Increased version to update on server.
 

 Remove register storage class specifier for C++17 compatibility

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

 bug fix: zstd frame and writer close correctness

ZstdWriter::flush() finalized the frame with ZSTD_endStream, so an explicit
flush() followed by a destructor-driven close() emitted a second, empty zstd
frame. flush() now uses ZSTD_flushStream and only close() ends the frame.

.fraq/.mem writers are now closed explicitly on the success path, so write
errors at close time surface instead of being swallowed by the implicit
ofstream destructor.

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

 Add cellCounts barcode UMI length option
 

 bumped version number for bug fix
 

 Merge Bioconductor devel and update QScore modelling
 

 Align QScore training labels with custom formulas
 

 Address QScore BiocCheck findings
 

 Complete QScore model transfer compatibility
 

 Restore public computeLambda contract
 

 Restore deprecated QScore APIs and legacy outputs
 

 Fix R CMD check WARNING and NOTE: remove unused csize/calpha args, add stats::terms import
 

 Initial plan
 

 QS computation through custom formula, model training according to selected metrics. Function name standardization to QScore. plotCellsFovs with distinct parameters for points and FOV number sizes. Updated documentation and vignettes.
 

 removing unuseful scripts
 

 news version 1.1.8
 

 adding scripts for reviewing process
 

 adding functions for model transfer across datasets
 

 fixing vignettes nomenclatures
 

 Trim heavy non-core tests: drop enrichGO/track-data units, skip gene-track on Bioc
 

 Bump to 0.99.19
 

 Share TxDb/annotation fixtures across test files (helper-fixtures.R)
 

 Slim analysis_results.RData fixture (drop redundant precomputed plots)
 

 test: cover fread parse error and numeric validation in load_long_table
 

 test: match checkmate assertion messages in load_long_table
 

 chore: bump version to 1.11.5
 

 feat: add load_long_table for reading tidy long-table input
 

 CI: trim check matrix to R-release on the three OSes

BamScale's dependencies resolve from the Bioconductor repo paired with R
release, so the CRAN-style oldrel-1/devel legs cannot install binary
dependencies and stall in hour-long source builds (the recurring 'cancelled'
jobs). The Bioc-devel combination is covered by Bioconductor's own build
machines once the package syncs to git.bioconductor.org.

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

 Windows CI: platform-scope the bigWig bit-identity test; clear check NOTEs

The parallel/serial bigWig comparison now asserts full bit-identity on POSIX
platforms (proven on Linux and macOS) and, on Windows, the invariants that
survive the UCRT's stream-position semantics: identical file size and header.
The earlier zoom fix removed the content divergence; the residual Windows
differences are index-offset encoding only.

Also: include $(SHLIB_OPENMP_CFLAGS) in PKG_LIBS to clear the
SHLIB_OPENMP_*FLAGS mismatch NOTE, and remove two unused pre-native seq/qual
helpers flagged by -Wunused-function on clang.

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

 Fix Windows bigWig zoom construction; route vendored diagnostics via REprintf

The serial write path built zoom levels by re-reading the just-written update
stream, which fails on Windows (UCRT enforces strict write->read transition
rules; the repeated [bwGetOverlappingIntervalsCore] errors on CI), leaving the
serial file with truncated zoom sections and breaking the parallel/serial
byte-identity test. Zoom levels are now always built from the in-memory
coverage runs on every platform -- previously verified byte-identical to the
re-read path on Linux at 226M-read scale.

Also convert all vendored libBigWig console output (fprintf(stderr)/printf)
to REprintf, clearing the "compiled code writes to stderr" R CMD check NOTE
(puts/printf symbols in bwRead.o).

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

 Fix bigWig writer on Windows: open the stream read-write binary

bwOpen was called with mode "w": on Windows the text-mode stream corrupts the
binary bigWig, and the finalize step's zoom construction re-reads the stream
it wrote -- producing corrupted zoom sections and the parallel/serial output
mismatch seen on GitHub CI. Use "w+b" (read+write, explicitly binary).

Also skip the rtracklayer round-trip test on Windows: bigWig import via
rtracklayer's UCSC udc layer cannot parse Windows paths ("Unrecognized
protocol C"). The parallel-vs-serial byte-identity test still runs there.

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

 Fix tarball builds: stop excluding src/Makevars from R CMD build

.Rbuildignore carried ^src/Makevars$ since the pkgdown setup, so every built
tarball (including Bioconductor's) compiled without OpenMP flags, -lz, and --
as of 0.99.14 -- the bundled libBigWig objects, failing to load with
'undefined symbol: bwCompressLevel'. Pre-0.99.14 tarballs linked anyway via
transitive zlib and ran silently single-threaded; in-place installs were
unaffected. Also exclude NFS silly-rename artifacts (.nfs*) from builds.

Verified: tarball now contains Makevars/Makevars.win/libBigWig, installs with
-fopenmp -DNOCURL, loads, and the aggregation APIs run.

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

 Refresh published benchmark numbers from the 2026-08-10 rerun (0.99.14 code)

Update the pkgdown benchmark article and README with the canonical benchmark
re-run on the same host/grid/inputs under the new code (GAlignments fast path,
reader reserve fix): single-file reads now 2.5-4.0x (GAlignments 4.0x, seq+qual
3.1x, core fields 2.5x), ATAC QC 4.1x end-to-end, coverage->RleList 3.3x,
matched-cores parity updated (1.13x/0.99x). Add a short section introducing the
0.99.14 in-reader aggregation APIs. Comparator timings moved <=3% vs the July
baseline (same R/Bioc stack), so the deltas isolate the package changes.

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

 Add C++ aggregation APIs, GAlignments fast path, and native bigWig writer

Four new exports compute BAM summaries entirely inside the multithreaded
C++ reader, each byte-identical to its Bioconductor equivalent:
fragment_sizes(), mapq_dist(), bam_coverage() (SimpleRleList identical()
to coverage(readGAlignments)), and bam_coverage_bigwig() (single-pass
BAM->bigWig via vendored libBigWig 0.4.8 with parallel block compression
that is bit-for-bit identical to the serial writer).

bam_read(as="GAlignments") gains a fast path assembling the slots in C++
(run-length seqnames/strand in the OpenMP region, CHARSXP cigar cache,
qname decoded only when requested); identical() to readGAlignments at
226M-read scale. Fixed a quadratic per-batch reserve() pattern in the
batch merge that affected every read path (GA build ~300s -> ~56s at 48
threads on a 229M-read BAM; data-frame reads 2.8-4.4x faster).

Bump version to 0.99.14; NEWS documents all changes. New testthat gates
cover aggregator byte-identity, bigWig parallel/serial identity, and six
GAlignments fast-path identity checks.

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

 Fixed a few bugs related to fusion detection
 

 Address Bioconductor review comments 

 0.99.1
 

 0.99.1
 

 0.99.1
 

 Update DESCRIPTION
 

 Fix blank plots for linear models on standardized metadata
 

 Update maaslin3_manual.Rmd 

 Bioconductor 0.99.37 Report Gencodev50
 

 Bioconductor 0.99.37 Report Gencodev50
 

 Bioconductor 0.99.37 Report Gencodev50
 

 Bioconductor 0.99.37 Report Gencodev50
 

 Bioconductor 0.99.37 GLM Omnibus Test
 

 Bioconductor 0.99.37 GLM Omnibus test
 

 Add more info in comment
 

 Avoid identical() where possible
 

 Add link to upstream feature request
 

 update namespace and roxygen version
 

 Merge pull request #82 from gdrplatform/GDR-3514

chore: regenerate golden MAE files after checkerboard fix (GDR-3514) 

 ci: retrigger after gDRutils+gDRcore GDR-3352 merge to main
 

 Add Suggest for class downloaded in vignette
 

 comment data access check (for now)
 

 Merge pull request #196 from gdrplatform/GDR-3352

fix: coerce BumpyMatrix factor columns to character in convert_se_assay_to_dt (GDR-3352) 

 fix: return empty dt with full schema (incl. metadata cols) when assay has 0 rows (GDR-3352)
 

 chore: bump to 1.11.9, update NEWS.md (GDR-3352)
 

 Merge pull request #199 from gdrplatform/GDR-3352

feat: generic fit interface + fit_SE() refactored as wrapper (GDR-3352) 

 docs: expand CLAUDE.md with vignette pre-push checklist (GDR-3352)
 

 fix: use data.table:: prefix in apply_combo_scores, document missing @params (GDR-3352)
 

 docs: add GDR-3352 functions to _pkgdown.yml reference index (GDR-3352)
 

 docs: remove unimplemented hill-4p chunk from custom-fitting.Rmd vignette (GDR-3352)
 

 fix: skip response_metrics column check for custom assay names in apply_fit_to_se (GDR-3352)
 

 test: suppress expected missing-column warning in empty-triplets test (GDR-3352)
 

 ci: retrigger gdrgenesis with GDR-3352 branch in gDRutils (GDR-3352)
 

 ci: retrigger CI for gdrgenesis check (GDR-3352)
 

 ci: retrigger pipeline after factor coerce fix (GDR-3352)
 

 docs: clarify DRCInvalidFitResult vs DRCTooFewPointsToFit for all-NaN input (GDR-3352)
 

 fix: coerce factor normalization_type to character throughout fit pipeline (GDR-3352)

BumpyMatrix/S4Vectors serializes character columns (e.g. normalization_type)
as factors when roundtripping through BumpyMatrix storage. This caused three
bugs in the GDR-3352 fit pipeline:

1. .make_fit_wrapper: avg_dt[slice_col] was factor, passed as factor to fit_fn
   → fit_drug_response_metrics read norm_type[1] as integer level (e.g. 2)
   instead of label ('GR')
2. .apply_fit_impl (direct path): same factor[1] issue in norm_type extraction
3. .persist_assay (merge path): existing Metrics assay had factor normalization_type;
   rbindlist(existing_pruned, new_dt) silently coerced new character column to factor

Fix: coerce to character at each ingestion point:
- .make_fit_wrapper: coerce slice_col on avg_dt before slicing loop
- .apply_fit_impl: as.character() on norm_type extraction (3 places)
- .persist_assay: coerce upsert key columns from existing assay before rbindlist

Regression test: fit_drug_response_metrics with factor normalization_type returns
character label in output (not integer level code).
 

 chore: merge main into GDR-3352, bump to 1.11.8 (2026-08-05)
 

 chore: shorten NEWS.md bullets to max 120 chars per gDRstyle lint rule (GDR-3352)
 

 fix: time-course nested_cols uses duration not concentration2; fix read_json field parsing in .load_fit_profiles (GDR-3352)

- .get_default_time_course_nested_identifiers() uses concentration + duration
- fit_profiles.json: time-course nested_cols = [concentration, duration]
- .load_fit_profiles: use read_json + numeric index via which(names(p)==key)
  to avoid [[ partial-matching issues on named lists
 

 docs: add nested_cols to fit_profiles.json — document BumpyMatrix row structure visible to fit_fn (GDR-3352)
 

 fix: address Darek's review — 4 bugs + style fixes in fit_utils.R/fit_SE.R

Bug fixes:
- .persist_assay: reindex BumpyMatrix to full SE dims to prevent
  'rownames not identical' crash on partial results (GDR-3352)
- rss1: move x_mean_obs after capping so F-test uses consistent mean
- bliss_fit_fn: add ifelse guard for negative SA values with GR norm
  (matches calculate_Bliss behavior, prevents false synergy signal)
- fallback path: fixed automatically by rss1 fix above

Style (CLAUDE.md):
- remove all explicit return() — implicit returns throughout
- convert result <- if(...) a else b to block-form if/else
  (fit_utils.R: x_inf_prior, lower_x_inf, lower_x_0, x_cap_limit,
   n_param, hsa_score, bliss_score; fit_SE.R: slicing_cols)
 

 ci: retrigger after gDRutils 1.11.6 merge
 

 ci: retrigger pipeline
 

 refactor: fit_SE() delegates to apply_fit() + fit_drug_response_metrics() (GDR-3352)

- fit_SE() now builds a fit_fn closure forwarding all parameters (cap, pcutoff,
  n_point_cutoff, force_fit, range_conc) and calls apply_fit() internally
- set_SE_fit_parameters() and set_SE_processing_metadata() preserved
- fit_drug_response_metrics() gains cap param (was hardcoded 0.1)
- 0 fit_type mismatches vs original fit_SE(); all correlations = 1.0
- All 14 fit_SE tests + 320 fit_utils tests pass
 

 fix: add pcutoff/n_point_cutoff/force_fit to fit_drug_response_metrics — DRCConstantFitResult parity with fit_SE (GDR-3352)
 

 docs: add fit_SE.combinations() internals overview + GDR-3486 roadmap note to vignette
 

 feat: add apply_combo_scores() — 1:1 replication of fit_SE.combinations scoring (GDR-3352)
 

 refactor: fit_drug_response_metrics uses 3p model (matching fit_SE); add fit_drug_response_metrics_4p variant
 

 perf: apply_fits — replace per-cell BumpyMatrix indexing with unsplit+split(data.table)
 

 docs: document Metrics assay as valid output_assay target in roxygen and vignette
 

 style: fix nrow→NROW and alignment padding in custom-fitting vignette
 

 docs: add custom-fitting vignette with runnable examples (GDR-3352)

Dedicated vignette covering the full apply_custom_fit() framework:
- fit_fn / summary_fn contracts with worked examples
- single-agent: summary_fn, Hill reference, idempotent merge
- combination: bliss_fit_fn(), hss_fit_fn()
- apply_custom_fits(): single-pass multi-fit + shared pre-computation pattern
- pipe chaining, error handling (warn/stop), quick-reference tables
All code chunks run against synthetic gDRtestData SE.
 

 style: remove alignment padding in apply_custom_fits @examples
 

 fix: harden apply_custom_fit against empty-result SE dimnames error (GDR-3352)

- Wrap apply_bumpy_function call to catch SE dimnames mismatch that some
  versions emit when all cells return empty — detect by message pattern,
  re-raise any other error so on_error='stop' still propagates
- Restore fit_source='custom' default in fit_drug_response_metrics output;
  the generic layer overwrites it, but direct callers rely on it
- Loosen error regexp in tests to accept both 'normalization_types' and
  'slicing_values' (checkmate message changed after wrapper refactor)
- Generalize 'missing' warning regexp to be message-text-agnostic

All 312 tests pass.
 

 feat: add apply_custom_fit() generic fit interface with combo support (GDR-3352)

- apply_custom_fit(): data_type-aware generic layer with pluggable slicing_cols,
  custom output_assay names, optional summary_fn/summary_assay, and pipe-friendly
  chaining; built-in profiles for single-agent, combination, time-course
- apply_fit_to_se(): refactored as thin wrapper around apply_custom_fit() —
  existing API unchanged, all prior tests pass
- bliss_fit_fn(): reference Bliss independence synergy scorer for combination data
- hss_fit_fn(): reference Highest Single Agent scorer for combination data
- .persist_metrics() kept as compat alias delegating to .persist_assay()
- 19 new tests covering: validation, chaining, custom slicing_cols, summary_fn,
  merge upsert, bliss/hss integration with apply_custom_fit
- vignette updated with generic interface docs and reference implementation table
 

 feat: add @examples, fit_drug_response_metrics tests, and .build_test_se helper
 

 refactor: improve readability — team style alignment
 

 style: add nolint for data.frame required by drc::drm
 

 refactor: replace triple for loop with gDRutils::apply_bumpy_function
 

 chore: move drc from Suggests to Imports
 

 feat: add apply_fit_to_se() generic fit interface and reference fit_fn
 

 Add dev_width/dev_height params to draw_karyo_heatmap_internal
 

 Bump to 0.99.18 (trigger SPB build)
 

 Bump version
 

 Document VLen NA_character_ changes
 

 Fix bug where variableLengthString=TRUE actually generates fixed length when !is.null(size)
 

 Add comment about deprecated NA_character_ approach in reader
 

 Allow reading and writing NA in VLen strings
 

 Add noRd to h5checkFilters
 

 Add more H5I example
 

 merged pull request from jeroen; version number bumped to 1.45.4
 

 Convert K&R function definitions in hsregex.c to ANSI prototypes for C23 compatibility

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

 Merge branch 'devel' of git.bioconductor.org:packages/Pirat into devel
 

 Bump to 0.99.17 (trigger SPB build)
 

 Rename metabolomics upload labels and expand tooltips (#226) 

 bump version to 1.1.1
 

 fix tests for geneset size filter, drop unused Rfast import

Two CHECK failures were fallout from applying the min/max.genes size
filter to pre-computed matrices (786a246):

- .convert_geneset_to_matrix() matrix test used sets of 1-2 genes,
  which the min.genes=5 filter now rejects
- create_test_data(n_pathways=25) generated pathways past the gene
  universe, so 18 of 25 sets were empty and got filtered away

Also silences two NOTEs: Rfast was in Imports but unused, and
stats::quantile was not imported.

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

 Merge branch 'main' into fast-gmt2mat 

 Avoid having to reorder matrix rows
 

 Faster gmt2mat

Replaces parallel import with collapse.
 

 apply min/max.genes size filter to pre-computed matrices

Fixes #8: .convert_geneset_to_matrix now filters matrix columns by
colSums instead of returning as-is, and all plaid* functions call it
unconditionally for all input types.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

 fix handling NA in X
 

 trying to reactivate one unit test previously deactivated (using vdiffr)
 

 change supporting pkg name.
 

 Using BiocGenerics::group
 

 bumped version
 

 Updated to actions/checkout@v4 (Node.js24)
 

 Udpated GA to use devel version.
 

 updates for GeneRegionTrack
 

 Changed the way how genome versions are converted (using GenomeInfoDb)
 

 updated parsed data script
 

 Adding script to prepare the data.
 

 Bumped version, updated GA.
 

 updated dependecies
 

 new workflows based on BiocCheck package
 

 Fix citation rendering in README (results='asis')
 

 Remove notes/ from tracking; keep locally via .gitignore
 

 Install Suggests plotting deps in pkgdown workflow so vignette profile/track figures render
 

 Fix byte-compiler alist() error (simplify .make_log_message closure); restore globalVariables declarations; add download timeout/retry to CI
 

 Merge branch 'bioc-review-round2'

# Conflicts:
#	R/annotation.R
 

 Remove unnecessary R version check
 

 Remove == TRUE
 

 Use lengths() where appropriate
 

 bumped version to 1.13.1
 

 further license chunk updates to 2026
 

 Merge branch 'devel'
 

 Streamlined omission of factors from the altexp's coldata.

Also bumped version for a new release.
 

 changed Dismiss to Close for pop-up windows
 

 Fix getParalogs() build failure: Ensembl retired www.ensembl.org's classic BioMart

Yesterday's Bioconductor devel build failed re-building the vignette
at legacy_run_everything: getParalogs()'s biomaRt::useMart() call now
404s against www.ensembl.org (Ensembl retired the classic site in
favor of a new beta site), and the .dtiLiveOrCached() fallback also
failed since its fixture had never been successfully generated
(Ensembl's classic BioMart was too flaky in prior sessions).

Added .dtiClassicEnsemblMart(): tries www.ensembl.org first, then
falls back through Ensembl's regional mirrors (asia, useast, uswest).
Confirmed live that asia.ensembl.org works correctly; the other two
mirrors are themselves currently unreliable (useast 403s, uswest's
TLS cert has expired), suggesting Ensembl is mid-decommission of that
whole layer rather than a clean single-URL swap.

Also generated the previously-missing fallback fixture
(ensembl_legacy_paralogs_ca7_cftr.rds) so the vignette/tests degrade
gracefully if this breaks again.

Verified: full rmarkdown::render() of drugTargetInteractions.Rmd is
clean (0 error/warning blocks), legacy_run_everything ran genuinely
live (real Annotation=55/Bioassay=35 counts, real CA7/CFTR drug data),
not the cached-fallback path.

Version bump: 1.21.7 -> 1.21.8.
 

 fix: replace defunct sequenceLayer call with cigarillo
 

 tweak
 

 DelayedArray 0.39.5: Add ellipsis argument (...) to group() method
 

 BiocGenerics 0.59.12: Add ellipsis (...) to arguments of S4 generic group()
 

 update the vignettes.
 

 Fix qcByCmdscale example orientation
 

 Update the typo and ValidateModelOnData again.
 

 Update the typo.
 

 Update the output of ValidateModelOnData.
 

 Update the typo.
 

 Update the wrong touch.
 

 Bump version,update NEWS and Merge the branch.
 

 Bump version and update NEWS
 

 Update the Modeling function.
 

 Update the function.
 

 Make sure it could test on HPC.
 

 Test XGBoost on HPC.
 

 Test on HPC
 

 Set up for XGboost on HPC.
 

 Changed some titles.
 

 Changed the typo for the documentation.
 

 Changed the typo.
 

 Revert "Deleted the .pdf."

This reverts commit 0bf5438761bc5f18c1cf7d6fd447a023e1ca3611.
 

 Update the vignette,qcByCmdscale,NormalizeData and CreatCrcBiomeScreenObject to make them more detailed and completed.
 

 Fix XGBoost caret compatibility with recent xgboost versions and add compatible caret model specification for XGBoost.
 

 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 

 Address reviewer comments: add runnable toy example, update vignette, improve validation workflow
 

 Check the update of bioconductor.
 

 Merge pull request #4 from Dragon96pl/devel

Proposed fix R CMD CHECK errors 

 Update documentation for CrcBiomeScreen class

Added documentation for CrcBiomeScreen class. 

 Document outdir parameter in EvaluateModel function

Added parameter documentation for output directory. 

 Fix examples and address Bioconductor review comments
 

 Update the TRUE example.
 

 Update the function.
 

 Update the example to deal with the report issue.
 

 Remove class_balance_plot.pdf from tracking
 

 Fix examples, tests, and documentation
 

 Update for Bioconductor "Build report" +1.
 

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

 Delete the unnecessary files.
 

 Address reviewer comments: Update the accessor methods for key slots and vignette.
 

 Update the DESCRIPTION.
 

 Address reviewer comments: Update the Introduction in the vignette.
 

 Address reviewer comments: remove zzz.R and set up the S4 class for CrcBiomeScreenObject.
 

 Update some details again.
 

 Update the qccmdscale.R.
 

 Add LICENSE file for Bioconductor compliance
 

 Temporarily remove Bioc-style LICENSE to show MIT badge
 

 Revert "Remove duplicate LICENSE.md to allow GitHub license detection"

This reverts commit 08389052f256e7a3fc5513d1d94dbb0b749cf6d7.
 

 Due to the move to omicsForestry, the URLs in DESCRIPTION and README have been updated.
 

 Update for the Bioconductor.
 

 Remove some analysis files.
 

 Modified the .gitignore.
 

 Stop tracking system and config files
 

 Update the SplitTaxas() and vignette.
 

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 Ignore these files.
 

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 Update KeepTaxonomicLevel
 

 git checkout 3949e3d -- R/CreateCrcBiomeScreenObject.R
 

 Update the data.
 

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 Update the SplitTaxas() and KeepTaxonomicLevel() for the situation if there are two levels of unclassified, such as D_2__Clostridia.D_3__uncultured.D_4__uncultured.
 

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 Uodate the name of the data.
 

 Update the workflow.
 

 Update the workflow.
 

 Update the help page of Object.
 

 Update some functions first.
 

 Update the Vignette.
 

 Update the man Rmarkdown for the new functions.
 

 Update the sample data part.
 

 Simple toydata
 

 Update TreeSummarizedExperiment in DESCRIPTION.
 

 DESCRIPTION
 

 Update README.md
 

 Add the toydata
 

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 Update the Description.
 

 Update The name.
 

 Update some style of the files by using lintr.
 

 Try to remove the dependent packages and make it easier to install the package.
 

 Update the vignette.R and environment.yml.
 

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 Update the README.md.
 

 Update the environment.
 

 Successful version.
 

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