Remove html
 

 Fix connectivity raincloud regression and restore p-value subtitles
 

 version
 

 Remove dependency on Organism.dplyr (package removed in Bioc 3.24)
 

 igblastr 1.3.1: Fix representation of missing values in custom annotations

We cannot use the string NA to represent missing values in the custom "ndm"
or ".aux" files that we create, because this crashes IgBLAST!
So now we use the following special values instead:
  o "N/A" for missing character values;
  o -1 for missing integer values.
See long comment at the top of R/igdata-IO.R for more information.
 

 Bump version to 0.99.1
 

 Remove local history and system files
 

 R version updated
 

 hexasticker updated
 

 Bump version to trigger webhook build
 

 remove swap file
 

 fix missing semicolon
 

 Merge branch 'devel' of github.com:BiocStaging/ontoProc2 into devel
 

 Merge remote-tracking branch 'bioc/devel'
 

 Merge upstream/devel: resolve version conflict
 

 Fix: suppress mbest warnings in function_run_cytoGLMM and update test expectations
 

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

 fix vignettes
 

 update
 

 1.40.2
 

 Optimize tests for SPB build time
 

 making changes according to the reviewer's suggestions
 

 Reduce SPB runtime and bump version
 

 upd doi cov data
 

 Update docker files
 

 Update Rscript command to install packages with remotes 

 Replace devtools with remotes for package installation in Docker 

 Bump version
 

 Merge pull request #28 from microbiome/tracker

Code tracker, general observers and exports 

 Add general observers, code tracker and exports
 

 Enable vignettes, citation and session buttons
 

 Add tracker prototype
 

 Split landing page definition into multiple functions
 

 Renamed runPca() arguments for centering scores per block.

We also respect the C++ default (which is now the same as the R default).
 

 Merge remote-tracking branch 'upstream/devel'
 

 Streamlined spike-in sections with dedicated scrapper functions.
 

 Update to scran_variances.
 

 Bump version and reduce Bioconductor check time
 

 refactor: fix and reformat group_mz_int
 

 update info to description
 

 change 1:length(x) to seq_along(x)
 

 devel notes suggestions
 

 Merge branch 'main' of https://github.com/MuyaoXi9271/MsCoreUtils
update
 

 Merge branch 'rformassspectrometry:main' into main
 

 Merge branch 'main' of https://github.com/MuyaoXi9271/MsCoreUtils
 

 add documentations for this function
 

 add test file for the function "group_mz_int"
 

 Merge branch 'rformassspectrometry:main' into main
 

 Merge branch 'rformassspectrometry:main' into main
 

 test
 

 upd zenodo link
 

 incl doi/biocCheck badge
 

 test revision
 

 Final revisions
 

 Fix pkgdown
 

 Fix vignette: add library(dplyr) to comparison-table chunk
 

 Fix pkgdown: add missing topics to reference index
 

 Fix Ci8
 

 Fix Ci6
 

 Fix Ci4
 

 Fix Ci2
 

 Fix CI4
 

 Fix CI2
 

 Fix CI: use Rscript -e for R commands
 

 Fix enrichplot::cnetplot deprecated arguments
 

 Fix target assignment priority and distal stats bugs2
 

 Fix target assignment priority and distal stats bugs
 

 Merge pull request #1 from Bisaloo/bioc-review

Misc fixes from Bioconductor review 

 fixed
 

 Remove redundant `choices` arg from match.arg
 

 Use anyNA() where appropriate
 

 v bump post doi upd
 

 update NEWS
 

 Bioconductor 0.99.17 Rcmd Time
 

 Bioconductor 0.99.15 Report
 

 Bioconductor 0.99.15 Report
 

 v bump
 

 Removed bam2junctions() from current release
 

 dynamically adjust citation to reflect v bump
 

 Bump version
 

 Fix bool v3 datatype
 

 version patch bump after minor doc upd
 

 upd v bumps and readme.
 

 Run devtools::document()
 

 Fix typo
 

 Generalized conversion functions to work with all NN results.
 

 Add conversion functions from findKNN output to sparseMatrix, SelfHits (#33)

Co-authored-by: LTLA <infinite.monkeys.with.keyboards@gmail.com> 

 Update devel branch
 

 Bioconductor tests updates (#39) 

 Bioconductor tests

* version bump: 0.99.0 -> 0.99.1

* Fix: shorten Rd example comments to comply with line width limits

* version bump: 0.99.2 -> 0.99.3

* Fix .gitignore: remove regex-problematic comments and ensure newline at EOF

* version bump: 0.99.3 -> 0.99.4

* Simplify .gitignore: remove problematic patterns and comments

* version bump: 0.99.4 -> 0.99.5

* Remove CITATION file: no doi yet for new package

* version bump: 0.99.5 -> 0.99.6

* Tests fixed

* Fix issues

* Skip tests

* Bump version

* Fix issues

* Bump version

* Fix .gitignore

* Bump version

* Fix tests

* Bump

* Fix issues

* Fix tests

* Fix tests

* Speed up examples

* Fix coding style 

 Fixed a bug related to enricher_internal function.
 

 Bump version from 1.19.0 to 1.19.1 

 updated NEWS
 

 Updated various libraries to their latest versions.
 

 Check for IRLBA convergence in scoreGeneSet, because why not.
 

 Updates to align to the updated C++ option defaults.

Specifically we remove overrides in sanitizeSizeFactors, subsampleByNeighbors,
because now we can just use defaults directly from the corresponding Options.
 

 Respect IRLBA's default extra_work for better performance.

Also provide the option to modify the convergence tolerance.
 

 Preserve assay dimnames for QC functions to match to character subsets.
 

 Cleaned up docstrings, minor elaboration to test, import stats.

Also some minor changes for a roxygen update.
 

 Added SE-friendly wrapper for variance decomposition with spike-ins.
 

 Tidied up the C++ code.

- Use sanisizer consistently for resizing, reserving, container creation.
- Avoid copying of weight vectors for aggregate_across_genes.
- Reduce duplicate code for output vector creation in combine_factors.
 

 Optionally skip trend fit or block averages in modelGeneVariances.
 

 replace limma topTableF by topTable 

 version bump 1.15.1
 

 add .Rbuildignore and update .gitignore
 

 add chunk labels to vignette

assisted-by: Gemini CLI gemini-3-flash-preview
 

 require full question in askUserYesNo
 

 remove BiocDeveloper-package.R
 

 add package to Suggests
 

 Updated the vendored version of igraph.
 

 chore: remove task number from NEWS.md
 

 Version bump
 

 Update example_data
 

 Revert "feat: allow different jaspar DB sources"

This reverts commit 2a431581923b58831b8f3c0916773e3790f7c23a.
 

 Use multi-signal SPB detection so skip actually fires on SPB

testthat::skip_on_bioc() only checks IS_BIOC_BUILD_MACHINE, which is
not set on Bioconductor's Single Package Builder (verified across
0.99.10-0.99.14: testthat consistently ran the full suite and 0.99.14
hit the 10-min check WARNING with all skipped tests still running).

Replace skip_on_bioc() with .skip_on_bioc_spb() in 4 slow test files;
the helper checks four signals (biocbuild user, bbs- in R.home(),
BBS_HOME, IS_BIOC_BUILD_MACHINE). Inert on devtools::test, CI, and
user installs - same default coverage as before.

This fixes the only remaining issue from 0.99.14 (Status OK, 10-min
WARNING). Local SPB-simulated check: 25s build + 3m23s check.
 

 add .BBSoptions to .Rbuildignore
 

 version bump 1.31.3
 

 update roxygen 8.0.0 and resolve notes
 

 Fix BiocCheck 80%-runnable-examples ERROR and SPB testthat timeout

Examples (man + roxygen sources kept in sync):
- 7 pipeline-function examples (annotateCluster, callEnhancer, clusterTSS,
  consensusCluster, deGene, shapeCluster, shiftPromoter) rewritten to
  display the corresponding pre-computed slot of exampleTSSr instead of
  re-running expensive computation. Examples are now runnable and fast,
  satisfying BiocCheck's "80% must have runnable examples" rule.
- 6 plot-function examples (plotCorrelation, plotDE, plotInterQuantile,
  plotShape, plotTSS, plotTssPCA) had \donttest{} removed; they run on
  pre-computed slots and finish in seconds.
- Roxygen @examples blocks in R/AnnotationMethods.R, R/ClusteringMethods.R,
  R/ConsensusMethods.R, R/EnhancerMethods.R, R/ExpressionMethods.R,
  R/ShapeMethods.R, R/ShiftingMethods.R updated so roxygenise() will not
  regenerate the old slow examples.
- Result: 0 of 28 man pages now use \donttest{} (was 13).

Tests:
- test-analysis.R top-level setup (mergeSamples → ... → consensusCluster)
  is now gated behind a Bioconductor-build-machine detection guard. This
  was the actual cause of the SPB testthat TIMEOUT in 0.99.11: the heavy
  pipeline ran outside any test_that block, where skip_on_bioc() cannot
  reach. Multi-signal detection (biocbuild user, bbs- in R.home(),
  BBS_HOME, IS_BIOC_BUILD_MACHINE) keeps SPB safe; everywhere else the
  setup runs normally.
- test_that bodies in test-{analysis,workflow,clustering,vapply-lapply}.R
  use standard testthat::skip_on_bioc() (Bioconductor's canonical idiom.

Local SPB-simulated R CMD check (IS_BIOC_BUILD_MACHINE=true): build 25s,
check 3m23s, Status OK, tests 0 FAIL / 16 SKIP / 118 PASS. Bumps version
to 0.99.14 to trigger SPB rebuild.
EOF
)
 

 passing check, repaired an issue with synonym filtering
 

 use vector for double bracket subset
 

 add all options to event argument
 

 Bump version to 0.99.11 to trigger SPB rebuild
 

 Wrap heavy examples in \donttest{} to fix SPB R CMD check timeout

The 0.99.9 build hit a 15-minute timeout in 'checking examples'.
Wrap pipeline-level examples (clustering, annotation, DE, shifting,
shape, plots) in \donttest{} so R CMD check parses but skips them.
Lightweight examples (data load, accessors, exports) still run.

Bump Version to 0.99.10 and Date to trigger SPB rebuild.
 

 Remove pkgdown GitHub Actions workflow

The pkgdown workflow built a static site into docs/ and pushed it back
to master on every commit. This conflicts with reviewer feedback on
issue #2222 (hpages, 2026-02-03, item 5):

  "All the stuff in the docs/ folder is static and was generated in
   2021! How do we know it's still in sync with the content of the
   package? My bet is that it's probably not, and there's no easy way
   to know, which is why this kind of static content is strongly
   discouraged. Please consider removing this folder."

We removed docs/ in commit 9d930bbf and added it to .gitignore. The
workflow has been failing on every push since (git add docs/ blocked
by .gitignore). Removing the workflow entirely is the cleanest fix
and aligns with the reviewer's direction. Once the package is
accepted, Bioconductor itself will build documentation pages.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 

 TSSr 0.99.9: address Bioconductor reviewer feedback (issue #2222, hpages 2026-02-03)

DESCRIPTION
- Bump version to 0.99.9; date 2026-05-01.
- Bump R dependency to >= 4.6.0 (Bioc 3.23 devel).
- Move rmarkdown from Imports to Suggests.
- Drop GenomicAlignments dependency (only seqnames was used).
- Add txdbmaker (>= 1.0.0) to Imports for makeTxDbFromGFF.
- Add withr to Suggests (used by tests).
- Add NSF funder ('fnd' role) to Authors@R.

NAMESPACE
- Import makeTxDbFromGFF from txdbmaker (fixes undefined global NOTE).
- Drop GenomicAlignments imports.

R code style (BiocCheck NOTEs)
- Replace all sapply() with vapply()/lapply() as appropriate.
- Replace cat()/print() with message() outside show methods.
- Replace = with <- for assignment throughout R code.
- Replace == "TRUE"/"FALSE" string comparisons with isTRUE()/isFALSE().

R/Aclasses.R
- Add TSSr() constructor with input sanity checks (per reviewer item 1).
- Add validity method on TSSr S4 class.
- Replace deprecated representation() with slots = list(...).

R/ImportFunctions.R
- getTSS() now checks file existence and fails gracefully when input
  BAM/BED/BigWig is missing (per reviewer item 2).
- Replace direct @seqnames slot access with seqnames() accessor.
- Remove spurious stringsAsFactors = FALSE from data.table() calls
  (data.table does not accept this argument; created phantom column).

R/NormalizationMethods.R
- Remove unused .getGenome() call; normalization no longer requires
  loading a BSgenome.

R/ConsensusMethods.R
- Guard single-sample case in consensusCluster (was reverse 2:1 loop
  causing crash when only one merged sample).

R/ExportMethods.R
- Replace direct @seqnames slot access with seqnames() accessor.

R/FilteringMethods.R
- Remove duplicated .filterWithPoisson() definition.

man/
- Add runnable examples (no donttest/dontrun) to all 18 man pages
  flagged by reviewer: callEnhancer, clusterTSS, exportClustersTable,
  exportClustersToBed, exportDETable, exportEnhancerTable,
  exportShapeTable, exportShiftTable, exportTSStable,
  exportTSStoBedgraph, getTSS, plotCorrelation, plotDE,
  plotInterQuantile, plotShape, plotTssPCA, plotTSS, shapeCluster,
  shiftPromoter.
- Rewrite exampleTSSr.Rd Format section to correctly describe the
  S4 TSSr class (was misleadingly worded as
  'RangedSummarizedExperiment:TSSr').
- Replace 'Large List' \value descriptions with concrete return types.
- Document TSSr() constructor with examples.

tests/testthat/
- Add test-bugfixes.R (regression coverage for v3 audit findings).
- Add test-constructor.R (TSSr() constructor + validity).
- Add test-getTSS-error.R (graceful failure on missing input files).
- Add test-vapply-lapply.R (assert no sapply remains in R/).
- Add test-export.R, test-export-methods.R, test-plot.R, test-analysis.R,
  test-workflow.R for broader functional coverage.

vignettes/vignette.Rmd
- Reduce eval=FALSE chunks to the minimum (only chunks needing BAM
  inputs not bundled in package).
- Add proper Introduction section and headers.

Removed
- docs/ (static pkgdown output from 2021; out of sync, strongly
  discouraged per reviewer item 5).
- Meta/vignette.rds (generated by R CMD build, should not be tracked
  per reviewer item 6).

Bioconductor dependency review
- All Imports verified against actual code usage under R/.

Local checks (R 4.6.0, Bioc devel 3.23, BiocCheck 1.48.0):
- R CMD check: 0 ERROR, 0 WARNING.
- BiocCheck: 0 ERROR, 0 WARNING, 6 NOTES
  (style/recommendation only: function length, line width,
  biocViews suggestion, R version recommendation, indent multiples,
  mailing-list subscription detection).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 

 Fix BiocCheck issues: add funder, fix code style and formatting
 

 version bump 1.31.1
 

 update vignette with LC
 

 Links updated in DAA page (#855)

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

 Minor fix
 

 Added scColPairRatios
 

 Fixed tests
 

 Post-release update
 

 improved manual page for bam2junctions
 

 reduce repetitive catalog code in examples
 

 version bump 1.9.2
 

 simplify lapply call in import TENxSpatialList
 

 Updated build number
 

 Bumped version
 

 Update example_data
 

 Merge branch 'main' of https://github.com/carmonalab/scECODA
 

 Version bump
 

 example_data restructured
 

 Minor fix
 

 Minor fix
 

 Merge remote-tracking branch 'origin/master' into devel
 

 Minor fixes
 

 Merge branch 'master' of github.com:edyp-lab/DaparToolshed
 

 fix reviewers comment
 

 Remove unwanted files 

 Add tests
 

 Add tests
 

 Add files via upload 

 Update DESCRIPTION file
 

 Fixing error and warning 

 Update .gitignore file
 

 Add a test case with an anchor adjacent to a TSS
 

 Update date of revision
 

 Update to 99.34
 

 changes
 

 Update NEWS
 

 plot_pca: fixed "Number of cell types/genes" showing number of samples
 

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

 1. Removed the rols package and developed custom internal functions for retrieving tissue ontology.
2. Removed the scran and scuttle packages, and related functions are replaced with counterparts in bluster and scrapper respectively.
 

 Fixed attachCellScores
 

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

 NEWS.md: align top-level header with DESCRIPTION Version (1.23.0)

The Phase-19 rebase inherited Bioc's post-RELEASE_3_23 version bump
(DESCRIPTION 1.23.0) but the NEWS.md header still said
"1.21.1 (development)". Aligning the two so the release-tag body
reads coherently against the actual version.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
 

 Phase 19 - Consolidated NEWS.md, final BiocCheck audit, and Bioconductor release

* NEWS.md: added Phase 14-18 supplement under the existing 1.21.1
  stanza (Bug fixes for #100/#92/#76/#89/#94/#66/#65/#42/#91; new
  consensusMethod feature for #87/#48/#33; documentation overhaul
  for #13/#49/#71/#99 plus run-donttest example hardening).

* Migrated three legacy DCF stanzas (1.6.1, 0.99.1, 0.1.0) from
  the deprecated NEWS file into NEWS.md; removed the legacy NEWS
  file (resolves BiocCheck "More than 1 NEWS file found" note).

* vignettes/sangeranalyseR.Rmd: moved `eval=FALSE` from a global
  knitr::opts_chunk$set() to per-chunk on the 13 user-recipe
  blocks. The 4 infrastructure chunks (style, setup,
  locate-fixture, session-info) now evaluate at build time,
  resolving BiocCheck's earlier "global eval=FALSE" warning while
  keeping the recipes (which reference user paths and Shiny apps)
  unevaluated.

Final audit:
- testthat: 1451 / 1451 PASS.
- R CMD check (--no-manual): 0 errors / 0 warnings / 0 notes.
- BiocCheck: 1 ERROR (Support Site HTTP 504 - environmental),
  2 WARNINGS (devel y-parity false positive + intentional vignette
  chunk evaluation choice), 15 NOTES (all stylistic /
  environmental). See plans/19_final_release_log.md for the full
  enumeration.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
 

 Phase 17 - Resolved Sprint 3 consensus issues (#87, #48, #33)
 

 Phase 16 - Resolved Sprint 2 robustness issues and fixed reply formatting
 

 Phase 13 - Final audit + Bioconductor upstream sync

* Final audit results captured in plans/13_final_release_log.md:
  - devtools::test():   1360 / 1360 PASS
  - rcmdcheck:          0 errors / 0 warnings / 0 notes (strictly clean)
  - BiocCheck:          1 / 1 / 17, all known environmental / advisory
                        items documented in Phase 9-10 logs
                        (Support Site, devel-branch y-parity, sapply,
                        <<-, function lengths, etc.)

* Lingering ignore-file housekeeping committed:
  - .Rbuildignore + ^\.positai$
  - .gitignore + .positai

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
 

 Phase 11 - Overhauled README and finalized documentation
 

 Phase 9 - Automated UI tests, dependency cleanup, and clean BiocCheck
 

 Phase 7 - Ported peakvalues logic to Rcpp for native performance
 

 Add Phase 5 E2E validation report and profiling artifacts

Runs the full SangerAlignment pipeline (8 ABIF reads, 4 contigs from the
ACHLO fixture) under both M1 and M2 trimming, captures per-stage wall
times and an Rprof sample, and validates 15 structural / determinism /
slot-equality invariants. All checks PASS.

Headline timing: full ingest + trim + assemble + cross-align ~1.85 s
under M1 and ~1.74 s under M2 (~225 ms per read). updateQualityParam
re-trim costs ~53% of a from-scratch run (skips ABIF parse + base
calling).

Profile finding: the dominant costs are NOT IO or DECIPHER alignment.
- Biostrings::translate (3 reading frames per read) ~35% of total
- MakeBaseCallsInside (peakvalues inner loop) ~32% (~16% self)
- DECIPHER alignment ~16%
- read.abif IO ~9%
- setValidity / S4 dispatch ~3%

Lazifying calculateAASeq and Rcpp-ising peakvalues are the two highest-
leverage local wins. BiocParallel migration of the per-SangerRead
construction loop (~84% of total wall time) remains the biggest
parallelism opportunity.

Artifacts under plans/phase5_artifacts/: run_e2e.R reproducer, full
stdout log, timings CSV, raw Rprof samples (compatible with profvis),
summaryRprof text breakdowns for M1 and M2, accuracy / slot-invariant
PASS logs.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
 

 Add comprehensive testthat coverage for validators, axes, and invariants

* Re-enable test_check() in tests/testthat.R so R CMD check runs the
  suite (was commented out).

* Fill the previously-empty test-Constructors.R with smoke tests for
  the SangerRead / SangerContig / SangerAlignment wrappers.

* New test files:
  - test-Validator-EdgeCases.R: 21 negative tests covering invalid
    extensions (.Xfa, .Xab1, .ab2, .fast), empty / corrupt / truncated
    .ab1 files, malformed CSVs (4 schema variants), out-of-range
    scalars (10 variants).
  - test-OrthogonalAxes.R: 6 cells of inputSource x processMethod x
    TrimmingMethod, asserting each combination yields a valid
    SangerAlignment.
  - test-SangerRead-SlotInvariants.R: byte-equality between SangerRead
    raw slots and the sangerseq parent class (guards a future slot
    refactor).
  - test-IO-Batching.R: hidden-file / nested-directory behaviour and a
    list.files call-count regression baseline.
  - test-Coverage-Smoke.R: breadth coverage for qualityBasePlot,
    MakeBaseCalls, readTable, writeFasta, updateQualityParam.
  - test-Validator-Helpers.R: direct unit tests for the new dot-prefixed
    helpers in UtilitiesFuncInputChecker.R (via asNamespace).
  - test-Regex-Boundary.R: pins the escaped extension regex against
    .Xfa, .Xab1, .fast, .faa, .ab1.bak, etc.
  - test-S4Validity.R: confirms the new setValidity methods reject
    malformed instances after slot mutation.
  - helper-Fixtures.R: 11 synthetic-fixture builders writing to
    tempdir(), used by the negative tests.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
 

 fix: FLAMES bulk quantification sample name error
 

 altered cellCounts for supporting single-cell junction detection.
 

 Removing bamsignals dependency and adding regionCounts to compute read counts. Removing C++11 flag from Makevars.
 

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

 Merge branch 'devel' of github.com:jtlandis/plyxp into devel
 

 Merge pull request #7 from mikelove/devel

update language on the two packages 

 update language on the two packages
 

 Update vctrs-S4-unchop.R
 

 We can save time when we know there are no groups.
 

 Update NEWS
 

 Adding note about recent error
 

 Merge branch 'devel_groups_on_DFrame' into devel
 

 version bump
 

 typo
 

 We should support "vctrs_vctr" as well
 

 This should cause plyxp github pages to render... finally
 

 Update test_dplyr_summarize.R
 

 Update NEWS
 

 no docs
 

 need to prevent recusion case
 

 Update NEWS
 

 use the correct group_data accessor
 

 remove type attribute and instead store group information on rowData and
colData
 

 add loadImage argument to TENxVisium(HD) constructors and classes, closes #24
 

 Bump version
 

 Bump version
 

 Bump
 

 Bioconductor 3.24 devel
 

 Bioconductor 3.23 release
 

 Bioconductor 3.24 devel
 

 Bioconductor 3.23 release
 

 Fix tests
 

 Add skip_on_bioc
 

 Fix coding style
 

 removed wrong return on null grouping and fillNULL=TRUE
 

 added missing import
 

 explicit Matrix imports
 

 minor speedup
 

 keep background data sparse, improve var computation
 

 Merge pull request #186 from gdrplatform/GDR-3369

GDR-3369: update author email address 

 chore: trigger CI
 

 chore: trigger CI
 

 chore: fix version bump in DESCRIPTION
 

 chore: update author email address
 

 chore: trigger CI
 

 chore: resolve conflict, bump version to 1.11.3
 

 chore: update author email in R source files
 

 chore: update author email address
 

 Fix tests
 

 Add warning message when the input is not unique for genomicElementDistribution.
 

 Added partisub, updated other libraries.
 

 Bump version
 

 version bump
 

 text improvements
 

 Update maintainer
 

 add NEWS entry for 0.99.1
 

 Merge pull request #193 from gdrplatform/GDR-3366

GDR-3366: fix handling of NA Duration 

 chore: merge main and update version to 1.11.2
 

 fix: handle NA Duration in Day0 detection and GR value calculation
 

 chore: merge main and update version to 1.11.2
 

 GDR-3366: replace hardcoded Duration values with NA_real_
 

 bump version
 

 update R requirement
 

 Fix issues
 

 Fix tests
 

 Bump version
 

 Bump version
 

 Merge upstream devel changes
 

 Skip tests
 

 Tests fixed
 

 Remove CITATION file: no doi yet for new package
 

 Simplify .gitignore: remove problematic patterns and comments
 

 Fix .gitignore: remove regex-problematic comments and ensure newline at EOF
 

 Fix: shorten Rd example comments to comply with line width limits