Multi() then either failed when it subset the SummarizedExperiment ([,j] index out of bounds: NA) or, when the NA-padded vector was at least as long as the cohort, treated it as "run on all samples" and skipped the intended subsetting. Example on 1.5.3: 50 ER+ / 45 ER- / 5 NA gives a 105-element subset with 10 NA entries for a 100-sample cohort. Both lapply bodies now use which(), as makeCalls.ssBC() already does, so samples with missing status are excluded. Cohorts with complete ER/HER2 values return identical subsets. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-auto-subsetting.R covers a mixed cohort with missing ER and an ER- cohort with missing ER and HER2 (subset shorter than the cohort). Both fail on the previous code. </pre> </div> Package: BreastSubtypeR Commit: 2f8ea71201a742d0d0957ff8228ba2fdbc21d3be Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:05:00 +0200 Commit message: Fix ROR-C risk group column: use criskgroups, not cpriskgroups In RORgroup() (R/NC_functions.R) the data frame built when hasClinical = TRUE assigned the combined + proliferation groups (cpriskgroups) to both "ROR-C Group (Subtype + Clinic)" and "ROR-PC Group (Subtype + Clinic + Prolif)". The ROR-C groups (criskgroups, thresholds -0.1 and 0.2 on the combined score) were computed but never reported. The ROR-C group column now uses criskgroups; the ROR-C score and every other column are unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-ror-groups.R adds a synthetic RORgroup() input in which the ROR-C and ROR-PC groups differ (high/low/med vs low/high/med) and checks that the ROR-C group is reproducible from the reported ROR-C score. The test fails on the previous code and passes with this change. Package: BreastSubtypeR Commit: 9ab99af8b9cf337614a30a61c3e0ce1c264df049 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-09-18 13:00:00 +0200 Commit message: Tests: run the nested testthat suite via test_check() tests/testthat.R contained a single inline test_that() block and never called test_check(), so tests/testthat/test-tn-cohort-detection.R (added in 1.5.1) was not executed by R CMD check; the Bioconductor devel check log shows only the inline test running. tests/testthat.R now calls test_check("BreastSubtypeR") and the inline BS_Multi() test moved unchanged to tests/testthat/test-bs-multi-manual.R. DESCRIPTION: Config/testthat/edition: 3 and testthat (>= 3.2.0) in Suggests, matching the edition-3 expectations used by the tests added on this branch. No version bump. Package: BreastSubtypeR Commit: a4b23b2aba07ba19b33669ac1e8d8361fd1139ab Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:59 +0200 Commit message: Merge pull request #135 from yqkiuo/main update to 1.5.2 Package: BreastSubtypeR Commit: b19c1c3f629d11a8f12e57526162b16e41e605c6 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-06-22 17:15:30 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: 0c0c47c87dcd6e560bedcd536f828dca642e7933 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-06-22 17:38:39 +0300 Commit message: Merge pull request #134 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: edeb030317e854cd706a351f12b93dbd722f232e Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 17:22:45 +0300 Commit message: Finalize NEWS entry for TN detection fix (#133) Package: BreastSubtypeR Commit: b8d6bf4b5bb037d8e101287e92d209fdb1e869a5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:59:04 +0300 Commit message: Update NEWS and documentation for TN detection fix (#133) Package: BreastSubtypeR Commit: d8eeff0e85113512842b1e4976fce6eed1142e39 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2026-06-22 16:25:06 +0300 Commit message: Fix TN-only cohort detection (#133) Package: BreastSubtypeR Commit: cd515ab92fffbbf8a3496cfc70e65299b77457ba Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2026-02-20 12:09:07 +0100 Commit message: v1.3.3 Package: BreastSubtypeR Commit: 0770ee5c0a5283fd1f073cf9c170464431eac2d3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2026-02-20 11:59:28 +0100 Commit message: Merge pull request #129 from yqkiuo/main AUTO - NA Package: BreastSubtypeR Commit: 9b740667ac781cede13f2884763f47576f5778cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:30:22 +0100 Commit message: Merge pull request #128 from yqkiuo/BranchManos Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: ebac3daf14161981995520818d552a8c894faa21 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2026-02-19 18:27:35 +0100 Commit message: Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127) Package: BreastSubtypeR Commit: 122fae948ba3ab93589046d4fc9f564a95db3805 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-12-21 07:08:46 +0100 Commit message: Merge pull request #125 from yqkiuo/main Update Package: BreastSubtypeR Commit: ab9e6c7e715a77c3d9d0c93f0d96794531b39afc Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:48:57 +0100 Commit message: Merge pull request #124 from yqkiuo/BranchManos cIHC.itr: return distances as numeric matrix, preserve dimnames Package: BreastSubtypeR Commit: 1cdd290182105e8d9dd1cf38a2f1cc2748045aba Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:41:20 +0100 Commit message: cIHC.itr: return distances as numeric matrix, preserve dimnames - Coerce mean_distance and mean_distance.Subtype to double matrices with sample/centroid dimnames; negate once. - Ensure testData is numeric matrix. - Use explicit getsuffix(calibration=..., internal=...). Closes #112 Package: BreastSubtypeR Commit: e626336705e6981d3f43c1e307381875acc4dbf5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:18:30 +0100 Commit message: Merge pull request #123 from yqkiuo/BranchManos feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to can… Package: BreastSubtypeR Commit: bf244ea222946de979dc528b6764b074b9a7492e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-12-10 11:17:59 +0100 Commit message: feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to canonical forms - Add `.normalize_er_her2_tn()` utility and call it inside `Mapping()` to coerce common variants to: * ER → {ER+, ER-} * HER2 → {HER2+, HER2-} (HER2 "2+" left unchanged/unevaluable) * TN → {TN, nonTN} Accepts Positive/Negative, Pos/Neg, Yes/No, True/False, 1/0, AMP→HER2+, etc. - Preserve original values in `colData` when fields are absent; only touch present columns. - Emit explicit warnings on ambiguous/unmappable values (e.g., HER2 "2+"). - Roxygen: expand `Mapping()` docs with required Column metadata for AUTO/ssBC/cIHC/PCAPAM50 and numeric TSIZE/NODE (0/1) for ROR; document the canonical receptor coding and the automatic normalization behavior. Closes #122 Package: BreastSubtypeR Commit: d4200b8f8fa6a230b1aed6bd8d5a271856dcf9c5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 10:04:54 +0100 Commit message: Merge pull request #120 from yqkiuo/BranchQiao Formatting Package: BreastSubtypeR Commit: 855146c3797560a923b044683b223aa09c5ab6b6 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 10:04:04 +0100 Commit message: Formatting Package: BreastSubtypeR Commit: 7e1546b848212ca92df006f0625e1f0213a5d825 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:57:27 +0100 Commit message: Merge pull request #119 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 13081dbdf8d5faead48468a7121455f68f226262 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-11-23 09:56:57 +0100 Commit message: Warning: nonASCII Package: BreastSubtypeR Commit: e872818d9f7db70dd95b04e56306c5f986b4cb2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-11-23 09:48:36 +0100 Commit message: Merge pull request #118 from yqkiuo/main 1.3.1 Package: BreastSubtypeR Commit: e837d4a4b93480e5921dc6220d336f390e08cfa9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:56:26 +0100 Commit message: Merge pull request #117 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 24282cdd95efcb545c8a516d2a4c52c333451e37 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:55:43 +0100 Commit message: docs(NEWS): updated to include latest changes/bug fixes Package: BreastSubtypeR Commit: d3e819ea9cb6036119018581de03f7c0ca6c03e9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 13:45:26 +0100 Commit message: shiny/preflight: reset cached data_input on source change (uploads/example) to fix stale cohort display Package: BreastSubtypeR Commit: f7ad9d6399c959146fad253c76e4b8a093367674 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:06:08 +0100 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: 33bc7cabda598a10d06781255a4ff477d64ec373 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:05:55 +0100 Commit message: Merge pull request #116 from yqkiuo/main Main to BranchManos unmerged changes Package: BreastSubtypeR Commit: c1164715171e92993dba23d51ed4d2739a9db33a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 12:03:31 +0100 Commit message: Include ssBC in robust singleton handling Package: BreastSubtypeR Commit: 0c0c39cd7cb7bdde99192d4a877cc9990b98b6c4 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:32:17 +0100 Commit message: v1.3.1 Package: BreastSubtypeR Commit: ed479c4a0a715bd078874a465956416cb58e999b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:30:33 +0100 Commit message: Minor typo for Shiny exports Package: BreastSubtypeR Commit: fca34d14be09269bd6a9e83f9b169b3f49e3b27d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:16:28 +0100 Commit message: ssBC.v2: include sample IDs in singleton fallback warnings; surface warnings in Shiny - Warnings now list subgroup + n + sample IDs (truncated for long lists). - Shiny wraps runs in withCallingHandlers() to show warnings via showNotification(). Package: BreastSubtypeR Commit: 5beba6624617ea57bd33a664a2c9ccddbe01f5d2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-11-19 11:15:25 +0100 Commit message: ssBC.v2: robust singleton handling + ROR guards - Use uncentered expression for n=1 fallback (avoid zero-vector Spearman→NA). - Add canonical 4-class name normalizer before RORgroup; create missing cols; enforce order. - Shorten Mapping() completion notification duration in Shiny. Package: BreastSubtypeR Commit: 6f8593d8659200d5b054e45ae6deb7ff624bf02f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 23:31:32 +0200 Commit message: Merge pull request #115 from yqkiuo/BranchManos fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: ae32dd867386460a3d6abcff63cd519bcebdd098 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-21 23:25:49 +0200 Commit message: fix(mapping): robust ENTREZID coercion in Mapping() Package: BreastSubtypeR Commit: 01a86e199d7353c526b1ddec6693b6c5d87a53e1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:51:52 +0200 Commit message: Merge pull request #114 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: aee5223fca7ad466234702b83f9d465092e65fec Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:50:18 +0200 Commit message: update documentation (.Rd) files & NEWS.md Package: BreastSubtypeR Commit: e3852e46bc7c708db9534558669b18e492bbcb44 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:38:36 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: f13b835df4329f494e2a1fe1242a1927657629f9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging -Name unnamed chunks Closes #113 Package: BreastSubtypeR Commit: 815edf2ed0faa1dc708fecc282da22945d861490 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-21 14:24:40 +0200 Commit message: fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging Package: BreastSubtypeR Commit: 27a8e42ca0dd5a06b976bd6e59aeedf3337c8ad1 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:41:55 +0200 Commit message: Merge pull request #111 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6ed1cf770b44ea3eeaa0fe5d284760692df203e Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:40:32 +0200 Commit message: feat(shiny): show ER/HER2 subgroup tallies (±TN) in AUTO preflight Package: BreastSubtypeR Commit: a85dec5c9e7f261e7d9ea94febbbfc063dc07992 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-16 15:04:55 +0200 Commit message: fix(shiny): guard switch() inputs to prevent length>1 errors; harden AUTO preflight & ssBC option handling Package: BreastSubtypeR Commit: 8b4e57129dabde362d8c811661e7586dc633c396 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:49:16 +0200 Commit message: feat(shiny): TN-aware AUTO preflight summary and messaging Package: BreastSubtypeR Commit: 83b469a296627e4a81983655692766813d8540b2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 10:48:42 +0200 Commit message: docs: convert wording to American English (standardized, normalization, visualize) Package: BreastSubtypeR Commit: 1c86f875473cf413e91da628410278915a9b19cb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-15 00:28:47 +0200 Commit message: Merge pull request #110 from yqkiuo/BranchManos v1.1.9: feat(app): add example-data loader and AUTO preflight cohort … Package: BreastSubtypeR Commit: bcb7486f49afd2f9c719d1b047c89b96421040b5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-15 00:26:27 +0200 Commit message: v1.1.9: feat(app): add example-data loader and AUTO preflight cohort stats; harden AIMS/sspbc outputs; renamed FPKM GEX example file Package: BreastSubtypeR Commit: 3e5ae1bae1910f63b576690d0f5965c092929197 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-14 22:26:00 +0200 Commit message: Merge pull request #109 from yqkiuo/BranchManos Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: 643629b4f37a82e8eb4fc1d4b8b7d47a1d0140e5 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-14 22:08:03 +0200 Commit message: Return the full matrix for sspbc (Posterior probabilities, etc) Package: BreastSubtypeR Commit: f0bb013273724583dc640776f5253a650e71deb7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-11 19:07:21 +0200 Commit message: Merge pull request #106 from yqkiuo/main v1.1.8 Package: BreastSubtypeR Commit: e519bba6330b28527eba397178b5db68259cd335 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 17:48:34 +0200 Commit message: Merge pull request #105 from yqkiuo/BranchManos Minor text improvements Package: BreastSubtypeR Commit: 7ef4c516f1e02b2667908e42c91db1f81587e183 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 17:35:16 +0200 Commit message: Minor text improvements Package: BreastSubtypeR Commit: bba02a162aae8a104830c2762903a95b4b24a086 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-11 16:30:43 +0200 Commit message: Merge pull request #104 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: c6bb89109d53b3cbfc61069dad0b97c43fc01a59 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 08:38:02 +0200 Commit message: v1.1.8: feat(auto): enforce v2-only for ER/HER2-defined cohorts; add TN cutoff (18); sync docs Package: BreastSubtypeR Commit: 104a9d3c962648e2421f86b970452b6ae8094add Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-11 00:03:52 +0200 Commit message: v1.1.7: Fixed bugs & Clarified guidance in AUTO logic Package: BreastSubtypeR Commit: 3a0c352910e74d2016eaaa4f0d229db74b6428b1 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:11:23 +0200 Commit message: Merge pull request #103 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: c23f9312cfe6399587682872db5168e726949468 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-08 07:10:55 +0200 Commit message: v1.1.6 Package: BreastSubtypeR Commit: bda41efb6523b351c335cbbbfe93eda3e294159a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-08 07:01:46 +0200 Commit message: Merge pull request #102 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 01fbf08f95785bd96121416f08a42a0723db9bb5 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:31:43 +0200 Commit message: Merge pull request #101 from yqkiuo/BranchManos Update citation Package: BreastSubtypeR Commit: 819b86fcb1f32f68d8d6551ae67675e59d55cbc2 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:29:59 +0200 Commit message: Update citation Package: BreastSubtypeR Commit: 18426cd1996f6d437078579a397e594ac858b422 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-07 23:18:10 +0200 Commit message: Merge pull request #100 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5cd622f0dfdcbf4ebd2612e2f3bce0d4d130a1dd Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:10:24 +0200 Commit message: Update to v1.1.6 Package: BreastSubtypeR Commit: 0168bb1d064c170c27904604ce944664052ffc4c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-07 23:00:02 +0200 Commit message: Fix CITATION error & update CITATION Package: BreastSubtypeR Commit: efcf440f930e3e0216161a7bfaa1f8a839796ffc Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:28 +0200 Commit message: Merge pull request #99 from yqkiuo/main v1.1.5 Package: BreastSubtypeR Commit: 522570c1925152201b4738888c70a9b479569b4d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-06 19:45:10 +0200 Commit message: Merge branch 'BranchQiao' into main Package: BreastSubtypeR Commit: caa57d7c96c2b3621ba3153a63704780fb67943c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: eca7fd305351bee53a3359193d31d6efb3bd239c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:26:16 +0200 Commit message: Merge pull request #98 from yqkiuo/BranchManos Bump version to 1.1.5, merge from BranchManos Package: BreastSubtypeR Commit: 3d6d84a04f652c46b098e7daf6b9433783c59317 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 19:17:29 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 08be34439c7ec15f3aab940989e7fc5881500a38 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:28:50 +0200 Commit message: Minor styler changes to comply with BiocCheck Package: BreastSubtypeR Commit: c33c626c748776d83aec78b69c2c5c2d78b40d94 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 18:00:25 +0200 Commit message: Remove Styler ignore file Package: BreastSubtypeR Commit: a756018eea737c57128fecbe2ed656a5c8bd8c89 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:53:48 +0200 Commit message: After styler formatting Package: BreastSubtypeR Commit: 0fb6775cf7105ccdfeac0f78d671c8220fa00a07 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-10-06 17:43:21 +0200 Commit message: Before styler formatting Package: BreastSubtypeR Commit: f462a35c15affb83307240678fdb8b5c31f1e1af Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-10-06 15:06:41 +0200 Commit message: Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos Package: BreastSubtypeR Commit: d58720a8654c148543e56efe3c8504e50f7a06f9 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Fix LaTeX errors, @importFrom issues, deprecated mutate_at(), tightened Mapping() Package: BreastSubtypeR Commit: 8cab29a01c0412be9b9a83d9c729c77b273c03f9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:33:33 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 2909f655c9c2686e9c562762e27c7cb78eb63544 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-10-03 12:28:41 +0200 Commit message: Merge pull request #97 from yqkiuo/BranchQiao Fix LaTeX errors Package: BreastSubtypeR Commit: f1d92deeed7ff76170c4ba8a70d0ac75e0dab7eb Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-10-03 12:28:10 +0200 Commit message: Fix LaTeX errors Package: BreastSubtypeR Commit: 9112d81e8538f3debb6c101255008486d052c326 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-12 19:39:12 +0200 Commit message: Merge pull request #96 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 977c1a7f7a5dd3700b51fe154e0a9509d6a960b1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 19:38:48 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: b2ba716538df0e23e684ec1118866c96560cab9b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:14:24 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: e25016431d3c00bfd81d941f4b8a71a2b7357ba1 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:07:19 +0200 Commit message: v1.1.3 Merge branch 'BranchQiao' of github.com:yqkiuo/BreastSubtypeR into BranchQiao # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit. Package: BreastSubtypeR Commit: 0f3624d0ed05aa4d2f2cb9759acb59d815fea297 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 16:04:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 8a340b6a4117f80791ae664c5741a0fe8627c9c3 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 15:44:48 +0200 Commit message: Fix BreastSubtypeRobj to include only the object itself (exclude environment variables) Package: BreastSubtypeR Commit: f969bcf09e03aa226de3839a68cf76cc01011ef3 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-12 14:52:15 +0200 Commit message: v1.1.3 Package: BreastSubtypeR Commit: 693c829f364caedb2161a940d196d1830bd19d87 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-12 10:21:35 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 8582fb3b897e60ecc6da91040e32b42b19641154 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 17:06:26 +0200 Commit message: Added publication badge Package: BreastSubtypeR Commit: bd0b6cab935e607efd4bb001e3b75b02b37cc1fe Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:47:02 +0200 Commit message: Fixed bug: When running BS_Multi() omitting the first method; Minimal fix (drop nothing after removing row_id) Package: BreastSubtypeR Commit: 234ccbe269d45bd2c407358b711253629fe59203 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-11 14:12:28 +0200 Commit message: Polishing README.md & Vignette Package: BreastSubtypeR Commit: b3d5c232a32097ee9b4f83908a9c89f6ca621be8 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:41:14 +0200 Commit message: DOI update and text Package: BreastSubtypeR Commit: bacb13657f301643a682a3fcd7e82a22091a3b6c Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-11 00:01:14 +0200 Commit message: Added DOI, Updated exported with version info, method, etc Package: BreastSubtypeR Commit: 787b3119148e345c0b2d4fa8638b3d6dd37600ee Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 19:17:32 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: c856d8dc615f688ae8f5d27eeb47ab297ead6b11 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:36:22 +0200 Commit message: Delete .github/workflows/sync-to-forks.yml Package: BreastSubtypeR Commit: 8d235ce12beccf9d394146a458ae135fec2f0fb3 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:18:15 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: ad15f75e9de9028eb6d93fb5efb3ca05220ce975 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 18:04:51 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 917d62c7bc428fc67ff97c513022feb210fed94c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:58:05 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 9258dd1803aac507ecae1ec05d30a55c7c91827c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:54:22 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 8864ea4a8bda1bee1b6496aaf185e8bb76af5257 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:57 +0200 Commit message: Update sync-to-forks.yml Package: BreastSubtypeR Commit: 71735535741a019e7ba9299e47783038edbd3714 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:51:00 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f165c7df5636588c76360b10a42e792e9bf53614 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:50:26 +0200 Commit message: Create sync-to-forks.yml Package: BreastSubtypeR Commit: f2d85acb23f2c38ec3b3062fbab841c29115d38e Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:47:46 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 792bc0ab92f80b7405d69c45516dd131ffd7663c Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:43:18 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 99d3102b66482953013f265d00464c8c3a4c2b25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:34:13 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 212e09ee660df8daaffea11a7af00d53321895aa Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 17:04:17 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 7cea1e782fedda5fef57f559c77dc39db8aceb9d Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:56:40 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: f33f344a6b0d06d3de393a783a23383e4ef5cac4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:33:26 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: adccaf9e7d8ce2b6234a1960e93e5d1543d98e09 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:31:34 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: a9e9e80f2f1063aae332963e474ea2f5804487b7 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:27:58 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 4151dfa20943c89acdd55c5e1dec18a03da01e2f Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 16:14:01 +0200 Commit message: Update sync-to-org.yml Package: BreastSubtypeR Commit: 1ab513bde94a41e4ab34856ca5e4f5ba5a6413e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-10 15:59:19 +0200 Commit message: Create sync-to-org.yml Package: BreastSubtypeR Commit: f9f0ea202177840660c02d39e203f67d4003e2cd Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:09:58 +0200 Commit message: Added description for new example dataset (TCGABRCAobj), updated the BreastSubtypeRobj with the 3 new medians info, tiny text improvements Package: BreastSubtypeR Commit: 056545172113202bb55a0ea0c2918851096fa0f2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:05:10 +0200 Commit message: Created a new example dataset (TCGABRCAobj) from TCGA-BRCA with Raw Counts, and similar results as OSLO2EMIT0obj Package: BreastSubtypeR Commit: 6de103db09589a53624341851237a8f547684ceb Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:02:19 +0200 Commit message: Updated BreastSubtypeRobj with 3 more published medians Package: BreastSubtypeR Commit: 6acd15688f6e60db4e1f2ef151c103e865ce5663 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 15:00:19 +0200 Commit message: Guard docalibration, Improve External calibration, UX, and minor text improvements Package: BreastSubtypeR Commit: 8f7e3790ac94fead82f77e6564d87c542fcf5097 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-10 11:11:22 +0200 Commit message: Fixed error in BS_Multi() in AUTO Mode, when ssBC has <50 PAM50 genes: Add safe row-aligning cbind helper, made RORgroup() tolerant to missing ESR1/ERBB2 rows, and made BS_Multi() assemble results by PatientID Package: BreastSubtypeR Commit: 06bd9bce269ca12b4ca9f052f3d81cd730212a68 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 21:20:25 +0200 Commit message: Fixed the issue with pre-loading third-party libraries before initializing the Shiny app, Updated Help files Package: BreastSubtypeR Commit: ee560564150a7a5f11c00e8750583438a6c084e6 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:55 +0200 Commit message: Updated NEWS.md with major changes Package: BreastSubtypeR Commit: abd132463b65390c813f04ea50c530fd4b058507 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:50:18 +0200 Commit message: Minor typos Package: BreastSubtypeR Commit: 74b20b933030517c45e68826a469dd88d79aa0b9 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:24:07 +0200 Commit message: Added a TCGA-BRCA subset, with clinical & annotation data, for testing the RawCounts normalization pipeline Package: BreastSubtypeR Commit: d4fedc4c9b2a241b2652e563c2300d423f787287 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 18:21:08 +0200 Commit message: iBreastSubtypeR: UX polish, AUTO explainer, export refactor, AIMS constraint & bug fixes Package: BreastSubtypeR Commit: fb7c21f7ebc4f50be7610c8c0a023036f1559358 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 13:24:32 +0200 Commit message: Include three pre-computed Medians (external) as an option to Shiny App Package: BreastSubtypeR Commit: d1a90080950c9b5ddcad737979d072bdc177e038 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 11:34:43 +0200 Commit message: ssBC fixes: No crashes when < 50 PAM50 genes, No accidental subtype calls when a sample’s distance row is all-NA, Won't error when a subgroup has zero samples, qCtr won't produce NaN from zero range Package: BreastSubtypeR Commit: 10644b50e4721efe7b0d9f65445d30e1fdcf5a26 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-08 10:05:57 +0200 Commit message: Add our reference to Mapping() & BS_Multi() Package: BreastSubtypeR Commit: 5ea0dd73f932fbdd278f4e299de7270698d855c1 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 23:10:17 +0200 Commit message: New preflight for AUTO to prevent errors, new customizations, included new polished text for PAM50 to guide users, and more Package: BreastSubtypeR Commit: 3b08eed750427d72842bec852ff85c2446138cbe Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 13:21:06 +0200 Commit message: Fix issue when HER2 missing and user runs AUTO Package: BreastSubtypeR Commit: 16b805c817e0b7e3883b1aa7defd6da04f6a57f4 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:20:14 +0200 Commit message: Included a Prelight check for ER/HER2/Tn status availability in Clinical data BEFORE Running subtyping, avoiding App crashing due to missing values Package: BreastSubtypeR Commit: f003e4ecbfadb6a2a293ff39d838581dea5a0086 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 12:01:32 +0200 Commit message: Synchronized changes in BreastSubtypeR_methods.R and NC_functions.R, Created a theme to match the logo, made things unified, text improvements Package: BreastSubtypeR Commit: a66b4796231c8054f2093c6795ca4e67f2cb04de Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-07 10:08:20 +0200 Commit message: Parker original when calibration=None, or external calibration returns error: Fixed by Making NA equivalent to "medianCtr" (sync eith Parker et al.), and -1 to No calibration. Also, avoid requiring PatientID for BS_parker() when hasClinical = FALSE, included extra controls for hasClinical in all NC functions, polished help text, corrected typos (also tried to correct the 2nd error for ssBC, when < 50 genes, but will work more on this and come back with another Commit) Package: BreastSubtypeR Commit: 53ca58ec99d200f998a8be6896bab45f47d789e3 Author: Emmanouil Sifakis <sifakise@gmail.com> Date: 2025-09-05 19:36:25 +0200 Commit message: Major changes: Multi method with AUTO mode added, Description text for each method with Refs added, Subtype 4-class selection Package: BreastSubtypeR Commit: bdf3bf291b59939171d85ff61f895b2ffc222b8d Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:18:47 +0200 Commit message: Fix UI so the drop down menus are easier to select Package: BreastSubtypeR Commit: c0ed93ab5eed4a965f478a0dcac17355f8f91501 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 15:01:42 +0200 Commit message: Changed HasClinical with a Tick box, included many controls to check whether TSIZE, NODE are available, added different help functions for GEX and Annotation, improved text, and more Package: BreastSubtypeR Commit: 277869bea9c0c7d2747370cc657b2e87cb4e7dd2 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 14:59:23 +0200 Commit message: Replaced the T -> TSIZE Package: BreastSubtypeR Commit: fd063a60aa8db3651975e89237ddb398d62c1100 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:28:48 +0200 Commit message: Minor edit Package: BreastSubtypeR Commit: 31e6bbfa2c897aa87caa09254cd2d4d2074b790f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:25:40 +0200 Commit message: Renamed folder to Shinny->Sniny, renamed data files with clear names Package: BreastSubtypeR Commit: 5ef9dd73efdccab438ee51f1ea0441ac565ca984 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-09-05 11:20:19 +0200 Commit message: Fix server.R bug Package: BreastSubtypeR Commit: c4c205e993f8791683fddf05392533aadded4b75 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-04 11:49:00 +0200 Commit message: refine shiny Package: BreastSubtypeR Commit: 304cb68143558163b4dd070c2498631f62a650e5 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-04 10:40:17 +0200 Commit message: Merge pull request #95 from yqkiuo/main Merge pull request #94 from yqkiuo/BranchQiao Package: BreastSubtypeR Commit: 6cbc1cb1b18907119b3414e3c0dafec607480a99 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:27:20 +0200 Commit message: Merge pull request #94 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 298458b861686b4ed9bfa17c070e5ffea513f3dd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-02 08:27:00 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: a50d8d4c3bea22f65836df6d099b269da685d8c2 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:25:43 +0200 Commit message: Merge pull request #93 from yqkiuo/main v1.1.2 Package: BreastSubtypeR Commit: 65b18fd8734f90e579fff40e53bbc51799b2c4ad Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:28 +0200 Commit message: Merge pull request #92 from yqkiuo/BranchManos Branch manos Package: BreastSubtypeR Commit: 5d09b44a5785c08a10d3d652d2a01db94678a1de Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-02 08:23:21 +0200 Commit message: Merge branch 'main' into BranchManos Package: BreastSubtypeR Commit: 8f4056fc16de285798c18e8c36e5399e5cd1fd23 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-09-01 10:18:12 +0200 Commit message: Merge pull request #91 from yqkiuo/BranchQiao v1.2.2 Package: BreastSubtypeR Commit: e11ffcd934d71dd5ee42c3816cabf93b997e6c64 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-09-01 10:17:53 +0200 Commit message: v1.2.2 Package: BreastSubtypeR Commit: 0969e8fa4d71d310d1d2f58c788af7a94566de25 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-31 22:18:46 +0200 Commit message: Merge pull request #90 from yqkiuo/BranchQiao v1.1.2 Package: BreastSubtypeR Commit: c575280eed4e562e90ba6b9b7a6675353e532725 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-31 22:18:25 +0200 Commit message: v1.1.2 Package: BreastSubtypeR Commit: 031beb8e23f96e6f4894f56b550dd49d0c2a729b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-29 16:04:28 +0200 Commit message: Updated code to include separate cut-offs for ERpos & ERneg, as well as separate cut-offs ER(pos/neg)/HER2 (independent of HER2 status) based on the above cut-offfs. Note: The combined cut-offs will be released in the next submission Package: BreastSubtypeR Commit: 93ba44156f95a90bb74440d472157107e5ef0908 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 20:13:37 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: efee177e7f94d079d424ad79467615a63ce71698 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 2c6cfcacdc3550df0916ecb54833275bf2b9f04f Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:34:19 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: d0154df0200108179568a150e1487e592a34e20a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 6a0be72275efbb8b9828b8765834d1ce97521134 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:26:55 +0200 Commit message: Resolve merge conflicts in README.md Package: BreastSubtypeR Commit: 3cf5afd43c31eeec90045902e6a082d82013bbf7 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: e91120bb63753900c47f80206b0662aef090c98a Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 19:17:28 +0200 Commit message: Minor edits Package: BreastSubtypeR Commit: c09d132b8993a81ad16143b2ddbd5fb6b6f36f8b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 18:32:39 +0200 Commit message: Updated NEWS.md, BreastSubtypeR_methods.R, and minor updates to Utilities.R and data_doc.R Package: BreastSubtypeR Commit: 10f36184b66a9a0703d4296c9311b5ed1fc03e23 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 15:16:50 +0200 Commit message: Shiny app normalization clarification Package: BreastSubtypeR Commit: 24740ca0d3f45e43e674d247778b8e003871361c Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:57:22 +0200 Commit message: Replaced the adaptive filtering as it was producing a reduced gene list for NC-based methods. Instead I introduce the calculation of UQ in the positively expressed subset and apply those calculcated factors to the full matrix. Package: BreastSubtypeR Commit: 347114047eeba2318371d4245043ae1d3b6bce86 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-28 14:34:21 +0200 Commit message: Include adaptive gene filtering so UQ normalization can work under real data Package: BreastSubtypeR Commit: f3bd9cdae36176a3857de89fac0c794bd8df369b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 16:29:18 +0200 Commit message: RawCounts test code include & help files updated Package: BreastSubtypeR Commit: c248d0fe615e9d6e3f4401bb6658908341de9208 Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 16:07:29 +0200 Commit message: Shiny app: added descripted text Package: BreastSubtypeR Commit: 52bea350827dc0fba939551f50149d60acb3887b Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 15:12:56 +0200 Commit message: Updated text in overview files Package: BreastSubtypeR Commit: 5b87399978a5d1cca09a82d5249a2b8863a553ea Author: Emmanouil Sifakis <emmanouil.sifakis@ki.se> Date: 2025-08-27 15:10:09 +0200 Commit message: CITATION added Package: BreastSubtypeR Commit: e8fcac0bcab82793b586f5ffc8c930a0002ac609 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-08-21 11:29:40 +0200 Commit message: Merge pull request #89 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 0c75bf90f3070408ec5a156edf84b9c0bc70250b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:29:14 +0200 Commit message: update new features Package: BreastSubtypeR Commit: a99a93e94a90d6a715d64daedbe2e1f886f87917 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-08-21 11:27:58 +0200 Commit message: update new features Package: BreastSubtypeR Commit: c9f28c19c39695ad8a84ee4aa929c352be00e229 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 18:11:51 +0200 Commit message: Merge pull request #88 from yqkiuo/BranchQiao Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: e4a62355017220fe89ec8ea09376a0a56060de7c Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 18:11:26 +0200 Commit message: Fix: added BiocStyle to Suggests for vignette build Package: BreastSubtypeR Commit: 1993ab3e50725d01e8980a00eeaec8f0b0b766c4 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:48:10 +0200 Commit message: Merge pull request #87 from yqkiuo/BranchQiao 1.1.1 Package: BreastSubtypeR Commit: 5d928ed37d8d0f47dd0392057846c43dc12e3dea Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:47:44 +0200 Commit message: 1.1.1 Package: BreastSubtypeR Commit: 52faaf9d7980c6d36524bcabbdcffe1f0fb92a0a Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-07-17 17:39:51 +0200 Commit message: Merge pull request #86 from yqkiuo/BranchQiao 1.0.1 Package: BreastSubtypeR Commit: 35eef13e343edd2f9c6a1c26d780c97f470ac6c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-07-17 17:38:55 +0200 Commit message: 1.0.1 Package: BreastSubtypeR Commit: 6abaf3b4ae3d1772babec19c83d49c04728daa06 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-27 09:49:16 +0200 Commit message: Merge pull request #85 from yqkiuo/BranchQiao general update Package: BreastSubtypeR Commit: 453e9aac8dc81b86987e53e60659f2c97f6ba403 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-27 09:48:42 +0200 Commit message: general update Package: BreastSubtypeR Commit: 226607c2ae42706346a1e8911d1f2f82a5ca1490 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 19:12:11 +0200 Commit message: Merge pull request #84 from yqkiuo/BranchQiao v1.1.1 Package: BreastSubtypeR Commit: d773d4401e93ec12006f4e79122cbee8247d80d7 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 19:02:45 +0200 Commit message: v1.1.1 Package: BreastSubtypeR Commit: e74e86a2cfdf6daf92ed180095d27619cd45cd54 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:44:06 +0200 Commit message: Merge pull request #83 from yqkiuo/BranchQiao Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: fd30082d86b34d3ced41b7a7c385e01448c19794 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:41:43 +0200 Commit message: Bug fixes: updated version, resolved minor issues Package: BreastSubtypeR Commit: 74145000a4ce350ca0e787fe5c459b79318b3edb Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 18:25:01 +0200 Commit message: Merge pull request #82 from yqkiuo/BranchQiao Bug fixes and minor improvements Package: BreastSubtypeR Commit: 1a5cb6636acfbd2ad1fc7c290bfba875dd2b22b0 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 18:24:35 +0200 Commit message: Bug fixes and minor improvements Package: BreastSubtypeR Commit: 4a895b8a8a149e0199b85eeaa19b6769dd8382df Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:27:17 +0200 Commit message: Merge pull request #81 from yqkiuo/BranchQiao Branch qiao Package: BreastSubtypeR Commit: 4a03138457415f0164139373ee34038bd07ad300 Author: Qiao Yang <qiao.yang@ki.se> Date: 2025-06-26 13:21:40 +0200 Commit message: Update DESCRIPTION Package: BreastSubtypeR Commit: 856c6f8f91de5339988cf4c315bcaf96247f37d5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-26 10:39:20 +0200 Commit message: general update Package: BreastSubtypeR Commit: e35db8756a5fa3f30bf4addbeacd58145589e16b Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:18:47 +0200 Commit message: general update Package: BreastSubtypeR Commit: 2e60c2222d3e9fdf48d3262ba087b447a95119a9 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 23:03:00 +0200 Commit message: general update Package: BreastSubtypeR Commit: 7cfcfe95b2761178d17cc2af122f61883e7dc666 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:50:06 +0200 Commit message: update general Package: BreastSubtypeR Commit: b30131f2c073711d4b42e38af49bef1849da20c5 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-25 22:48:53 +0200 Commit message: Update RawCounts para Package: BreastSubtypeR Commit: 6fa4d83d00b30727be9b1d4fd3798015fad0442a Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:32:10 +0200 Commit message: debug ROR Package: BreastSubtypeR Commit: ba045196fcd4a3bff148b3497a82f3f87d6bb324 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:31:55 +0200 Commit message: refine "-1" in parker.original Package: BreastSubtypeR Commit: b5e6254539fd38e41109056b2ddff7d36e0f9c19 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:15:41 +0200 Commit message: refine "-1" in parker.orignal Package: BreastSubtypeR Commit: bc7d097164cb411bfc4b40d5513073ae1bac35d8 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:39 +0200 Commit message: 0.00.0 Package: BreastSubtypeR Commit: 5d966c161e4cdae464dd16d48421f6d5a4e26461 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:30 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 81f77832a0d7f8f5b8b70403616fe165ff96862d Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:01:08 +0200 Commit message: debug data type Package: BreastSubtypeR Commit: 8471668b9b9b43c3e27a87faa458488a8fba7f05 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:56 +0200 Commit message: debug BS_Multi Package: BreastSubtypeR Commit: 01fa8b576ca237667ed8a792477638cd4b023dbd Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:34 +0200 Commit message: clear author Package: BreastSubtypeR Commit: a86f573778ed992a3d2dbb698b4c9c00a15619c4 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-21 19:00:20 +0200 Commit message: clear authors Package: BreastSubtypeR Commit: 00d2b9c5d71c6830e845dcddcb810b9640666207 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:33:01 +0200 Commit message: debug AUTO Package: BreastSubtypeR Commit: 8b3f7c2ef2d45cf772511a7290ba0a31baa43b62 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 23:32:46 +0200 Commit message: debug bad PCAPAM50 Package: BreastSubtypeR Commit: c70f4c9b0d64da1940659ae9a826d8221be05a32 Author: Qiao Yang <yq.kiuo@gmail.com> Date: 2025-06-20 09:32:30 +0200 Commit message: debug PCAPAM50 </div> </div>
Fix ROR-C risk group column: use criskgroups, not cpriskgroups In RORgroup() (R/NC_functions.R) the data frame built when hasClinical = TRUE assigned the combined + proliferation groups (cpriskgroups) to both "ROR-C Group (Subtype + Clinic)" and "ROR-PC Group (Subtype + Clinic + Prolif)". The ROR-C groups (criskgroups, thresholds -0.1 and 0.2 on the combined score) were computed but never reported. The ROR-C group column now uses criskgroups; the ROR-C score and every other column are unchanged. Present in Bioconductor release 1.4.0 and devel 1.5.1. tests/testthat/test-ror-groups.R adds a synthetic RORgroup() input in which the ROR-C and ROR-PC groups differ (high/low/med vs low/high/med) and checks that the ROR-C group is reproducible from the reported ROR-C score. The test fails on the previous code and passes with this change.
Tests: run the nested testthat suite via test_check() tests/testthat.R contained a single inline test_that() block and never called test_check(), so tests/testthat/test-tn-cohort-detection.R (added in 1.5.1) was not executed by R CMD check; the Bioconductor devel check log shows only the inline test running. tests/testthat.R now calls test_check("BreastSubtypeR") and the inline BS_Multi() test moved unchanged to tests/testthat/test-bs-multi-manual.R. DESCRIPTION: Config/testthat/edition: 3 and testthat (>= 3.2.0) in Suggests, matching the edition-3 expectations used by the tests added on this branch. No version bump.
Merge pull request #135 from yqkiuo/main update to 1.5.2
Merge branch 'BranchQiao' into main
Merge pull request #134 from yqkiuo/BranchManos Branch manos
Finalize NEWS entry for TN detection fix (#133)
Update NEWS and documentation for TN detection fix (#133)
Fix TN-only cohort detection (#133)
v1.3.3
Merge pull request #129 from yqkiuo/main AUTO - NA
Merge pull request #128 from yqkiuo/BranchManos Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127)
Fix AUTO NA handling in ER/HER2 subgroup counts (na.rm=TRUE) (closes #127)
Merge pull request #125 from yqkiuo/main Update
Merge pull request #124 from yqkiuo/BranchManos cIHC.itr: return distances as numeric matrix, preserve dimnames
cIHC.itr: return distances as numeric matrix, preserve dimnames - Coerce mean_distance and mean_distance.Subtype to double matrices with sample/centroid dimnames; negate once. - Ensure testData is numeric matrix. - Use explicit getsuffix(calibration=..., internal=...). Closes #112
Merge pull request #123 from yqkiuo/BranchManos feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to can…
feat(Mapping): accept flexible ER/HER2/TN encodings; normalize to canonical forms - Add `.normalize_er_her2_tn()` utility and call it inside `Mapping()` to coerce common variants to: * ER → {ER+, ER-} * HER2 → {HER2+, HER2-} (HER2 "2+" left unchanged/unevaluable) * TN → {TN, nonTN} Accepts Positive/Negative, Pos/Neg, Yes/No, True/False, 1/0, AMP→HER2+, etc. - Preserve original values in `colData` when fields are absent; only touch present columns. - Emit explicit warnings on ambiguous/unmappable values (e.g., HER2 "2+"). - Roxygen: expand `Mapping()` docs with required Column metadata for AUTO/ssBC/cIHC/PCAPAM50 and numeric TSIZE/NODE (0/1) for ROR; document the canonical receptor coding and the automatic normalization behavior. Closes #122
Merge pull request #120 from yqkiuo/BranchQiao Formatting
Formatting
Merge pull request #119 from yqkiuo/BranchQiao Branch qiao
Warning: nonASCII
Merge pull request #118 from yqkiuo/main 1.3.1
Merge pull request #117 from yqkiuo/BranchManos Branch manos
docs(NEWS): updated to include latest changes/bug fixes
shiny/preflight: reset cached data_input on source change (uploads/example) to fix stale cohort display
Merge branch 'BranchManos' of https://github.com/yqkiuo/BreastSubtypeR into BranchManos
Merge pull request #116 from yqkiuo/main Main to BranchManos unmerged changes
Include ssBC in robust singleton handling
v1.3.1
Minor typo for Shiny exports
ssBC.v2: include sample IDs in singleton fallback warnings; surface warnings in Shiny - Warnings now list subgroup + n + sample IDs (truncated for long lists). - Shiny wraps runs in withCallingHandlers() to show warnings via showNotification().
ssBC.v2: robust singleton handling + ROR guards - Use uncentered expression for n=1 fallback (avoid zero-vector Spearman→NA). - Add canonical 4-class name normalizer before RORgroup; create missing cols; enforce order. - Shorten Mapping() completion notification duration in Shiny.
Merge pull request #115 from yqkiuo/BranchManos fix(mapping): robust ENTREZID coercion in Mapping()
fix(mapping): robust ENTREZID coercion in Mapping()
Merge pull request #114 from yqkiuo/BranchManos Branch manos
update documentation (.Rd) files & NEWS.md
fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging -Name unnamed chunks Closes #113
fix(ssBC): honor TN cohorts when methods are specified manually - Run ssBC with s="TN" and ssBC.v2 with s="TN.v2" when TN cohort detected - Add internal ._msg() helper and replace message() calls accordingly - Fix samples_ERHER2.icd typo and align with AUTO outputs - Improve TN cohort detection and informative logging
Merge pull request #111 from yqkiuo/BranchManos Branch manos
feat(shiny): show ER/HER2 subgroup tallies (±TN) in AUTO preflight
fix(shiny): guard switch() inputs to prevent length>1 errors; harden AUTO preflight & ssBC option handling
feat(shiny): TN-aware AUTO preflight summary and messaging
docs: convert wording to American English (standardized, normalization, visualize)
Merge pull request #110 from yqkiuo/BranchManos v1.1.9: feat(app): add example-data loader and AUTO preflight cohort …
v1.1.9: feat(app): add example-data loader and AUTO preflight cohort stats; harden AIMS/sspbc outputs; renamed FPKM GEX example file
Merge pull request #109 from yqkiuo/BranchManos Return the full matrix for sspbc (Posterior probabilities, etc)
Return the full matrix for sspbc (Posterior probabilities, etc)
Merge pull request #106 from yqkiuo/main v1.1.8
Merge pull request #105 from yqkiuo/BranchManos Minor text improvements
Minor text improvements
Merge pull request #104 from yqkiuo/BranchManos Branch manos
v1.1.8: feat(auto): enforce v2-only for ER/HER2-defined cohorts; add TN cutoff (18); sync docs
v1.1.7: Fixed bugs & Clarified guidance in AUTO logic
Merge pull request #103 from yqkiuo/BranchQiao Branch qiao
v1.1.6
Merge pull request #102 from yqkiuo/main v1.1.5
Merge pull request #101 from yqkiuo/BranchManos Update citation
Update citation
Merge pull request #100 from yqkiuo/BranchManos Branch manos
Update to v1.1.6
Fix CITATION error & update CITATION
Merge pull request #99 from yqkiuo/main v1.1.5
Update sync-to-org.yml
Merge pull request #98 from yqkiuo/BranchManos Bump version to 1.1.5, merge from BranchManos
Minor styler changes to comply with BiocCheck
Remove Styler ignore file
After styler formatting
Before styler formatting
Fix LaTeX errors, @importFrom issues, deprecated mutate_at(), tightened Mapping()
Fix LaTeX errors
Merge pull request #97 from yqkiuo/BranchQiao Fix LaTeX errors
Merge pull request #96 from yqkiuo/BranchQiao Branch qiao
v1.1.3
v1.1.3 Merge branch 'BranchQiao' of github.com:yqkiuo/BreastSubtypeR into BranchQiao # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit.
Fix BreastSubtypeRobj to include only the object itself (exclude environment variables)
Minor typos
Added publication badge
Fixed bug: When running BS_Multi() omitting the first method; Minimal fix (drop nothing after removing row_id)
Polishing README.md & Vignette
DOI update and text
Added DOI, Updated exported with version info, method, etc
Delete .github/workflows/sync-to-forks.yml
Update sync-to-forks.yml
Create sync-to-forks.yml
Create sync-to-org.yml
Added description for new example dataset (TCGABRCAobj), updated the BreastSubtypeRobj with the 3 new medians info, tiny text improvements
Created a new example dataset (TCGABRCAobj) from TCGA-BRCA with Raw Counts, and similar results as OSLO2EMIT0obj
Updated BreastSubtypeRobj with 3 more published medians
Guard docalibration, Improve External calibration, UX, and minor text improvements
Fixed error in BS_Multi() in AUTO Mode, when ssBC has <50 PAM50 genes: Add safe row-aligning cbind helper, made RORgroup() tolerant to missing ESR1/ERBB2 rows, and made BS_Multi() assemble results by PatientID
Fixed the issue with pre-loading third-party libraries before initializing the Shiny app, Updated Help files
Updated NEWS.md with major changes
Added a TCGA-BRCA subset, with clinical & annotation data, for testing the RawCounts normalization pipeline
iBreastSubtypeR: UX polish, AUTO explainer, export refactor, AIMS constraint & bug fixes
Include three pre-computed Medians (external) as an option to Shiny App
ssBC fixes: No crashes when < 50 PAM50 genes, No accidental subtype calls when a sample’s distance row is all-NA, Won't error when a subgroup has zero samples, qCtr won't produce NaN from zero range
Add our reference to Mapping() & BS_Multi()
New preflight for AUTO to prevent errors, new customizations, included new polished text for PAM50 to guide users, and more
Fix issue when HER2 missing and user runs AUTO
Included a Prelight check for ER/HER2/Tn status availability in Clinical data BEFORE Running subtyping, avoiding App crashing due to missing values
Synchronized changes in BreastSubtypeR_methods.R and NC_functions.R, Created a theme to match the logo, made things unified, text improvements
Parker original when calibration=None, or external calibration returns error: Fixed by Making NA equivalent to "medianCtr" (sync eith Parker et al.), and -1 to No calibration. Also, avoid requiring PatientID for BS_parker() when hasClinical = FALSE, included extra controls for hasClinical in all NC functions, polished help text, corrected typos (also tried to correct the 2nd error for ssBC, when < 50 genes, but will work more on this and come back with another Commit)
Major changes: Multi method with AUTO mode added, Description text for each method with Refs added, Subtype 4-class selection
Fix UI so the drop down menus are easier to select
Changed HasClinical with a Tick box, included many controls to check whether TSIZE, NODE are available, added different help functions for GEX and Annotation, improved text, and more
Replaced the T -> TSIZE
Minor edit
Renamed folder to Shinny->Sniny, renamed data files with clear names
Fix server.R bug
refine shiny
Merge pull request #95 from yqkiuo/main Merge pull request #94 from yqkiuo/BranchQiao
Merge pull request #94 from yqkiuo/BranchQiao Branch qiao
v1.1.2
Merge pull request #93 from yqkiuo/main v1.1.2
Merge pull request #92 from yqkiuo/BranchManos Branch manos
Merge branch 'main' into BranchManos
Merge pull request #91 from yqkiuo/BranchQiao v1.2.2
v1.2.2
Merge pull request #90 from yqkiuo/BranchQiao v1.1.2
Updated code to include separate cut-offs for ERpos & ERneg, as well as separate cut-offs ER(pos/neg)/HER2 (independent of HER2 status) based on the above cut-offfs. Note: The combined cut-offs will be released in the next submission
Resolve merge conflicts in README.md
Minor edits
Updated NEWS.md, BreastSubtypeR_methods.R, and minor updates to Utilities.R and data_doc.R
Shiny app normalization clarification
Replaced the adaptive filtering as it was producing a reduced gene list for NC-based methods. Instead I introduce the calculation of UQ in the positively expressed subset and apply those calculcated factors to the full matrix.
Include adaptive gene filtering so UQ normalization can work under real data
RawCounts test code include & help files updated
Shiny app: added descripted text
Updated text in overview files
CITATION added
Merge pull request #89 from yqkiuo/BranchQiao Branch qiao
update new features
Merge pull request #88 from yqkiuo/BranchQiao Fix: added BiocStyle to Suggests for vignette build
Fix: added BiocStyle to Suggests for vignette build
Merge pull request #87 from yqkiuo/BranchQiao 1.1.1
1.1.1
Merge pull request #86 from yqkiuo/BranchQiao 1.0.1
1.0.1
Merge pull request #85 from yqkiuo/BranchQiao general update
general update
Merge pull request #84 from yqkiuo/BranchQiao v1.1.1
v1.1.1
Merge pull request #83 from yqkiuo/BranchQiao Bug fixes: updated version, resolved minor issues
Bug fixes: updated version, resolved minor issues
Merge pull request #82 from yqkiuo/BranchQiao Bug fixes and minor improvements
Bug fixes and minor improvements
Merge pull request #81 from yqkiuo/BranchQiao Branch qiao
Update DESCRIPTION
update general
Update RawCounts para
debug ROR
refine "-1" in parker.original
refine "-1" in parker.orignal
0.00.0
clear authors
debug data type
debug BS_Multi
clear author
debug AUTO
debug bad PCAPAM50
debug PCAPAM50
