Update DESCRIPTION and NEWS
 

 fix test to stricter
 

 pass fileName to backendInitialize()
 

 ci: trigger build
 

 chore: bump version to 1.11.5
 

 next bioc submission
 

 Trim vegan dependency, add seed/print UX, progress bar (v1.1.5)

Move vegan from Imports to Suggests: PERMANOVA F is computed directly and
adonis2 is never called at runtime, so users no longer install vegan and its
transitive dependencies. vegan is retained in Suggests for the vignette's
benchmark comparison only.

Remove unused stats imports (aov, as.dist, t.test) and an unreachable t-test
pre-filtering branch. Replace per-permutation messages with a progress bar.
Add an optional seed argument and a 'melsi' S3 class with a print() method;
the return value is still a list so $ access is unchanged.

All statistical results are byte-identical to 1.1.4, verified on fixed-seed
pairwise and multi-group runs; the method is unchanged.
 

 test: add skip_long_checks() guards to reduce Bioc check time (#84)

* chore(DESCRIPTION): bump version to 0.99.3.9000

* test: add skip_long_checks() guards to reduce Bioc check time

* test(makeQset): skip calculateCGEnrichment under skip_long_checks

The test also fails in CI due to strand<- not being found in the MEDIPS
namespace, on top of being slow. Guarding with skip_long_checks() stops
the error without removing the test for local runs.

* docs(NEWS): update to include PR numbers

---------

Co-authored-by: Steven Hill <8912559+Steven-M-Hill@users.noreply.github.com> 

 Document BPPARAM parallel permutation testing (v1.1.4)

Surface the existing BPPARAM argument to melsi() with worked examples in
the README and vignette and a NEWS entry. Pass a BiocParallelParam object
(e.g. MulticoreParam(workers = 8)) to run the permutation loop in parallel;
default NULL runs sequentially.
 

 FIX: Correct version number for Bioconductor devel
 

 Update documentation
 

 plot_boxplot: added parameter plot_signif to prevent clutter if many cell types and/or groups are plotted
 

 Add addtional tests and fix bug
 

 Add new tests
 

 Add addtional tests
 

 Fix bugs and add tests
 

 Fix notes and failing test in Mac
 

 Remove formatting from RNA-seq analysis questions (#43) 

 Bump version to 2.21.1 and document efficiency improvements in NEWS
 

 Speed up filter dedup, sparse-distance scatter, dendro coercion and adjacency

Four optimisations in R/netboost.R:

* nb_filter: replace unique(t(apply(filter,1,sort))) with vectorised
  unique(cbind(pmin,pmax)) (byte-identical).
* nb_mcupgma (dense hclust path, <30k features): vectorise the per-edge
  scatter of sparse distances into the lower-triangle vector
  (byte-identical).
* tree_dendro: storage.mode()<-integer instead of element-wise
  apply(...,as.integer) (byte-identical).
* calculate_adjacency (Pearson/Spearman): for <=~7900 features compute
  the correlation matrix once and index edges (byte-identical); above
  that, where a dense p x p matrix neither fits nor stays under R's 2^31
  vector limit, use a chunked edge-wise standardised crossprod that
  scales to >50k features (e.g. 60k in ~1s). The crossprod evaluates the
  identical Pearson formula and differs from WGCNA::cor only by
  floating-point rounding (~machine epsilon for the scaled data used in
  the pipeline). Kendall keeps the per-edge loop.
 

 Merge pull request #122 from gdrplatform/GDR-3439

fix: fall back to Background section barcode in EnVision parser 

 ci: trigger build
 

 fix: fall back to Background section barcode in EnVision parser

Some EnVision exports have the barcode only in the Background
information section, not in the Plate information header. This caused
plates to be silently skipped during import.

GDR-3439
 

 Logo rebranding
 

 Get rid of huge inefficiency in create_region_db() and family

With this change, install_IMGT_germline_db(), install_custom_germline_db(),
and reset_germline_dbs() are about twice faster.
 

 put a stop threshold on findLQR
 

 Fix a bug in featureAlignedExtendSignal when input is GAlignmentPairs.
 

 version bump 1.53.4
 

 update color.pathway.by.objects to use new kegg/webapp/color_url docs

authored-by: gemini 3.5 flash
 

 update NEWS
 

 add orthology examples and unit tests
 

 replace organism with genome in keggList, organism error stands, refers to #30
 

 Fix the coordinates issue for init.
 

 feat(topics): add unsupervised approach NMF for topic clustering (#106) 

 version bump, 0.99.1
 

 added info on core iSEE + extension writing
 

 Add Sabuj (#832) 

 updated version number to 2.27.4
 

 Fix the issue applied the coordinates twice.
 

 update URL of the file listing intergenic releases*
 

 Merge branch 'bioc_devel' into bioc_master
 

 Merge branch 'bioc_devel' into bioc_master
 

 version bump
 

 adding support for salmon mixed references
 

 Remove section
 - resources no longer available
 

 added BiocStyle to Suggests
 

 more figures saved just in case, also silly animation of how amplican works
 

 Merge upstream devel
 

 Resolve DESCRIPTION merge conflict
 

 Added URL and BugReports to DESCRIPTION 

 Update vignette
 

 refactor: enforce alphabetic ordering of files (issue #20)
 

 update check bioc yml to latest version of bioc
 

 update checkbio file
 

 Update simReads to define effective transcript length in the same way as RSEM, kallisto and Salmon.
 

 remove white spaces around = . version bump to v2.2.3
 

 Merge branch 'issue-18' into devel
 

 docs: stamp NEWS dev section as 2.81.21 (2026-06-13); add #162 ref

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
 

 Merge branch 'devel' of https://github.com/seandavi/GEOquery into devel

# Conflicts:
#	DESCRIPTION
 

 feat: optional BiocFileCache-backed download cache (#171) (#193)

The historical "cache" only re-uses files already present in destdir, which
does not persist across sessions, guard partial downloads, or key on the
source URL. Add a proper persistent cache backed by BiocFileCache:

- geoCache() returns the BiocFileCache (default tools::R_user_dir("GEOquery",
  "cache"); override with options(GEOquery.cache.path=)); clearGEOCache() wipes
  it. Both exported.
- downloadFile() consults the cache (lookup by URL -> copy into place) and
  populates it on a miss, all wrapped so a cache failure never breaks a
  download.
- Opt-in via options(GEOquery.cache = TRUE); default off preserves current
  behavior for one cycle.

Adds BiocFileCache to Imports and an offline test of store/lookup/clear. Bumps
version to 2.77.20.

Refs #171

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 docs: narrative pkgdown articles + lean indexing vignette (#156) (#191)

Restructure the documentation around descriptive, narrative pkgdown articles
that explain the why and the how -- GEO entity types and file formats, the
SOFT vs Series Matrix code paths, ExpressionSet vs SummarizedExperiment, NCBI
RNA-seq quantifications, the single-cell inspect->decide->load workflow, and
downstream analysis with links to limma/DESeq2/edgeR and the single-cell
ecosystem.

- new vignettes/articles/: geo-data-formats, rnaseq, single-cell,
  downstream-analysis (executed code disabled; prose-first, pkgdown-only)
- vignettes/GEOquery.qmd is now a concise quick-start that indexes the articles
  (satisfies the Bioconductor vignette requirement, builds without network)
- remove the old single-cell vignette (folded into the richer article)
- .Rbuildignore vignettes/articles so R CMD check never builds them; pkgdown
  renders them from source

Also dedupe a repeated NEWS bullet. Bumps version to 2.77.18.

Closes #156

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 feat: geoSingleCellUnits() loadable-unit view (#158) (#189)

* feat: geoSingleCellUnits() loadable-unit view (#158, SC2)

Collapse a single-cell manifest into one row per loadable unit (sample +
format) with a completeness assessment: a 10x Matrix Market unit is "complete"
only when matrix+barcodes+features are all present; single-file formats are
complete; others are "unsupported". The `loadable` flag drives reader
decisions. Pure logic (.sc_units), tested offline including the incomplete-
triplet and empty-manifest cases.

This is the decision layer between the manifest and the readers (next PR).
Bumps version to 2.77.16.

Refs #158

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* fix: handle empty input in .classify_sc_files (no supp files)

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 feat: getGEO returnType argument for SummarizedExperiment (#168) (#187)

Stage 1 of ADR-0002. Adds getGEO(..., returnType = c("ExpressionSet",
"SummarizedExperiment")). GSE Series Matrix results can now be returned as
SummarizedExperiment; SOFT S4 results (GDS/GPL/GSM/GSE) are unaffected.

- default stays "ExpressionSet" with a one-time rlang::inform that the default
  will change, so nothing breaks for current users
- coercion happens at the getGEO boundary via the new exported
  as_SummarizedExperiment() (wrapping
  SummarizedExperiment::makeSummarizedExperimentFromExpressionSet), so existing
  results can be modernized without re-downloading
- the internal .applyReturnType() handles list / single / non-ExpressionSet

Offline tests cover coercion and pass-through. roxygen + man/ updated by hand.
Bumps version to 2.77.14.

Refs #168 (the default flips to SummarizedExperiment in a later stage).

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 test: gate live-network tests behind GEOQUERY_INTEGRATION (#169) (#185)

The live-NCBI tests are non-deterministic and intermittently fail PR CI (e.g. a
transient getGEO("GSE53986") failure). Add a skip_if_no_integration() helper
(skips unless GEOQUERY_INTEGRATION=true, and always on CRAN) and apply it to the
network-dependent tests across test_GSE/GPL/GSM/GEO_conversions/fetch_GPL_false/
geo_rnaseq/supp_files. Offline tests -- including the bundled-data tests in
test_GDS and the GPLbroken case in test_GSE -- are left running on every PR.

Adds a weekly `integration` workflow (Bioc devel container, GEOQUERY_INTEGRATION=
true) that runs the live suite on a schedule and on demand, so GEO format drift
is still caught -- just not on the PR critical path.

PR CI now runs only the deterministic offline tests, making merge-when-green
trustworthy. Bumps version to 2.77.12.

Refs #169

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 test: confirm getGPL = FALSE skips GPL for local series matrix (#18) (#183)

#18 reported that getGEO(filename=..., getGPL=FALSE) still downloaded the GPL.
The current code forwards getGPL correctly (parseGEO -> parseGSEMatrix), so
featureData is empty and no GPL is fetched. Add an offline regression test
(via the synthetic fixture) to lock the behavior. No code change needed.

Bumps version to 2.77.10.

Closes #18

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 docs: modernize DESCRIPTION and biocViews (#71) (#181)

The Description called GEO "a public repository of microarray data" and
described SOFT parsing as if it were primary, though GSEMatrix=TRUE (Series
Matrix -> ExpressionSet) is the default and the package now also handles
RNA-seq, single-cell supplementary data, and GEO search. Rewrite the
Description to match, and broaden biocViews (GeneExpression, Transcriptomics,
RNASeq, Sequencing, SingleCell, ThirdPartyClient).

Also collapse the NEWS development header to the version-free
"(development version)" form so per-change z-bumps don't churn it.

Bumps version to 2.77.8.

Closes #71

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 fix: build supplemental-file URLs with url_join, not file.path (#131) (#178)

file.path() mangles 'https://' into 'https:/' and produces double slashes
when the base ends in '/'. Add a small vectorized url_join() helper and use it
where supplemental-file URLs are returned as strings: getGEOSuppFiles(
fetch_files = FALSE) and getGEOSeriesFileListing(). The actual download path
already used httr2::req_url_path_append() and was unaffected.

Note: the original #131 suggestion (fs::path) is itself wrong -- it also
collapses 'https://'. url_join() preserves the scheme. Adds offline tests.

No version bump (reconciliation deferred to the 3.0 batch).

Closes #131

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 fix: tolerate NA in GDS ID_REF in GDS2eSet (#21) (#177)

A single NA (or empty) ID_REF (e.g. GDS3666) produced row names with missing
values and broke ExpressionSet construction ("row names contain missing
values"). Sanitize NA/empty ID_REF to a usable name and make.unique(), mirroring
the series-matrix path. Adds an offline synthetic-GDS regression test.

No version bump (reconciliation deferred to the 3.0 batch).

Closes #21

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 fix: thread parseCharacteristics through to parseGSEMatrix (#60) (#175)

parseCharacteristics was accepted by getGEO() but dropped before reaching
parseGSEMatrix(): getAndParseGSEMatrices() and parseGEO() did not forward it,
so getGEO(parseCharacteristics = FALSE) still parsed characteristics (and
could crash, e.g. GSE23397).

- forward parseCharacteristics in getAndParseGSEMatrices() -> parseGSEMatrix()
- add parseCharacteristics to parseGEO()'s signature and forward it in the
  series-matrix branch; getGEO() now passes it on the local-file path too
- document the new parseGEO() argument (roxygen + man/parseGEO.Rd)
- add an offline regression test exercising the parseGEO forwarding path

No version bump / NEWS-header change: the DESCRIPTION-vs-NEWS version lineage
reconciliation is deferred to the 3.0 batch. NEWS bullet added under the
existing header.

Closes #60

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 ADR-0004: single-cell reader architecture (TENxIO + anndataR) (#167)

Records the decision to read single-cell formats via Bioconductor importers
-- TENxIO for 10x .mtx/.h5, anndataR for .h5ad -- in-package, in Suggests,
behind requireNamespace() guards, using their SingleCellExperiment
assemblers. DropletUtils and BPCells remain optional. Rejects DropletUtils
as a default (heavy compiled chain; broke Windows CI in #166), zellkonverter
(Python/basilisk), Seurat, and hand-rolled Matrix assembly.

Updates ROADMAP SC2/SC3/SC5 and the dependency-architecture section to match.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 Add contributor scaffolding and changelog conventions (#165)

- PR template with NEWS / tests / document / version / BiocCheck checklist
- Issue forms: bug report (accession + reprex + sessionInfo), feature request,
  config routing usage questions to the Bioconductor support site
- CONTRIBUTING.md documenting the dev loop, tidyverse NEWS style with PR links
  and @credits, version-bump rule, and required checks
- CODEOWNERS for auto review-request
- pkgdown development: mode auto (renders the "(development version)" banner)
- .Rbuildignore CONTRIBUTING.md (non-standard top-level file)

No package version bump: all changes are build-excluded.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 CI: add concurrency cancel-in-progress to workflows (#164)

* Add CLAUDE.md and ADR process

- CLAUDE.md: build/test commands, architecture overview, conventions
- adr/: Architecture Decision Records with template and ADR-0001
- .Rbuildignore: exclude adr/ and CLAUDE.md from package build

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* Add improvement roadmap and API-design ADRs

- ROADMAP.md: prioritized roadmap from multi-dimension audit (bugs, features,
  UX, docs, CI/CD, triage automation), issue staleness/feasibility triage,
  and a dedicated Single-Cell & Spatial section
- ADR-0002: staged ExpressionSet -> SummarizedExperiment return-type migration
- ADR-0003: getGEO extension policy (freeze signature; new verbs -> functions,
  IO config -> options, output-shape -> coercer)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* Exclude ROADMAP.md from package build

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* Add GEOquery 3.0 milestone and paper framing to roadmap

Maps roadmap items into the 3.0 must-ship batch vs post-3.0, with the
paper as a downstream capstone (venue, prerequisites, sequence).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* CI: add concurrency cancel-in-progress to push/PR workflows

Prevents stacked/overlapping runs when commits land in quick succession
(needed for a parallel worktree -> PR loop). No package version bump:
.github/ is build-excluded.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com> 

 we are on 1.35.1 now
 

 pkgdown on successful check
 

 further doc links fixing
 

 pre-download data in image
 

 fix NA logp
 

 removed scran imports, version bump
 

 removed mention that pairwise tests are through scran
 

 Replaced scran::findMarkers in findDoubletClusters() with a homebrew version.

findMarkers is now deprecated and its replacement does not report p-values. To
avoid changes to the results, we implement a homebrew version of the pairwise
t-tests based on scrapper's modelGeneVariances that is a drop-in substitute.
 

 bump version
 

 removed debug output
 

 disabled junction detection in cells with no valid barcodes.
 

 igblastr 1.3.10

Rename the infer_cdr3_ends_from_*() functions -> solve_cdr3_ends_using_*().

In addition to solve_cdr3_ends_using_fwr4_aa_comparisons(), the new
solve_cdr3_ends_using_fwr4_dna_comparisons() function now is also used
internally by install_IMGT_germline_db() to solve missing "cdr3_end"
values in the "auxiliary data" that gets included in the germline db,
when possible. For example, it succeeds with ferret allele IGKJ2*01.
 

 Merge remote-tracking branch 'upstream/devel'
 

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

 Convert vignette from Sweave/PDF to R Markdown/HTML

Replace qPLEXdata.Rnw (LaTeX/Sweave) with qPLEXdata.Rmd rendered as a
BiocStyle HTML document. The R code (including the contrast fix) is
unchanged; this removes the LaTeX build dependency and follows current
Bioconductor vignette conventions. Add rmarkdown and BiocStyle to Suggests
and bump version to 1.31.2.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
 

 disabled Visium HD + BCL input mode
 

 added dual index support for BCL
 

 Speed up image background plot
 

 excluded cell.barcode parameter when it is visium HD.
 

 write all spots for junction detection in visium HD.
 

 Add cell segmentation for gene expression plot.
 

 Deprecated
  requsted on bioc-devel
 

 vignette updates
 

 fix: resolve undeclared BSgenome import warning from BiocCheck

R/motif_proximity.R called BSgenome::getSeq() but BSgenome was not
declared in DESCRIPTION, which triggered the R CMD check warning about
an undeclared '::' import. Since getSeq is a Biostrings generic (already
imported) and BSgenome only supplies the method, switch the call to
Biostrings::getSeq(), matching how match_bkg.R already extracts
sequences from a BSgenome. Also add BSgenome to Suggests so the
genome-sampling code paths guarded by requireNamespace() can be
installed and exercised in the check environment.

While here, fix a quiet/quietly typo in two requireNamespace() example
blocks (sequence_complexity and utils-sequence) and their generated Rd.
 

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

 Fix DO.MultiDGE now implements glmGamPoi test after subsetting for each cell type
 

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

 bugfix
 

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

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

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

 fix bug in function DO.MultiDGE
 

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

 Addition of glmGamPoi to DO.MultiDGE analysis in pseudoBulk approaches -> additional arguments method_pb and design_fit_glm
 

 fixed multiple accumulation of read counts
 

 modified getline to fgets for windows
 

 changed the default soft-clipping enabling: enable when junction is disabled.
 

 done visium hd read mapping
 

 Bump version
 

 chore: bump version to 0.99.3 (#79) 

 fix(check): resolve R CMD check TIMEOUT and BiocCheck NOTEs (#77)

* Fix indentation: convert 2-space to 4-space per Bioconductor style guide

Applies styler::style_dir() with scope=indention, indent_by=4
across all R/ source files and vignettes/

* style: fix function argument alignment to use 4-space indentation

Replace paren-aligned continuation lines with 4-space indents in
R/buildQset.R, calculateEnrichment.R, classes.R, combineQsets.R,
makeDMRs.R, makeQset.R, mixQsets.R, plotting.R, qseaCNV.R,
qseaExtra.R, and utilityFunctions.R to satisfy BiocCheck indentation note

* refactor: fix 4-space indentation in glue strings and function signatures

Fix BiocCheck NOTE "Consider multiples of 4 spaces for line indents"
by removing leading whitespace from continuation lines inside glue::glue()
strings and aligning function parameter lists to 4-space indent.

Files changed: R/PCA.R, R/alterQset.R, R/makeDMRs.R, R/makeQset.R,
R/plotting.R

* refactor(makeDMRs,plotting): fix remaining non-4-space indents in string literals

Remove leading whitespace from continuation lines inside warning()/glue()
strings and restore correct } else { alignment in makeDMRs.R.
Clears the final 3 lines flagged by BiocCheck indentation NOTE.

* style: fix 2-space to 4-space indentation in sampleQC and utils

* style: fix over-indented continuation lines in asValidGranges

* style: reapply indentation after main rebase

* Fix plotly PNG device error on headless build servers

- Skip plotly::ggplotly() during non-interactive builds in pca.Rmd
  (plotly internally opens a PNG device which fails without X11)
- Add dev = pdf to knitr::opts_chunk() in all 5 vignettes
  to prevent the default PNG device being used on headless servers

* style: add missing chunk labels to all vignettes

* fix(vignettes): use pdf device in pca vignette chunks

Switch the knitr chunk device in  from PNG to PDF
to avoid graphics device issues in headless build environments.

* docs: update NEWS.md and regenerate man pages for v0.99.3

- Add v0.99.3 NEWS.md entry summarizing style and vignette fixes
- Regenerate man/ documentation to reflect any updated roxygen2 tags

* style: normalize R and vignette indentation to 4 spaces for BiocCheck

* style: remove trailing whitespace-only indent lines flagged by BiocCheck

* style(R/qseaCNV.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/buildQset.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/PCA.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/qseaExtra.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/makeDMRs.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/analyseDMRs.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/alterQset.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/calculateEnrichment.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/dplyrVerbs.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/genome.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/makeQset.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/mixQsets.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/classes.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/combineQsets.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/plotting.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/sampleQC.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/utilityFunctions.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/utils.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/utilityFunctions.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/alterQset.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/analyseDMRs.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/calculateEnrichment.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/combineQsets.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/dplyrVerbs.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/mixQsets.R): wrap lines > 80 chars to satisfy BiocCheck note

* style: wrap lines longer than 80 characters

* fix: restore vignette YAML front matter

* fix: restore roxygen metadata to 7.3.3

* style: wrap reported R source lines

* style: wrap reported vignette lines

* style: wrap remaining core source findings

* style: wrap remaining helper source findings

* style: wrap remaining vignette findings

* style(r): wrap long lines in helper sources

* style(r): normalize wrapping in plotting helpers

* docs(vignettes): reflow examples and prose

* docs(man): regenerate man files with roxygen

* style: add final line to .Rbuildignore

* refactor(r): remove paste from condition signals

* docs: guard poolSamples example with dontrun

* style: move roxygen version to the same position as in main (it was moved accidentally during debuggin)

* docs: update NEWS with all the changes made in style/wrap-lines-from-format-notes

* fix(check): resolve TIMEOUT, qsea import NOTE, and global-var NOTE

- Fix skip_long_checks() to use getOption() instead of options();
  the old call returned a named list so the guard never fired and
  slow BAM-processing tests always ran, exceeding the 15-min limit.
- Add options(skip_long_checks = TRUE) in tests/testthat.R so
  R CMD check skips long-running tests.
- Add @import qsea via R/mesa-package.R and regenerate NAMESPACE to
  resolve 'Package in Depends field not imported from' NOTE.
- Replace all qsea::: and janitor::: calls with public-API equivalents
  (qsea::getParameters()[["BSgenome"]], slot assignment @, tileGenome)
  to resolve 'Unexported objects imported by :::' NOTE.
- Declare five data-object names in utils::globalVariables() to
  resolve 'no visible binding for global variable' NOTE.

* fix(qseaCNV): correct makeGenomeWindows to use fixed-width tiles + rebase

tileGenome(..., cut.last.tile.in.chrom=FALSE) distributes tiles evenly
across chromosomes, producing wrong window widths and boundaries that
break the hmmCopyGC/hmmCopyMap overlap check in addHMMcopyCNV.
Replace with a direct reimplementation using GRanges/IRanges/Seqinfo
public APIs: fixed-width tiles, last partial window dropped — identical
to the original qsea:::makeGenomeWindows behaviour.

Also rebases fix/rcmd-check-notes onto style/wrap-lines-from-format-notes
and regenerates man/ with devtools::document().

* test: reset global mesa options before state-sensitive assertions

Calling devtools::test() in a dirty interactive session carries over
options like mesa_parallel, mesa_TxDb, mesa_genome, and mesa_annoDb,
causing expect_error(annotateWindows()) and expect_false(getMesaParallel())
to fail. Explicitly reset to NULL/FALSE at the start of the relevant
test blocks so tests are robust to session-state pollution.

* test: cache qsea fixtures and gate slowest blocks to fit 15-min budget

Add tests/testthat/helper-fixtures.R with a memoised cachedExampleQset()
so repeated qsea::getExampleQseaSet() builds in test-editQset.R and
test-DMRs.R reuse a single simulation per (repl, depth). Gate the
heaviest blocks (test-DMRs.R "Calculating DMRs", test-exampleQset.R
"Testing general functionality", test-pca.R "UMAPs") behind
skip_long_checks() so R CMD check stays under the Bioconductor 15-min
tests budget while devtools::test() still runs everything locally.

* docs: update man files' documentation

* docs(NEWS): add PR #77 links to all entries from this branch

* docs(NEWS): add missing addHMMcopyCNV makeGenomeWindows bug fix entry

* style: wrap lines > 80 chars in mixQsets.R, utils.R, plotting.R, qseaExtra.R, sampleQC.R

* docs(PCA,buildQset): replace getExampleQseaSet() in examples with exampleTumourNormal

* docs(buildQset): wrap addNormalisation examples in \donttest{}

exampleTumourNormal is filtered to CpG_density >= 5 and has no
low-density background windows; getExampleQseaSet() is retained
for these examples but hidden from R CMD check timing.

* docs: documented man/addNormalisation.Rd and man/getDimRed.Rd

* docs: mesa version updated to 0.99.2.9000

* docs: mesa version updated to 0.99.2.9000

* docs(NEWS): condense PR #77 entries; use ragg_png vignette device

Tighten the 0.99.2.9000 NEWS section: fold the three BiocCheck NOTE
resolutions into one bullet and trim wording, and drop the duplicate
### FIXED block that repeated the same #77 fixes under the old 0.99.0
heading.

Switch all vignette chunks to dev = "ragg_png" and add ragg to Suggests,
matching the NEWS entry.

* docs(ENCODEbadRegions): unwrap @source URL to fix pkgdown build and stay under 80 chars

* docs(ENCODEbadRegions): regenerate Rd to match unwrapped @source URL

Regenerate man/ENCODEbadRegions.Rd from the roxygen source so the
\source{} block no longer wraps the URL in a \url{} tag. pkgdown's
Rd parser fails on a \url{} tag that spans a line break, which aborted
build_reference() (and the pkgdown deploy) on this topic. The plain
wrapped URL parses cleanly and keeps every line under 80 characters.

* fix(qseaCNV): correct window-start seq() call in addHMMcopyCNV

The makeGenomeWindows reimplementation passed each chromosome length
positionally to seq() (matching 'from') while also supplying from = 1L,
which errors with "formal argument 'from' matched by multiple actual
arguments" and broke addHMMcopyCNV(). Use an explicit closure so the
chromosome end maps to 'to'.

* fix(sampleQC): guard BSgenome check against length-0 comparison

After dropping qsea:::getGenome(), addHyperStableFraction() compared the
BSgenome parameter directly, which throws "argument is of length zero"
when that parameter is NULL. Use identical() for a safe, intentional
error path.

* fix(mixSamples): report missing sample names instead of stopifnot

Replacing qsea:::checkSamples() with stopifnot() produced an unhelpful
"... is not TRUE" error. Compute the missing names with setdiff() and
stop() naming them.

* fix(mixThreeQsetSamples): report missing sample names instead of stopifnot

Same fix as mixSamples(): replace the generic stopifnot() with a
setdiff()-based check that names the missing sample(s).

* docs(utils): mark remove_almost_empty_cols internal, drop stale Rd

remove_almost_empty_cols() is an unexported, internally-used-only helper,
but its roxygen block (lacking @noRd) generated a help page. Add @noRd so
no man page is produced and remove the orphaned Rd. Also corrects the
@details text, which still claimed the removal message came from an
internal janitor helper after the code switched to a plain message().

* docs(NEWS.md): remove irrelevant change

---------

Co-authored-by: fperezmartinez <felipe.perezmartinez@manchester.ac.uk> 

 style: standardize 4-space indentation and fix vignette build issues per Bioconductor style guide (#75)

* Fix indentation: convert 2-space to 4-space per Bioconductor style guide

Applies styler::style_dir() with scope=indention, indent_by=4
across all R/ source files and vignettes/

* style: fix function argument alignment to use 4-space indentation

Replace paren-aligned continuation lines with 4-space indents in
R/buildQset.R, calculateEnrichment.R, classes.R, combineQsets.R,
makeDMRs.R, makeQset.R, mixQsets.R, plotting.R, qseaCNV.R,
qseaExtra.R, and utilityFunctions.R to satisfy BiocCheck indentation note

* refactor: fix 4-space indentation in glue strings and function signatures

Fix BiocCheck NOTE "Consider multiples of 4 spaces for line indents"
by removing leading whitespace from continuation lines inside glue::glue()
strings and aligning function parameter lists to 4-space indent.

Files changed: R/PCA.R, R/alterQset.R, R/makeDMRs.R, R/makeQset.R,
R/plotting.R

* refactor(makeDMRs,plotting): fix remaining non-4-space indents in string literals

Remove leading whitespace from continuation lines inside warning()/glue()
strings and restore correct } else { alignment in makeDMRs.R.
Clears the final 3 lines flagged by BiocCheck indentation NOTE.

* style: fix 2-space to 4-space indentation in sampleQC and utils

* style: fix over-indented continuation lines in asValidGranges

* style: reapply indentation after main rebase

* Fix plotly PNG device error on headless build servers

- Skip plotly::ggplotly() during non-interactive builds in pca.Rmd
  (plotly internally opens a PNG device which fails without X11)
- Add dev = pdf to knitr::opts_chunk() in all 5 vignettes
  to prevent the default PNG device being used on headless servers

* style: add missing chunk labels to all vignettes

* fix(vignettes): use pdf device in pca vignette chunks

Switch the knitr chunk device in  from PNG to PDF
to avoid graphics device issues in headless build environments.

* docs: update NEWS.md and regenerate man pages for v0.99.3

- Add v0.99.3 NEWS.md entry summarizing style and vignette fixes
- Regenerate man/ documentation to reflect any updated roxygen2 tags

* style: normalize R and vignette indentation to 4 spaces for BiocCheck

* style: remove trailing whitespace-only indent lines flagged by BiocCheck

* docs: update man/ files

* fix(vignettes): switch figure device from pdf to ragg_png

Replaces dev = "pdf" with dev = "ragg_png" in all five vignette setup
chunks. The pdf device produced poor-quality embedded figures in HTML
vignette output. ragg_png renders high-quality PNG without requiring
Cairo or X11, resolving the headless build server issue cleanly.

Adds ragg to Suggests in DESCRIPTION.

* docs: mesa version updated to 0.99.2.9000

* docs: mesa version updated to 0.99.2.9000

* docs(NEWS.md): switch figure device from pdf to png, as it was like that on 0.99.2

---------

Co-authored-by: fperezmartinez <felipe.perezmartinez@manchester.ac.uk> 

 Replace mzR with RaMS for mzML reading

mzR pulls in netCDF/HDF5 system libraries and requires Rcpp
compilation, which makes installation slow and often fails on
fresh/CI/Docker environments. RaMS is a pure-R mzML reader with only
lightweight CRAN dependencies, so it installs in seconds.

getmzml() output is unchanged: a data.frame with mz, intensity, and rt
(seconds) columns. RaMS reports retention time in minutes, so it is
converted to seconds. Verified byte-for-byte identical output against
mzR on a 9.8M-row file.

Bump version to 1.1.0 (Bioc devel).

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

 Merge branch 'RELEASE_3_23' into devel
 

 fix typo
 

 fix hvg selection
 

 +scater
 

 track changes v1.2.0-.1
 

 bug fix: overwrite of 'th'
 

 order deps alphabetically
 

 scrapper: seq-crc
 

 scrapper updates: Visium HD (binned) workflow
 

 scrapper updates: seq-deconvolution chapter
 

 wording
 

 scrapper updates: seq-intermediate-processing chapter
 

 scrapper: ind-clu
 

 scrapper: ind-norm
 

 formatting
 

 auto-update gitignore
 

 scrapper: img-ccc
 

 scrapper revision: img-qc
 

 scrapper revision: img-workflow-cos/xen
 

 scrapper updates: seq-QC chapter
 

 scrapper revision: crs-workflow-xenvis
 

 install beachmat.hdf5
 

 remove manual installation of dependency packages (SPE, AUCell)
 

 remove manual installation of dependency packages (SPE, AUCell)
 

 # update DESCRIPTION
 

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

 refactor(ucsc): centralize RestUri calls with rtracklayer user agent

All UCSC REST API calls now identify as "rtracklayer" via a shared
wrapper, consistent with rtracklayerGET/POST.

Refs lawremi/restfulr#4
 

 Merge branch 'main' into devel 

 Merge pull request #67 from pnnl/view-fix

updated biocviews to fix dependency issue and use BiocFileCache 

 updated examples to use BiocFileCache

I hope this will make the build more reliable
 

 Merge pull request #66 from pnnl/z-test-update

Z test update 

 tried to fix hg pages
 

 updated examples to use BiocFileCache

I hope this will make the build more reliable
 

 Update both readme files
 

 update version number
 

 Finish adding plotting methods to the LRT vignette
 

 Split into three separate vignettes for simulation, rate estimation and likelihood ratio testing
 

 Add LRT vignette
 

 Fix return variable name in LRT function 

 Fix geneId assignment in betaTblIdx 

 Refactor runEMH1FkLRT to use h0Beta values 

 Bugfix for mainExpectationMaximizationFkH0 

 add likelihood ratio test functions for fk

Add likelihood ratio test for fk

- Add one-line call in likelihoodRatioTest() to run fk LRT
- Implement fk LRT pipeline (computeFkLRT, computeFkLRTParams, runEMH0FkLRT, runEMH1FkLRT) adapted from beta LRT
- Reuse constructBetaLRTTable() to build fk LRT output 

 updated
 

 bump version
 

 updated help pages and bumped ersion
 

 version bump 1.1.2
 

 bump version
 

 allow additional attributes in SquaregffBy
 

 Bump version
 

 Specify types in benchmarks
 

 Add test for writing NA warning
 

 Remove debug escape hatch
 

 Error on unsupported codec
 

 Merge pull request #17 from KlausVigo/devel

Devel 

 further typos...
 

 fix sf on row subset
 

 fixed more tests...
 

 fixed wrong param name
 

 removed sanity check based on old scrna pipeline
 

 fixed typo
 

 handle se inputs to agg
 

 more updates for scrapper...
 

 first shot at moving to scrapper...
 

 Merge pull request #60 from gdrplatform/GDR-3420

GDR-3420: add custom annotation support to import_data 

 chore: bump version to 1.11.3
 

 Merge pull request #197 from gdrplatform/GDR-3420

GDR-3420: allow custom annotations in merge_data 

 docs: regenerate man pages
 

 feat: allow custom annotations in merge_data and cleanup_metadata

Add optional cell_line_annotation and drug_annotation parameters to
merge_data() and cleanup_metadata(). When provided, these bypass the
automatic package-based lookup (gDRinternal/gDRtestData), enabling
open-source users to supply their own annotation CSVs.
 

 fix: use backtick formatting instead of \pkg{} in vignette

The raw \pkg{ggplot2} LaTeX macro is valid in roxygen/Rd files but
undefined in the vignette's LaTeX preamble, causing an 'Undefined
control sequence' error that broke the Bioconductor vignette build.
Replace it with the plain inline-code form used elsewhere for package
names.
 

 Merge pull request #79 from gdrplatform/GDR-3417

GDR-3417: add workshop drug annotations 

 docs: remove Dimensions column from DepMap dataset table
 

 fix: correct version to 1.11.4 and simplify NEWS entry
 

 chore: bump version to 1.11.4
 

 igblastr 1.3.9

Replace arguments 'with.intdata' and 'with.auxdata' with 'intdata'
and 'auxdata' in function install_custom_germline_db().

The new arguments can be NULL, or "auto", or a data.frame containing
custom annotations (internal or auxiliary data}, or the path to a file
containing custom annotations.

Setting 'intdata' or 'auxdata' to "auto" achieves the same as setting
the old 'with.intdata' or 'with.auxdata' arguments to TRUE, that is,
it tells install_custom_germline_db() to compute and add the annotations
to the new germline db.

Alternatively, the user can now supply their own custom annotations
by passing a data.frame -- or the path to a file containing annotations --
to 'intdata' or 'auxdata'.

See '?install_custom_germline_db' for more information.
 

 Update
 

 Merge pull request #9 from sa-lee/claude/bioc-build-failure-0rdfv7

ci: test against Bioconductor devel (3.24) to catch build failures 

 fix(vignette): build TxDb from local GTF via useHub=FALSE

The Bioconductor 3.24 (devel) build fails when re-building the vignette at
the tximeta-run chunk:

  Quitting from fluentGenomics.Rmd:189-194 [tximeta-run]
  Error: error in evaluating the argument 'x' in selecting a method for
  function 'bfcadd': object 'bfc' not found
   1. tximeta::tximeta(coldata, dropInfReps = TRUE)
   2.  getTxDb(txomeInfo, useHub = useHub, skipFtp = skipFtp)
   3.   checkViaAHub(txomeInfo, srcName, ensSrc, dbType)
   4.    BiocFileCache::bfcadd(bfc, ...)

This is an upstream regression in tximeta 1.31.2: its internal
checkViaAHub() references an unbound variable 'bfc' on the AnnotationHub
code path (the default useHub = TRUE). Older tximeta (Bioc 3.22) is
unaffected, which is why this only shows up on devel.

Pass useHub = FALSE so tximeta builds the TxDb directly from the local GTF
already registered by makeLinkedTxome in the setup chunk, avoiding the
broken checkViaAHub path. This is also more robust for the build machines
since it does not depend on AnnotationHub.
 

 fix sequence search API
 

 version bump 1.1.1
 

 use local file df in cloud_compare.R
 

 add transfer script --dry-run
 

 Merge branch 'devel' of https://github.com/BorchLab/scRepertoire into devel
Getting hex sticker fixed
 

 update documentation
 

 Fixing warnings
 

 Update data files
 

 Update DaparToolshedData
 

 Calling DNAMultipleAlignment from MultipleAlignment not Biostrings
 

 Update DaparToolshedData
 

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

 Merge branch 'main' into devel 

 Minor changes
 

 Update DaparToolshedData
 

 Untrack file DaparToolshedData.Rproj
 

 Merge pull request #16 from KlausVigo/master

Add citation 

 Merge pull request #15 from KlausVigo/master

remove ignored files 

 Bioconductor 0.99.29 nlme fit, CpG bacthing, Methylation scale, these changes were made to improve performance
 

 illustrate use of percent_mutation() in the vignette
 

 update bioc version
 

 update bioc version
 

 adding functions to vignette and bump version to 0.99.5
 

 Adding user functions to load data and validate h5
 

 Merge branch 'devel' into update_clampdata_readers 

 Update vignette to use new CLAMPData reader functions
 

 uploaded summary for results in get_started
 

 Address Bioconductor revision 1
 

 fixed missing )
 

 Bump version
 

 Fix comment in source code

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

 Fix typos in help page of saveHDF5GSVA() and loadHDF5GSVA()

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

 Update unit tests for serialization, update example for saveHDF5GSVA() / loadHDF5GSVA
 

 Removed unnecessary parameter from the internal .pull_param() helper function
 

 version bump
 

 Merge pull request #388 from rformassspectrometry/jomain

docs: better explain parallel processing 

 bump version
 

 import write.phylip from MultipleAlignment and fix example for saveAlignments.
 

 doc: remove column with no info
 

 chore: as per review
 

 doc: add prism data
 

 doc: update data description
 

 chore: update data description
 

 feat: add motif_proximity() for enrichment near genomic anchors

motif_proximity() and plot_motif_proximity() test whether a motif's hits
are spatially enriched near a set of anchor coordinates, genome-wide. It
is the distance-based sibling of motif_peaks(): binomial (default),
anchor-randomisation permutation, and KS nulls; hit- and anchor-counting
modes; strand-aware directional (upstream/downstream) testing; and either
precomputed hits or internal scanning of an XStringSet or BSgenome.

motif_peaks() gains a seq.strand argument that orients local mode by
feature strand, so mirror-image peaks across strands combine, and its
examples now document the windowed genome-coordinate recipe.

Also fix two stale motif_peaks(sequences, motif=) calls (the
implant_motifs example and the SequenceSearches vignette) left over from
the CentriMo rewrite, and add a proximity-enrichment section to that
vignette.
 

 update example to generate calls
 

 Adaptations for BioC 3.24; version number bumped to 1.45.1
 

 feat: add no.overlaps option to motif_coocc()

Forward scan_sequences2()'s no.overlaps / no.overlaps.by to the
internal-scan path. Because motif_coocc()'s Fisher test is on
per-sequence presence/absence, collapsing overlaps never removes the
last hit from a sequence, so the p-/q-values are unchanged; the option
only affects the descriptive spatial columns under max.distance, where
it stops tandem/overlapping matches of one motif being counted as
separate instances. Dedup stays within each motif (relying on
scan_sequences2()'s no.overlaps.by.motif = FALSE) so between-motif
overlaps, i.e. heterodimer footprints, are preserved. Default FALSE,
matching scan_sequences2()/enrich_motifs2(); ignored with a warning on
the precomputed-hits path. Adds roxygen, NEWS note, and tests.
 

 # added MultipleAlignment
 

 Bioconductor 0.99.28 SVA matrix plot out of range
 

 feat: geom_motif/geom_logo layers and motif_tree2 tip logos

Add ggplot2 layers that embed sequence logos into arbitrary ggplot
constructions, reusing the view_motifs() logo renderer:

- geom_motif()/annotate_motif() take universalmotif objects (honouring
  use.type); geom_logo()/annotate_logo() take bare row-named numeric
  matrices. annotate_*() place one logo at fixed coordinates; geom_*()
  position from aesthetics (bounding box, or x/y anchor with
  width/height) and can draw a different motif per group via a named
  list plus a `motif` selector aesthetic. Built on shared ggproto
  objects GeomMotif/StatMotif/StatLogo; letter colours are resolved
  internally so the layers never touch the plot's fill scale.

- motif_tree2() now draws aligned tip logos by default (tiplogo = TRUE,
  aligned via view_motifs2()), the motifs serve as tip labels. Its
  default layout changes to "rectangular"; tip logos are drawn only on
  rectangular/slanted layouts (others warn and skip) and not for dist
  input. New args: tiplogo, tiplogo.align, tiplogo.width,
  tiplogo.height, tiplogo.offset.

Also fix a pre-existing renderer bug shared with view_motifs()/
view_logo(): with a small min.height, letters shorter than their
per-letter y.spacer allotment were scaled by a negative height and
flipped below the baseline. The spacer is now capped at half the
letter height.

Replace the cowplot side-by-side tree+motifs vignette section with a
motif_tree2() example, and document the ggtree >= 3.13 requirement for
tip labels (ggtree's empty() calls the removed ggplot2:::is.waive()
under ggplot2 4.0). Adds tests and NEWS entries.
 

 fix test, update news and description
 

 Fix DOI, update Date, reword Description field

- Correct DOI from 10.2174/1389202924666230517115655 to
  10.2174/0113892029264990231013112156 (was returning 404)
- Update Date to 2026-06-07
- Reword Description to not start with package name (R CMD check NOTE)

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

 Fixed bug in addSpecificityProxyScore
 

 Merge pull request #169 from jorainer/jomain

fix: address all SQL injection security issues 

 define updateObject() methods for MultipleAlignment derivatives
 

 major fix in Unload.gdsn()
 

 Bioconductor 0.99.25 Correcting PARAM = empty to NULL
 

 import DNAMultipleAlignment from MultipleAlignment.
 

 small tweak to README.md