DRIMSeq dependency removed
 

 Roxygen refresh and fixes
 

 Speed up exportToTrack() when qLow and qUp are given.

Build the BED12 blocks of all clusters at once: compute the candidate
starts and ends of the up to three blocks of each cluster in matrices
with one column per cluster, create all the blocks with a single call to
IRanges(), and split them by cluster with relist() and
PartitioningByEnd().  This replaces a loop that built and concatenated
IRanges objects cluster by cluster, which took ~2.5 ms per cluster.

On exampleCAGEexp, exporting tag clusters with quantiles is 12-19x
faster and consensus clusters 10x faster, and the results, including
the BED12 files written by rtracklayer, are identical.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 Simplify
 

 Announce the changes in consensus-cluster expression in NEWS.

Describe in the development-version section that tpmThreshold of
aggregateTagClusters() now only selects the tag clusters that define
consensus-cluster boundaries, that consensus-cluster expression is the
sum of the CTSSs passing filteredCTSSidx() when aggregateTagClusters()
is run, and that the hidden filters removed from aggregateTagClusters()
and CustomConsensusClusters() change expression values, outOfClusters,
and the number of consensus clusters.  Also announce the deprecation of
excludeSignalBelowThreshold.

Explain how that argument behaved: up to CAGEr 1.20 (Bioconductor 3.6),
TRUE summed in each sample the signal of the tag clusters passing
tpmThreshold, as announced in the 1.2.7 entry, whereas from CAGEr 1.22.0
(Bioconductor 3.7) it discarded the individual CTSSs below tpmThreshold
in every sample.  The switch to per-CTSS filtering came with commit
5447ae1 (2017-09-14), whose message does not mention it, and the 1.22.0
NEWS entry did not announce it.

This entry is kept in its own commit because the development-version
section of NEWS.md does not exist on the release branch: a backport of
the code changes needs its own NEWS entry.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 Correct the documentation of flagLowExpCTSS() to match its code.

flagLowExpCTSS() keeps (TRUE) the CTSSs whose signal is strictly above
the threshold in at least nrPassThreshold samples, nrPassThreshold
being capped at the number of samples, and flags (FALSE) the others.
The documentation said instead that CTSSs with a signal below the
threshold are flagged, while a signal equal to the threshold is flagged
too, and that CTSSs are flagged when their signal is below the
threshold in at least nrPassThreshold samples, which describes a
different filter: with the default nrPassThreshold = 1, only the CTSSs
that are at or below the threshold in all samples are flagged.

The behaviour of the function does not change.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 Add tests for consensus-cluster expression in aggregateTagClusters().

Add a testthat (edition 3) suite built on a small synthetic CAGEexp
object (three samples, a dozen CTSSs, and a padding CTSS that sets
library sizes so that TPM values are simple multiples of the counts).
Expected values are derived by hand from the definitions of consensus
clusters and written as arithmetic in the comments.

The tests check that a broad cluster made only of low CTSSs is kept,
that cluster expression is the sum of the CTSSs passing
filteredCTSSidx(), that expression in a sample does not depend on the
number of samples in the object, that cluster boundaries follow the
tag clusters with score >= tpmThreshold, that outOfClusters is
consistent with that, that excludeSignalBelowThreshold is deprecated
and ignored, and that CustomConsensusClusters() keeps clusters made of
low CTSSs while its threshold and nrPassThreshold arguments still work.

The CTSS filtering thresholds used in the tests do not fall on a count
or TPM value of the synthetic data, so that the results do not depend
on whether flagLowExpCTSS() compares signal strictly with the
threshold, a point on which its documentation and code disagree.
testthat 3.1.5 is required for expect_no_warning().

Most of these tests fail until the hidden CTSS filters applied after
consensus-cluster construction (the excludeSignalBelowThreshold filter
and the sum-over-samples filter in .CCtoSE()) are removed.  The tests
for cluster boundaries and for the explicit filters of
CustomConsensusClusters() already pass.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 Merge pull request #18 from rformassspectrometry/jomain

feat: add support for MsBackendSql backends 

 feat: add support for MsBackendSql backends

- Add alabaster and plain text stash format support for `MsBackendSql`
  backends (for certain supported database systems).
 

 example contexts, readme and vignette updates
 

 Merge pull request #71 from gdrplatform/GDR-3739

fix: keep the rendered report when only the publication step fails 

 chore: reword the NEWS entry with a known verb
 

 test: cover the clean-up after a failed publication step
 

 added author
 

 Merge remote-tracking branch 'origin/main' into GDR-3703

# Conflicts:
#	DESCRIPTION
#	NEWS.md
 

 feat: show the recorded fits and processing steps in the processing reports
 

 adjusted news
 

 Subtract the squared background means in place to save memory
 

 updated doc
 

 motif reliability and variability
 

 added kNN smoothing
 

 added fpc
 

 fixed variance
 

 Fix glued variable in error message when annotation package is not installed
 

 added example contexts
 

 replaced adjusted P value with FDR
 

 Bump package version to 0.99.8
 

 Address reviewer feedback for discovery-aware analysis
 

 Merge pull request #13 from rformassspectrometry/gabri

fix: metadata download after changes in JSON parsing 

 fix: metadata download after changes in JSON parsing
 

 fix: issue Check if issues from MsBackendMetaboLights are also a problem here
Fixes #11 . Fix bug in parsing file name with "+"
 

 Add Allen's phylogenetic entropy and Rao's quadratic entropy to addAlpha (#845) (#847)

Co-authored-by: Tuomas Borman <tvborm@utu.fi> 

 Fix/alpha rarefaction bug (#854)

Co-authored-by: Tuomas Borman <tvborm@utu.fi>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 Add reference sections to pkgdown site (#128) 

 fix: use importFrom syntax for magrittr
 

 Deprecated split z and split by cell components in transcript spots and dealt with failed unit tests
 

 feat: add alabaster stash for MsBackendOfflineSql

- Add alabaster stash format for `MsBackendOfflineSql` with all related unit
  tests and documentation.

Note that we are still not importing from the *MsBackendSql* package, but only
listing this package in *Suggests* to keep the dependency tree of *SpectraStash*
somewhat manageable.
 

 bump version
 

 Replace BiocParallel::bpiterate(), which is not supported by the
DoparParam back-end, by calls to bplapply() in rounds of one block per
worker, when socket or foreach workers receive blocks of an in-memory
input from the main process. The main process frees the blocks of each
round before taking the next ones, and the copies it holds are now
included in the memory budget given by 'maxmem' and in the memory
estimated before the calculations start. Added doParallel and foreach to
Suggests, for a new unit test on the DoparParam back-end.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 Add additional resources, retrievable from GitHub
 

 Merge Bioconductor devel into main
 

 tests: add unit test for as.data.frame.Chromatograms
 

 fix: update wrong variable
 

 address Johannes comments
 

 Merge branch 'main' into gabri
 

 refactor: function from chromatograms to data.frame
 

 Merge pull request #69 from rformassspectrometry/jomain

Add citation 

 refactor: move ggiraph to Suggests to decrease dependencies
 

 Add logo
 

 refactor: change ggplot function for color
 

 Merge branch 'main' into phili
 

 feat: add parameter to hide axis to ggplot
 

 Merge branch 'main' into gabri
 

 Merge pull request #64 from rformassspectrometry/paper-revision-jo

Update Supp 3 

 Update and restructure README
 

 Update Supplementary_Material_3_interoperability_chromExtract.qmd
 

 Merge pull request #61 from rformassspectrometry/paper-revision-jo

refactor: adapt to the large-scale data 

 feat: update from plot to ggplot
 

 Merge remote-tracking branch 'origin/main' into paper-revision-jo
 

 Update/fix format of supplements
 

 Merge pull request #60 from rformassspectrometry/chrom-extract-ref

perf(chromExtract): avoid re-validating backend when matching chromData 

 Update title
 

 Small update
 

 rename supp material 3
 

 perf(ChromBackendSpectra): avoid re-validating Spectra when setting chromSpectraIndex
 

 Update helpers.R
 

 prototype-qmd
 

 Remove stale tests
 

 refactor: peakBoundary for efficiency
 

 Write obs_names/var_names as the index of obsm/varm data frames (#501)

* Write obs_names/var_names as the index of obsm/varm data frames
* Cover data frames in the obsm/varm roundtrip tests
* Check the index of R generated obsm/varm data frames with h5diff
* Test obsm/varm data frames with missing values

Co-authored-by: Witold Wolski <wewolski@gmail.com>
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 

 Error instead of skip when Python tests are required (#533)

* route python skip helpers through one helper

* add test for strict python test mode

* error instead of skip when python tests are required

* document strict python test mode

* fix lint

* update news

* bump version 

 Bump dawidd6/action-download-artifact from 21 to 27 (#529)

Bumps [dawidd6/action-download-artifact](https://github.com/dawidd6/action-download-artifact) from 21 to 27.
- [Release notes](https://github.com/dawidd6/action-download-artifact/releases)
- [Commits](https://github.com/dawidd6/action-download-artifact/compare/v21...v27)

---
updated-dependencies:
- dependency-name: dawidd6/action-download-artifact
  dependency-version: '27'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

 pkgdown workflow: run on devel, build against Bioconductor devel (3.24) with spicyR from its GitHub devel branch, as lisaClust's

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 

 1.99.39: pkgdown reference sections from roxygen @concept tags (has_concept), not a hand-kept list

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 

 pkgdown: calibrationCheck in the reference index

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 

 1.15.6: simpler vignette (defaults no longer passed, one-step survival vector, colTest() matching by name, coord_cartesian zoom, bcells fix)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 

 1.99.38: colTest() takes subject, reports group medians with the Wilcoxon test, and matches rows to a named condition

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 

 Bump to 1.1.7: make the gene-order test invariant to eigenvector sign

R-CMD-check failed on Linux CI for 1.1.6 in test-label-value-integrity.R:
shuffling the genes passed to get_pca_plot() returned both PCA axes negated
-- the same embedding, mirrored -- and the permutation-invariance test read
that as an order dependence. The test shuffles with sample() and no seed, so
it was a coin flip on that BLAS build; 1.1.5 passed by chance and nothing in
1.1.6 caused it. It is the failure c22fd55 fixed for the snapshots, in a test
that fix did not reach.

Orient the PCA (PC1/PC2) and MDS (Dim1/Dim2) axes with canon_axis() before
comparing, as the snapshots already do. canon_axis() moves to helper-data.R
so both files share one definition. A new test pins the property: negating
an axis passes, moving a point still fails, and without orientation the flip
fails as it did on CI.

Test-only change; no user-visible behaviour changes.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 1.99.35: writeCellStore() writes the cells of each image as a points element, so the table annotates elements of the store

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 

 1.99.33: writeCellStore() takes a SpatialExperiment; plotImage() without a pair shows every cell type; vignette store section on the SpatialExperiment

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 

 site: remove the gap between the navbar and the home page hero

Quarto's main.content has a 1em top margin that the negative hero margin only
partly cancelled (a ~14px light strip showed under the navbar).

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 

 site: remove the redundant Articles section

Fold the unique content (polishing options table and held-out genes,
SVG/GPU calls, polish memory budget, static GPU benchmark with caveats,
polishNB pointer) into Get started and delete site/articles and
scripts/article-setup.R along with the navbar and home links.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 

 docs(site): show total Bioconductor downloads (computed at build time) instead of the rank badge; weekly rebuild

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 

 docs(site): home page with logo, authors, download stats and CI status; add SpaNorm logo

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 

 site: make every read-only logging-handler stream property assignable (torch's _StderrHandler)

reticulate's output capture failed on torch._logging._internal._StderrHandler, a
different class from logging._StderrHandler that the previous shim patched. Patch all
Handler subclasses with a read-only stream property, including ones defined later
(torch is imported after the shim runs).

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 

 ci(site): build on R 4.5 so the pinned reticulate 1.44.1 compiles

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012hFT9QMAZMopnJeA2VW41B
 

 fix: compute the dispersion winsorisation cap on finite log-dispersions only

A single NaN psi made psi.max NaN and turned every gene's logPAC/Pearson/
median-bio output into NaN; psi = 0 (log -Inf) dragged the median to -Inf.
Shared internal helper .psiMax() used by winsorisePsi() and subsetFitGenes().
Bump to 1.7.16.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
 

 docs: combined R/Python Quarto website, built and deployed by GitHub Actions

Replaces pkgdown with a single Quarto site serving SpaNorm (R) and spanormpy
(Python): tabbed R|Python Get started, articles, R and Python reference, and an
R vs Python page. Only site sources are committed (site/ is in .Rbuildignore);
.github/workflows/quarto-site.yaml renders and deploys to gh-pages.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 1.21.10: parallel test passes with a single-threaded BLAS (Bioconductor build machines)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 

 Export internal functions to workers, so they are available when using PSOCK
 

 Bump patch version
 

 Update version to upcoming release
 

 1.31.8: CITATION reads without a declared encoding

inst/CITATION spelled one author name with a literal non-ASCII character
(Szabó, the MM285 paper). utils::readCitationFile() without a declared
encoding refuses non-ASCII input, so BiocCheck warned "Unable to read
CITATION file" (bioc R-universe, 1.31.7). The name is now the escape
"Szabó": the file is pure ASCII and renders the same.
 

 fix: add missing sf-signature spatialMatch/spatialJoin methods (0.99.28)

spatialMatch/spatialJoin had no method for a plain sf object. An sf is a
base S3 class (c("sf", "data.frame")), not an S4Vectors::DataFrame, so
the existing DataFrame-signature methods never matched it -- calling
either with a real sf object errored with "unable to find an inherited
method" rather than falling through to anything.

This is purely a missing signature, not an S3/S4 dispatch limitation:
setMethod(generic, c(..., "sf"), ...) dispatches on the class vector
directly, no setOldClass() bridging needed. Fixed by adding
c("DuckDBDataFrame", "sf") for spatialMatch, and both
c("DuckDBDataFrame", "sf")/c("sf", "DuckDBDataFrame") for spatialJoin,
delegating to the same existing DuckDBSpatial calls (which already
handle sf input correctly as of DuckDBSpatial 0.99.8).

Added regression tests for all three new signatures. Full test suite:
0 failures.
 

 fix: add missing spatialJoin mixed-dispatch methods (0.99.28)

spatialJoin was missing the mixed-type method pair
(c("DuckDBDataFrame", "DataFrame")/c("DataFrame", "DuckDBDataFrame")) that
spatialMatch already has. A call with one out-of-core DuckDBDataFrame
side and one in-memory DataFrame side (in either order) therefore had no
applicable method more specific than MultiAssaySpatialExperiment's own
c("DataFrame", "DataFrame") fallback, which materializes both sides'
geometries fully into memory via st_as_sfc() -- silently defeating the
out-of-core path for exactly the mixed case a caller joining a lazy layer
against a small in-memory one would hit.

Found via user feedback flagging that geometries were still loading into
memory. Fixed by adding the missing method pair, delegating to
DuckDBSpatial::st_join_table()/sf::st_join() the same way the existing
c("DuckDBDataFrame", "DuckDBDataFrame") method does (both already accept
a mixed lazy/in-memory pair as of DuckDBSpatial 0.99.8).

Added a regression test covering both argument orders in
test-spatial-dispatch.R. Full test suite: 0 failures.
 

 remove NOTE caused by LICENSE file
 

 bump version
 

 compute the classic Fisher test of the propagated calls without topGO, with the same results, and move the topAnat classes and their methods to their own files
 

 small fix
 

 ci: update
 

 all NOTEs
 

 chore: full pixi support (#74) 

 Memory footprint (#5)

* fast covariance calculation

* fixed dependencies

* fixed bugs

* added test 

 set eval=FALSE to avoid errors because of unstable internet
 

 chore: advance development version to 1.5.9

Official devel remains 1.5.8 and release remains 1.4.1 with no RELEASE_3_24 branch. Apply the author-approved next unused development version; no Bioconductor synchronization.

Prepared with Codex assistance.
 

 fix(mapping): preserve singleton rows for max selection

Keep singleton measurements unchanged while retaining the existing max calculation for groups with multiple probes. Add focused regression and preservation tests for issue #178.

Prepared with Codex assistance under the author-approved singleton-preservation scope.
 

 docs(readme): remove external Bioconductor badge labels 

 Bump to 1.1.6: independent equivalence check, edgeR QL option, tximport fixes

Verification
- benchmark_vista_equivalence() now compares VISTA with reference
  DESeq2/edgeR/limma pipelines that share none of VISTA's code, matched by
  identifier; a test enforces the separation, and injected defects in
  VISTA's own helpers must be reported.

edgeR
- New edger_test = c("LRT", "QL") in create_vista(), run_edger_analysis(),
  benchmark_vista_equivalence() and validate_vista_deep(). LRT stays the
  default; calls that rely on it get a notice that QL becomes the default
  in VISTA 1.4.0 (see ?VISTA-deprecated). The test used is recorded in
  cutoffs(v)$edger_test and in the report.

Bug fixes
- Untested genes were stored with pvalue = 1; they keep the engine's NA.
- Filtering a consensus table on padj returned the union in intersection
  mode.
- DEG-count plots dropped comparisons with no DEGs.
- limma MA plots used log10(log2-CPM + 1) on the x axis.
- An explicit intercept in design_formula survived for edgeR and limma.
- tximport abundance/length could be imported as counts; unscaled tximport
  counts are now converted to lengthScaledTPM (matching tximport), with
  tx2gene summarised as summarizeToGene() does.
- DESeq2 now accepts estimated counts, rounded after a shared filter.
- Negative values are refused; exact TPM/CPM or log-scale input warns.
- RSEM TPM/FPKM columns could be imported as counts.

Also: provenance records VISTA, R and engine versions; the code-economy
vignette computes its tallies; docs and NEWS updated.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

 1.99.32: cellWeights (a vector of cell weights or a soft cell type membership matrix) in spicy(), kontextualEngine() and getPairwise(); weighted random-labelling sums in the core

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 

 After testing, I remembered that .assays is reserved in masks...
 

 Speedup optim 5: dont walk names twice, call both functions in each
iteration
 

 speedup optim 4: plyxp_group_ids2 uses `[[` alot, convert object to list
for faster operator
 

 speedup optim 2: calling tibble is slow - construct raw data.frame with
`df0`
 

 testing various parts of the S4 vctrs interface
 

 work in progress
 

 ensuring active bindings are read only
 

 testing different branches of simple slice
 

 Forgot to commmit these tests
 

 had a typo
 

 misc
 

 Update test_S4_list_unchop.R
 

 taking inspiriation from biocmask side project
 

 This is not yet needed and was not much used
 

 logical bug, missing argment. testing other branches
 

 testing error paths
 

 Many more group tests, including group_split
 

 testing peek_ctx and poke_ctx. So far not used too often. questioning
its relevance
 

 Unused at the moment
 

 Update test_plyxp_utils.R
 

 Revert 'some work'...

This commit reverts 23cdc8aebed7950d7f85865041d91f0bfbebdfb6

prior commit implements col_data/row_data generics for internal use. Not
ready for devel/bioc
 

 formatting
 

 shouldnt have used roxygen tag here...
 

 Allow new quosure to mimic its parent quosure transform value
 

 air formatting
 

 plyxp_quos defaults to exclude empty. ungroup now retains empty quos and
has granular behavior
 

 enabled .features and .samples as grouping options
 

 An unused function. It should be removed soon
 

 small refactor
 

 enforce_matrix() is no longer needed. replaced with enforce_2d_size()
 

 this function is no longer used, it was inlined to .bind_self
 

 Merge remote-tracking branch 'origin/main' into GDR-3718

# Conflicts:
#	NEWS.md
 

 chore: update the package date
 

 Merge pull request #216 from gdrplatform/GDR-3586

fix: restore CIScore_50/80 and the single-agent arm fit for combinations 

 chore: update the package date
 

 Merge pull request #207 from gdrplatform/GDR-3718

fix: add a co-dilution fit profile and allow refitting a processed SE 

 fix: set SE metadata over an entry that holds a sessionInfo
 

 bump version to 1.99.4
 

 feat: accept in-memory sf objects in st_join/st_join_table (0.99.8)

st_join.DuckDBTable/st_join_table only accepted lazy DuckDBTable/
DuckDBDataFrame objects for x/y. Closes a real gap flagged by a user
comparing against duckspatial::ddbs_intersects(), which accepts sf
objects on either side.

New internal .as_duckdb_table() materializes an in-memory sf object (or
a data.frame with an sfc or raw-WKB-list geometry column -- the latter
matching the shape as.data.frame() on a DuckDBDataFrame's own geometry
column produces) by converting its geometry to WKT (the same idiom
.geom_to_sql() already uses for a single geometry), copying it into a
temp DuckDB table via copy_to(), then casting back to native GEOMETRY
with ST_GeomFromText(). Temp-table naming reuses DuckDBArray's
PID+counter convention to avoid the dbplyr::unique_table_name()
global-RNG collision class fixed there in 0.99.9. Chosen over
writeGeoParquet()+tempfile since that would pull in nanoparquet as a
hard dependency and add disk I/O for what's typically the small side of
a join.

Three independent review passes (two rounds, four reviewer agents total)
caught and fixed real problems before this shipped:
- The redirect errors added to .geom_to_sql() pointed at spatialMatch()/
  spatialJoin(), which don't exist in this package (those are
  BiocDuckDB-level MultiAssaySpatialExperiment methods) -- corrected to
  layerSpatialMatch(), st_join(), and st_join_table().
- .as_duckdb_table()'s raw-WKB branch crashed on any NULL entry (the
  common case of a DuckDBDataFrame's own geometry column, which
  represents missing geometries as NULL), since sf::st_as_sfc.WKB()
  asserts every element is raw with no NULL tolerance. Fixed by
  substituting an empty geometry per NULL entry, wrapped in the same
  tryCatch-to-friendly-error pattern writeGeoParquet() already uses.
- Hardened the generated ST_GeomFromText("") SQL against a geometry
  column name containing a literal double quote.

Also removed .spatialMatch_sql()'s dead else branch (DuckDBDataFrame-
spatial.R): it attempted the same DuckDBDataFrame(as.data.frame(table))
call that didn't actually work, but its only caller (layerSpatialMatch())
never reaches it with a non-DuckDBTable table, taking a separate
in-memory sf::st_intersects() path instead -- unreachable, untested dead
code.

Added regression tests for all of the above, including sf-on-either-side
joins, the NULL-geometry fix, and the corrected error-message text. Full
test suite: 0 failures.
 

 feat: add st_join_table for sparse joins between two lazy spatial tables (0.99.8)

st_intersects_table() only ever supported testing x against a single
reference geometry -- its y goes through .geom_to_sql(), which has no
case for another lazy table -- so there was no way to get a sparse match
table between two out-of-core layers short of materializing the full
attribute join via st_join(). This blocked spatialJoin(DuckDBDataFrame,
DuckDBDataFrame) in BiocDuckDB, whose sparse=TRUE branch called
st_intersects_table(x, y) and always errored with "unsupported geometry
type: DuckDBDataFrame" when both sides were out-of-core.

Added st_join_table(x, y, join = st_intersects, sparse = TRUE), modeled on
the existing st_join.DuckDBTable: same INNER JOIN ... ON (...)
approach and the same .st_predicate_sql_name() mapping to honor join=,
but projecting a sparse (id_x, id_y) row-pair table instead of full
attributes.
 </pre>
    </div>
  
    

      Package: CEMiTool

      Commit: 325dddd3fc11c4c18eec095ae1f968aedf561f40

      Author:  Pedro Russo <pedrostrusso@gmail.com> 

      Date: 2026-10-20 09:06:05 -0300

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: CEMiTool

      Commit: 3630f2a726ec1e290cb6558ad40802ded423bfb9

      Author:  Pedro Russo <pedrostrusso@gmail.com> 

      Date: 2026-10-20 09:02:13 -0300

      Commit message:


	  
		
 Mirroring changes in master to devel
 
    
  
    

      Package: OmnipathR

      Commit: 9ce957c453451091c2d2ac65a94746c5b8a95b5e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-20 12:23:32 +0100

      Commit message:


	  
		
 Bump version: 4.1.0 → 4.1.1
 
    
  
    

      Package: OmnipathR

      Commit: 644c8a1280a5ec8cf7dc75713af05ab06a3a5fbe

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 02:45:11 +0100

      Commit message:


	  
		
 NEWS for 4.1.1

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 730cb57407b77a3095252f681d6d577c372a910c

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 02:44:37 +0100

      Commit message:


	  
		
 CITATION: ASCII quotes, so that readCitationFile() reads it

BiocCheck reads the file without a declared encoding and gives a
warning for non-ASCII characters.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 4af5333194c429fd99ff19faf24580ad7fdd34be

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 00:54:40 +0100

      Commit message:


	  
		
 docs rebuild

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: ee5ad33716fbe7738990c52ef86c9a36cef67783

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 00:54:40 +0100

      Commit message:


	  
		
 resources: use a cached resource list for one hour at most

Resources are added to and removed from the server often, so a resource
list older than one hour is downloaded again.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: f57ef9609c83810a158c54113184b0dac6fee2f4

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 00:54:40 +0100

      Commit message:


	  
		
 omnipath_cache_remove: max_age and min_age remove only the matching versions

When status was not given, the version filter kept no version at all, so
omnipath_cache_remove(max_age = 30) emptied the whole cache instead of
removing what is older than 30 days. Without status, versions of any state
are now kept. The manual now describes status as it works: the states to
keep.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: e561784371addd03657df181fdee1e7ca01c3425

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 00:11:42 +0100

      Commit message:


	  
		
 Live web service tests do not run on Bioconductor build machines

A short outage of the OmniPath web service must not fail the Bioconductor
build. Other machines, our daily build server included, still run them.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: c714f9dfb8f66191bf12582ded0e6a7946a53518

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-13 00:11:42 +0100

      Commit message:


	  
		
 resources: download with retries and cache, fix category filter

resources() read the resource list with readLines(), with no retry and no
cache, on every query that names resources. One failed connection failed
the query. It now uses the package downloader, like the other functions.
The generic_categories argument looked for a key that the service does not
send, so it always gave an empty result. It now reads the key categories.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: ba43e096a988ee4d47955a66313c8ad09ccc411d

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-12 23:08:14 +0100

      Commit message:


	  
		
 docs rebuild

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 38528ff92def0e4d302c75e931c6caf14321e1df

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-12 23:08:14 +0100

      Commit message:


	  
		
 Runnable examples for 29 more manual pages

Examples of functions that download data run again: on build servers these
functions return early, so the examples stay fast. Small offline helpers
have new examples. The cache and configuration examples work on a temporary
directory, and never change the user's cache or configuration.
wikipathways_metabolites_sparql() returns early on build servers like the
other download functions. The show_network() example calls show_network().

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 8907449f2bb545a0288ddc3d7a295544ab55f5f0

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-12 23:08:14 +0100

      Commit message:


	  
		
 subnetwork: select the vertices with V(), add examples to graph helpers

subnetwork() called igraph_vs(), which does not exist, so the function
failed on every call. It now selects the given nodes with V(), or all nodes
when none is given. ensure_igraph(), subnetwork() and graph_interaction()
have offline examples.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 466c2a7025d7723bfa2bfba0fd3126581becf1fa

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-12 23:02:28 +0100

      Commit message:


	  
		
 Vignettes build when a third-party server does not answer

Chunks that download from g:Profiler, UniProt, the OBO Foundry or a
publisher show the error instead of stopping the vignette build. The text
next to each such chunk tells the reader why the output can be missing.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 9c6de4f542099aeb253f1c25b85fa68239d42c01

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-12 23:01:20 +0100

      Commit message:


	  
		
 Build-server detection also reads OMNIPATHR_BUILDSERVER

A local R CMD check under any user can now skip the slow examples the same
way as the Bioconductor and Saez Lab build servers.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: a7c05f9a876c08a8e0e33d9c32a930fbf2cf3491

      Author:  jannikfranken <Jannik8513@gmail.com> 

      Date: 2026-09-30 15:34:36 +0200

      Commit message:


	  
		
 `oma_organisms`: robust to header changes, re-download malformed cache

OMA now serves its species table from Zenodo with 5 comment lines and a
column header row instead of 3 comment lines. The hard-coded `skip = 3L`
made readr return a single column table, without `ncbi_tax_id`, which
broke the organism name translation (`taxon_name`, `latin_name`, etc.).

Now all lines starting by "#" and the header row are removed, the columns
are read with fixed names and types, and the result is validated. If the
table is malformed (e.g. a previously cached bad parse), the cache entry
is removed and the file is downloaded again.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: OmnipathR

      Commit: 5897de4085b65dd462b4da5fcdfce7b7cea20883

      Author:  jannikfranken <Jannik8513@gmail.com> 

      Date: 2026-09-28 16:29:02 +0200

      Commit message:


	  
		
 KEGG: use list/genome, the list/organism endpoint returns 400

The KEGG REST endpoint `list/organism` has been retired and now fails
with HTTP 400. This broke `kegg_organisms()`, `kegg_organism_codes()`
and, through the argument validation in `kegg_query()`, any KEGG call
that checks organism codes (e.g. `kegg_conv("compound", "pubchem")`).

- `kegg_request()` now transparently requests `list/genome` whenever
  `list/organism` is asked for, so `kegg_list("organism")`,
  `kegg_request("list", "organism")` and `kegg_organisms()` work again.
- New internal `kegg_genome_to_organisms()` reshapes the two column
  output of `list/genome` ("T01001", "hsa; Homo sapiens (human)") by
  splitting the second field on "; " into `kegg_name` and `latin_name`.
- Removed the obsolete `list/organism` entry from `KEGG_COLUMNS`.
- Updated the `kegg_list()` docs to the new return shape.

Breaking change: the organism table now has 3 columns (`genome`,
`kegg_name`, `latin_name`) instead of 4. The `phylogeny` column is
dropped, as `list/genome` does not provide it; nothing in OmnipathR
used it. The code remains in the 2nd column, so `kegg_organism_codes()`
is unaffected.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: MetaboCoreUtils

      Commit: 3f40f43f37002a0deee0715af1edb2294ddfc78d

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2026-10-20 11:37:37 +0200

      Commit message:


	  
		
 Merge pull request #89 from rformassspectrometry/jomain

feat: add parameter nomatch to translate() 
    
  
    

      Package: MetaboCoreUtils

      Commit: 9077c8175e5a34cb47b7d67841365ffd42b325d0

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2026-10-19 07:24:21 +0200

      Commit message:


	  
		
 feat: add parameter nomatch to translate()

- Add parameter `nomatch` to the `translate()` function to configure the
  behaviour if a name could not be translated/matched. Add also parameter
  `warning` that allows to disable warning messages.
 
    
  
    

      Package: geneslator

      Commit: e7b7161780f2f622eb3614cec05e012af3eca3c6

      Author:  GMicale <gmgmicky@gmail.com> 

      Date: 2026-10-20 11:08:31 +0200

      Commit message:


	  
		
 Updated README
 
    
  
    

      Package: geneslator

      Commit: 10aae9e9cbacd29d346b4d6d0f473a4342a6b05c

      Author:  GMicale <gmgmicky@gmail.com> 

      Date: 2026-09-24 19:19:39 +0200

      Commit message:


	  
		
 Merge branch 'main' of github.com:knowmics-lab/geneslator
 
    
  
    

      Package: geneslator

      Commit: b825a4f5fb156f01fad889fcde03b9f0e6f71f77

      Author:  Giovanni Micale <gmgmicky@gmail.com> 

      Date: 2026-09-04 17:10:34 +0200

      Commit message:


	  
		
 Update README.md 
    
  
    

      Package: biomaRt

      Commit: ba00684e7d8282b927ea8d650f96d218483d6ce4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-19 09:38:41 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: biomaRt

      Commit: 3d1eaf5520af3e09583664594fe28d9d309b77d9

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-19 09:53:09 +0200

      Commit message:


	  
		
 Use fetch = FALSE in vignette as well
 
    
  
    

      Package: biomaRt

      Commit: f88dd09c86169861e243b5cc6f958fa3de6c6a1c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-19 09:38:26 +0200

      Commit message:


	  
		
 Avoid hits on ensembl latest release
 
    
  
    

      Package: gDR

      Commit: c98efa763cefe1baa5946a5187791a139f363210

      Author:  Arek Gladki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-10-20 09:45:05 +0200

      Commit message:


	  
		
 Merge pull request #70 from gdrplatform/GDR-3728

fix: show one legend per page in the Incucyte analysis report 
    
  
    

      Package: gDR

      Commit: 8ebe3144c8670a34c1df3718b45b412ec6e26c3a

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-10-19 13:38:58 +0200

      Commit message:


	  
		
 fix: show one legend per page in the Incucyte analysis report
 
    
  
    

      Package: limma

      Commit: 595fd2c4d7fe23168182dfbc4486eea5bc4cb8ae

      Author:  Mikael Jagan <jaganmn2@gmail.com> 

      Date: 2026-10-20 00:17:02 -0400

      Commit message:


	  
		
 no longer using methods-internal class
 
    
  
    

      Package: geNetClassifier

      Commit: 781ddcfba595cc5f3076c88257eaeda45ec44553

      Author:  Mikael Jagan <jaganmn2@gmail.com> 

      Date: 2026-10-20 00:07:58 -0400

      Commit message:


	  
		
 no longer using methods-internal class
 
    
  
    

      Package: S4Vectors

      Commit: 904dc54db14b1e9fa111e3d9e66ba135f5911b7a

      Author:  Mikael Jagan <jaganmn2@gmail.com> 

      Date: 2026-10-20 00:00:23 -0400

      Commit message:


	  
		
 no longer using methods-internal class
 
    
  
    

      Package: Category

      Commit: adc36989fed922abd0e34197565f79bf1c4d3b6e

      Author:  Mikael Jagan <jaganmn2@gmail.com> 

      Date: 2026-10-19 23:29:27 -0400

      Commit message:


	  
		
 no longer using methods-internal class
 
    
  
    

      Package: igblastr

      Commit: 0b6fab6efd2a12a47d93c25b47514454c848fb44

      Author:  J. Kim <juyeongkim@users.noreply.github.com> 

      Date: 2026-09-18 13:27:26 -0700

      Commit message:


	  
		
 Build and push docker image for igblastr (#12)

* Build and push docker image for igblastr

* Ignore `RELEASE_3_22` branch 
    
  
    

      Package: sesame

      Commit: c304730fac5a4e97e8e15028f94c6fad56b435ef

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-19 16:50:17 -0400

      Commit message:


	  
		
 1.31.7: heatmap annotation tracks (zwdzwd/sesame#220), follow-up fixes

#220 (Pancreas-Pratik) adds CpG-context and Ensembl Regulatory Build tracks
under the visualizeRegion() heatmap, built on first use and cached in
BiocFileCache; biomaRt is in Suggests and needed only for the regulatory
track. On top of the merge:

- @param for show.cgi, show.regulatory, show.beta.legend and
  show.annotation.legend, which R CMD check flagged as undocumented.
- NAMESPACE regenerated by roxygen; imports and exports are unchanged.
- A plain visualizeRegion() call is silent again: it no longer prints
  "Heatmap annotations not requested."
- sesameAnno_buildHeatmapAnnotations() checks for biomaRt before reading
  the manifest, so a missing package fails before any download.
- The regulatory legend title is "Ensembl Regulatory Build Feature" in
  every layout; the beta legend label takes sample.name.fontsize instead
  of an empty argument.

R CMD check: 0 errors, 0 warnings (R 4.6.0, sesameData 1.31.1).
 
    
  
    

      Package: sesame

      Commit: 4109d7d99b167166552359313c46adeed4c15559

      Author:  Wanding Zhou - Bioinformatics <zhouwanding@gmail.com> 

      Date: 2026-10-19 16:21:20 -0400

      Commit message:


	  
		
 Merge pull request #220 from Pancreas-Pratik/devel

Add heatmap annotations to visualizeRegion 
    
  
    

      Package: sesame

      Commit: 522b2e9ba7538a63310eb93c77c3cce5d0b6c385

      Author:  Pratik Mehta <pratikmehta00@gmail.com> 

      Date: 2026-09-23 15:08:28 -0400

      Commit message:


	  
		
 Address review comments: add CpG and Ensembl regulatory heatmap annotations
 
    
  
    

      Package: sesame

      Commit: 57926125eada5b3a774742008532e6d511051212

      Author:  Pratik Mehta <pratikmehta00@gmail.com> 

      Date: 2026-09-20 10:27:18 -0400

      Commit message:


	  
		
 Add heatmap annotations to visualizeRegion
 
    
  
    

      Package: BreastSubtypeR

      Commit: 67d982cb324ec376ea599929eb41837a50fd09b3

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 14:43:28 +0200

      Commit message:


	  
		
 Merge pull request #174 from JohanHartmanGroupBioteam/fix/prepublication-review-1.5.8

Correct clean-session Shiny behavior and clarify unpublished 1.5.8 maintenance findings 
    
  
    

      Package: BreastSubtypeR

      Commit: 840b190524d989a7f9c2aaa7cf43888196ec5822

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 11:11:44 +0200

      Commit message:


	  
		
 Clarify maintenance provenance and remove unused plotting dependency
 
    
  
    

      Package: BreastSubtypeR

      Commit: 0ec9682928dc81edb090e624cdc8fc50f0afc5b8

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 10:58:31 +0200

      Commit message:


	  
		
 Represent undefined additional ROR-PC categories as missing values
 
    
  
    

      Package: BreastSubtypeR

      Commit: 647e5c9f5b8d9f779e27baddb274fc93e14a8b75

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 10:56:00 +0200

      Commit message:


	  
		
 Fix Shiny namespace lookup and empty silent-error reporting
 
    
  
    

      Package: BreastSubtypeR

      Commit: 0921e85b2d7eeed72b4679df43fc5dce379c5087

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 07:35:15 +0200

      Commit message:


	  
		
 Merge pull request #173 from JohanHartmanGroupBioteam/maintenance/1.5.8-candidate

Prepare provisional 1.5.8 maintenance candidate and document ROR limitations 
    
  
    

      Package: BreastSubtypeR

      Commit: 107d0388ff2b596b2fedb18dcc5421f09b5e287d

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 06:45:23 +0200

      Commit message:


	  
		
 Prepare provisional 1.5.8 candidate with ROR interpretation and boundary disclosures
 
    
  
    

      Package: BreastSubtypeR

      Commit: aea84bd07b126c122b7445d34895c7a43c0ef000

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 05:43:52 +0200

      Commit message:


	  
		
 Merge pull request #171 from JohanHartmanGroupBioteam/ci/bioccheck-account-checks

Stabilize BiocCheck CI by separating maintainer account checks 
    
  
    

      Package: BreastSubtypeR

      Commit: d4198abc26711036ee77f36f80a4a2e85d1f9924

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 05:18:04 +0200

      Commit message:


	  
		
 Stabilize BiocCheck CI by separating maintainer account checks
 
    
  
    

      Package: BreastSubtypeR

      Commit: b34d561fda860d6b2b1e2d1bf0e7fd3196846106

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-19 05:13:48 +0200

      Commit message:


	  
		
 Merge pull request #170 from JohanHartmanGroupBioteam/docs/readme-shiny-screenshot

Synchronize README screenshot and refine publication links and logo 
    
  
    

      Package: BreastSubtypeR

      Commit: cb8123928f133393889e9e302eaa8a8d03a24227

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 04:46:21 +0200

      Commit message:


	  
		
 Increase README logo height to 120 pixels
 
    
  
    

      Package: BreastSubtypeR

      Commit: 856f0e603cc1cd4b13e7b140a8ad29de88b4bfce

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 04:43:53 +0200

      Commit message:


	  
		
 Link Editor's Choice references to the BreastSubtypeR entry
 
    
  
    

      Package: BreastSubtypeR

      Commit: 4cf3fd342d6d9026ee3cc4fa749e7528fd936f33

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 04:35:58 +0200

      Commit message:


	  
		
 Synchronize README Shiny screenshot after visualization refresh
 
    
  
    

      Package: BreastSubtypeR

      Commit: 7a1085ca489663118cbb50505770e46056cff010

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 04:25:53 +0200

      Commit message:


	  
		
 Merge pull request #169 from JohanHartmanGroupBioteam/maintenance/visualization-refresh

Refresh approved visualization styling with exact scientific preservation 
    
  
    

      Package: BreastSubtypeR

      Commit: 06ab3d61496a49fbf301c19d40fb9dc1d7729313

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-19 00:39:54 +0200

      Commit message:


	  
		
 Refresh approved visualization styling without changing scientific results
 
    
  
    

      Package: BreastSubtypeR

      Commit: de820e700d3de2290d8ddf6c4c1d2a275a32c16a

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-18 23:35:41 +0200

      Commit message:


	  
		
 Merge pull request #165 from JohanHartmanGroupBioteam/docs/documentation-refresh-oslo-20261018

docs: refresh documentation and correct OSLO example provenance 
    
  
    

      Package: BreastSubtypeR

      Commit: 7bc7e954d017ac340e1c0f72408f3e5c2af713a9

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 23:09:20 +0200

      Commit message:


	  
		
 docs: align Shiny workflow and add verified example screenshot
 
    
  
    

      Package: BreastSubtypeR

      Commit: 97dbcbc719e59eabb0c9880fe474df9dd697b57a

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 23:09:20 +0200

      Commit message:


	  
		
 Merge main into documentation refresh
 
    
  
    

      Package: BreastSubtypeR

      Commit: 38d4f5811c0793f64b53de2ed4b8ae3ceacae07c

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 22:33:19 +0200

      Commit message:


	  
		
 Merge pull request #167: clarify the local Shiny workflow

Clarify the local Shiny workflow and compact its presentation. 
    
  
    

      Package: BreastSubtypeR

      Commit: f6da04e571907207b6a3dc9c0448e82937fa4efe

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 22:03:59 +0200

      Commit message:


	  
		
 test: cover Shiny workflow and pending AUTO presentation
 
    
  
    

      Package: BreastSubtypeR

      Commit: 22a79b3e4b4ed143349496d8193e0a56c50fcc60

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 22:03:44 +0200

      Commit message:


	  
		
 ui: clarify AUTO state and Shiny presentation
 
    
  
    

      Package: BreastSubtypeR

      Commit: 047970d859fac312afd0f3b8465d2667d936859b

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 17:32:44 +0200

      Commit message:


	  
		
 docs: label release and devel build badges
 
    
  
    

      Package: BreastSubtypeR

      Commit: 463e77b1c84705242b2f91758aba73366beb435e

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 16:53:58 +0200

      Commit message:


	  
		
 docs: correct OSLO example expression provenance
 
    
  
    

      Package: BreastSubtypeR

      Commit: 8951b7a1fbc8e21b9087e826c84b4bbee01ab323

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 16:53:50 +0200

      Commit message:


	  
		
 docs: refresh README and publication recognition
 
    
  
    

      Package: BreastSubtypeR

      Commit: b90c15f9b0869e71b2c0cbfaafcb71fa2b6a3aba

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 16:53:43 +0200

      Commit message:


	  
		
 docs: synchronize workflow vignette
 
    
  
    

      Package: BreastSubtypeR

      Commit: 669bcb93f97f491ab58fca7064129eb3d26a26d5

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 16:53:35 +0200

      Commit message:


	  
		
 docs: clarify method interpretation and reference help
 
    
  
    

      Package: BreastSubtypeR

      Commit: 84ec049322ced442c7ceced8af4fac30deb248c4

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 11:51:05 +0200

      Commit message:


	  
		
 Merge pull request #162 from JohanHartmanGroupBioteam/codex/input-coverage-161

Report model-specific input coverage in R and Shiny 
    
  
    

      Package: BreastSubtypeR

      Commit: d8cd0828b3a1addb763960603357b275b718b8ba

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 11:15:56 +0200

      Commit message:


	  
		
 feat: display current input coverage in Shiny
 
    
  
    

      Package: BreastSubtypeR

      Commit: c08079b9fc310ee80eb0bb6687872190369fc051

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-18 11:12:53 +0200

      Commit message:


	  
		
 feat: report model-specific input coverage in R
 
    
  
    

      Package: BreastSubtypeR

      Commit: 6ba679745411451c9548ce9727705f1b468ea9f0

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-17 20:34:48 +0200

      Commit message:


	  
		
 Merge pull request #160 from JohanHartmanGroupBioteam/codex/issue-159-ssbc-quantile-provenance

Clarify ssBC.v2 quantile provenance and references 
    
  
    

      Package: BreastSubtypeR

      Commit: e004e7bc3b5e134a9dcf58b11983fce1c691f104

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-17 07:47:29 +0200

      Commit message:


	  
		
 docs: clarify ssBC.v2 quantile provenance and references
 
    
  
    

      Package: BreastSubtypeR

      Commit: 746bf2a0c83e2f4848b137bed51fc8d254d68aef

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-17 06:45:15 +0200

      Commit message:


	  
		
 Merge pull request #158 from JohanHartmanGroupBioteam/codex/issue-152-pam50-confidence

Fix PAM50 Confidence calculation to match Parker 
    
  
    

      Package: BreastSubtypeR

      Commit: 550ed744eb19d892e3c5cc552bd68a609dc7bbf1

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 22:32:35 +0200

      Commit message:


	  
		
 Merge origin/main into codex/issue-152-pam50-confidence
 
    
  
    

      Package: BreastSubtypeR

      Commit: 207870e520e6d38dba55f8eb59e4c400b402da33

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-16 22:08:50 +0200

      Commit message:


	  
		
 Merge pull request #157 from JohanHartmanGroupBioteam/codex/issue-154-ror-boundaries

Fix subtype-specific ROR-PC risk-group boundaries 
    
  
    

      Package: BreastSubtypeR

      Commit: 6f68e09e7ad342faee62f3b01766c64c230f0834

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 20:02:22 +0200

      Commit message:


	  
		
 fix: restore Parker PAM50 Confidence calculation
 
    
  
    

      Package: BreastSubtypeR

      Commit: 66272ca3adfcf1e64f6aa09f04aa90e3b2dfddf2

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 19:59:10 +0200

      Commit message:


	  
		
 fix: correct subtype-specific ROR-PC cutoff boundaries
 
    
  
    

      Package: BreastSubtypeR

      Commit: 59e0e2c692ec6a00fe28b863a1cff8bee8e01626

      Author:  Emmanouil Sifakis <sifakise@gmail.com> 

      Date: 2026-10-16 19:09:49 +0200

      Commit message:


	  
		
 Merge pull request #155 from JohanHartmanGroupBioteam/codex/issue-153-node-documentation

Clarify NODE counts in clinical ROR documentation 
    
  
    

      Package: BreastSubtypeR

      Commit: 181c5c0fc96290e13dcb7a0ffd1b50d49d87883e

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 18:46:24 +0200

      Commit message:


	  
		
 docs: refine clinical ROR help and cutoff wording
 
    
  
    

      Package: BreastSubtypeR

      Commit: d4c63e9ef64c8f6ff7275c3ad103a861ed761fe1

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 18:18:03 +0200

      Commit message:


	  
		
 docs: clarify NODE counts for clinical ROR grouping
 
    
  
    

      Package: BreastSubtypeR

      Commit: 58e200cd460591c53daba5dc3db53ca291e2fd9e

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-16 18:18:02 +0200

      Commit message:


	  
		
 test: cover existing NODE and TSIZE handling in ROR
 
    
  
    

      Package: PADOG

      Commit: dbc3d6fd21e7aed9930b2907bf7d8ef8598cadae

      Author:  Adi Tarca <atarca@med.wayne.edu> 

      Date: 2026-10-19 13:53:38 -0400

      Commit message:


	  
		
 improved compPADOG. bumped version
 
    
  
    

      Package: GSVA

      Commit: b446e6d707d0ab08294ce5362cd50064f8aef8c6

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-10-19 18:10:27 +0200

      Commit message:


	  
		
 Fix on the GSVA random walks with missing values, which now run only over the non-missing genes of each column
 
    
  
    

      Package: GSVA

      Commit: d008fda511c0674c84b3ad3c662b83cb66560148

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-10-19 17:10:04 +0200

      Commit message:


	  
		
 Handle undefined GSVA random walk scores produce by either maximal or singleton gene sets. In the C code, avoid integer overflows in a couple of places, and also free a couple of missing memory allocations
 
    
  
    

      Package: GSVA

      Commit: 20ee1a42db3527a2bfca7772c55c1b86d053d5fd

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-10-19 16:17:44 +0200

      Commit message:


	  
		
 Discard duplicated gene identifiers in gene sets
 
    
  
    

      Package: smoothclust

      Commit: b06dd0c5d2b69529596ea81521a0d54a21b3a336

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-10-13 00:16:02 -0400

      Commit message:


	  
		
 documentation updates and minor updates
 
    
  
    

      Package: smoothclust

      Commit: 5bdf79ab127b9b5619c015fd9c2d19336fca830b

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-10-12 23:36:36 -0400

      Commit message:


	  
		
 change 'adjust' argument to logical
 
    
  
    

      Package: smoothclust

      Commit: c2f482c9005045f872ab13779c5c471bd2808c8b

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-10-11 11:18:42 -0400

      Commit message:


	  
		
 documentation updates
 
    
  
    

      Package: smoothclust

      Commit: e213f2195e0ed4f9bc152fb8f7bcb514b350a016

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-10-11 10:56:23 -0400

      Commit message:


	  
		
 version
 
    
  
    

      Package: smoothclust

      Commit: baacc9bf2e4a129168349703167a2edee0b80492

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-10-11 10:56:06 -0400

      Commit message:


	  
		
 documentation updates
 
    
  
    

      Package: smoothclust

      Commit: e52f62199934d3cd7af0fd3200503aaf555aa045

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-10-11 10:39:30 -0400

      Commit message:


	  
		
 documentation updates
 
    
  
    

      Package: smoothclust

      Commit: e1d4085c2833a7db7327fe6cd726a7c1eb56c228

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-10-11 09:27:11 -0400

      Commit message:


	  
		
 bugfix when coordinates coincide; rebuild package
 
    
  
    

      Package: smoothclust

      Commit: 642e469ed8fee0dc3407e15fc47e276744bb04ef

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-07-26 11:25:34 -0400

      Commit message:


	  
		
 vignette example - number of neighbors parameter
 
    
  
    

      Package: smoothclust

      Commit: 5a13a610319caf81d628562b4baa6c625a351a8f

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-07-26 11:03:00 -0400

      Commit message:


	  
		
 version
 
    
  
    

      Package: smoothclust

      Commit: 1ae49c99484cf6555020d371e55022923e089c77

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-07-26 11:02:53 -0400

      Commit message:


	  
		
 update NEWS
 
    
  
    

      Package: smoothclust

      Commit: 26b73a343ebebe825d3b43f0570e5dd1ee38d0be

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-07-26 11:02:06 -0400

      Commit message:


	  
		
 simplify boundary density calculations
 
    
  
    

      Package: smoothclust

      Commit: 44ca80d57a1f395482e410035c7ff41948b3c6f9

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-07-25 15:24:10 -0400

      Commit message:


	  
		
 allow size factors for zero counts
 
    
  
    

      Package: smoothclust

      Commit: d1129c8013efc229245b95f7b0bc51e5127aba37

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-07-20 18:08:28 -0400

      Commit message:


	  
		
 version
 
    
  
    

      Package: smoothclust

      Commit: 24b1f1fa4471d08d9c03af50dda3a615648ccb27

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-07-20 18:08:22 -0400

      Commit message:


	  
		
 add NEWS
 
    
  
    

      Package: smoothclust

      Commit: 6bdae00e954bf6eda76c6da984ccacde4d1d0127

      Author:  Lukas Weber <weberlm3@gmail.com> 

      Date: 2026-07-20 18:08:01 -0400

      Commit message:


	  
		
 updates for library size normalization and log transformation
 
    
  
    

      Package: exploreSE

      Commit: f0a4ced85fe30f6c5be4bc0ec82cab07d61af680

      Author:  Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com> 

      Date: 2026-10-19 16:36:53 +0200

      Commit message:


	  
		
 bug fix in get.gos and get.gsea
 
    
  
    

      Package: BiocCheck

      Commit: 5595f6db80aa00b45ea869d85a3bfd6ce6a81130

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-10-19 09:47:49 -0400

      Commit message:


	  
		
 Updates

 - pkgType now takes BiocType in Description into account
 - Fix Size check for non software packages
 
    
  
    

      Package: multipointR

      Commit: 9832d7d6ab386eeaa299e7dbbd223499de480df0

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2026-10-19 15:46:28 +0200

      Commit message:


	  
		
 version bump and exponential kernel default
 
    
  
    

      Package: multipointR

      Commit: f74fbfc08c3fb33154bb5e2c190b4b4db544ef5e

      Author:  Martin Emons <55688661+mjemons@users.noreply.github.com> 

      Date: 2026-10-19 15:28:57 +0200

      Commit message:


	  
		
 Rewrite towards allowing adaptive selection and Cox models (#4)

* allow relaxed fit

* option to standardise scales and permutation test for coefficients

* rmin for kppm and new lambda default

* fixed many bugs for kppm models

* adapted to matern kernel and polish vignette for kppm

* updated docs

* made examples shorter

* reducing test and example compute time/mem

* reduce test compute memory 
    
  
    

      Package: SpaNorm

      Commit: f79061de670f032ecb1ea872bd6ea19eecf0c302

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun157.hpc.net.uq.edu.au> 

      Date: 2026-10-19 19:18:02 +1000

      Commit message:


	  
		
 Move repository to BhuvaLab: update URLs (DESCRIPTION, pkgdown, README, vignette)

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: c12e5e57a9ee24036a32a178f1dd4466d4679ab4

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun038.hpc.net.uq.edu.au> 

      Date: 2026-09-30 06:15:55 +1000

      Commit message:


	  
		
 Merge feature/block-design: tpsBasis(), nbBlockDesign() compact block designs for polishNB, singular-block fix (1.7.15)

- tpsBasis(): SpaNorm's tensor natural-spline basis of position, exported;
  built on reference coordinates and evaluated anywhere, centred on the
  reference (identical to the internal bs.tps() on its own coordinates)
- nbBlockDesign(): a compact [X | Z_1 | ... | Z_G] design for polishNB(),
  nbProfilePsi() and nbNewtonSolver(), each group's q x q block removed by a
  Schur complement; at spiDE's depth = "spatial_spline" shape (30k cells, 50
  patients, 759 block columns, 1,000 genes) 3.3x faster than the dense
  grouped absorption with coefficients equal to 2.3e-13 (job 29111836)
- polishNB: a block the grouped solver cannot factor now flags that gene
  singular instead of stopping every gene's polish (regression test)

R CMD check (job 29107531): tests, examples and vignette OK.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JfUYckeFijW2ogSFn5hPNq
 
    
  
    

      Package: SpaNorm

      Commit: d5bec965f6bc93f697b8ac9be0dd1d733e1b048c

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun038.hpc.net.uq.edu.au> 

      Date: 2026-09-30 05:42:43 +1000

      Commit message:


	  
		
 NEWS: nbBlockDesign() timing at spiDE's spatial_spline shape (job 29111836)

One index type as spiDE builds it -- 30,000 cells, 50 patients, 1-3 sections
each, 759 block columns (6-31 per patient), 10 dense columns -- 1,000 genes,
profile dispersion, one dedicated core:

  intercept-only model     0.345 s/gene   ( 5.8 min)
  spline, dense grouped    1.571 s/gene   (26.2 min)
  spline, compact          0.480 s/gene   ( 8.0 min)

Per-gene factorisation 0.120 s dense vs 0.009 s compact; same Newton
iteration counts (20.0 per gene); all 1,000 genes polished on both paths,
coefficients within 2.3e-13, log-likelihoods within 2.5e-16 relative.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JfUYckeFijW2ogSFn5hPNq
 
    
  
    

      Package: SpaNorm

      Commit: b00d4c10ae13d617539ec01b348e7877f0b98bc4

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun038.hpc.net.uq.edu.au> 

      Date: 2026-09-30 05:02:36 +1000

      Commit message:


	  
		
 benchmarks: polishNB on spiDE's depth = "spatial_spline" design, dense vs compact

block_design_spide_shape.R builds spiDE's design for one index type exactly
as spiDE's .indexDesign() + .depthBlocks() do (checked equal to spiDE's own
functions when a spiDE tree is given: same W, absorb and pen): per patient an
intercept and, per section, [l | l * B] with B the section's 3x3 (2x2 below
200 cells, none below 100) spline basis, plus niche and condition x niche
columns. It fits it with polishNB() on spiDE's dense grouped absorption and
as a compact nbBlockDesign (group = patient, each patient's block columns
padded with zero columns to the widest; spiDE's 1e-3 ridge keeps the padding
at 0, so the fit is the dense fit), with the intercept-only model as the
reference cost.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JfUYckeFijW2ogSFn5hPNq
 
    
  
    

      Package: SpaNorm

      Commit: 9854052c196ab78121320bc9975b1ebad41caf25

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun038.hpc.net.uq.edu.au> 

      Date: 2026-09-30 00:42:19 +1000

      Commit message:


	  
		
 SpaNorm 1.7.15: NEWS, timing benchmark for nbBlockDesign()

benchmarks/block_design_timing.R (build-ignored) times polishNB() per gene on
simulated data at spiDE's spatial_spline shape -- 45 patients, 40 dense
columns, a 10-column block per patient (intercept + l x 3x3 spatial spline)
-- in four arms: the dense grouped design, the compact nbBlockDesign, and the
intercept-only model (patient intercepts alone) as a dense logical absorb and
as a q = 1 block design. Run on one dedicated core, one BLAS thread, 3 genes,
profile dispersion (SLURM job 29107530, results committed alongside):

  cells    intercept   spline dense   spline compact   dense/compact
  20,000     0.40 s        1.92 s          0.34 s            5.6x
  60,000     0.88 s        4.56 s          0.86 s            5.3x
  150,000    2.24 s       10.64 s          2.17 s            4.9x
  300,000    3.94 s       13.89 s          3.69 s            3.8x

The per-gene factorisation is 8.0-13.2x faster than the dense grouped one;
coefficients, log-likelihoods, dispersions and iteration counts agree between
the two layouts in every arm. .Rbuildignore also drops `.git`, which is a
file (not a directory) in a git worktree and so was shipped by R CMD build.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JfUYckeFijW2ogSFn5hPNq
 
    
  
    

      Package: SpaNorm

      Commit: 4e113aeb7443a59daec3b2daa51f8dafa9968d1d

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun038.hpc.net.uq.edu.au> 

      Date: 2026-09-30 00:41:25 +1000

      Commit message:


	  
		
 nbBlockDesign: as.matrix() without the sparse-coercion warning

as.matrix() filled the block part through as.matrix(), which
Matrix warns about on every large coercion (1 GiB at 300,000 cells x 490
columns). It now fills each group's rows directly; the values are the same.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JfUYckeFijW2ogSFn5hPNq
 </pre>
    </div>
  
    

      Package: SpaNorm

      Commit: cc54e712fc74fac24f03f4b653dfc9bd2385d89c

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun038.hpc.net.uq.edu.au> 

      Date: 2026-09-29 23:52:31 +1000

      Commit message:


	  
		
 nbBlockDesign(): compact per-group block designs for polishNB

A design [X | Z_1 | ... | Z_G] whose block columns are non-zero only on their
group's cells -- a per-patient intercept plus a per-patient spatial
library-size spline, say -- can now be passed to polishNB(), nbProfilePsi()
and nbNewtonSolver() as W = nbBlockDesign(X, Z, block): the dense cells x p_x
columns, one cells x q matrix of each cell's own block values, and the group
of every cell. The dense n x (p_x + G q) matrix is never built. The linear
predictor and the score go through a sparse copy of the block part (n q
entries) or, for a batch of 5+ genes, group-by-group BLAS products; the
per-gene factorisation scales each group's pre-split rows once and takes the
group's share of X'WX, B_g = X_g'W Z_g and C_g = Z_g'W Z_g + diag(pen) from
them, absorbing every C_g by a Schur complement. Cost per Newton step is
O(n (p_x + q)^2) whatever G is.

The coefficient layout is as.matrix(D)'s: X's columns, then group 1's q
columns, group 2's, ... lambda.a and start.cols may be given for [X | Z]
only (the Z part then applies to every group). The results are the dense
grouped path's (as.matrix(D) with absorb = rep(1:G, each = q)): the tests
hold coefficients, log-likelihoods, dispersions, polish flags, the Schur
complement S, the cross block B, each C_g^-1, the Newton step and xcov() to
1e-8 or tighter against it and against the full dense inverse, for both
engines, profile and fixed dispersion, warm starts, vector and matrix
offsets, unequal group sizes, gene blocking and a nearly aliased group
(condition ~1e10).

Degenerate groups are handled rather than failed: each C_g is scaled to unit
diagonal and Cholesky-factorised, and one whose smallest squared pivot falls
below rank.tol (1e-10; a variance inflation above 1e10) -- fewer cells than
columns, a level with no cells, an unpenalised column constant over the
group -- is inverted by a truncated eigendecomposition (a generalised
inverse). The step is then zero along the group's null directions, which do
not enter the linear predictor, and the fit equals the dense fit with the
aliased columns removed (tested for an empty level and a 2-cell group). The
dense grouped path flags such a gene singular. The factorisation state
carries S, B, per-group H with C_g^- = H H', and the per-group rank, for a
caller that needs the Schur pieces (e.g. a sandwich).

CPU only: a device backend, absorb/absorb.batch, and the batched/device
helpers (nbNewtonSolverBatch, nbGramBatch, nbAbsorbGramBatch) refuse a block
design with a message. The matrix path is unchanged: the design helpers
evaluate the same expressions on a base matrix.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JfUYckeFijW2ogSFn5hPNq
 
    
  
    

      Package: SpaNorm

      Commit: d5c9eb12a61db8bb17645f9d0cee15f188a55d13

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun038.hpc.net.uq.edu.au> 

      Date: 2026-09-29 23:43:30 +1000

      Commit message:


	  
		
 tpsBasis(): export SpaNorm's spatial spline basis

The tensor product of per-axis natural splines that SpaNorm's fit is built
from (the internal bs.tps()), exported so a downstream model can use the same
smooth functions of position -- e.g. a per-patient spatial library-size
spline. On its own coordinates it is bs.tps() bit for bit (tested with
identical(), and against the biology columns of a real SpaNorm fit). It can
also be built on reference coordinates (knots at the reference quantiles,
boundary knots at its range, df from its ranges) and evaluated anywhere, with
the columns centred by the REFERENCE means, so two subsets of one section
share one basis. `df` may be one value (bs.tps()'s aspect-ratio rule) or one
per axis.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JfUYckeFijW2ogSFn5hPNq
 
    
  
    

      Package: SpaNorm

      Commit: 7a4bc385647bcb3c463349ceba158f74398e47dc

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun038.hpc.net.uq.edu.au> 

      Date: 2026-09-29 23:43:20 +1000

      Commit message:


	  
		
 polishNB: a block the grouped solver cannot factor flags the gene singular

When a per-group block of C = Z' diag(w) Z fails its Cholesky (an unpenalised
block with no cells, or with fewer cells than columns), the grouped solver's
factor() returns NULL. The per-gene engine handed that NULL back to solve(),
whose as_fac() treated it as a weight vector and stopped the whole polish in
sqrt(NULL); the batch engine stored it with `[[<-`, which deletes the list
element. One unfactorable gene thereby killed every gene's polish. as_fac()
now passes NULL through (solve() and xcov() already return NULL on it) and
the batch engine keeps the NULL with `[<-`, so the gene falls back to its
input fit flagged singular, as a singular Schur complement already did.
Regression test in test-polishNB.R (errors on master in both engines).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01JfUYckeFijW2ogSFn5hPNq
 
    
  
    

      Package: SpaNorm

      Commit: 4694532dceb43dc3218f5d11451053f43d096088

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-28 11:51:21 +1000

      Commit message:


	  
		
 Merge fix/polish-collinear-block: catch a collinear unpenalised block up front (macOS arm64 CI)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: b2b3085392c7d1542e776e122c3e47d9cda9a232

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-28 11:39:32 +1000

      Commit message:


	  
		
 polishSpaNorm: catch a collinear unpenalised block up front, not per gene

A batch matrix given with every level's indicator makes the unpenalised
block [(gmean), batch] collinear, so every gene's information is exactly
singular. The polish left that verdict to each gene's chol(), which turns on
rounding: x86 (Ubuntu, Windows) flagged all 20 genes of the test fixture,
macOS arm64 CI factored every one and polished gene 3 along the null
direction (5 failures in test-polishSpaNorm.R, run 36237141413).

One QR of the unpenalised columns now decides it for every gene: the
information X'WX + diag(pen) is positive definite exactly when those columns
have full rank. A collinear block marks the kept genes singular and
unpolished without calling polishNB(), and the warning names the cause. The
test mocks polishNB() to fail if reached, so it pins the up-front check on
every platform.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 521dc95bcc030ff38529a2d2359d14228f72b0db

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 20:53:12 +1000

      Commit message:


	  
		
 Merge feature/polish-nb: host the per-gene penalised-NB polish (polishNB) and add polishSpaNorm() (1.7.14)

polishNB(), nbProfilePsi() and the nb* Newton/gram solvers move here from spiDE
(outputs unchanged, pinned by spiDE's golden gate at tolerance 0). polishSpaNorm()
polishes the SpaNorm model itself (shared a1 fixed by default or joint, gmean
outside W, wtype ridge x ncells, zero-gene and zero-batch-level hold-outs), and
SpaNormSVG()/svgTest() pair the full and null fits by polish state and settings.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 0c3d870dfde0197fa7c1fa677b7bc045b1b2604f

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 16:06:38 +1000

      Commit message:


	  
		
 docs: scope the polish evidence to what was measured; the batch-level hold-out

NEWS and the vignette's "Polishing the fit" (final review M-4/M-5/M-6 and
the parked timing minor):

- The per-gene log-mean shift under ls = "joint" (median 0.03 and 0.09 SE,
  max 0.17 and 0.68) was measured on two cores (404_16, 709_51) over a
  random 50 genes each (task 10b §3); it is now stated that way.
- The 4-7x wall-time cost was measured at tol.ls = 1e-6, where every joint
  fit ran all 10 steps; the shipped 1e-3 stops sooner and the cost was not
  re-measured. Said so.
- "A handful" of SVG changes is replaced by the counts: 137 -> 123 on the
  395-cell core, 5 -> 5, 180 -> 178, 545 -> 551 (task 10 §2).
- NEWS: nbProfilePsi() takes an offset but no absorb/absorb.batch; the
  F.raw attribute is removed from user NEWS (the code comment stays).
- Vignette: the default psi.method = "fixed" converges the mean at
  SpaNorm()'s dispersion and keeps it; "profile" re-estimates it. The
  motivation no longer implies the default fixes an inflated dispersion.
- Vignette: the exact 33.2 s / 24.6 s become "about half a minute or more
  on one core".
- NEWS: the polishSpaNorm bullet gains the batch-level hold-out (held_out
  column, warning) and the unpolished-genes warning; the SpaNormSVG bullet
  lists psi.range among the paired settings under "profile".

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: ad1bc5fa15f540482e646449fa7bbed3e7466ae9

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 15:59:16 +1000

      Commit message:


	  
		
 tests: tighten the joint-stationarity assertions to a1's own SE

The recomputed pooled score was checked with |U| < 1e-3 * sum(Y), which is
2.85 a1-SEs on the fixture, and the recorded score against it with an
absolute tolerance of 1e-3 * sum(Y) (597, against |U| ~ 0.02). The only
tight check read the recorded score, not an independent one (final review
M-3).

Per the ruling, the stationary, all-zero-gene and profile joint tests now
assert |U| * ls.se < 1e-3 with U recomputed from the stored fit, and
|ls.score - U| < 1e-6 |U| + 1e-8. All pass on the fixture unchanged. A
mutation that returns a1 0.5 SE off its optimum, every gene re-polished
there and the recorded score left at the optimum's, passes all 15 old
expectations and fails both new ones (|U| * se = 0.501; |score - U| = 105).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 1b7d7b9bd36fd96ebd265310cc0e77091ec347a3

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 15:56:41 +1000

      Commit message:


	  
		
 polishSpaNorm(): record psi.range under "profile"; SpaNormSVG() forwards and compares it

Under psi.method = "profile" the dispersion's search interval is part of
the objective (a gene whose optimum is on a bound keeps its input psi), but
it reached polishNB() only through `...` and was never recorded. So
SpaNormSVG() polished a missing null at the default interval, and
.polishedAlike() accepted the pair. Final review X5, reproduced here: with
psi.range = c(0.02, 0.2), "polish the full fit, then SpaNormSVG()" and
"SpaNormSVG(), then polish both" gave nulls differing in psi on 6 of 40
genes and svg.F by up to 1.36, both passing as polished alike.

Per the M-1 ruling: .polishSpaNormFit() records psi.range in
@polish$settings when psi.method = "profile" (the value passed, else
polishNB()'s default, read from its formals); SpaNormSVG()'s null polish
forwards it; .polishedAlike() and .polishAlikeDiff() compare it under
"profile", a missing field (a fit polished before this) meaning the
default. The code's design implies the two routes should pair alike, not
be refused: the null polish is meant to use all of the full fit's recorded
settings. The X5 test asserts that: both routes record the range on all
four fits and give the same null psi, psi_bound and svg.F (1e-8). A
second test pins the comparison: a hand-made pair with different ranges is
not alike and svgTest() names 'psi.range'; a missing field matches the
default; "fixed" does not record it.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 81898363a8cbc3eb6f6e1aaea9af93da50b88016

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 15:52:12 +1000

      Commit message:


	  
		
 polishSpaNorm(): warn when genes passed to the polish stay unpolished

A gene the Newton engine cannot converge keeps its input fit
(polished = FALSE), and the fit is still marked polished. When that was
every gene (final review X2: a one-hot batch matrix with no intercept
column passes checkBatch(), leaving the unpenalised block collinear, so
all 20 genes are singular) the polish was a silent no-op: isPolished()
TRUE, coefficients and logcounts unchanged, no warning.

.polishSpaNormFit() now warns once per fit with the count of genes passed
to the polish that were not polished and how many of them were singular
(final review M-2 ruling). isPolished() stays TRUE and there is no entry
stop, since SpaNorm() accepted the design. Held-out genes are not counted
here; they have their own rule.

Test: the X2 design through SpaNorm(batch = model.matrix(~ 0 + b)); it
was silent before this change.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 933cd7d2bc28ea1696451ece22bcfcc8abd814b4

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 15:50:01 +1000

      Commit message:


	  
		
 polishSpaNorm(): hold out a gene with no counts in a whole batch level

Batch columns are unpenalised 0/1 indicators, so a gene with no counts in
every polished cell of one level has no finite optimum: that level's
coefficient runs to -Inf, the degeneracy the all-zero hold-out already
covers for the intercept. The polish drove it there and reported the gene
converged, and the normalisation then imputed the gene at full strength
where it was never observed. On the new batch fixture: batch coefficient
-0.174 -> -19.65 (-22.3 under ls = "joint"), and logcounts in the all-zero
level mean 1.54 -> 6.11, against 6.24 in the level it is expressed in.

The all-zero rule is generalised (final review I-2 ruling). The polished
cells are grouped by the unique rows of the unpenalised block of the
polish design (the (gmean) intercept and the batch indicators), and a gene
with zero total counts in some group is held out as an all-zero gene is:
polished = FALSE, input coefficients and dispersion kept, and under
ls = "joint" the new shared a1. The all-zero rule is the one-group case,
unchanged (still a verbose message only). Groups are formed only when every
unpenalised column besides the intercept is 0/1; otherwise only the
all-zero rule applies (documented). The reason is recorded per gene in a
new @polish$genes column, held_out ("all-zero" / "zero-batch-level" / NA),
and one warning per fit counts the batch-level cases, naming the fit
('SpaNorm' or 'SpaNormNull'). The null polish goes through the same path,
from polishSpaNorm() and from SpaNormSVG().

Tests: the grouping and hold-out helpers; a batch-factor fixture where one
gene is zero across a level (held out, input kept, warning, logcounts not
inflated); the other genes polished to their optimum with the batch
column unpenalised; the joint variant; SpaNormSVG() pairing and running on
the batch design with the gene held out of the null too. The all-zero test
now also asserts no warning and held_out = "all-zero".

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 017d045fbfde421bf049071b48b3068eedc3e7b0

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 15:23:19 +1000

      Commit message:


	  
		
 tests: check unpolished SpaNormSVG() against master's statistic, not a stored RDS

The unpolished-SVG regression test compared SpaNormSVG()'s output with
expect_identical() against an RDS computed on one node. The fits behind it
are rebuilt at test time (scran size factors, the IRLS, edgeR), so the
last bits follow the BLAS: on the same node the assertion fails with
OPENBLAS_NUM_THREADS=1 ("Objects equal but not identical"), and the final
review measured 9.1e-13 under OPENBLAS_CORETYPE=Prescott. Every CI
platform and Bioconductor builder uses another BLAS.

The test now runs SpaNormSVG(backend = "cpu") and asserts its statistics
equal master b5d3f8f's svgTest() body applied inline to the same full and
null fits, at tolerance 1e-10. It passes at 1 and 4 BLAS threads and under
Prescott, and fails on a 1e-8 relative drift in svg.F. The RDS had no
generator in the repository; it is removed.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 028d8e70d05bc8a2cf460036ed8c1bb70b84f27d

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 13:28:44 +1000

      Commit message:


	  
		
 docs: NEWS and vignette for polishNB()/polishSpaNorm()

Adds the user-facing NEWS.md entries for the polish machinery moved
from spiDE (polishNB(), nbProfilePsi(), the nb* Newton solvers), the
new polishSpaNorm()/isPolished() pair with the Task 10 ls = "fixed"
vs "joint" numbers and their caveats, and the SpaNormSVG()/svgTest()
polish-pairing rule (attr(, "F.raw")).

Adds a "Polishing the fit" section to vignettes/SpaNorm.Rmd covering
when to polish, the SVG pairing rule, and the ls choice; the demo
chunk is eval=FALSE (measured 33.2 s with null = TRUE, over the
vignette's ~30 s per-chunk budget).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: fca08ab848615bea8bbd2a8eac84a1246c66423c

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 11:55:20 +1000

      Commit message:


	  
		
 polishSpaNorm(ls = "joint"): lower the shared a1 stop to 1e-3

.LS_TOL asked for a1's standardised score |U|/sqrt(I) -- its distance
from the joint optimum in units of its own profiled SE -- below 1e-6,
far past what the inner per-gene polish can resolve. Measured on four
real YTMA cores (Task 10, jobs 28973894-98): all 8 joint fits hit the
ls.maxit = 10 cap and warned, although a1 had settled by step 3.

Lower the default to 1e-3 (a1 within a thousandth of its own SE, still
far inside its sampling error). .LS_MAXIT and the rest of the loop are
unchanged. Docs (polishSpaNorm()'s @details, man/polishSpaNorm.Rd) and
the tests that assumed the old default are updated to match; the
optim()-oracle test now passes tol.ls = 1e-8 explicitly, since it needs
a tighter stop than the package default to keep comparing against an
independent optimum. Adds a test that the default converges within the
cap and lands within 1e-3 * ls.se of a run forced to a much tighter
stop (via mocking .LS_TOL, since tol.ls cannot reach .polishSharedLS()
through polishSpaNorm()'s public ... -- it also reaches the cold-pass
polishNB() call first, which does not accept it).

devtools::test(): 1048 pass / 0 fail / 37 skip (was 1043/0/37).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: b2b3a387f120876a569ba2765fe40d3620343a84

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 09:56:45 +1000

      Commit message:


	  
		
 SpaNorm 1.7.14: polishSpaNorm() (fixed and joint library-size coefficient), polished SVG pairing

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: e441a9943755f83b814a9ad794003416a3dc71bc

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 09:46:51 +1000

      Commit message:


	  
		
 Fix round 1: joint loop stop, one gene set per step, no stop() on I <= 0

- .polishSharedLS() takes `...` before its options, so polishSpaNorm()'s
  per-gene maxit/tol no longer partial-match maxit.ls/tol.ls. The loop runs at
  its documented stop (|U|/sqrt(I) < 1e-6, 10 steps), and every warm
  re-polish receives the caller's maxit/tol. The loop's defaults live in one
  place (.LS_MAXIT, .LS_TOL) and are recorded as settings$ls.maxit and
  settings$ls.tol.
- The line-search total is summed over the same genes that formed U and I in
  that step. A gene left out for a singular information is still re-polished,
  but it can no longer stall the search or end it at a point that is not the
  maximum of the objective being compared.
- A non-positive profiled information warns and returns the fixed-a1 polish
  with the attempt recorded (ls.converged = FALSE), as the no-gene path does,
  in place of stop(). It is checked before the tolerance, so it is never read
  as convergence.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 16528811e73438867d7f6aeefb278e7f10f085e2

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 08:33:27 +1000

      Commit message:


	  
		
 polishSpaNorm(ls = "joint"): the pooled, profiled Newton step on the shared a1

The library-size coefficient a1 is shared by every gene of a SpaNorm model.
ls = "joint" alternates the per-gene polish with a Newton step on the
profile log-likelihood of a1: score U = sum_g w1' r_g and profiled Fisher
information I = sum_g [(w1^2)' D_g - c_g' H_g^-1 c_g], with H_g^-1 c_g from
nbNewtonSolver()'s factorisation. Each candidate re-polishes every gene
warm (and, under psi.method = "profile", re-profiles psi and re-polishes);
the step is halved until the total penalised log-likelihood over the
polished genes does not fall. It stops at |U|/sqrt(I) < 1e-6 or 10 steps.

The sums, the objective and the re-polish run over the polished genes
only. A gene whose information is singular is left out of both U and I
and counted (ls.singular). Held-out genes keep gmean/alpha[, -1]/psi and
take the new shared a1. With no polished gene, a1 is left unchanged with
a warning. settings record ls.iterations, ls.score, ls.se = 1/sqrt(I),
ls.singular and ls.converged.

Matches an optim() oracle to 5e-8 in a1; on the test fixture the joint a1
moves 1.013 -> 0.938 (15.8 profiled SEs) for +124 log-likelihood units.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 5516896e3de65a44a4e0f9ec6ddb9409b1a68f74

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 07:12:58 +1000

      Commit message:


	  
		
 Fix round 1: .polishedAlike() compares polish settings, not just isPolished()

Review (Important) reproduced a real defect: two separate polishSpaNorm()
calls -- one polishing only the full fit, with a different psi.method -- give
a pair that is isPolished() on both sides but scores a different LRT (median
svg.F +38%, FDR<0.05 calls 30 -> 33, on .polish_spe()). The original ruling
3's "consistent" check (isPolished() equality only) accepted this silently;
it is reachable through the public API, not only by hand-assembling a
mismatched pair.

.polishedAlike(full, null) is now the sole function either SpaNormSVG() or
svgTest() uses to decide comparability: TRUE iff both are unpolished, or both
are polished and their recorded psi.method/ls/cells agree (the three settings
that define the fitted objective; a1 and maxit/tol are deliberately excluded).
svgTest()'s guard now names what differs via .polishAlikeDiff(). SpaNormSVG()
gains a fourth pairing branch: when both fits are polished but their settings
differ, it re-polishes the null with the full fit's settings -- starting from
the stored SpaNormNullUnpolished when there is one, else refitting -- with a
message() naming the mismatch. Every branch that polishes a null now forwards
ALL of the full fit's recorded settings (psi.method/ls/cells AND maxit/tol),
not only the three .polishedAlike() compares.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 0948b530bcd25283c43571e626c8d6cbd0b66ad6

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 05:19:18 +1000

      Commit message:


	  
		
 SpaNormSVG() pairs the full and null fits by polish state; svgTest() refuses a mixed pair

svgTest() compares a full SpaNorm fit against a nested "technical" null by a
likelihood ratio, and that is only a comparison of nested models when both
sides are estimated the same way. SpaNormSVG() now keeps the two paired
(.svgPairedNull()): a missing null is fit and polished to match a polished
full fit, using the full fit's own polish settings; a stored null whose
polish state already matches is used as is; a stored null that does not
match is polished in place (with a message) when the full fit is polished
and the null is not, and refused (naming both states, pointing at
polishSpaNorm()) in the other direction, since silently un-polishing or
polishing the full fit here is not SpaNormSVG()'s job. svgTest() gains the
same guard directly, since it is reachable via SpaNorm:::svgTest().

svgTest() also records the unclamped LRT statistic as attr(df.svg, "F.raw")
(additive only; svg.F is unchanged). On the .polish_spe() fixture this is
mildly negative for some genes even for a correctly polished pair (psi.method
= "fixed" keeps each model's own fitNB dispersion, and svgTest() scores
winsorised psi/mu independently per model), so the nesting guarantee is
tested differently: the polished full fit's own penalised objective, at its
own optimum, is at least as large as that same objective evaluated at the
polished null's coefficients embedded in the full design (biology columns at
0, shared library-size coefficient held at the full fit's own value) --
confirmed on the fixture (max relative gap -5.8e-4, well inside the 1e-8
tolerance, on all 40 genes).

Existing unpolished-pair SVG behaviour is unchanged (tests/testthat/fixtures/
svg_baseline_unpolished.rds is the pre-change output, asserted identical()
after).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 6bc98c0a7d1d4e13d241163871547d31ba9bebc2

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 04:00:28 +1000

      Commit message:


	  
		
 tests: polishSpaNorm() refuses a fit with an unshared library-size coefficient

The plan's Review Focus 1: a fitNB()-style or hand-built fit whose alpha[, 1]
differs across genes is refused at the entry point with an error naming the
column, and nothing is written to the object before the refusal.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 87edfe6156122136d5c5a7fb82d8e272c73cdd00

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 03:51:02 +1000

      Commit message:


	  
		
 polishSpaNorm(): converge each gene of a SpaNorm fit, SPE and Seurat methods

A new exported generic that converges every gene of a stored SpaNorm fit to
its own penalised-NB optimum under SpaNorm's model (ls = "fixed": the shared
library-size coefficient held; gmean an unpenalised per-gene intercept; the
wtype penalties times ncells), through polishNB(). It stores the polished fit
as 'SpaNorm' and the input as 'SpaNormUnpolished', polishes a stored
'SpaNormNull' alike, drops stale SVG columns with a warning, and rewrites the
normalised assay from the polished fit.

- Genes with no counts in the polished cells are not passed to polishNB():
  they keep their input fit bit for bit and are recorded polished = FALSE.
- An already polished fit is refused unless overwrite = TRUE, which polishes
  again from 'SpaNormUnpolished', never from the polished fit.
- A non-integer counts assay is refused at the entry point.
- @polish holds settings (psi.method, ls, cells, maxit, tol, pen, a1.input,
  a1, SpaNorm) and per-gene diagnostics (polishNB()'s, plus loglik).
- ls = "joint" is a stub (.polishSharedLS()) until the pooled step lands.
- The SPE and Seurat methods share one core; the normalisation block size
  comes from .normaliseBlockSize().

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 99e708997dfbb2cb7f2bf8197027f6db9db1a1f0

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 02:53:45 +1000

      Commit message:


	  
		
 Extract .normaliseBlockSize() from .spaNormCore()

The DelayedArray block-size rule for normaliseBlocked() moves into its own
helper so polishSpaNorm() can share it. Pure refactor: no behaviour change.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: aa1abbe0f403e9c95cb1d2f132d74eb6c729fe20

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 02:23:57 +1000

      Commit message:


	  
		
 SpaNormFit gains a polish slot, isPolished(), and .spaNormPolishProblem()

Groundwork for polishSpaNorm() (Task 7): a `polish = "list"` slot
(prototype list(), so existing callers of SpaNormFit()/fitSpaNorm() are
unaffected), the exported isPolished() predicate and internal
.polishSlot() accessor (both go through methods::.hasSlot() rather than
`@`/`$`, since those error on an object saved before this slot existed
-- verified against a real RDS written under the installed pre-slot
SpaNorm 1.7.13), a show() line for a polished fit, and a validity check
that `polish` is either empty or carries `settings`+`genes`.

.spaNormPolishProblem() (R/polishSpaNormModel.R) maps a SpaNorm-model fit
(gmean/alpha/W/wtype parameterisation) onto the generic per-gene
penalised-NB problem polishNB() solves: the shared library-size
coefficient becomes a per-cell offset, gmean becomes an explicit
unpenalised "(gmean)" design column, and the wtype-keyed penalty is
reconstructed to match fitSpaNorm()'s own (R/mainSpaNorm.R).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 579d02e25dc53eccc377a12c7d6780389d09aa45

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-26 01:27:46 +1000

      Commit message:


	  
		
 tests: port spiDE's array-batch and .segmentSum tests

Task 5's move of the polish machinery to SpaNorm left these internals
(.setRows, .mulRows, .scaleCols, .asHost, .matmulB, .rowsFinite,
.rowMeansB, .colsOf, .maskedRowMin, .asLike, .rowMaxB, .asHostMat,
.segmentSum) untested here. Port spiDE's tests/testthat/test-array-batch.R
(11 test_that blocks) and the .segmentSum block from test-inference.R,
from spiDE commit 26997f0 (before deletion), into
tests/testthat/test-nbArrayBatch.R.

spiDE:::.foo becomes .foo and SpaNorm::toRMatrix/is_torch_tensor become
unprefixed, consistent with every sibling test file in this package.
Every torch half that builds a real CPU tensor is gated with
skip_if_no_gpu() instead of skip_if_not_installed("torch"): torch 0.17 on
a CPU device aliases R memory without keeping it alive, so results depend
on GC timing (a deferred engine follow-up). Base-R halves are ungated and
run everywhere.

devtools::test(filter = "nbArrayBatch"): 15 pass, 0 fail, 12 skip (GPU
halves only, no GPU on this node). Full devtools::test(): 763 pass, 0
fail, 37 skip, against a baseline of 748/0/25 at fbc7d67 -- the +15/+12
delta matches the focused run exactly.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: fbc7d67b115be029be983fd00204828cec0ce210

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 21:30:17 +1000

      Commit message:


	  
		
 SpaNorm 1.7.13: polishNB() and the penalised-NB Newton machinery; RhpcBLASctl in Suggests

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 2e3a3b66d6bc8e8a166dd5f999b4f6ae84fc41a3

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 20:46:02 +1000

      Commit message:


	  
		
 tests: gate the CPU-tensor engine tests on a GPU

On a CPU device torch 0.17's torch_tensor(, float64) wraps R's
memory without copying or holding it, so a tensor made from an R temporary
reads reused memory after a garbage collection. The engine's .asLike() and
.nbLoglikBatch() build tensors that way, and a second identical
.polishBatch() call in one process was measured returning wrong
coefficients. Every test that runs the polish engines' or the batched
solvers' tensor path on the CPU now uses skip_if_no_gpu() instead of
skip_if_no_torch(), with a comment at each: test-polishEngine.R (NB
kernels, the zero-dispersion loglik, mixed dispersions, .psiProfileBatch,
.polishBatch on tensors, the offset tensor path) and test-nbSolver.R
(.newtonSolverBatch, .absorbBatch). The engine fix is deferred; no engine
code changed.

test-polishNB.R: the comment that pointed to test-polishEngine.R for the
offset tensor path now says that test is gated too.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: SpaNorm

      Commit: cce4cad0033b0ef5b43c8fdc36e0968c8bfa50e0

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 20:45:55 +1000

      Commit message:


	  
		
 polishNB(): remove the unread gpu.mem.budget argument

Moved from .polishFit(), which accepted it and never read it; the batched
working set is sized by batch.size or options(SpaNorm.polish.mem.budget).
The argument and its doc are removed; nothing else threaded it.

Test (RED: the argument was present): it is no longer a formal.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: ece0cc52da8f4d935603523fb9fd07e3e36e7de2

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 20:45:35 +1000

      Commit message:


	  
		
 Multi-worker dispatch needs RhpcBLASctl only when it is installed

.singleBLAS() is now bpnworkers > 1 && .hasBLASctl(), where .hasBLASctl()
is requireNamespace("RhpcBLASctl", quietly = TRUE). Without the package
(it moves to Suggests), dispatch is plain bplapply() and the workers keep
the BLAS thread count they inherit, instead of erroring inside every
worker. With it, nothing changes.

The probe is a package function so a test can mock it. testthat 3.3.0
will mock requireNamespace() only in base (.package = "base"), which
would change it for every caller in the process for the whole test.

The BPPARAM doc says the workers go single-threaded when RhpcBLASctl is
installed, and what to do when it is not.

Test (RED: "Can't find binding for `.hasBLASctl`"): with the probe FALSE
and .workerBLAS() mocked to fail, a 2-worker MulticoreParam dispatches
without calling it (forked workers inherit the mock), and polishNB() and
nbProfilePsi() match the serial run. A mutant without the guard fails it.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: a7e356653db371287dc0e30fb298bb6c0fca44bf

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 20:44:41 +1000

      Commit message:


	  
		
 polishNB docs: the integer-count guard reads the first 20 genes only

The moved guard (unchanged) checks the first 20 genes. It catches an assay
that is non-integer throughout, such as a back-transformed log-count
matrix, but not a stray non-integer value in a later gene. @details now
says so.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 1cea5979277c01b4435bca063ce8feff46b36027

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 20:44:18 +1000

      Commit message:


	  
		
 polishNB()/nbProfilePsi(): shape checks at entry; a scalar psi recycles

.polishShapes() stops, naming the argument and both sizes, when
nrow(W) != ncol(Y), nrow(alpha) != nrow(Y), ncol(alpha) != ncol(W), or
length(psi) is neither 1 nor nrow(Y). Both entry points call it. The
first case used to pass silently on the per-gene engine: with Y 2 x 50 and
W 100 x 2, each gene's counts were recycled against a 100-cell mean and
came back polished = TRUE with wrong coefficients. The batch engine failed
with an opaque BiocParallel error. Neither changes a valid call.

nbProfilePsi() recycles a scalar psi to nrow(Y). Left scalar, psi[gi]
gave NA to every at-bound gene after the first.

Tests (RED: no error on the gene engine, an opaque remote error on the
batch one, NA for the scalar psi): every mismatch in both functions, and
a scalar psi identical() to the equivalent vector.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 8d04c83a4e95f06df407bea11ba0063348ea0ac5

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 19:42:40 +1000

      Commit message:


	  
		
 polishNB docs: drop a stray roxygen fragment from the move

The move copied spiDE R/inference.R:12-72, which overran into the first
lines of .ptByCol()'s roxygen block ("Apply a t tail to a statistic
matrix..."). Roxygen merged that orphan fragment into polishNB()'s block,
so man/polishNB.Rd carried the wrong title. The fragment is deleted;
comments only, no code change.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 44fab76b0048aea4d7bbedc6a7a47bbe684c3a46

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 19:39:05 +1000

      Commit message:


	  
		
 tests: move spiDE's re-profile kernel test with nbProfilePsi()

".reprofilePsi uses the same kernel as the batched engine" builds W
directly and tests the function that moved to SpaNorm as nbProfilePsi(),
so it moves too (Task 3 left it for this task): spiDE::: dropped,
.reprofilePsi() -> nbProfilePsi(), assertions and tolerances unchanged.
An at-bound gene keeps its incoming psi, and a free gene's dispersion is
the batched kernel's answer to 1e-12.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: fcfc386821390d3fd9fec802e5c23fb0e3c9a64e

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 19:36:24 +1000

      Commit message:


	  
		
 nbNewtonSolver docs: parse cleanly, and describe the batch arguments

`\code{W' diag(w) W + diag(pen)}` opened an R string at the apostrophe
inside \code, which gave 6 Rd parse warnings on every document(). It
now reads `\code{crossprod(W, w * W) + diag(pen)}`, the same matrix in
valid R. document() and tools::checkRd() are silent on every man page.

penalty_diag, backend, cell.tile and parts said "see polishNB()", which
does not document them; each is described here instead. The
\link{polishNB} in the description now resolves.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 91b189478e04885d187a5993f170413725133d6b

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 19:36:24 +1000

      Commit message:


	  
		
 tests: name the far-start offset test for what it tests

"the sane start subtracts the mean offset" never reached the sane start:
a0 = 40 has a fitted log-mean of 43, which is not degenerate, and Newton
converges from it in 44 iterations with restarted = FALSE. It is renamed
"a far start converges to the intercept net of a constant offset", its
comment corrected, and it now asserts expect_false(r$restarted). The
sane start with an offset is tested by "the sane start is the log mean
net of the offset, in both engines".

Also in test-polishNB.R: the batch-size test reads the opening progress
message with capture_messages() instead of expect_message(), so the other
verbose lines no longer leak into the test output.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: b875e8e26ac4561603182773683423990bf5cb47

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 19:36:24 +1000

      Commit message:


	  
		
 Delete .polishCovBatchSize() and its three constants

Copied from spiDE's .covBatchSize() in the engine move, but nothing in
SpaNorm calls it (the polish is sized by .polishBatchSize() alone) and
nothing in the plan will: POLISH_TENSOR_MULT_COV, POLISH_BUDGET_FRACTION,
POLISH_COV_MEM_BUDGET_CPU and the SpaNorm.cov.mem.budget option go with
it. spiDE keeps its own copy for inference. The file header no longer
mentions it.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 477b05b3eef538b6ace88740e3112f30293183a8

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 19:31:26 +1000

      Commit message:


	  
		
 polishNB(offset =, psi.range =): threaded to both engines, checked at entry

- offset: NULL, a per-cell log-scale vector or a genes x cells matrix,
  checked once by .polishOffset() (shape, finiteness; a Matrix made base,
  a torch tensor refused with a message). A NaN used to stop both engines
  with "missing value where TRUE/FALSE needed" and an Inf returned the input
  fit flagged singular. A matrix is sliced to each sub-batch's genes
  (.rowsOf(offset, gi[ii])) and to each gene on the per-gene engine,
  straight from the whole matrix, so no block-sized copy is held; it stays
  on the host and the engine moves it.
- sizing: with an offset the auto batch size counts one more genes x cells
  matrix (the .offsetRows() expansion at every mean evaluation), two for a
  matrix (plus the batch's held rows), through a new `mats` argument to
  .polishBatchSize(). POLISH_GENE_CELL_MATS is unchanged and a NULL offset
  adds 0, so that path sizes exactly as before.
- psi.range: forwarded to both engines (the default is theirs), checked to
  be two increasing positive numbers.

NULL offset and default psi.range: 20 saved outputs of the move commit
(both engines, both psi rules, blocks/batches, warm, absorb none/logical/
grouping, the mocked device path, MulticoreParam, nbProfilePsi) are
identical().

Tests (RED: unused arguments): each gene's zero penalised score at
exp(W a + offset) in both engines, vector and matrix; a matrix offset
sliced with the counts across block and batch layouts equals each gene
alone (a row mis-slice in either engine is caught); every bad shape
refused by name; Matrix made base; the device path receives exactly each
sub-batch's rows; the batch size at 6/7/8 matrices; psi.range bounds the
search in both engines.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: a2ef9458a793f5256df6a98dde596ca61bc305c1

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 19:11:32 +1000

      Commit message:


	  
		
 nbProfilePsi(): the moved .reprofilePsi(), exported, with an offset

spiDE's variance-component loop re-profiles the dispersion after its warm
passes and will call this once the move lands, so it is exported
(@keywords internal) rather than left as a SpaNorm internal that spiDE
could reach only through :::. The body is .reprofilePsi()'s; the one
change is `offset = NULL`, appended to the signature and passed to
.muBatch() through .offsetRows() for the block's genes. Without it the
dispersion would be profiled at the wrong mean with no error. NULL gives
the pre-offset mean bit for bit.

.polishOffset() is the one check of an offset's shape (NULL, a
per-cell vector, a genes x cells matrix; finite; Matrix-class made
base; a torch tensor refused). polishNB() uses it from the next commit.

Tests (RED: could not find function "nbProfilePsi"): the dispersion
equals the profile ML at the given mean, a gene with no spread keeps
its input psi, blocking is exact, and a vector or per-gene matrix offset
moves psi to the ML at the offset mean. The optimize() oracle is
compared at 1e-6 because it places a flat optimum only to about
sqrt(eps).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: b46c600ef33256c2e22aa5e1938d55abca4864f3

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 19:06:43 +1000

      Commit message:


	  
		
 polishNB(absorb.batch =): the 1x1 absorption for the shared-factor solver

The per-gene solver takes `absorb`, which for a random-slope fit is a
per-sample grouping with multi-column blocks. The shared-factor batched
solver (built inside .polishBatch() on a device) absorbs 1x1 blocks only,
and a grouping cannot be reduced to its 1x1 subset generically. So
.polishBatch(nested =) now gets `absorb.batch` when given; otherwise a
logical `absorb` unchanged; otherwise the dense batched solver (exact,
slower). spiDE passes its nested-indicator logical here, reproducing the
nested_batch split .polishFit() made from re_group.

`absorb.batch` must be NULL or a logical with one value per column of W.

Tests (RED: "unused argument (absorb.batch = d$nested)"): on the device
path, mocked onto the CPU, .polishBatch() receives absorb.batch with
shared.factor = TRUE, a grouping alone arrives as all-FALSE, a logical
absorb passes through, and all three agree with the CPU polish to 1e-5.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 80753dbe8e917b55e83304ce4185ef14175c2612

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 19:03:56 +1000

      Commit message:


	  
		
 Tests for polishNB(): the optimum, engine parity, integer guard, zero gene

The plan's four tests. They failed before the move with
`could not find function "polishNB"`. Two of the plan's thresholds were
tighter than the moved engine's documented precision, which the move may
not change:

- the zero-score check at 1e-6 * sum(y) now passes tol = 1e-12. The
  default tol = 1e-8 stops on the relative log-likelihood gain and leaves
  up to 2.6e-6 on this fixture; 1e-12 gives 3.4e-8.
- engine parity is checked at a held dispersion (alpha to 1e-8; the two
  agree to 1e-16), then under "profile" to optimize()'s tolerance (psi to
  1e-4, alpha to 1e-6): the per-gene engine profiles psi with optimize()
  and the batch one by bisection, measured 1.9e-5 apart on log psi.

The zero-gene test asserts finite alpha and psi for both genes and a
polished first gene; the zero gene comes back polished, capped at maxit,
psi on its bound (kept at the input), intercept -27.45.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: bbe687d6d3d0740059c189ada4a1ceeec14fe008

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 19:01:15 +1000

      Commit message:


	  
		
 polishNB(): the gene-blocked polish driver, moved from spiDE

The body of spiDE's .polishFit() (R/polish.R) becomes the exported
polishNB(), with .reprofilePsi() from the same file and the helpers it
dispatches through from R/inference.R (.chunkGenes, .singleBLAS,
.workerBLAS, .bplapplySingleBLAS; spiDE keeps its own copies). The five
helpers are byte-identical after deparse; polishNB() differs from
.polishFit() only by:

- signature: pen -> lambda.a (kept as `pen` internally), covtype ->
  start.cols (the logical, taken directly; spiDE keeps the
  covtype == "CellType" derivation), re_group dropped, arguments reordered,
  psi.method = c("profile", "fixed") with match.arg();
- absorb = NULL means no absorption (rep(FALSE, ncol(W))); the re_group
  fallbacks for the per-gene and the shared-factor batched solver are
  spiDE-specific and stay there, so a grouping reaches the batched solver
  as the dense path;
- SpaNorm:: prefixes dropped;
- messages: the integer guard's last sentence is "Use the raw counts."
  and the lambda.a length error no longer mentions re.celltype.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 763f109b3a48c1e76664a206a456b6563cc16e4b

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 18:39:25 +1000

      Commit message:


	  
		
 Optional per-cell offset in the per-gene and batched polish engines

.polishGene(), .polishBatch() and .muBatch() take offset = NULL, a log-scale
offset added to every linear predictor: the Newton's starting mean, each
line-search candidate, the degenerate-start check, and the sane start,
which is now net of the offset's mean over the same cells. In the batch
engine every linear predictor goes through .offsetRows(), which slices a
per-cell vector (the same for every gene) or a genes x cells matrix to the
rows being computed. .polishBatch() refuses any other shape, and .muBatch()
refuses a bare vector that would otherwise recycle down its columns.

offset = NULL is the pre-offset engine bit for bit (16 saved result sets,
identical()).

Tests: the four from the plan, plus five that each fail when the offset is
dropped or mis-sliced at one site the four do not reach (the degenerate
check, the sane start with and without start.cols, per-gene row slicing
on a path where the active rows are not 1..B, the torch branch), and one
for the shape guards.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 774dadd68ef83ecbd5e321e0d54c6fe924906886

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 17:44:56 +1000

      Commit message:


	  
		
 Per-gene and batched polish engine, moved from spiDE

Verbatim move of spiDE's damped-Newton polish engine on the penalised
negative binomial likelihood:

- R/polishEngine.R <- spiDE R/polish.R: .MU_FLOOR, .nbPenLoglik,
  .polishGene; plus the exported nbMuFloor() (returns exp(-30)).
- R/polishEngineBatch.R <- spiDE R/polish-batch.R, all of it; plus a copy
  of spiDE's .covBatchSize() as .polishCovBatchSize() with the three
  constants it reads (spiDE keeps its own for inference).

Renames only: ct_cols -> start.cols; psi.method "moderated" -> "fixed";
SPIDE_POLISH_GENE_CELL_MATS -> POLISH_GENE_CELL_MATS and the copied
SPIDE_* constants -> POLISH_*; SpaNorm:: prefixes dropped. The two memory
budget options read SpaNorm.polish.mem.budget / SpaNorm.cov.mem.budget
first and fall back to the spiDE option names, so an existing setting
keeps working.

Tests: every direct-W test of spiDE's test-nb-batch.R, test-psi-batch.R
and test-polish-batch.R, in tests/testthat/test-polishEngine.R. Two stay
in spiDE: "spiDE() can reach the reference polish engine" (spiDE(),
buildNiches, .toySPE) and ".reprofilePsi uses the same kernel as the
batched engine" (.reprofilePsi moves with polishNB()).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 50e4ff41d4f54346c440b1c0e804c88b542db308

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 17:33:12 +1000

      Commit message:


	  
		
 Penalised NB Newton solvers and batched grams, moved from spiDE

Task 2 of the polish-to-spanorm plan: the per-gene and batched linear
algebra that fitNB's polish stage needs, moved verbatim from spiDE
(feature/polish-to-spanorm) into SpaNorm as the base for polishNB().

R/nbSolver.R <- spiDE R/polish.R: .absorbBlocks, .newtonSolverBlocked,
.newtonSolver.

R/nbSolverBatch.R <- spiDE R/inference-batch.R: .gramBatch, .segmentSum,
.absorbBatch, .cholBatch, .cholSolveBatch, .newtonSolverBatch, and the
backend helpers (.rowsOf, .setRows, .mulRows, .scaleCols, .asHost,
.matmulB, .rowsFinite, .rowMeansB, .colsOf, .maskedRowMin, .rowMaxB,
.asHostMat, .asLike, .subsetState).

Bodies are byte-identical to the spiDE source modulo stripping the
SpaNorm:: prefix (verified programmatically by extracting all 23
functions from both trees and diffing). .absorbSpec() was left in
spiDE: it is not in this task's function list and is a caller-side
helper for .polishFit(), not part of the solver.

Four thin exported aliases with one roxygen page (man/nbNewtonSolver.Rd,
@keywords internal): nbNewtonSolver, nbNewtonSolverBatch, nbGramBatch,
nbAbsorbGramBatch.

Tests: all 15 test_that() blocks from spiDE's test-solver-batch.R,
test-solver-slope-absorb.R and test-absorb-batch.R moved into one new
tests/testthat/test-nbSolver.R (none call fitSpiDE/spiDE()/toySpiDE/
.toyClustered, so nothing stayed behind). spiDE:::/SpaNorm:: rewritten
to bare calls; the two torch-vs-CPU agreement tests now use SpaNorm's
skip_if_no_torch()/gpu_tol() from helper-gpu.R instead of spiDE's own
pattern.

devtools::test(filter = "nbSolver"): 58/58 pass (torch usable on this
node, so the torch-backed tests ran rather than skipping).
devtools::test() (full suite): 464 pass, 0 fail, 0 warn, 17 skip (all
pre-existing GPU/MPS-only skips) -- no regressions.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: b5d3f8f3ec905467e49311f0e3e3c8b92b39834b

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun156.hpc.net.uq.edu.au> 

      Date: 2026-09-25 13:35:43 +1000

      Commit message:


	  
		
 Merge fix/technical-lambda-scaling: scale the SVG null's ridge penalty by ncol(Y) (1.7.12)
 
    
  
    

      Package: SpaNorm

      Commit: f07f7232c095eecabc6519b914d3d2b8d74173ef

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun148.hpc.net.uq.edu.au> 

      Date: 2026-09-23 14:27:31 +1000

      Commit message:


	  
		
 Scale the null model's ridge penalty by ncol(Y) in fitSpaNormTechnical()

fitSpaNorm() passes lambda.a.vec * ncol(Y) to fitSpaNormNB() but stores the
raw lambda.a in the SpaNormFit. fitSpaNormTechnical() rebuilt the penalty
from that stored raw value and did not rescale it, so the nested null used
by SpaNormSVG()/svgTest() was penalised ncol(Y) times less on the
library-size terms than the full model (1e-4 vs 0.0395 on a 395-cell core),
making the likelihood-ratio test inconsistent and slightly deflating svg.F.

The stored lambda.a stays raw: matchLambda() compares it against the
user-supplied argument to decide whether a cached fit can be reused.

fitSpaNormTechnical() now also stops if ncol(Y) differs from the full
fit's ncells. Adds a regression test that intercepts the penalty handed to
fitNBGivenPsi() in both fits. Bumps to 1.7.12.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 9f40301bfd31d45b5fa768a6e80488dabffc846d

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun154.hpc.net.uq.edu.au> 

      Date: 2026-09-08 21:22:15 +1000

      Commit message:


	  
		
 Skip the torch tests when libtorch/lantern is not installed

CI installs the torch R package (it is in Suggests) but never runs
torch::install_torch(), so the libtorch/lantern shared libraries are
absent and every tensor call errors with "Lantern is not loaded".
test-quasilik.R's cpu_tensor() guarded only on skip_if_not_installed(
"torch"), which sees the R package and passes, so the three CPU-tensor
parity tests errored instead of skipping.

The GPU tests were unaffected: checkGPU() -> getBackendDevice() already
tryCatch()es that failure down to "cpu".

Guard them with a new skip_if_no_torch() that probes torch by actually
building a tensor rather than trusting requireNamespace(), resolved once
per run. With the backend absent the suite is FAIL 0 | SKIP 20 | PASS
395 (was FAIL 3); with torch working the tensor branch still runs.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01MNyqumfPxayw9k2AZmrAv1
 
    
  
    

      Package: SpaNorm

      Commit: de6959484faebb82de605c1cebd6369102ba314b

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun154.hpc.net.uq.edu.au> 

      Date: 2026-09-08 12:04:19 +1000

      Commit message:


	  
		
 qlMomentTable(): one shared moments table for a blocked caller

qlDispersion() built its (log mu, log phi) table from each call's own
range, so a caller scoring genes in blocks got results that depended on
how the genes were split. qlMomentTable() builds the table once over a
range the caller fixes and qlDispersion(table = ) uses it; lookups outside
the range clamp to the edge, where the moments are asymptotically flat.
Tested: identical per-gene dispersions whole and in two blocks, on the CPU
and on tensors.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: dd63989420abc67370388f94214a90b6c1531b67

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun154.hpc.net.uq.edu.au> 

      Date: 2026-09-08 09:38:34 +1000

      Commit message:


	  
		
 Quasi-likelihood dispersion (edgeR v4) as generic NB-GLM machinery, CPU and torch

nbUnitDeviance() is the NB unit deviance elementwise over genes x cells,
on the CPU or on the device of a torch tensor input. nbDevianceMoments()
obtains the unit deviance's first two moments under the fitted NB by direct
summation over the pmf -- the definition edgeR's Chebyshev tables
approximate -- and matches them to a scaled chi-square (w0 rescales the
deviance, w1 is the observation's effective df). qlDispersion() gives each
gene's adjusted deviance, effective residual df and their ratio; with
moments = "table" (the default) the moments are evaluated once on a shared
(log mu, log phi) table and bilinearly interpolated onto every gene and
cell, so the per-gene work is elementwise and runs on the accelerator when
the counts and means are tensors. The per-gene grid and per-cell paths are
kept for the oracle tests, which hold the whole pipeline to
edgeR::glmQLFit() at 3e-3 and the table to the per-cell moments at 2e-3.

Used by spiDE 0.99.18 for the standard-error scale of its niche tests.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: cc381206e51eb7a02e5c0bf3adae47a71fad0f4e

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun133.hpc.net.uq.edu.au> 

      Date: 2026-08-13 09:03:38 +1000

      Commit message:


	  
		
 Add a supplied-dispersion (psi) passthrough to fitNB()

fitNB() gains `psi = NULL`. When a numeric vector of per-gene NB
dispersions is supplied, the outer dispersion loop is bypassed entirely:
the loop's convergence test exists only to decide when psi has settled,
and a supplied psi is settled by definition. The coefficients therefore
come from a single inner IRLS fit at the given psi. edgeR::estimateDisp
is never called, no dispersion subsample is drawn (the returned
`sampling` factor carries no "dispersion" level -- cells are "glm" if
used for fitting, else "all"), maxit.psi is ignored, and the returned
loglik has one element.

Supplied dispersions are used AS-IS: not re-estimated, and not
winsorised -- the caller owns them, and in the intended use they come
out of a previous fitNB run. They need not come from an identical
design: dispersions estimated on a design nested in (or equal to) the
fitting design are appropriate -- e.g. pooled across a coarser
per-patient model -- which errs conservative.

Validation: numeric, length nrow(Y), finite and strictly positive
(psi feeds size = 1/psi). `psi` composes with `offset`; supplying both
is the motivating downstream use (spiDE stage 1: raw-count fit with the
normalisation linear predictor as a fixed offset and a dispersion pooled
per patient). psi = NULL is a strict no-op, verified as identical output
on a shared seed.

Tests in tests/testthat/test-fitNB-psi.R (30 assertions). The load-
bearing ones, chosen against the deceptive failure mode where psi is
validated and echoed back but the fit runs at something else:

  * the returned loglik must equal the literal NB log-likelihood at the
    returned coefficients and the SUPPLIED psi -- this pins which psi
    the fit actually ran at;
  * fits at p0 and 2*p0 must differ (identical alphas mean the supplied
    psi never reached the IRLS), and the working-weight Wald SEs at
    2*p0 must exceed those at p0 for every gene and coefficient, the
    direction implied by w = mu/(1 + psi*mu) decreasing in psi;
  * refitting at an estimated psi reproduces the original fit within
    IRLS stopping slack (measured ~4e-3; the inner loop's relative-
    loglik tolerance of 1e-4 is not reachable from fitNB()'s arguments,
    so warm- and cold-started fits stop at different points near the
    same optimum -- documented in the test);
  * the pinned-column offset equivalence holds at a supplied psi to
    ~1e-15, exercising the psi bypass and the offset threading together.

Both deliberate breakages are confirmed caught, with the injection
itself verified before each run (deparse at width 500 + a stopifnot
that the substitution took -- last round a line-wrapped deparse made a
mutation silently not apply): (A) supplied psi ignored, outer loop runs
anyway -> psi identity, loglik identity and the p0-vs-2p0 divergence all
fail; (B) psi validated and returned but a different vector handed to
the IRLS -> the psi identity check alone stays green, exactly the
deceptive case, and the loglik identity (off by 4.4e+2) and divergence
(exactly 0) fail.

Existing suite unchanged: 339 passed / 17 skipped, bit-identical per
file to the pre-change baseline. R CMD check: 0 errors, 0 warnings,
0 notes, before and after.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 0791ad9f0713928bc69d674a2336df0c869cb4c3

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun133.hpc.net.uq.edu.au> 

      Date: 2026-08-13 00:28:26 +1000

      Commit message:


	  
		
 Add a fixed offset to fitNB() and calculateMu()

Both gain an `offset` argument: a genes x cells matrix added to each
gene's linear predictor with its coefficient held at 1, so that
log(mu) = gmean + tcrossprod(alpha, W) + offset.

Why an offset and not another column of W. The motivating consumer
(spiDE's two-stage estimator) needs to remove a library-size effect
SpaNorm has already estimated while modelling all of the biology itself,
from scratch. Added as a design column, that LS term's coefficient floats
during the fit and can absorb biology correlated with sequencing depth --
and depth does correlate with biology, which is exactly why SpaNorm's own
LS spline needs a biology anchor to keep from over-correcting. Held at
exactly 1, the known effect is subtracted rather than re-estimated, and
that leak is closed.

The offset enters in four places, not one:

  * the log-likelihood (.blockedNBLoglik);
  * the IRLS alpha update, where the working response becomes
    Z - gmean - O, since the offset's contribution is not being fitted;
  * the is.spanorm gmean fold, for the same reason;
  * edgeR::estimateDisp()'s own offset -- the easiest of the four to
    miss and the most quietly damaging, because dropping it leaves the
    coefficients plausible while inflating every gene's dispersion, and
    with it the Wald variances a downstream caller derives from psi.

It is subset by `idx` alongside the counts and sliced per gene-block in
step with them. All offset slicing goes through one helper
(.blockOffset), because a mis-sliced offset neither errors nor fails to
converge -- it converges to the wrong answer.

offset = NULL is a strict no-op, so every existing caller is untouched:
all 15 calculateMu() call sites, SpaNorm(), SpaNormSVG(), SpaNormPCA().
The existing test suite passes unchanged, 287 passing expectations and
16 GPU skips, identical before and after.

New tests in tests/testthat/test-fitNB-offset.R. The two that matter:

  * EQUIVALENCE. Fitting design [(1+c)w, x] with no offset, and design
    [w, x] with offset c*w, are the same model written two ways; both
    start from the same alpha initialisation, so every iteration must
    coincide -- same log-likelihood, same dispersions, same fitted means
    -- while the coefficients differ by exactly what a unit coefficient
    on the offset accounts for. Holds to ~1e-15, including for the Wald
    standard errors built from the fit, and separately for a gene-varying
    offset and in the small-n regime the downstream consumer runs in.
  * MULTI-BLOCK. A gene- and cell-varying offset gives identical results
    (~1e-15) at 1, 2 and 5 gene-blocks and in the one-gene-per-block
    limit.

Both carry controls, because an identity that holds trivially proves
nothing: a fit frozen at its initialisation would satisfy either one, so
each asserts the fit moved; and an offset rotated by one gene, or by one
cell, must move the answer (it does, by ~1e-1 against a 1e-10 tolerance).

Each site above was then broken deliberately, one at a time, to confirm
the assertions fail when it is: dropping the offset from the log-mean or
from the working response breaks the equivalence by 1.9; dropping it from
the gmean fold breaks gmean by 9.8e-3 against a 1e-8 tolerance; and
dropping it from the dispersion offset -- either inside the helper or by
never passing it at the call site -- moves psi by 0.27 and the Wald
standard errors by 23%, while leaving the coefficients within 1%. That
last one is why the equivalence fixture uses a CELL-VARYING offset: under
a constant offset, edgeR's per-gene intercept absorbs it, the dispersion
step is genuinely indifferent to whether it is passed at all, and an
assertion on psi cannot fail. The first version of these tests had that
blind spot; the mutation pass is what found it.

The GPU path is IMPLEMENTED BUT UNVERIFIED. It is written through the
same backend-agnostic helpers as the rest of the fit (toGPUMatrix,
add_vec_mat_gpu, tcrossprod_gpu), so it should follow, but no h100 was
free to run the fp64 smoke and no accelerator has ever executed this
code. test-fitNB-offset.R carries a skip_if_no_gpu()-guarded
blocked-vs-unblocked test that will exercise it on the first run on a
real device; until that passes, treat the GPU path as unproven. Use an
h100-class device to check it: fp64 digamma inside the dispersion step
fails on an a100, and not at startup, so a toy fit green-lights it
wrongly.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 1fa360e159a2a1368ce87243eb3cc776fb0011c2

      Author:  dbhuva <d.bhuva@uq.edu.au> 

      Date: 2026-07-27 12:51:43 +1000

      Commit message:


	  
		
 Fix getGPUMemoryBudget() reporting the physical GPU's memory instead of the assigned MIG slice's

nvidia-smi's `-i` flag, given a bare integer index, targets its own
system-wide physical-GPU enumeration -- unaffected by CUDA_VISIBLE_DEVICES.
Under NVIDIA MIG partitioning the job scheduler confines a process via
CUDA_VISIBLE_DEVICES=MIG-, but nvidia-smi never sees that
restriction, so `-i=<torch::cuda_current_device()>` silently queried the
whole card's free memory rather than the assigned slice's -- a many-fold
overestimate that fed directly into downstream batch-sizing and caused
real CUDA OOMs (reported via spiDE on a MIG-partitioned A100).

torch's R package exposes no MIG-aware alternative: cuda_memory_stats()/
cuda_memory_summary() report only PyTorch's own allocator bookkeeping, and
cuda_get_device_properties() isn't exported. Fixed by resolving the
correct nvidia-smi `-i` target through CUDA_VISIBLE_DEVICES instead of the
bare index (also fixes a latent non-MIG bug where a job restricted to
e.g. CUDA_VISIBLE_DEVICES=2,3 would have queried physical GPU 0). Adds
setGPUMemoryBudget() so callers can bypass auto-detection entirely when
it remains unreliable.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: SpaNorm

      Commit: 186ffd3682b77a255839d843fcd2cb8ba90dd257

      Author:  dbhuva <d.bhuva@uq.edu.au> 

      Date: 2026-07-24 21:26:21 +1000

      Commit message:


	  
		
 Fix R CMD check failure: guard getBackendDtype()'s example against a missing Lantern install

getBackendDtype() calls torch::torch_float64()/torch_float32() unconditionally
(unlike every other torch-touching helper in this file, which gates on
checkGPU()), so its own standalone example crashed R CMD check on the macOS
CI runner where torch is installed but its native Lantern library isn't
loaded -- halting the combined example script before any function
alphabetically after it could run. Gate the example the same way every
other GPU-aware example in this file already does.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: 0d5eaea99a55204c5af8832356ddb2a7709e2a34

      Author:  dbhuva <d.bhuva@uq.edu.au> 

      Date: 2026-07-24 19:48:16 +1000

      Commit message:


	  
		
 Export the generic GPU device/tensor layer for downstream packages

spiDE calls SpaNorm::calculateMu()/invert_mat() directly for its own
per-gene Wald inference, outside fitNB(), so it never benefited from
the memory-aware GPU blocking added to fitNB()'s internal IRLS loop.
Exports the reusable device/dtype resolution, memory-budget detection,
tensor conversion, and generic linear-algebra helpers from gpuFunctions.R
(no NB-specific logic), adds a batched invert_mat_batched() for
per-gene/per-feature covariance workloads SpaNorm itself never needs
(its own model shares one coefficient across all genes), and makes
calculateMu() dispatch to the accelerator when requested (backend
defaults to "cpu", preserving its exact prior behaviour for existing
internal callers that assume a plain matrix comes back).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
 
    
  
    

      Package: SpaNorm

      Commit: b32dadec2cd8593d1fd5178468acb53579f58ff9

      Author:  dbhuva <d.bhuva@uq.edu.au> 

      Date: 2026-07-24 09:26:29 +1000

      Commit message:


	  
		
 Add memory-aware gene-blocked GPU fitting to avoid OOM on limited-VRAM GPUs

Auto-detects available accelerator memory (nvidia-smi for CUDA, a
system-memory fraction for MPS) and fits the IRLS model in contiguous
gene-blocks sized to the budget, overridable via a new gpu.mem.budget
parameter. The blocked and non-blocked code paths are unified into a
single implementation (a single whole-gene block when the problem
already fits), removing ~150 lines of duplicated tensor-fitting logic.

Verified against the pre-existing CPU/GPU baseline and a block-count
sweep on both real (HumanDLPFC) and simulated data: results match
within a small floating-point tolerance from summation-order
differences; CPU results are unaffected regardless of block count.

Bump version to 1.7.5; document the feature in NEWS.md and the
vignette's "Scaling to large datasets" section.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
 
    
  
    

      Package: gDRimport

      Commit: 72351b459390999483042ee1088304a14b6e6e38

      Author:  Arek Gladki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-10-19 10:56:38 +0200

      Commit message:


	  
		
 Merge pull request #128 from gdrplatform/GDR-3637

fix: let an explicit instrument read .tsv results files 
    
  
    

      Package: gDRimport

      Commit: 1d2257ab23f442ef6f001210676738d347efd95d

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-10-16 11:45:12 +0200

      Commit message:


	  
		
 docs: say when a .tsv results file is read as long_tsv
 
    
  
    

      Package: gDRimport

      Commit: f8d58c6aed46c0a4ad5cf0b888b707935146499c

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-10-14 08:17:52 +0200

      Commit message:


	  
		
 fix: let an explicit instrument read .tsv results files
 
    
  
    

      Package: exploreSE

      Commit: e5c572753b226e6228473ef30d4e510004b23688

      Author:  Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com> 

      Date: 2026-10-19 10:06:58 +0200

      Commit message:


	  
		
 readme and vigentte fixes
 
    
  
    

      Package: exploreSE

      Commit: 13b7940605474486251404029426282870d515e8

      Author:  Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com> 

      Date: 2026-10-19 09:49:41 +0200

      Commit message:


	  
		
 edit readme
 
    
  
    

      Package: MGnifyR

      Commit: 60edae14f4438ffab5d05c5f3cfc0ffd2b37e9d8

      Author:  Tuomas Borman <tvborm@utu.fi> 

      Date: 2026-10-19 11:02:40 +0300

      Commit message:


	  
		
 Document package with "_PACKAGE" instead of deprecated @docType

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    

      Package: MGnifyR

      Commit: cd8da38b488c8e4b338c8c09109f6d1a622db86e

      Author:  Tuomas Borman <tvborm@utu.fi> 

      Date: 2026-10-19 10:58:55 +0300

      Commit message:


	  
		
 getResult returns NULL with a warning instead of failing when no data could be fetched
 
    
  
    

      Package: SpatialFeatureExperiment

      Commit: 5dccfd78b644f8d31959f95e5dacfb0d5621d9a6

      Author:  Lambda Moses <lambda.calc29@gmail.com> 

      Date: 2026-10-19 15:49:36 +0800

      Commit message:


	  
		
 Still prefer scater for PCA
 
    
  
    

      Package: SpatialFeatureExperiment

      Commit: ea1913f9a9338a216cf01df7ee08a5b5525f88a3

      Author:  Lambda Moses <lambda.calc29@gmail.com> 

      Date: 2026-10-19 15:49:16 +0800

      Commit message:


	  
		
 Fixed image misalignment in Visium
 
    
  
    

      Package: SpatialFeatureExperiment

      Commit: 17f9946d671e40864454be55dc725339dafdbaed

      Author:  Lambda Moses <lambda.calc29@gmail.com> 

      Date: 2026-10-09 17:25:51 +0800

      Commit message:


	  
		
 Draft
 
    
  
    

      Package: tidySummarizedExperiment

      Commit: cb3f3a8fa4bbe1e0591ef52b43137036dcb4c918

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-10-19 11:44:37 +1030

      Commit message:


	  
		
 Merge pull request #126 from tidyomics/copilot/fix-filter-non-syntactic-names

Preserve non-syntactic colData names in filter() 
    
  
    

      Package: tidySummarizedExperiment

      Commit: 1bd6062d0e95d0f46fad2de2c368c6b77399c42a

      Author:  copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> 

      Date: 2026-08-20 04:56:40 +0000

      Commit message:


	  
		
 Preserve non-syntactic colData names in filters

Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
 
    
  
    

      Package: tidySummarizedExperiment

      Commit: 28a5bbd10c9fef8d24fea8f2bdd9446b273473e5

      Author:  copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> 

      Date: 2026-08-20 04:49:41 +0000

      Commit message:


	  
		
 Initial plan
 
    
  
    

      Package: OmicsMLRepoR

      Commit: 336d44dcee49cad9d655c08e54ce3a1aa5ee0035

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-10-18 20:51:26 -0400

      Commit message:


	  
		
 version bump

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: OmicsMLRepoR

      Commit: 68b948dd348d7439c1475c7bb7506adefed362ef

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-10-18 17:39:54 -0400

      Commit message:


	  
		
 add citation information for the Database paper

Add inst/CITATION with the bibentry for Long et al. (2026), Database
2026:baag027, so citation("OmicsMLRepoR") returns the paper rather than
R's auto-generated package default. Add a matching Citation section to
the README.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: AnnotatedBCGEData

      Commit: 78b87775b3157092ebc4f84cfea9aca0abe6b0f3

      Author:  Heidi <heidi.climber@gmail.com> 

      Date: 2026-10-18 15:05:54 -0600

      Commit message:


	  
		
 updates to final mapping files
 
    
  
    

      Package: systemPipeRdata

      Commit: 1752dc0d29f7aa254cca06352dd0e11cc015b8ad

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-18 13:22:04 -0700

      Commit message:


	  
		
 Version bump 2.17.2
 
    
  
    

      Package: systemPipeRdata

      Commit: 3de4470146d822653d55072ec5877cf5e6ae0eab

      Author:  tgirke <tgirke@citrus.ucr.edu> 

      Date: 2026-10-18 13:22:04 -0700

      Commit message:


	  
		
 Fix BiocCheck errors: Authors@R, install.packages, runnable examples; ExperimentData biocViews

- DESCRIPTION: Authors@R replaces Author/Maintainer; biocViews switched to
  ExperimentData terms (BiocCheck classified the package as Software);
  crayon added to Suggests (used via crayon:: in vignettes)
- R/dataenv.R: drop unreachable install.packages('remotes') (remotes is
  in Imports); NAMESPACE: drop utils::install.packages import
- NAMESPACE: import stats::setNames
- Runnable examples for genWorkenvir_gh, getParam_gh (small GitHub repos,
  written to tempdir()) and getData_gh (no-manifest case, no download);
  getSPRdata example wrapped in if (interactive()) (175MB download)
 
    
  
    

      Package: gDRcore

      Commit: f2cfbde8ceee48a4a0eddb842d24835b50987ced

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-10-18 22:24:37 +0200

      Commit message:


	  
		
 Merge pull request #215 from gdrplatform/GDR-3701

feat: record the import step in the SE provenance 
    
  
    

      Package: gDRcore

      Commit: 967bff8b86514dca87d9b33f34e0f9755435e0b7

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-18 18:47:11 +0200

      Commit message:


	  
		
 Merge branch 'GDR-3699' into GDR-3701

# Conflicts:
#	DESCRIPTION
#	NEWS.md
 
    
  
    

      Package: gDRcore

      Commit: 6582d86b764d673e1886a2922162fe05e539e311

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 20:16:55 +0200

      Commit message:


	  
		
 Merge branch 'GDR-3699' into GDR-3701
 
    
  
    

      Package: gDRcore

      Commit: f3c3b6d7fd64bf05b24d06cab830dc88ee903178

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 12:52:49 +0200

      Commit message:


	  
		
 chore: bump version to 1.11.21 and update NEWS
 
    
  
    

      Package: gDRcore

      Commit: 7d3805a9501c778d630dd8e8ca7cb6a828936e08

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 12:52:49 +0200

      Commit message:


	  
		
 test: cover the import step and merge_data() keeping the record
 
    
  
    

      Package: gDRcore

      Commit: 5cdfee34cc1f3eb81aee49532cd6253ffc8ae413

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 12:52:49 +0200

      Commit message:


	  
		
 feat: record the import step from the gDRimport record of the input data
 
    
  
    

      Package: Rsubread

      Commit: 782507abca1ef2223906ed327d4e27ae4d93bb52

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-10-19 07:23:21 +1100

      Commit message:


	  
		
 removed a warning caused by unused variable in Makevars.Linux.
 
    
  
    

      Package: gDRcore

      Commit: 1a3b068e1d8d57b5b1d54791c007792f379b4d7f

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-10-18 21:59:45 +0200

      Commit message:


	  
		
 Merge pull request #214 from gdrplatform/GDR-3699

feat: record the processing steps in the SE provenance 
    
  
    

      Package: gDRcore

      Commit: 2badd81d257c9648241c1a2921f86c21df7428f5

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-18 18:43:50 +0200

      Commit message:


	  
		
 Merge branch 'GDR-3698' into GDR-3699

# Conflicts:
#	DESCRIPTION
#	NEWS.md
 
    
  
    

      Package: gDRcore

      Commit: e7cad49ab271b18c7cad9a26b2065e2b88e39de9

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 20:16:54 +0200

      Commit message:


	  
		
 test: check the message about missing GR values
 
    
  
    

      Package: gDRcore

      Commit: 4496b42c8a811e2b112aa330757b2e2e9bd20189

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 20:16:54 +0200

      Commit message:


	  
		
 fix: log the cell lines without a GR value as one short line
 
    
  
    

      Package: gDRcore

      Commit: fbbf615d07749e771885abd4f0fbe4c9443fdcef

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 20:15:46 +0200

      Commit message:


	  
		
 Merge branch 'GDR-3698' into GDR-3699
 
    
  
    

      Package: gDRcore

      Commit: 4f5f1520bca14b1ffd000778690c9d5d1313ddca

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 10:13:31 +0200

      Commit message:


	  
		
 test: check that re-running the pipeline on its output records the same steps
 
    
  
    

      Package: gDRcore

      Commit: ff557e11aa48f5f45efb71995e3b811cbe58b566

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 10:13:31 +0200

      Commit message:


	  
		
 fix: keep the input format out of the create step so a re-run from an MAE matches
 
    
  
    

      Package: gDRcore

      Commit: 7b0dfbceee41360c6b5a059d2a171485166b8246

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 09:22:57 +0200

      Commit message:


	  
		
 chore: bump version to 1.11.20 and update NEWS
 
    
  
    

      Package: gDRcore

      Commit: 7c68dc354db29a1c20666ff063ffb6a7bdd61822

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 09:22:57 +0200

      Commit message:


	  
		
 test: cover the provenance of the processing steps
 
    
  
    

      Package: gDRcore

      Commit: 43a0ad788ad0a3d884a89e85baffd61625e37963

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 09:22:57 +0200

      Commit message:


	  
		
 feat: record the create, normalize and average steps in the provenance
 
    
  
    

      Package: gDRcore

      Commit: 173f54b339a22ca7ae6b4ca143de1f6a3b23c842

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 09:22:57 +0200

      Commit message:


	  
		
 refactor: share the GR method choice between calculate_GR_value() and normalize_SE()
 
    
  
    

      Package: GExPipe

      Commit: ab9f23fa643a891feb3964ac5821a29607a6a635

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-10-19 00:53:08 +0500

      Commit message:


	  
		
 Sync with GitHub main: GExPipe 0.99.116
 
    
  
    

      Package: gDRcore

      Commit: 7a3913712a7368faa2b2295c819a960ec056ee10

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-10-18 21:32:26 +0200

      Commit message:


	  
		
 Merge pull request #213 from gdrplatform/GDR-3698

feat: record the provenance of gDRcore fits 
    
  
    

      Package: gDRcore

      Commit: 21c3b541e19b3bbf05a01c68da8b1d4b30a9790d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-18 18:39:54 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into GDR-3698

# Conflicts:
#	NEWS.md
#	tests/testthat/test-fit_SE.R
 
    
  
    

      Package: gDRcore

      Commit: fe8c12366a9e9bb889b76f7c3b1e760961644a32

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 20:15:18 +0200

      Commit message:


	  
		
 test: check that fit_SE.timecourse() rejects fit_args with the default fit
 
    
  
    

      Package: gDRcore

      Commit: 9e1dff1f31c65488577677f42cad7e5f6a2bb72b

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-15 20:15:18 +0200

      Commit message:


	  
		
 fix: reject fit_args in fit_SE.timecourse() when the default fit would drop them
 
    
  
    

      Package: gDRcore

      Commit: b3cf69aa5bac08df1d5b52b4c8b635ca8ec76af8

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-14 16:34:06 +0200

      Commit message:


	  
		
 chore: bump version to 1.11.19 and update NEWS
 
    
  
    

      Package: gDRcore

      Commit: deca4236bbf0b5d8c05f25f24f8b298cfdfe256f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-14 16:34:06 +0200

      Commit message:


	  
		
 test: cover the provenance of single-agent, combination and time-course fits
 
    
  
    

      Package: gDRcore

      Commit: a61dd7ea30a0669200e09b3786c61229ff150c0d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-14 16:34:05 +0200

      Commit message:


	  
		
 docs: explain fit provenance in the custom fitting vignette
 
    
  
    

      Package: gDRcore

      Commit: 11829cf6b6a8c47085850fbf4014a4bf8a8b2a51

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-10-14 16:34:05 +0200

      Commit message:


	  
		
 feat: describe the combination and score functions in their recipes
 
    
  
  


</div>

</div>