forgot to remove one data_dir stanza
 

 Merge pull request #335 from kvittingseerup/devel

Fixed bug in genomic_domain_position 

 BiocCheck fixes
 

 Fixed bug in genomic_domain_position
 

 IDR consequences bug fix (#332)

* IDR consequences calculation bug fix

* Updated example data 

 Merge branch 'master' into devel 

 Proteomics data handling and predefined switches import (#329)

1. Added function importPredefinedSwitches()
2. Added handling proteomics data imported from predefined switches:
    - switchAnalyzeRList gets new flag omicDataType, set to 'transcriptomics' or 'proteomics'
    - importGTF() reads only CDS instead of exon
    - CPAT/CPC2 are disabled
    - consequences that are based on non-coding regions are disabled
    - proteomics mode is added to high-level functions (Part1, Part2, and Combined)
3. Fixed phase reading from GFF/GTF files 

 Merge pull request #326 from kvittingseerup/devel

Merge from devel 

 see NEWS (#324)

* Critical bug fixes

* Documentation mismatches fixes

* Stale links fixes

* analyzeInterProScan implementation

* Stale references fixes

* Added a contributor 

 Merge pull request #322 from chunxubioinfor/update-citations-v2

Update package citation to IsoformSwitchAnalyzeR v2 

 Merge pull request #309 from elena-iri/devel

Added R-CMD-check github actions workflow and fixed bugs related to issue #307 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 Added R-CMD-check workflow
 

 Merge pull request #305 from elena-iri/devel

Added trailing new lines to man files 

 Merge pull request #300 from elena-iri/feat_type_casting

Feat type casting 

 Added autocast of numerica variables warnings and switch
 

 Tutorial_iCluster2b_scRNA+ATAC.Rmd update
 

 add mergeRegion.R, mergeRegion.Rd
 

 update tutorials
 

 Force an empty line between writeRmd calls, streamline output suppression.
 

 Streamlined report generation and compilation.

- Make sure to add trailing lines for non-terminating writeRmd calls, otherwise
  some aspects of markdown formatting might not work.
- Directly suppress all output when compiling the report.
- Some rewording and typo fixes for the normalization section.
- More symmetric handling of the lfc.threshold=NULL case for runVoom.
 

 Optionally append an empty line in writeRmd.

This is useful for pipeliens that perform multiple calls to writeRmd and want
to make sure that there's some space between the content added in each call.
 

 Merge pull request #285 from waldronlab/amr-vocab

attributes.tsv: resistance to beta-lactam and resistance to carbapenems (1.7.9) 

 attributes.tsv: resistance to beta-lactam and resistance to carbapenems (1.7.9)

Names bugphyzzExports gives these AMR terms when it pairs resistant and
sensitive values (waldronlab/bugphyzzExports#83).

Co-authored-by: Claude Code <noreply@anthropic.com>
 

 Stop importing NMF so loading the namespace does not change search path

NMF's .onLoad attaches Biobase (and thereby BiocGenerics and generics).
Because NAMESPACE had importFrom(NMF, aheatmap), loading clusterExperiment
changed the search path, which R CMD check reports as a WARNING for
data("rsecFluidigm") (the stored object references the clusterExperiment
namespace). All NMF calls already use NMF::, so drop the import.

This exposed base-R and Biobase functions that were used without being
imported (they resolved only via NMF's side effect). Import them explicitly
in the new R/imports.R and add utils and Biobase to Imports.

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

 Use limma::voomLmFit for DEMethod="limma-voom"

limma (>= 3.99.x, Bioc 3.24) now emits a message from voom() recommending
voomLmFit, which caused expect_silent() failures in test-getBestFeatures.R
on the Bioconductor build. Replace voom() + lmFit() with voomLmFit() in
getBestFeatures, update docs, vignette and NEWS, require limma (>= 3.99.3),
and bump version to 2.33.1.

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

 1.99.54: continuous conditions (slope of each pair's effect) and an overall test for more than two conditions

spicy() (cell method) takes a numeric condition with more than two values as continuous: each pair's per-image
effect is regressed on it in the frailty model (Paule-Mandel tau2 under the design), the slope tested by CR2 with
Satterthwaite df; covariates and adjustAbundance as for groups. With more than two groups, each pair has an
overall test: the CR2 Wald test of every level equal to the reference with the HTZ F (Tipton and Pustejovsky
2015), new design_joint_test in the core (checked against a dense reference and clubSandwich::Wald_test).
spicyBoxPlot() draws a scatter with the fitted slope, signifPlot() halves at the mean -/+ 1 SD, calibrationCheck()
counts the overall test. Two-condition results are unchanged.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0138g2Rr8cawMNxSNRUG9zyT
 

 1.99.52: no M_PI in the core (MSVC, spicyr-py Windows build)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0138g2RrVSxr2MSzg4HTEgAP
 

 1.99.50: self-pair allocation variance with a radius from 50 sampled cells per image by default (selfVariance = "sampled"; "exact", "geometricSampled", "geometric"; selfVarianceCells)

Counting shared neighbours for every cell grows with cells x neighbours^2: NeoTRIP at r = 200 took 13 min exact,
72 s sampled, with self-pair p-values within 2% and no discovery changed (r = 50, 100, 200). The sample is seeded by
each image's size and first cell, so results are reproducible and the same in R and Python. Cross pairs, the count
effect and kNN are unchanged.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0138g2RrVSxr2MSzg4HTEgAP
 

 R-path tables: columns filled when a pair has no image rows (more than two conditions); side NA for untested pairs

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Xua3VYycDCVczTsN6gfg93
 

 1.99.48: help, vignette and NEWS for the exact self-pair variance, room guard, standard CR2 and not_tested

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Xua3VYycDCVczTsN6gfg93
 

 Use the exact ZINB score for nonzero counts in the weight functions
 

 Organism names from the Ensembl organisms species.json

The Ensembl species page is not available any more, and the translation
of organism names failed (#130). The Ensembl organisms now come from
species.json on the EBI FTP, with more than 11,000 organisms. On build
servers, a slim copy at rescued.omnipathdb.org is the first choice.

The Ensembl organism IDs are the BioMart dataset names, from a table in
the package: BioMart does not change any more, and the IDs derived from
the scientific names collide for the new, larger set of organisms.

If one resource of organism names fails, the others are still used, and
the incomplete table is not saved to the cache. The database cache keys
contain the package version, so an upgrade builds the databases again.

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

 fix: add_sequence() on new StringSet objects

new versions of StringSet objects set sequence and names during their
as.data.frame method unlike before, so we need to construct the record
differently for add_sequence() to work the same.
 

 bug fix: restore vignette engine so the vignette is built
 

 bug fix: size-factor alignment and numerical stability of weights

- Keep size factors aligned with their samples in two-group tests.
- Improve numerical stability of NB/ZINB weight estimation, including
  glm.nb dispersion fits and large dispersion values.
- Correct the variance used in the mean test.
- Add regression tests.
 

 Merge pull request #284 from waldronlab/bioc-3.24-prep

Release prep for Bioconductor 3.24 (1.7.8) 

 Release prep for Bioconductor 3.24 (1.7.8)

- importBugphyzz(): read only bugphyzz_*.csv from the Zenodo zip; the
  archive now also contains sources/*.csv.gz
- makeSignatures(): "bugphyzz:" prefix for discrete signatures (#256)
- attributes.tsv: fix group typo, plural, trailing semicolon and the
  unused mixed-case group on the butyrate row (#281)
- skip download tests when offline; physiologies() example in dontrun (#266)
- rlang listed in Imports only

Co-authored-by: Claude Code <noreply@anthropic.com>
 

 Merge pull request #280 from waldronlab/bacdive-id-character

BacDive import: read id columns as character (fixes devel test failure) 

 Add attribute_synonyms.tsv and apply it in physiologies() (1.7.7)

Maps source terms (BacDive shape and aerophilicity terms, 2020 Bergey's
"vibriod cell", biosafety strings, disease association spellings) to the
controlled vocabulary in attributes.tsv before the export validates them.
Only TRUE rows are mapped, since some mappings are lossy. Adds a test that
every discrete value from every sheet and source maps.

Closes #264, closes #229.

Co-authored-by: Claude Code <noreply@anthropic.com>
 

 Merge pull request #278 from waldronlab/ncbi-refseq-source

Add NCBI_RefSeq to attribute_sources.tsv (1.7.6) 

 README and NEWS: name the NCBI RefSeq source and both bugphyzzExports links

Co-authored-by: Claude Code <noreply@anthropic.com>
 

 Merge pull request #277 from waldronlab/readme 

 README: document the pipeline and related repositories

Co-authored-by: Claude Code <noreply@anthropic.com>
 

 Split only multi-valued BacDive columns; test the split and the cache

The ';' split now applies to the twelve columns where references can
disagree, leaving halophily, the metabolite columns and the paired
temperature and biosafety columns alone. Fixture covers a two-valued
oxygen tolerance cell, an untouched halophily cell, and a cached second
read. From review of #276.

Co-authored-by: Claude Code <noreply@anthropic.com>
 

 NEWS: list the user-facing changes in 1.7.4

Co-authored-by: Claude Code <noreply@anthropic.com>
 

 importBugphyzz(): separate MCC and R2 thresholds, deprecate v (#271)

* importBugphyzz(): separate MCC and R2 thresholds, deprecate v

Defaults mccThreshold = 0.7 and r2Threshold = 0.5 match the manuscript;
the old v = 0.8 kept ASR for four attribute values and no numeric
traits. excludeRarely now also drops "never". Validation joins are
case-insensitive so attributes such as "COGEM pathogenicity rating"
are no longer dropped. Closes #263.

* Address review: tests on mocked inputs, NA checks

Move the ASR filter into .filterAsr() and add tests that mock
.downloadResource() and .validationData(), covering the per-type
thresholds, the case-insensitive join, v deprecation, excludeRarely and
threshold validation. Reject NA thresholds with a clear message and keep
dropping rows with NA Frequency, as before.

* NEWS: note that unvalidated ASR rows are dropped

* Join whole-attribute validation rows only for binary and numeric

Same guard as waldronlab/bugphyzzExports#67: multistate values repeat across physiologies, so binary and numeric attributes match only rows with physiology == attribute.

---------

Co-authored-by: Claude Code <noreply@anthropic.com> 

 .Rbuildignore: exclude inst/backup and unused workflow figures

Co-authored-by: Claude Code <noreply@anthropic.com>
 

 Enable Zarr v2 VLen-UTF8 test datasets (#14) 

 gbCounts: nombres de junctions robustos y error informativo
 

 Add st_as_sf()/st_crs(), make st_as_sfc() materialize to match sf

A user expected st_as_sfc() to collect a lazy DuckDBTable's geometry
column into memory as an sfc; instead it stayed lazy, building more
SQL. She then tried st_collect() instead and found it combined every
row into one MULTIPOINT via DuckDB's own ST_Collect aggregate - a
different operation whose name happens to collide with the "collect
into memory" expectation. Neither materializes; nothing in the
package did.

Add st_as_sf(x, ..., geom = "geometry"): materializes a DuckDBTable/
DuckDBDataFrame into an in-memory sf object, one feature per row.
Converts every GEOMETRY-typed column (not just the active one, so a
second geometry column doesn't survive as inert raw WKB), substitutes
real empty-geometry WKB for SQL-NULL cells, and forwards ... to the
inner sf::st_as_sf() call.

Add st_crs(x, geom = "geometry") for DuckDBTable/DuckDBDataFrame and
st_crs(x) for DuckDBColumn: reads a lazy geometry column's CRS via
DuckDB's own ST_CRS SQL function without collecting - needed by
st_as_sf(), and something the package had no way to do at all before.

Having shipped st_as_sf() as materializing while st_as_sfc() stayed
lazy left two sibling sf generics disagreeing on the one axis they
never otherwise differ on, which is the direct, confirmed root cause
of the user's whole chain of confusion. In plain sf, st_as_sfc() and
st_as_sf() are both always materializing; nothing in this package
internally relied on st_as_sfc()'s laziness either (every real call
site already collected first, then called plain sf::st_as_sfc() on
the in-memory result). So: flip st_as_sfc.DuckDBTable/.DuckDBColumn
to materialize too, matching upstream sf exactly, package-wide, no
exceptions. A column already GEOMETRY-typed is collected and tagged
with its own st_crs(), honoring an explicit non-NA crs= override the
same way plain sf does; a WKT/GeoJSON/WKB column not yet
GEOMETRY-typed is collected as-is and handed to plain sf::st_as_sfc()'s
own parsers, substituting an empty geometry for NA/NULL cells on
either path. The still-lazy, SQL-side parse (for chaining further lazy
spatial ops at out-of-core scale without collecting) remains
available, just honestly named: sql_call(x, "ST_GeomFromText") (or
"ST_GeomFromWKB"/"ST_GeomFromGeoJSON") instead of borrowed from a
generic whose name promises something else. This is a deliberate
breaking change; the package is still pre-1.0/devel.
 

 Merge remote-tracking branch 'upstream/devel'
 

 Update force nbSim to be set at 1 and other small validations change.
 

 Update function specificSNVColKeep
 

 Merge branch 'RAIDS2preliminary' of https://github.com/belleau/RAIDS into RAIDS2preliminary
 

 Merge pull request #18 from adeschen/RAIDS2preliminary

Adding unit tests for RAIDSparam class 

 Merge pull request #17 from adeschen/RAIDS2preliminary

Update vignette 

 Merge pull request #16 from adeschen/RAIDS2preliminary

Raids2preliminary 

 Update vignette
 

 Update vignette
 

 Merge pull request #15 from adeschen/RAIDS2preliminary

Raids2preliminary 

 Update vignette
 

 Merge pull request #14 from adeschen/RAIDS2preliminary

Raids2preliminary 

 Update vignette
 

 Update vignette
 

 Merge pull request #12 from adeschen/RAIDS2preliminary

Raids2preliminary 

 Update vignette
 

 Merge pull request #11 from adeschen/RAIDS2preliminary

Raids2preliminary 

 Update vignette
 

 25 becomes chr25
 

 Merge pull request #10 from adeschen/RAIDS2preliminary

Update vignette 

 Update founding information
 

 Update vignette
 

 Merge pull request #9 from adeschen/RAIDS2preliminary

Raids2preliminary 

 Merge pull request #8 from adeschen/RAIDS2preliminary

Raids2preliminary 

 Update vignette
 

 Merge pull request #7 from adeschen/RAIDS2preliminary

Raids2preliminary 

 Merge pull request #14 from belleau/RAIDS2preliminary

Raids2preliminary 

 Merge pull request #6 from adeschen/RAIDS2preliminary

Update vignette 

 Merge pull request #5 from adeschen/RAIDS2preliminary

Adding Acknowledgments section 

 Adding Acknowledgments section
 

 Adding funding in the authors
 

 Merge pull request #3 from adeschen/RAIDS2preliminary

Raids2preliminary 

 Update citation section
 

 Correct typos and line length
 

 Add functions for admixture in GDS reference and a parameter cleanADMIXTUREFiles
 

 Change parametersRAIDS for RAIDSparam in documentation
 

 Update function for syntheticJSD and add call it in computeAdmixtureProportion
 

 Update function for ADMIXTURE with RAIDSparam_class
 

 Update ancestryInferencePCAKNN and cascade for RAIDSparam_class
 

 Update prepPedSyntheticRef for RAIDSparam_class
 

 Update getRefSuperPop2 for RAIDSparam_class
 

 Update profileGenoSynthesis dispatchParseReadCov generateProfileGenoCall generateProfileRawGDS2 selectForSynthetic syntheticGeno2 to RAIDSparam_class
 

 Merge branch 'RAIDS2preliminary' of https://github.com/belleau/RAIDS into RAIDS2preliminary
 

 Add getter and setter form genoType slot in RAIDSparam
 

 Update addGenotypeProfile to RAIDSparam_class
 

 Update pruningProfile2 to RAIDSparam_class
 

 Adding getter and setter for verbose in RAIDSparam
 

 Adding getter and setter for fieldPopInAnc in RAIDSparam
 

 Adding getter and setter for fieldPopInRef in RAIDSparam
 

 Adding getter and setter for kList in RAIDSparam
 

 Adding getter and setter for PCAalgorithm and eigenCount  in RAIDSparam
 

 Merge branch 'RAIDS2preliminary' of https://github.com/belleau/RAIDS into HEAD
 

 Update the computeAdmixtureProportion cascade
 

 Adding getter and setter for specificSNV in RAIDSparam
 

 Adding getter and setter for slideWindowMaxBP in RAIDSparam
 

 CHange offset to posOffset slot in RAIDSparam
 

 Adding getter and setter for pRecomb in RAIDSparam
 

 Merge branch 'RAIDS2preliminary' of https://github.com/belleau/RAIDS into RAIDS2preliminary
 

 Adding getter and setter for seqError in RAIDSparam
 

 Adding getter and setter for minCov and minProb in RAIDSparam
 

 Adding getter and setter for prefix and nbSim in RAIDSparam
 

 Adding getter and setter for sampleRef in RAIDSparam
 

 Adding getter and setter for inferenceType  in RAIDSparam
 

 Merge branch 'RAIDS2preliminary' of https://github.com/belleau/RAIDS into RAIDS2preliminary
 

 Adding getter and setter for fileReferenceAnnotGDS in RAIDSparam
 

 Merge branch 'RAIDS2preliminary' of https://github.com/belleau/RAIDS into HEAD
 

 MERGE
 

 Add commentaries in the code
 

 Adding getter and setter for paramAncestry in RAIDSparam
 

 Adding getter and setter for reference  in RAIDSparam
 

 Adding genoSource getter and setter for RAIDSparam object
 

 Adding examples in doc
 

 Adding unit test for getter and setter for the pedStudy slot in RAIDSparam class
 

 Adding getter and setter for the studyDFSyn slot in RAIDSparam class
 

 Adding getter and setter for the studyDF slot in RAIDSparam class
 

 Update tools for admixture
 

 Removing unused validation function
 

 Removing unused validation function
 

 Removing unused validation function
 

 Add function for P-matrix: prepPMatrix and writePMatrix
 

 Update RAIDSparam class and add unit tests
 

 Adding unit test for RAIDSparam() function
 

 Adding unit tests
 

 Add unit tests
 

 Adding unit tests
 

 Add unit tests
 

 Update RAIDSparam class, doc and tests
 

 Cosmetic change
 

 Update RAIDSparam class, doc and tests
 

 Update RAIDSparam class, doc and tests
 

 Update RAIDSparam class, doc and tests
 

 Update RAIDSparam function, doc, and tests
 

 Update doc for RAIDSparam()
 

 Add RAIDSparam() function
 

 Add Cancer Bioinformatics citation
 

 Add function profileGenoSynthesis adapted ancestryInferencePCAKNN
 

 Remove function for futur release avout lcwgs
 

 Update doc for paramRAIDS() function
 

 Update checkout action version 7
 

 Comment example that cause a problem because of GZIP
 

 Update doc for paramRAIDS() function
 

 Update validateParamRAIDS_subpart02() function
 

 Update paramRAIDS validation functions
 

 Update indents in functions
 

 Use selectForSynthetic in ancestryInferencePCAKNN
 

 Update man ecample for addGenotypeProfile
 

 Add the function dispatchParseReadCov
 

 Update man examples for computePCAProfile and computePCARefRMMulti2
 

 Correct variable names ingdsWrapper2_internal
 

 Renamed computePCARefRMMulti1 to computePCARefRMMulti2
 

 Update man example for prepPedSyntheticRef
 

 Update man example for computePoolSyntheticAncestryGr2
 

 Updated ecample for ancestryInferencePCAKNN
 

 Updated computeKNNRefSyn and a cascade of funtions
 

 Update man for ancestryAnalysis
 

 Change error in the name of the function selectHGDP1kgForSynthetic
 

 Update paramRAIDS doc
 

 Add missing import to readGenoVCF3() function
 

 Update doc for computePoolSyntheticAncestryGr2() function
 

 Update doc for snvListVCFRef() function
 

 Update doc for computePCAProfile() function
 

 Update doc for computeKNNProfileSubSet() function
 

 Update doc for addStudyGDSProfileSyn() function
 

 Update importFrom for functions
 

 Update doc for wrapperAncestry(), create getRefSuperPop2() doc
 

 Update import for getRefSuperPop() function
 

 Add missing imports to writeBedRef() and writeBedBimFilesProfileFilter()
 

 Change closefn to closefn.gds in addGenotypeProfile() function
 

 Add import for write_fam function in writeFamRef() function
 

 Update doc and format code for writeFamProfile() function
 

 Remove warning for not visible variables in validateParamRAIDS_subpart01() function
 

 Update check-bioc actions
 

 Update functions related to internal validation of parameters
 

 Divers update
 

 Adapted pruningProfile2 to HGDP1kgV0.1
 

 Added the function selectHGDP1kgForSynthetic
 

 Upadate for the new ref
 

 Clean up
 

 Create the function generateProfileLoadPhaseIGDS2 and cascade
 

 Add function generateProfileRawGDS2 and generateProfileGenoStdGDS2
 

 add the createProfile2 cascade of function
 

 Merge pull request #618 from adeschen/adeschen-patch-4

Adeschen patch 4 

 Merge branch 'KrasnitzLab:main' into main
 

 Update check-bioc.yaml 

 Deprecate
  - software deprecated in 3.18
 

 docs: correct benchmark numbers with density-aware fixtures

All benchmark fixtures for the .marginVars() and .check_gram_size() perf
entries on this branch were written via writeCoordArray() under
DelayedArray's dense-budgeted default block settings, not the
density-aware setAutoBlockSize(target_bytes / density) +
setAutoBlockShape("scale") correction this package's own writeCoordArray()
docs recommend for sparse arrays. Re-measured both with correctly
configured fixtures, and against deliberately uncorrected fixtures of the
same data, to check sensitivity to the resulting Parquet partition/
row-group layout directly.

.marginVars(): 1.6x-1.7x on the original 2000 x 300, ~60%-dense fixture
(vs. the previously reported 1.57x) and 1.8x-1.85x on a larger, more
realistic single-cell-like 20000 x 5000, 2%-dense fixture. The smaller
fixture writes to a single partition regardless of block settings (too
small to trigger the distortion); the larger one does differ materially
(1 file/5 row groups corrected vs. 4 files/8 row groups uncorrected), yet
the measured speedup is the same within run-to-run noise under both
layouts, consistent with the fix's benefit coming from eliminating a
redundant full-table scan rather than per-row throughput.

.check_gram_size(): 580x-840x across repeated runs (vs. the previously
reported 205x from a single run). This fix is structural (skips an entire
query execution: 1 query -> 0 queries), so it was not expected to be
sensitive to block/chunk layout, and measurement confirms this: corrected
vs. uncorrected fixture writes changed the number only from 813x to 839x,
within noise, while ambient DuckDB thread count/machine load (unrelated to
block configuration) moved it between 580x and 840x across sessions. 205x
sits below that range but is the same phenomenon, not an effect of the
block-shape methodology gap.
 

 Fixes #73
 

 Bump version
 

 Check that indices are at least whole numbers
 

 Relax restriction on chop_vec() x type
 

 Add test case from #288
 

 Merge pull request #61 from drake69/feat/organism-argument

Add the organism argument and correct the GSEA ranking (0.99.12) 

 Rank genes explicitly for GSEA in the reference pipeline

The pipeline passed only the p-value column and relied on the fallback.
It now builds stat = -log10(p) and passes scoreType = "pos", with a
comment on why the ranking has no sign: a CTD chemical set mixes genes
the chemical increases with genes it decreases, and a signed statistic
lets the two halves cancel. On this dataset the moderated t gives 172
chemicals at FDR < 0.05 against 257, and 3 of the 6 reference chemicals
against 5. Results are unchanged: 257 significant chemicals, 5 of 6.
 

 docs(vignette): describe what CAMERA adds without misjudging GSEA

The guidance on choosing a method said CAMERA controls "the inflated
false-positive rate that ORA/GSEA exhibit" on co-regulated gene sets.
Published benchmarks do not support that for GSEA: fgsea showed
unbiased p-values and a false positive rate close to 5%. The sentence
now says only what CAMERA does: it accounts for inter-gene
correlation, which ORA ignores.
 

 chore: ignore the outputs of the Yang replication script

The replication script writes the vignette tables to yang2024_outputs/
in the working directory, for comparison with the bundled copies; like
example_outputs/, it is generated, not authored. Also ignore the figure
folders rmarkdown can leave next to a vignette when a render stops.
 

 feat(vignette): compare Yang et al. and ctdR chemical by chemical

The Yang 2024 replication showed the same test on ctdR's sets and the
discovery ranking, but never put the two analyses' calls side by side.
Step 7 of the replication script now writes yang2024_comparison.tsv:
for every entry of the paper's tables, the authors' call next to ctdR's
call in discovery at 0.05, without correction (paper p-value against
ctdR's raw p-value) and with it (paper FDR within each class against
ctdR's Benjamini-Hochberg p-value over every chemical tested).

Without correction the calls agree on 82 of the 91 entries ctdR tests;
with correction 11 entries are significant only for the authors, the
cost of correcting over the whole catalogue. The vignette ends with the
two cross-counts and the entries that disagree, each explained:
parent terms enlarged with MeSH descendants, paper p-values just above
0.05, the transcription error on methyl parathion, and four entries
ctdR does not test.
 

 fix(scripts): seed the random number generator before GSEA

fgsea estimates p-values by sampling, so the full GSE311566 pipeline
returned different GSEA results on every run with the same input: up
to 0.9 in a single p-value and 266 against 271 chemicals at FDR < 0.05.
Set a seed, declared in the configuration block, right before the GSEA
call. Two seeded runs now return identical results; enrichment scores
were never affected.
 

 docs(vignette): use words instead of symbols in the size filter table

The check, cross and greater-or-equal symbols in the table of size
filters and background universes stopped the vignette from rendering
to PDF with pdflatex. Write Yes, No, "at least" and n/a instead; the
HTML vignette reads the same.
 

 docs: present the introductory vignette as an application example

The introductory vignette is renamed "ctdR: an application example",
says so at the top and points to the replication vignette for how the
package was validated. It states the question ctdR answers, which
chemicals among all those in CTD are enriched, as distinct from
verifying chemicals chosen in advance, which is what the CTD Batch
Query and CTDquerier do. The replication vignette now says that the
published counts it compares against are the output of CTD's Batch
Query.

Corrections across the vignette, README, package help and the error
raised when no CTD data have been imported: the CTD file is read as
.gz, so the instruction to decompress it is gone; downloads go through
the CTD downloads page, which now asks for a browser check; the file is
about 40 MB compressed, not "several GB"; the import reads the column
names from the header rather than skipping 27 lines; the import is no
longer described as human-only. "Updating the CTD data" explains that
CTD keeps no past releases, so the file used must be kept. The
statement that no CTD data are bundled now says what is shipped: a
synthetic example and tables of counts and p-values.
 

 feat(import): pool species by symbol with organism = "all"

organism = "all" replaces NULL as the way to keep every species, so the
call states what it does. When species other than human are imported,
and always with "all", the symbol-keyed gene sets are forced to pool
genes across species by gene symbol, as the CTD website does: a mouse
Esr1 interaction counts as ESR1. This is orthology by homonymy, stated
as such in the documentation, the vignette and the import message; it
cannot be turned off. Entrez-keyed sets keep each species' own genes.

Whether a gene takes its HGNC symbol is decided on its Entrez ID, not
on the organism of the interaction, because CTD records some
interactions on a gene of another species than the experiment's. A
human-only import keeps the rule of every earlier version.

The species summary printed at import lists the ten largest species
and counts the rest, instead of every species on one line.
 

 feat(import): let import_CTD() keep species other than human

import_CTD() gains an organism argument. It defaults to 9606, so an
import with no further argument keeps only human interactions, as
before. It also accepts other NCBI Taxonomy IDs, several at once, or
NULL for every species in the file, which is what a published analysis
that pooled species needs in order to be repeated.

No orthology mapping is performed: each interaction keeps the gene CTD
curated it on. Entrez-keyed sets hold every species requested; the
symbol-keyed sets keep only genes with a human Entrez ID, because
symbols come from org.Hs.eg.db. The import reports how many
interactions each species contributes.

The provenance record now states which species were imported; records
written by earlier versions print as human. Version 0.99.12.
 

 docs: mark lifecycle as stable in README

The package has been accepted into Bioconductor and its public API is
no longer expected to change without notice. Planned extensions are
additive, so the experimental badge no longer reflects the package
status.
 

 M1: shared S4 track engine (builder/sender split, Track classes, loadTrack) (#201)

* refactor(tracks): split bed and bedGraph loaders into payload builders and senders

Add .bedTrackPayload, .bedGraphTrackPayload and .bedGraphUrlTrackPayload,
browser-free builders returning list(config, files); the exported loaders
keep their signatures and send the same messages. Add dev/m1-plan.md with
the igvR S4 class inventory and the M1 stage checklist.

* style(tracks): replace assert_data_frame banned by gDRstyle lint

* refactor(tracks): split remaining loaders into payload builders and senders

Add internal builders for the seg, VCF, GWAS, BAM (url, local file, local
data), CRAM (url, local), GFF3 (url, local) and splice junction (url, local)
loaders. Senders keep their signatures and send the same messages; builders
are tested without a session in test-trackPayloads.R.

* refactor(tracks): port igvR annotation and quantitative Track classes with loadTrack()

Add R/tracks.R with Track, igvAnnotationTrack, the DataFrame/GRanges/UCSC
annotation and quantitative track classes, trackInfo()/trackSize(), internal
.trackTable()/.trackPayload() builders reusing .bedTrackPayload and
.bedGraphTrackPayload, and the exported loadTrack() generic. Tests in
test-tracks.R; plan updated for stage 3.

* fix(tracks): build example GRanges without undeclared IRanges

* refactor(tracks): port remaining igvR Track classes and add loadTrack() for GWASTrack

* test(tracks): pin pre-split wire message keys of bed and bedGraph senders

* fix(tracks): build payloads before removing same-named tracks

A builder that rejects its input no longer leaves the browser without the
track it was meant to replace.

* fix(tracks): sanitize annotation trackConfig once and document unsent slots

* fix(tracks): accept trackConfig in loadTrack for GWASTrack and document VariantTrack limits

* fix(js): honour annotation Track slots in the bed and bedGraph handlers

loadBedTrackFromFile now uses message.displayMode when present and falls
back to the hard-coded "EXPANDED", so loaders that never send it behave
as before. loadTrack() forwards expandedRowHeight, squishedRowHeight,
maxRows, searchable and visibilityWindow for annotation tracks and
visibilityWindow for quantitative tracks; mergeExtraParameters applies
them. expandedRowHeight joins .validIgvTrackOptions (igv.js reads it).
nameField is documented as stored for igvR compatibility, not sent.

Adds an annotation-slots node harness scenario and R tests for the
config igv.js receives.

Gate review stage 3 P2 (#197).

* fix(js): honour VariantTrack displayMode, height and visibilityWindow

The loadVcfTrack handler now uses message.displayMode, message.height and
message.visibilityWindow when present and falls back to its hard-coded
EXPANDED, 100 and 1000000 otherwise, so loadVcfTrack() renders as before.
loadTrack() sends the three slots; slot options are merged
with .slotsOverConfig so trackConfig is sanitized once, by the builder.

Adds a variant-slots node harness scenario and an R test for the message
and the config igv.js receives.

Gate review stage 4 P2 (#198).

* feat: make getGenomicRegion, showGenomicRegion, removeTracksByName S4 generics

Each dispatches on its first argument (session); the previous body is the
default method for signature ANY, so every (session, id, ...) call keeps
working while a downstream package such as igvR can add methods for its
own class instead of masking these functions.

* feat(tracks): load a plain igv.js track config list with loadTrack()

Add a loadTrack() method for a named list, so any igv.js track type
read from a url (e.g. bigBed) loads without a dedicated loader. The
config needs name, url and type or format (checkmate), goes through
.sanitizeAndMergeOptions and the .validIgvTrackOptions allowlist, and is
built before any track is removed. A minimal loadTrackConfig handler in
igvShiny.js hands it to igv.js, filling in order when unset; a node
harness scenario covers it.

Related: #111

* fix(tracks): build seg and gwas payloads before removing a track

loadSegTrack and loadGwasTrack removed the track of the same name
before validating their input, so a bad table dropped the existing
track. Build the payload first, as loadSpliceJunctionTrackFromURL
already does.

* test(tracks): pin the literal wire keys of every loader message

The sender tests compared each message with the output of the builder
the sender itself calls, so they could not fail on a changed key. Pin
the names() of each loader message, in the order recorded from the
loaders before the builder/sender split (bd7a6a8).

* fix(tracks): allow genotype colors on variant tracks only

homvarColor, hetvarColor and homrefColor sat in the global
.validIgvTrackOptions, so loadBedTrack and the other non-variant loaders
forwarded them instead of warning and dropping them. Move them to
.variantTrackOptions and add them through a new 'allowed' argument of
.sanitizeAndMergeOptions for the vcf builder, VariantTrack, a 'variant'
config list and 'variant' startup tracks.

* fix(lint): wrap setGeneric bodies in braces, robust session_proxy test

Brace the multi-line function bodies of the three new setGeneric calls
(gDRstyle brace_linter). The module test now checks that a session_proxy
dispatches to the ANY method and calls through MockShinySession's own
sendCustomMessage instead of overriding a possibly locked binding.

* fix(tracks): check type and format of a config list each on their own

The 'or' assertion let an invalid type through when format was valid,
e.g. type = c('variant', 'bed') or NA. Assert each as an optional single
non-empty string and require at least one of them.

* fix(tracks): build every payload before removing the track it replaces

The bed, bedGraph, bedGraph url, vcf, bam, cram, gff3 and local splice
junction loaders, and the loadTrack() sender, removed the track of the
same name before building and validating their payload, so bad input
dropped the existing track. Build first, as the seg, gwas and splice
junction url loaders now do. The wire messages are unchanged.

* fix(tracks): ignore trackConfig on a config list with a warning

loadTrack(, trackConfig = ...) failed with an unused-argument
error. Accept trackConfig and validateReference like every other method;
a non-empty trackConfig is logged and ignored, as for a GWASTrack.

* fix(lint): wrap multi-line anonymous function bodies in braces

* fix(test): assert behaviour, not the log line, for an ignored trackConfig

* fix(tracks): keep BED12 exons and check local GFF3 against the reference

GRanges imported from BED12 kept only six columns, so a multi-exon
transcript drew as one solid feature; .bed12Columns() writes thick,
itemRgb and blocks back. A GFF3Track with a local table returned no
reference data, so validateReference never ran for it.

Codex review P1 on #197 and #198.

* fix(tracks): address Codex review P2 findings

- .slotsOverConfig() drops a malformed trackConfig on its own, so the
  slot options of an annotation track survive it
- alignment tracks take displayMode from trackConfig and sanitize it
  once (.alignmentConfig)
- add one show() method for the Track hierarchy (BiocCheck warning)
- a config list or startup track with a vcf format and no type keeps
  the genotype colors, as igv.js infers a variant track from it

* docs(news): cover loadTrack config lists and the S4 generics in 1.9.52

* fix(tracks): read factor GFF3 coordinates by value in the reference check

as.numeric() on a factor gives its level codes, so a valid GFF3 table
with factor start/end columns got false reference warnings.

Codex confirmation review P2 on #201.

---------

Co-authored-by: Claude <noreply@anthropic.com> </pre>
    </div>
  
    

      Package: augere.core

      Commit: 8c441d2830f33997272beab9fb5c23696918bdbc

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-11-05 17:02:19 +1100

      Commit message:


	  
		
 Clarified contents= description in compileReport manpage, reoxygenated.
 
    
  
    

      Package: augere.de

      Commit: ca71ad3947f0f894c3e0d86f9e315bca3cd574fc

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-11-05 16:57:07 +1100

      Commit message:


	  
		
 Bumped version, reoxygenated.
 
    
  
    

      Package: augere.de

      Commit: 7c9c0f078cc12b23f34fcfbf009bde5dc0657ff5

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-11-05 16:55:49 +1100

      Commit message:


	  
		
 Support edgeR's new QL-based quality weights in runEdgeR.

This is disabled by default, at least until we get some more experience.

Also replaced glmTreat with glmQLFit(lfc=) as this seems more modern.
 
    
  
    

      Package: augere.de

      Commit: 523deee27a1b176c5f6ed7e987b4d5b739a31940

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-11-05 15:53:18 +1100

      Commit message:


	  
		
 Cleaned up various diagnostic figures.

- Removed barplot of normalization factors and just show the samples with the
  biggest/smallest factors so that users can see the outliers.
- Store the various MD plots in a tabset rather than cramming them together.
  This requires some extra work to silence the subsection headers.
- Added missing caption for the voom plot.
 
    
  
    

      Package: humanHippocampus2024

      Commit: 2d8285adddea6aaa2c1898d18257099516581c4a

      Author:  CH <chrishou_0612@CH.lan> 

      Date: 2026-11-04 22:14:44 -0600

      Commit message:


	  
		
 version bump up in devel
 
    
  
    

      Package: humanHippocampus2024

      Commit: 206ab74d20df9672f124e41f91520b984c2afecb

      Author:  CH <chrishou_0612@CH.lan> 

      Date: 2026-11-04 22:14:26 -0600

      Commit message:


	  
		
 bug fix
 
    
  
    

      Package: humanHippocampus2024

      Commit: d02a741edb134565d315f96b0134dc3889748d5d

      Author:  CH <chrishou_0612@CH.lan> 

      Date: 2026-11-04 21:45:42 -0600

      Commit message:


	  
		
 version bump up in devel
 
    
  
    

      Package: humanHippocampus2024

      Commit: 47da7230b4ca84a6429dbfd358ea2ec3ca5668a0

      Author:  CH <chrishou_0612@CH.lan> 

      Date: 2026-11-04 21:45:06 -0600

      Commit message:


	  
		
 bug fix
 
    
  
    

      Package: augere.gsea

      Commit: f4566a19c3dd21ac97b220653fea200160901991

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-11-05 14:17:33 +1100

      Commit message:


	  
		
 Added voom caption, replace meaningless normalization factor barplot.

Now we just report the largest and smallest normalization factors to give
readers an idea of the spread and which samples are most extreme.
 
    
  
    

      Package: augere.gsea

      Commit: b532d18334b11d2265337f87778d41ba358ebc86

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-11-05 13:32:10 +1100

      Commit message:


	  
		
 Switch to voomLmFit and normLibSizes to avoid deprecation messages.
 
    
  
    

      Package: BiocDuckDB

      Commit: af31625f270d60a6ce73bad77eef1110901c46f3

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-11-04 16:49:45 -0800

      Commit message:


	  
		
 Fix PCA/beachmat fast path silently using raw instead of projected values

.duckdb_seed_to_sparse_matrix() (the beachmat/tatami fast path behind
initializeCpp,DuckDBArraySeed-method, used by BiocSingular::runSVD's
compute_center/compute_scale for PCA) materialized the seed's raw,
unprojected column instead of its logical (datacols-level) one.
tblconn(table, select = FALSE) deliberately skips column-selection, so
the connection it returns reflects the table's base columns, not
whatever SQL projection (e.g. a log1p() transform applied via
Math/Ops) is recorded in datacols; the subsequent select(conn,
all_of(datacol_name)) then picked that raw column up by name, which
silently succeeds whenever a transformed datacol keeps its original
name (the common case: Math/Ops rewrite a datacol's expression in
place, e.g. value to log(value + 1), without renaming it). The matrix
extraction itself was otherwise correct (right shape, right sparsity),
so this was silent: no error, just the wrong values feeding PCA
centering/scaling.

Reported with a reproducible fixture showing up to a 0.405 error in
PCA centering on a log-transformed assay versus the correctly-
projected result (down to ~1.3e-15, floating-point noise, after the
fix).

Checked before applying: git history shows select = FALSE was part of
the original feature commit with no documented rationale, not a
deliberate performance tradeoff; grepped all callers and the existing
test suite and confirmed nothing relies on or asserts the previous
(buggy) behavior.

Fix: tblconn(table, select = TRUE) (the generic's own default), so the
same select() call afterward operates on the already-projected
connection. Added regression tests covering both the direct value-
extraction path and an end-to-end runSVD/PCA comparison against a
log1p-transformed oracle; verified both fail without the fix and pass
with it.
 
    
  
    

      Package: SpaNorm

      Commit: b3cf5fd8cd24484bbb1b74c300fe534dde7a28d0

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun151.hpc.net.uq.edu.au> 

      Date: 2026-11-05 08:56:20 +1000

      Commit message:


	  
		
 Merge upstream/devel (reconcile rebased history with Bioconductor)

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

      Package: SpaNorm

      Commit: fa3985d6ed8f67bfaa2a155b796908695c748191

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun151.hpc.net.uq.edu.au> 

      Date: 2026-11-05 08:48:21 +1000

      Commit message:


	  
		
 Bump version to 1.7.17

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

      Package: SpaNorm

      Commit: ec43d4bfb90368f2d4e0ec29ebec18b07129a6d7

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun151.hpc.net.uq.edu.au> 

      Date: 2026-11-05 08:47:03 +1000

      Commit message:


	  
		
 tests: skip slow test files on Bioconductor builders

SpaNorm 1.7.16 timed out at 40 min in R CMD check on nebbiolo2 and taishan
while running tests. Add skip_on_bioc() to the nine slowest test files.

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

      Package: SpaNorm

      Commit: 3c9082e7c1c26fc1af57d46dd9d6ec3a05fada7e

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-22 14:45:13 +1000

      Commit message:


	  
		
 ci(site): install nbformat, nbclient and ipykernel so Quarto can execute the Python reference examples

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

      Package: SpaNorm

      Commit: a06998d15a11d531d0d784d018a6aa9b901c8f90

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-22 13:46:12 +1000

      Commit message:


	  
		
 site: executed Python reference examples and an output check

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

      Package: SpaNorm

      Commit: 7d6faffa4aec622a54723138593d5a08f81f5265

      Author:  Dharmesh D Bhuva <30132854+bhuvad@users.noreply.github.com> 

      Date: 2026-10-22 13:46:12 +1000

      Commit message:


	  
		
 site: shared fitted objects and executed R reference examples

The R and Python fits are built once per site build into _cache; every R reference page
that needs a fit loads it. reference-examples.yml lists which examples run and why any do not.

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

      Package: SpaNorm

      Commit: 04cd3594fd92c802597b937d9dae00c0e88a46b8

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

      Date: 2026-10-22 12:42:11 +1000

      Commit message:


	  
		
 DESCRIPTION: maintainer email is d.bhuva@uq.edu.au

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

      Package: SpaNorm

      Commit: 274f3d9b70724354ad9717f596ce0ca2464f34da

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

      Date: 2026-10-22 12:42:07 +1000

      Commit message:


	  
		
 CI: site workflow also triggers on DESCRIPTION, man, NEWS and the workflow figure

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

      Package: SpaNorm

      Commit: 2662cbe97123cc64321adfb55e54e466aff4b094

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

      Date: 2026-10-22 12:42:07 +1000

      Commit message:


	  
		
 Site: authors card generated from DESCRIPTION (ORCID icons, maintainer mailto)

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

      Package: SpaNorm

      Commit: ff0ac4171902cc05ee192fca5660d71638052e94

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

      Date: 2026-10-22 12:41:08 +1000

      Commit message:


	  
		
 site: run the plotSpatial reference example at build time and show its figures

An explicit allow-list (run_pages) replaces the blanket no-executable-chunk check; fits stay unexecuted.

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

      Package: SpaNorm

      Commit: 7c0182594e162056cf1afaed0f50fedc70187ed2

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun151.hpc.net.uq.edu.au> 

      Date: 2026-11-05 08:48:21 +1000

      Commit message:


	  
		
 Bump version to 1.7.17

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

      Package: SpaNorm

      Commit: ae0643c3379b588773a30055b14a94c984acbb39

      Author:  Dharmesh Bhuva (qris-uq) <uqdbhuva@bun151.hpc.net.uq.edu.au> 

      Date: 2026-11-05 08:47:03 +1000

      Commit message:


	  
		
 tests: skip slow test files on Bioconductor builders

SpaNorm 1.7.16 timed out at 40 min in R CMD check on nebbiolo2 and taishan
while running tests. Add skip_on_bioc() to the nine slowest test files.

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

      Package: scpdata

      Commit: 06825b70e66f257a761e850f7ec0c21590199c8d

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-11-04 22:31:45 +0100

      Commit message:


	  
		
 update news
 
    
  
    

      Package: scpdata

      Commit: 7edd22e8fe3142260c348ad871ea9361dffb6d3b

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2026-11-04 21:29:31 +0000

      Commit message:


	  
		
 Merge pull request #47 from AbiramiSnd/fix_broken_links

fixed the broken links from issue #19 
    
  
    

      Package: scpdata

      Commit: b63f6187fb37fd8ace174375391332cf36d4bbf2

      Author:  AbiramiSnd <abirami.sndrmty@gmail.com> 

      Date: 2026-11-04 12:29:53 +0100

      Commit message:


	  
		
 fixed the broken links from issue #19
 
    
  
    

      Package: AnnotationGx

      Commit: 9f617ab5f9bae7ad00ed504e782f0425990ea7b1

      Author:  Michael Tran <mtran256@uwo.ca> 

      Date: 2026-11-04 14:31:36 -0500

      Commit message:


	  
		
 chore: bump version to retry Bioconductor build
 
    
  
    

      Package: AnnotationGx

      Commit: 8b137d9a25b04e5d41be82ba9ed82f156e5730b3

      Author:  Michael Tran <mtran256@uwo.ca> 

      Date: 2026-11-04 14:27:09 -0500

      Commit message:


	  
		
 fix: finalize Bioconductor data licensing review
 
    
  
    

      Package: gDRutils

      Commit: de406a76bf90047eabea01ac35058297f64ccb5c

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

      Date: 2026-11-04 17:21:58 +0100

      Commit message:


	  
		
 Merge pull request #212 from gdrplatform/GDR-3776

fix: use the co-dilution fit of the matching ratio in predict_smooth_from_combo() 
    
  
    

      Package: gDRutils

      Commit: 3681f17ee5718771292f4849bd4af4ec2470dbf1

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

      Date: 2026-11-02 17:39:12 +0100

      Commit message:


	  
		
 fix: use the co-dilution fit of the matching ratio in predict_smooth_from_combo()
 
    
  
    

      Package: PECA

      Commit: a4c057571f8a0c37f975eaa5f80fe4b88fd9ecc3

      Author:  Tomi Suomi <tomi.suomi@utu.fi> 

      Date: 2026-11-04 17:53:36 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: f55b1daba03ba9664130814e35824c3188e4c0ee

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-03 18:04:32 +0100

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: e8654ee84eae8d015bd3dca82ab578acd4c26760

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-03 18:02:32 +0100

      Commit message:


	  
		
 Document VLen-UTF8 breaking change in NEWS
 
    
  
    

      Package: Rarr

      Commit: ff64b0284dfba84dbe2f6de2db73d6bee5ed0429

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-04 16:39:12 +0100

      Commit message:


	  
		
 Implement v3->v2 conversion only for little endian types
 
    
  
    

      Package: Rarr

      Commit: 53bf831ecd4b69dc9cb0e54dc2a5def395b1cd07

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-04 16:36:50 +0100

      Commit message:


	  
		
 Do not expose unrecommended v3 data types
 
    
  
    

      Package: Rarr

      Commit: 633f9f399aba41c6d088b10e5ff67d62676a3ebc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-03 18:00:42 +0100

      Commit message:


	  
		
 Fix lint
 
    
  
    

      Package: Rarr

      Commit: 16907dc3aa099b0dac5b5589ab8b28ed8540e220

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-02 15:44:14 +0100

      Commit message:


	  
		
 Mention v3 data types and vlen-utf8 writing in NEWS
 
    
  
    

      Package: Rarr

      Commit: c96af7689c8ec8153ff7735e91d379a99f51a43c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-02 15:41:40 +0100

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: Rarr

      Commit: 927b782928fd4c94288884c616239def1112612f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-02 15:38:25 +0100

      Commit message:


	  
		
 Use new syntax to write VLen-UTF8
 
    
  
    

      Package: Rarr

      Commit: 408ff3cf8fdd72ef47e27339527e797f6d4bbbfa

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-02 15:38:06 +0100

      Commit message:


	  
		
 Default to VLen-UTF8 if possible when writing

Progress towards #158
 
    
  
    

      Package: Rarr

      Commit: adb5860acd30ad0f8ac42b17aa810c9fe5e92aed

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-02 15:37:31 +0100

      Commit message:


	  
		
 Allow v3 data types specification for writing

Fix #263
 
    
  
    

      Package: Rarr

      Commit: 7827ec2bed1b6ecb05c74d20310a90e45662fc74

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-04 16:18:22 +0100

      Commit message:


	  
		
 Add comment with link to upstream bug report
 
    
  
    

      Package: Rarr

      Commit: bc5def4a6d618fe38253874fa529bff81f8cd58e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-04 15:28:08 +0100

      Commit message:


	  
		
 Make sure seq.int() returns an ALTREP vector
 
    
  
    

      Package: Rarr

      Commit: f27632af72e663fe1eb8baec0b401ea6246a6d8b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-04 11:33:59 +0100

      Commit message:


	  
		
 Update touchstone
 
    
  
    

      Package: Rarr

      Commit: 89732a3888e4e0520ac0e8b0de04a0fbf1b1d1c2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-03 15:43:02 +0100

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: c1a7674ff62c963b609524a13c89e3debb68930d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-03 15:42:25 +0100

      Commit message:


	  
		
 Mention unstandardized v3 codecs improvements in NEWS
 
    
  
    

      Package: Rarr

      Commit: 77e9807b1b1e14acb1d765b32d92a610d854a332

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-02 19:31:04 +0100

      Commit message:


	  
		
 Add warning when writing non standardized codecs
 
    
  
    

      Package: Rarr

      Commit: 7cee575e5e560b62a360b0bb38bae8dab8c8080d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-02 17:48:38 +0100

      Commit message:


	  
		
 Add numcodecs.zlib as an alias for zlib
 
    
  
    

      Package: Rarr

      Commit: 2ac9a4af3e24c4281324c5e0485be385b07516dc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-11-03 14:41:45 +0100

      Commit message:


	  
		
 Add more undesirable functions
 
    
  
    

      Package: augere.de

      Commit: 25714f814ecad33e4e84c77991cf054ada73c7ec

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-11-05 02:21:36 +1100

      Commit message:


	  
		
 Switch to voomLmFit and normLibSizes to avoid deprecation messages.
 
    
  
    

      Package: CalibraCurve

      Commit: c227051425c165606944f33f548bf9e6cb030d29

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-11-04 15:17:20 +0100

      Commit message:


	  
		
 fix description file
 
    
  
    

      Package: STRINGdb

      Commit: 88df545b77084805644c43a3e42ef29e626dd786

      Author:  Damian <damian.szk@gmail.com> 

      Date: 2026-11-04 15:15:04 +0100

      Commit message:


	  
		
 Fix wrong map() results, get_summary() default and payload images

map() gave wrong results without a warning in three cases:
- Missing (NA) or empty identifiers were mapped to a real protein. The
  normalization of the aliases (iconv from Windows-1252) turned aliases
  with bytes that Windows-1252 does not define, such as the hyphen U+2010
  in "spine-associated RapGAP 3", into NA, and merge() matched them to
  every NA identifier: for human, every row without a gene name got
  9606.ENSP00000222345, and removeUnmappedRows = TRUE kept those rows.
- With several identifier columns, the identifiers were written back by
  position after the rows had been reordered, so they no longer matched
  the rest of their rows.
- With takeFirst = FALSE, the identifiers came back upper-cased.

Now an NA or empty identifier is never mapped, every row keeps its own
identifiers as given, and the rows keep the order of the input. The
undefined bytes are kept as byte codes, so those aliases can be mapped, and
get_aliases() contains no NA aliases. The columns, their order and the
order of the repeated rows of takeFirst = FALSE are unchanged; for the
vignette's example and the human aliases of STRING 12.5 the output is
identical to before.

get_summary() gets the default required_score = NULL (the score_threshold
of the object), so get_summary(string_ids) works as documented.
post_payload() sends logo_imgF and legend_imgF with httr's upload_file
instead of RCurl's fileUpload, which the package no longer imports. New
offline unit tests; the help of map, multi_map_df and get_summary describes
the behaviour.
 
    
  
    

      Package: STRINGdb

      Commit: 92edb864a8e5fc14a7d0ef5434f0e61622e4e6cb

      Author:  Damian <damian.szk@gmail.com> 

      Date: 2026-11-04 14:31:53 +0100

      Commit message:


	  
		
 Bump version to 2.25.3 for the offline constructor
 
    
  
    

      Package: STRINGdb

      Commit: 2557f229344b62983a1cf3296d3fc07bf19be73b

      Author:  Damian <damian.szk@gmail.com> 

      Date: 2026-11-04 14:31:47 +0100

      Commit message:


	  
		
 Create STRINGdb objects for known versions without asking STRING

The constructor asked string-db.org for the current version and for the
list of available versions whenever an object was created, so it failed
offline and whenever string-db.org could not be reached. The Bioconductor
build machines failed this way with SSL connect errors, in the unit tests
and in the vignette.

The versions known to the package (11.0, 11.0b, 11.5, 12.0 and 12.5) and
their stable addresses are now bundled (KNOWN_STRING_VERSIONS), and an
object for one of them is created without any request to STRING. Without a
version, string-db.org is still asked for its current version, now with a
5-second timeout; when it cannot be reached, the newest known version is
used and a WARNING is printed. A version that the package does not know is
still looked up on string-db.org. A version that is not available, or that
cannot be checked, stops with an error that gives the reason and the
versions; the error message used to be empty. The lookups send
caller_identity.

Versions without a dot still get ".0", and the output without a version is
unchanged when STRING can be reached. New offline unit tests; the class
help documents the version field.
 
    
  
    

      Package: CalibraCurve

      Commit: dcd15a18b71614e72cd3178408e85e9cdfeed1cb

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-11-04 15:01:43 +0100

      Commit message:


	  
		
 solve version inconsistency
 
    
  
    

      Package: CalibraCurve

      Commit: b2abf5dc9f0a2955a567fae0e0d2a9744a041745

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-11-04 14:29:44 +0100

      Commit message:


	  
		
 improve documentation
 
    
  
    

      Package: CalibraCurve

      Commit: 3db892cbef63127e1705424ebd9b302354052f34

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-11-04 13:17:05 +0100

      Commit message:


	  
		
 some optimizations
 
    
  
    

      Package: CalibraCurve

      Commit: 859f71538e9d7142ad2931e439857af367aa3f2d

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-11-04 11:14:28 +0100

      Commit message:


	  
		
 allow plotting of blanks
 
    
  
    

      Package: CalibraCurve

      Commit: 93908d11573fa107159b3ef1c23733a3db6d27a7

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-10-27 17:35:10 +0100

      Commit message:


	  
		
 fix bug when multiple input files are used and at least one result cannot be computed
 
    
  
    

      Package: CalibraCurve

      Commit: 274d3a830089f14ec7f25bdb220db0bf3e75ada8

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-10-27 17:10:24 +0100

      Commit message:


	  
		
 fix checks
 
    
  
    

      Package: CalibraCurve

      Commit: 70327fbb367856acf4fd4dcc8a59d131250f48f8

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-10-27 16:59:18 +0100

      Commit message:


	  
		
 add some edge case tests
 
    
  
    

      Package: CalibraCurve

      Commit: 2fd28fd0452cce727208d3258394abc029e29454

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-10-27 16:45:11 +0100

      Commit message:


	  
		
 enhance response factor plots
 
    
  
    

      Package: CalibraCurve

      Commit: 7006150b7f681ad07104b970da841edafa997d95

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-10-23 15:42:06 +0200

      Commit message:


	  
		
 allow usage of column names (as alternative to column numbers) when reading data
 
    
  
    

      Package: CalibraCurve

      Commit: b0deb8347ab593ee09dbf76d7ad5ecd49a041109

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-10-23 14:56:30 +0200

      Commit message:


	  
		
 allow turning off log10 transformation of x-axis for plots
 
    
  
    

      Package: CalibraCurve

      Commit: 617cabc66296c88afff283053d62a7ee53bc422b

      Author:  KarinSchork <karin.schork@rub.de> 

      Date: 2026-10-23 13:26:49 +0200

      Commit message:


	  
		
 bump version and add warning if only 1 replicate per concentration level is present
 
    
  
    

      Package: CalibraCurve

      Commit: 8f6de139a5c5525c6dd6aad10dde83cf566cf159

      Author:  Karin Schork <karin.schork@rub.de> 

      Date: 2026-06-01 18:01:52 +0200

      Commit message:


	  
		
 Upgrade ImageMagick to version 7 in workflow

Updated ImageMagick installation from version 6 to 7 and commented out harfbuzz and fribidi installation. 
    
  
    

      Package: CalibraCurve

      Commit: 90f81309ec0f04650e57ac208bc82bf13c1cf8a9

      Author:  Karin Schork <karin.schork@rub.de> 

      Date: 2026-06-01 17:51:05 +0200

      Commit message:


	  
		
 Merge pull request #24 from mpc-bioinformatics/KarinSchork-patch-2

Add terms of use 
    
  
    

      Package: CalibraCurve

      Commit: 5f5b45af4340e425cbfc3a78c29399d2207aacda

      Author:  Karin Schork <karin.schork@rub.de> 

      Date: 2026-06-01 17:50:47 +0200

      Commit message:


	  
		
 Update LICENSE to retain organization and year

Removed the 3-Clause BSD License text while retaining the organization information. 
    
  
    

      Package: CalibraCurve

      Commit: 8e9cfe7fa973847e80f7ad64d2e830108d4bcb51

      Author:  Karin Schork <karin.schork@rub.de> 

      Date: 2026-06-01 17:42:05 +0200

      Commit message:


	  
		
 Upgrade actions/checkout and actions/cache versions 
    
  
    

      Package: CalibraCurve

      Commit: 174c5e142818f5738df9ebdf58ce4aff9fadc4a3

      Author:  Karin Schork <karin.schork@rub.de> 

      Date: 2026-06-01 17:23:21 +0200

      Commit message:


	  
		
 Update GitHub Actions checkout action version to v6 
    
  
    

      Package: CalibraCurve

      Commit: 1b1a196043edbdd8202a461e66b244821eb708da

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

      Date: 2026-06-01 14:04:33 +0000

      Commit message:


	  
		
 docs: add terms of use section to README.Rmd
 
    
  
    

      Package: CalibraCurve

      Commit: bfc3e419d98cc835a55e21f1006d789d4103e1b0

      Author:  Karin Schork <karin.schork@rub.de> 

      Date: 2026-06-01 16:00:44 +0200

      Commit message:


	  
		
 Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> 
    
  
    

      Package: CalibraCurve

      Commit: 66efb5f8c9de97537c342f3acb4c233a008454f5

      Author:  Karin Schork <karin.schork@rub.de> 

      Date: 2026-06-01 14:15:33 +0200

      Commit message:


	  
		
 Merge pull request #25 from mpc-bioinformatics/KarinSchork-patch-3

Include 3-Clause BSD License in LICENSE file 
    
  
  


</div>

</div>