docs: add the Track options reference vignette (#160)

* docs: add the Track options reference vignette (#159)

Replace the overview vignette with a reference of every track type and the
options it takes. The overview held install, minimal-app and custom-genome
sections that getting-started already covers better; its one unique piece,
the dataMode = "http" example, moves there.

Every option documented was checked against the unminified igv.js 3.8.4,
the build bundled in inst/htmlwidgets/lib. Names the library does not read
are left out rather than described - they are collected in #159.

Fills the two dead references to a "Track options reference" vignette that
getting-started has carried since it was written.

* docs: run the reference examples instead of showing them

BiocCheck warns when at least half the vignette chunks across the package go
unevaluated, and the overview vignette this PR removes was the one holding
that ratio down. Master sat at 41%; adding a reference of eval=FALSE loader
calls took it to 57%.

Padding the count would have been the wrong fix. The loaders are one-way
messages to a browser, so a session that prints instead of sending makes every
example runnable - and the printed message is better documentation than the
call alone, since it shows the defaults the loader fills in and what igv.js
actually receives. igvShiny() already builds outside a shiny session, so the
allowlist example runs too and prints the real warning.

Combined ratio is now 33%.

Also wraps the three table rows over 80 characters, moving the junction
vocabularies into a list below the table, and builds the remote genome URLs
with paste0 rather than file.path, which is what the vignette this text came
from did.

* docs: wrap the one vignette line over 80 characters 

 Improve base zstd detection
 

 Avoid file.info()
 

 Tidy ibdmdb data (#838) 

 Bump version
 

 Add title to sections
 

 Rename unused var
 

 feat(networks): Add metabolomics support to the Network Interpretation tab (#223) 

 Update installation with remotes::install
 

 Gate the PTM legend callout on PTM data presence (#107) 

 Filter RPCAInput  (#837)

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

 Update package loading message (#839) 

 version bump
 

 Bump version
 

 Run devtools::document()
 

 Default to base R zstd de/compression
 

 Updates.

 Committer: Erik Wright <Erik.Wright@bcm.edu>
 Changes to be committed:
	modified:   DESCRIPTION
	modified:   NAMESPACE
	modified:   R/BrowseSeqs.R
	modified:   R/InferRecombination.R
	modified:   R/MaskAlignment.R
	modified:   R/ReadDendrogram.R
	modified:   R/Treeline.R
	modified:   R/Zipline.R
	modified:   man/BrowseSeqs.Rd
	modified:   man/DistanceMatrix.Rd
	modified:   man/InferRecombination.Rd
	modified:   man/MaskAlignment.Rd
	modified:   man/ReadDendrogram.Rd
	modified:   man/Treeline.Rd
	modified:   man/WriteDendrogram.Rd
	modified:   man/Zipline.Rd
	modified:   src/ChainSegments.c
	modified:   src/Cluster.c
	modified:   vignettes/DECIPHERing.Rnw
	modified:   vignettes/GrowingTrees.Rnw
 

 Mention new read_zarr_consolidated_metadata() in NEWS
 

 Rename function for export
 

 Always return consolidated metadata as v3
 

 Add consolidate argument to read_consolidate_metadata
 

 restore random seed after knn impute

#34
 

 fix pqn ref_mean
 

 Fix some issues related with Bioconductor update
 

 Fix Shiny App link in README.md 

 Update README.md 

 Fix Shiny App link in README

Updated the link for the Shiny App badge to the correct URL. 

 Bump version to 0.99.13 and add NEWS

Version bump and NEWS entry for the Bioconductor devel sync: compatible
seq/qual XStringSet output built in C, GAlignments header seqlengths fix,
.onLoad C-callable provider loading, workflow benchmarks, and README refresh.

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

 Refresh README: latest benchmarks and Bioconductor status

Rewrite the README around the current results: a highlights block, a
single-file read-throughput table (2.3-3.2x vs scanBam/readGAlignments),
and an end-to-end workflow table framed by read fraction / Amdahl's law
(ATAC QC 3.7x down to coverage->bigWig 1.2x), with the byte-identical
correctness statement. Merge the overlapping Why/Compatibility and
benchmark sections, and tighten install, quick start, and the seq/qual
compact-vs-compatible notes.

Reflect that BamScale is accepted on Bioconductor (devel/3.24): use the
Bioconductor availability/build/downloads badges and lead installation
with BiocManager; keep the R-CMD-check and pkgdown badges.

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

 Compatible seq/qual XStringSet objects and correct GAlignments seqlengths

Return seq/qual as DNAStringSet/PhredQuality built directly from the shared
packed byte buffer in C (new src/xstringset_build.c using the IRanges/XVector
C-callable constructors), so the compatible read path no longer re-encodes via
character vectors; .bamscale_scanbam_biostrings is now a no-op fallback that only
fires if a plain character column reaches it. .onLoad force-loads the C-callable
providers (S4Vectors/IRanges/XVector/Biostrings) and GenomicAlignments so fresh
SnowParam SOCK workers resolve the constructors and the GAlignments class.

Fix .bamscale_build_galignments_seqinfo to carry the BAM-header sequence lengths
into the GAlignments Seqinfo (via GenomeInfoDb::Seqinfo). Previously seqlengths
were NA, so coverage() extended each seqlevel only to its max end and export.bw()
wrote truncated chromosome sizes, diverging from readGAlignments().

DESCRIPTION: GenomeInfoDb -> Imports; LinkingTo += S4Vectors, IRanges, XVector.

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

 bump version

Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
 

 update roxygen version and fix now unsupported multiline expressions

Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
 

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

 Merge remote-tracking branch 'upstream/devel'
 

 rprimer 1.17.1: Package now needs to depend on MultipleAlignment
 

 DEV: Satisfy roxygen2 multiline @importFrom complaint
 

 minor updates
 

 KEGG gene set description: KEGG list API update: organism -> genome 

 Biostrings 2.81.6: Tweak Biostrings:::.call_fun_in_MultipleAlignment
 

 Fix indentation
 

 Don't fail on BiocCheck
 

 Move BiocCheck earlier in the GHA workflow
 

 Add workflow_dispatch trigger

Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
 

 Bump version

Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
 

 Merge pull request #7 from jeroen/fix-arm64-msse2

Do not pass -msse2 on Windows ARM64 (aarch64) 

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

 Also install GenomicFeatures (GHA)
 

 Install also GenomicRanges in GHA
 

 Read genes.gtf to see what the problem is
 

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

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

 Changed p value fill limit calculation to address issue #21
 

 Typo fix for Kobak citation.
 

 fix: simplify experiment_md assignment by removing unnecessary if
 

 chore: bump version to 1.11.8 and update NEWS.md
 

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

 update GHA to not use depreciated versions

Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
 

 bump version

Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
 

 fix typo in documentation

Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
 

 Merge pull request #5 from jeroen/devel

Remove CFLAGS from C++ build 

 Script the Connect re-pin and warn when the live demo falls behind (#157)

* docs: script the Connect re-pin and write down the deploy routine

app.R runs the demo out of the installed package, so manifest.json's pinned
commit decides what the public demo shows - and moving that pin by hand means
keeping six fields in step: RemoteSha, GithubSHA1, the recorded Version and the
two file checksums. bump-pin.sh does all six from one argument, defaulting to
origin/master, and refuses an abbreviated sha (the GitHub API answers those
with silence, which reads like a missing commit).

--check reports drift without touching anything and exits non-zero, so it
doubles as a post-merge reminder that the live demo is behind.

Also re-pin to 559c5c8 (1.9.35), the commit that rebuilt the demos: the
manifest still pointed at 1.9.25.

Related: #64

* ci: warn when the Connect demo pin falls behind master

The pin gap is invisible by construction: CI stays green, the repo is correct,
only the live app is stale - which is how manifest.json ended up ten versions
behind. A push to master that touches the demos now runs bump-pin.sh --check
and files a single reminder issue, closing it once the pin catches up.

It deploys nothing. Republishing stays a click in Connect Cloud.

Related: #64

* fix: define the Connect pin drift by what the app installs, not by sha equality

Connect republishes on every master change by itself, so the manual step is the
pin, not the republish - the docs said otherwise.

The check was worse than wrong: requiring pin == HEAD is false immediately after
every merge, including the merge that moves the pin, so the workflow would have
filed a drift issue against its own landing commit. Compare the pinned commit
with master over R/, inst/ and DESCRIPTION instead - the only paths that reach
the served package - and stay quiet when they match.

Verified against both ends: the old 1.9.25 pin reports 33 changed files, while
the merge of this branch reports none.

Related: #64

* fix: separate the pin-check failure modes and check every manifest invariant

Review notes on this branch, all four valid:

- the workflow filed "the demo is behind" for any non-zero exit, including the
  script failing to run at all (missing jq/gh, unknown commit, API error). Only
  exit 1 means drift now; anything above fails the job instead of lying quietly
- --check looked at RemoteSha alone, so it passed a manifest whose README.md
  checksum was stale - which this branch had. It now verifies both sha fields,
  the recorded version and both file checksums, and the stale checksum is fixed
- drop base64 from the version lookup: -d/-D differs between GNU and macOS.
  The raw media type returns DESCRIPTION directly
- add a concurrency group; two runs could both find no open issue and both
  file one

--check reads the manifest against master and cannot observe what Connect has
deployed; the docs claimed otherwise. The footer version stays the one place
the deployment itself is verified.

Related: #64 

 Bump version
 

 Install openssl on mac CI
 

 Update bundled autoconf-archive utils
 

 Remove references to C99
 

 docs: record the tair10 gene track rename in NEWS (#143) (#155)

Before #143 the tair10 config carried its own "Genes TAIR10" track. The
registry entry supplies the annotation as "RefSeq All", so the track is
still there under a different name and removeTracksByName("Genes TAIR10")
in user code now matches nothing, without an error or a warning. hg19
losing Gencode v18 made NEWS; this did not.

The comment next to the config also overstated the change, implying data
has to be renamed to RefSeq accessions. The registry entry carries an
aliasURL, so chr1 and 1 both resolve; only the displayed name changes.
Verified in the browser on the bundled igv.js 3.8.4 with a track named in
both spellings. 

 Bump version
 

 Disable SSE2 on Windows arm64
 

 feat: load a splice junction track from a bed url (#103) (#153)

* feat: draw splice junctions from a bed url, the igv.js answer to #103

igv.js has no sashimi plot - grep for "sashimi" in the bundled 3.8.4 build
returns nothing. What it has is SpliceJunctionTrack, drawn from a bed file
of the shape STAR writes as SJ.out.tab, and a merged track to put it over
coverage. #103 has been waiting since November on advice that describes
desktop IGV instead.

loadSpliceJunctionTrackFromURL() sends such a bed to the "junction" type,
with indexed=false when no tabix index is given: igv.js otherwise guesses
url + ".tbi" and fails on a file that is not there.

The junction filters, thickness rules and labels reach igv.js through
trackConfig, so they are added to .validIgvTrackOptions. Their names come
from the 3.8.4 source, not from spliceJunctionTrack.html: that example
still sets labelUniqueReadCount and four siblings, and no such option
exists in the library any more - it reads labelWith/labelWithInParen.
The example is corrected here too.

Its three data files went 404 on s3.amazonaws.com/igv.org.demo, the same
dead bucket as #143; upstream moved them to igvteam/igv-data. The scanner
that would have caught this never looked at igv.js.examples, so the
directory joins its scope - which surfaced five more dead URLs in two
other examples, repointed or replaced by the stock genome the files
themselves named as the alternative.

The browser test serves its own bed fixture from 127.0.0.1 rather than
adding another third-party host to the suite.

* fix: treat an unusable indexURL as no index, not as JSON null

A NULL indexURL survives list(), so shiny sent it as JSON null and the
handler read .length off it. That throws: the track never loads and R
sees nothing, the failure showing up only in the browser console. Same
for a vector or an NA.

Normalising in R keeps it off the wire, matching what .sanitizeTracks()
already does for a track url.

Raised by CodeRabbit on #153. 

 Merge pull request #101 from gdrplatform/GDR-3471

feat: add lintRmdDeps() — static check for unresolved Rmd function calls (GDR-3471) 

 fix: add @importFrom data.table and utils::getParseData in rmd_linter.R — resolves R CMD check WARNING (GDR-3471)
 

 docs: add @keywords linter to lintRmdDeps so pkgdown finds it in reference index
 

 style: address Janina review — character(1) → string in @param/@return, data.frame → data.table (GDR-3471)
 

 style: fix paste_linter violations in rmd_linter.R (toString)
 

 Gviz 1.57.1: Resync with GenomicAlignments/cigarillo split

cigarRangesAlongReferenceSpace() and sequenceLayer() have moved
from GenomicAlignments to the new cigarillo package, and were renamed
cigars_as_ranges_along_ref() and project_sequences(), respectively.
 

 Merge branch 'devel' of git.bioconductor.org:packages/ontoProc2 into devel
 

 S4Vectors 0.51.6: S4Vectors:::anyMissing() is now defunct (was deprecated)
 

 Style
 

 BSgenome 1.81.1

Remove functions BSgenome::forgeMasksFile, BSgenome::forgeSeqFiles,
BSgenome::forgeSeqlengthsRdaFile, BSgenome::forgeSeqlengthsRdsFile,
BSgenome::forgeBSgenomeDataPkg, and BSgenome::forgeMaskedBSgenomeDataPkg.

These were deprecated in BioC 3.22 and defunct in BioC 3.23.
 

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

 mike made a typo
 

 updates to README for github pages
 

 Style changes
 

 Small bug in removing assays
 

 Document deprecations and breaking changes in NEWS
 

 Export h5writeAttribute.array()
 

 Remove fix_missing() shim for missing bit64conversion
 

 Pull index - 1L out of integer
 

 Use vectorized arithmetic instead of loop
 

 Remove dontrun
 

 Add note about naming high-level functions
 

 Simplify some branching patterns
 

 Mention no copy shortcut in NEWS
 

 3.23.4: add package anchors to Rd cross-references

Doc-only fix for the "Found Rd file(s) with Rd \link{} targets
missing package anchors" R CMD check NOTE. Anchors external \link{}
targets (GRanges, SummarizedExperiment, mcols, DESeqDataSet,
summarizeOverlaps, GreyList/calcThreshold, Dist, heatmap.2,
lattice/xyplot, vennPlot) to their packages across 14 man/*.Rd
files. No code change.
 

 Bump version
 

 Fix Windows ARM64 build by selecting SIMD flags per architecture (#33)

Co-authored-by: Claude Fable 5 <noreply@anthropic.com> 

 Add missing quote
 

 Update OS in workflow and add ARM variants for all families
 

 v0.99.15: tryCatch fixed
 

 v0.99.15: unified resolver, strict/P-P/metadata closed loop
 

 v0.99.15: hop=1 perf, lazy ego, neighbor cache, tests fix, column order, get_edge_ids
 

 v0.99.15: fix cross-platform vignette build (strip TxDb from RData, add magick)
 

 v0.99.15: triple-positive fix, chromatin boundary tests, doc sync
 

 v0.99.14: fix vignettes
 

 v0.99.14: Bioconductor review revisions minor fix
 

 v0.99.14: Bioconductor review revisions check
 

 v0.99.14: Bioconductor review revisions new functions fixed
 

 v0.99.14: Bioconductor review revisions new functions1
 

 v0.99.14: Bioconductor review revisions fix functions3
 

 v0.99.14: Bioconductor review revisions fix functions
 

 v0.99.14: Bioconductor review revisions updated documents
 

 v0.99.14: Bioconductor review revisions updated docu
 

 Remove figure/ from tracking (.gitignore now covers it)
 

 v0.99.14: Bioconductor review revisions updated function2
 

 v0.99.14: Bioconductor review revisions updated function
 

 v0.99.14: Bioconductor review revisions updated doc1
 

 v0.99.14: Bioconductor review revisions updated3
 

 v0.99.14: Bioconductor review revisions updated1
 

 v0.99.14: Bioconductor review revisions7
 

 Re-render README.md from updated README.Rmd
 

 v0.99.14: Bioconductor review revisions4
 

 v0.99.14: Bioconductor review revisions2
 

 v0.99.14: Bioconductor review revisions
 

 Refine code quality and algorithm coverage for Bioconductor review
 

 style: use .Library instead of .libPaths() in get_gDR_session_info test
 

 fix: compare package versions numerically in get_gDR_session_info (GDR-3499)
 

 Version bump
 

 Delete inst/extdata/metadata_zenodo_fixed.csv 

 Delete inst/scripts/make-metadata.R 

 Delete inst/extdata/metadata_zenodo_fixed.csv 

 Create README.md 

 Delete inst/extdata/metadata.csv 

 Fix bugs
 

 Fix bug bootstrap CIs
 

 Refactorization
 

 Increase coverage
 

 Remove NON-ASCII
 

 Improve plots
 

 Refactoring
 

 Fix references
 

 Merge branch 'stable' into devel 

 Upgrade TSENAT v.0.99.33 (#63)

Comprehensive audit and fix of statistical implementation bugs across 15 R source files, identified via systematic code review with numerical verification. Covers core statistical methods (Hochberg correction, GEE bias-correction, bootstrap CIs, AR(1) estimation, LMM/GEE model validation) plus jackknife diagnostics, M-estimation, paired bootstrap, Storey π₀, Westfall-Young permutation, and entropy/divergence helpers.

Also includes supporting code refactoring: pipeline stage extraction, input validation helpers, and modular assumption checks. 

 replace deprecated scran::convertTo with edgeR::SE2DGEList
 

 Update snapshot for v3 consolidated metadata
 

 Bump version
 

 Run ruff
 

 Merge pull request #42 from fmicompbio/fix-tests

Fix tests 

 Update NEWS
 

 Use ggplot2 for plotEISA(), add identity line and set aspect ratio to 1
 

 bump version
 

 update docs
 

 add missing import for setNames
 

 Merge pull request #191 from gdrplatform/GDR-3459

Optimize split_SE_components and df_to_bm_assay performance 

 fix: use S4Vectors::DataFrame instead of as.data.frame() in split_SE_components — avoids undesirable_function_linter warning while preserving identical() compatibility (GDR-3459)
 

 ci: retrigger after gdrin MR!107 merge
 

 style: fix NEWS.md entry to start with imperative verb
 

 ci: retrigger pipeline
 

 chore: merge main into GDR-3459, bump to 1.11.6
 

 chore: resolve merge conflicts with main
 

 refactor: apply code review suggestions for split_SE_components and df_to_bm_assay
 

 perf: optimize split_SE_components with data.table ops, vectorized paste, and uniqueN
 

 Version bump to v1.1.1
 

 Delete .BBSoptions

per email from Andres Wokaty 

 rcpp
 

 igblastr 1.3.17: Add net_charge() and extract_region_net_charge()

See '?net_charge' for the details.
 

 respond to biocCheck
 

 sync with bioc devel and bump version
 

 update checkout version
 

 Bump version to 1.37.1 for Bioconductor devel and update NEWS

Set the version to 1.37.1, one patch above Bioconductor's devel (1.37.0),
as required to push a change to devel; the odd minor is correct for the
devel branch (BioC 3.24). Retitle the release notes accordingly and fold
in the row-dendrogram change.

Record 1.18.0 through 1.37.0 as no significant updates, since that span is
only Bioconductor's automatic per-release version increments; the local
history had skipped straight from a stale "1.18.0 Forthcoming" entry.

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

 Add optional row dendrogram to heatmap_ic()

The heatmap gains a `row_dendrogram` argument that draws the biomarker
hierarchical clustering as a dendrogram beside the heatmap, restoring the
row dendrogram that superheat used to provide before it was replaced by
ggplot2. Biomarkers are ordered by the clustering whether or not the tree
is drawn, so the argument affects only the display; it defaults to FALSE
to keep the plain ggplot as the default return value.

When enabled, the dendrogram and heatmap are aligned and composed with
patchwork, so the returned object is a patchwork composition that still
inherits from ggplot. When there are too few biomarkers to cluster, the
dendrogram is silently omitted and the plain heatmap is returned.

The row clustering helper is split into cluster_fit() (returning the
hclust fit, reused to draw the tree) and cluster_order() (returning just
the ordering). Drawing the dendrogram adds ggdendro and patchwork to
Imports.

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

 Merge pull request #79 from nhejazi/topTable-rownames

 

 fixing topTable rownames in modtest_ic
 

 bump version 2.11.1 + NEWS
 

 [R][saveReport] fix for ntry=1
 

 [R][survivaAnalysis] fix coeff sum for correct model
 

 update docs
 

 export gsonKO and allows converting uniprot to ko
 

 get-ppi-network
 

 bayes-enrich
 

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

 feat: let loadGwasTrack callers map gwas columns, and show it in the demo (#144)

* feat: let loadGwasTrack callers map gwas columns, and show it in the demo

#142 wired the column mapping into the GWASTrack class. loadGwasTrack,
the function most callers reach for, still had no way to send one: the
trackConfig allowlist dropped "columns" as an unsupported igv.js option.

Adds it to the allowlist and documents both it and colorTable on the
loadGwasTrack parameter.

The Connect Cloud demo gains a button that renames the gwas table's
columns to names igv.js cannot guess, then loads it with explicit column
numbers and a chromosome color map - the two features have nowhere else
to be seen. Verified in a headless browser: 2438 features parsed from the
renamed table, chr19 purple, everything else gray from the "*" entry.

* test: check loadGwasTrack passes the column mapping to igv.js 

 feat: send the gwas column mapping and chromosome colors to igv.js (#142)

* feat: send the gwas column mapping and chromosome colors to igv.js

GWASTrack has taken chrom.col, pos.col and pval.col since it was written,
stored them in the S4 object, and never sent them anywhere. igv.js was
left guessing the layout from the header names it knows (chr/bp/p), so a
table spelled any other way drew an empty track - the flexibility #32
asks for was already in the signature, just not wired up.

display() now sends columns={chromosome,position,value}, which the igv.js
gwas parser reads 1-based, exactly as the constructor takes them.

The same message carries the new chromosomeColorMap argument through as
igv.js colorTable (#46), where a "*" entry colors every chromosome not
named explicitly. Both ride mergeExtraParameters, so no JS changes.

Column numbers are checked in the constructor: out of range meant an
empty track with no complaint from either side.

* fix: satisfy the gDRstyle linters and reject a repeated chromosome

toString() for paste(collapse) and NCOL() for ncol(), both flagged by
gDRstyle::lintPkgDirs. A colorTable is a JSON object, so a chromosome
named twice quietly loses one of its colors - the sanitizer now says so.
Adds the show() color-line coverage review asked for.

* test: check the out-of-range message names the offending column 

 Bump version and added suggests dependencies
 

 corrected bug with newer Rcpp versions
 

 Additional bug review
 

 Improve documentation
 

 Update README structure
 

 Revert circleci config
 

 Update news
 

 Fix circleci
 

 Remove trash from test
 

 Fix bugs and related tests
 

 Remove duplicated
 

 Increase tests coverage (#61)

Increase test coverage. 

 ci: check Linux on pull requests, the full matrix on master and nightly (#140)

macOS and Windows spend roughly 70 of their 80 minutes compiling the Bioc devel
dependency tree from source. Devel publishes no binaries for either system and
moves daily, so the package cache can never cover it - measured on 2026-07-26,
Install BiocGenerics and the two dependency passes alone were 24, 22 and 8 minutes,
against a 2-minute R CMD check. Linux runs inside the Bioconductor container and
gets through the same work in a fraction of the time.

Pull requests now check Linux only, so the answer arrives in about 15 minutes. The
full matrix still runs where a slow answer is still useful: every push to master -
so nothing reaches Bioconductor unchecked - plus a nightly schedule and any pull
request labelled full-ci, for changes that touch the JS or the track loaders.

A macOS or Windows regression now surfaces at the merge to master rather than on
the pull request that caused it; the label is the escape hatch when a change looks
platform-sensitive. 

 Restored sanity checks for expected results that match text descriptions.

Basically copied from OSCA, but should be more robust given the relative
control we have over the dependencies.
 

 ci: use --ignore-vignettes so skipped vignettes do not fail the check

Skipping vignette building on push and pull request left the package without
an inst/doc directory, which made "checking files in 'vignettes'" and
"checking package vignettes" warn. With error_on = "warning" those two
warnings failed the run even though the check was otherwise clean.

--no-vignettes only suppresses running vignette code and rebuilding outputs;
it leaves the inst/doc consistency checks active. --ignore-vignettes skips
all vignette tests and is the flag that belongs with --no-build-vignettes, so
it replaces --no-vignettes rather than joining it. The scheduled and manually
dispatched full check is unaffected: it still builds vignettes, so inst/doc
exists and the checks run normally.
 

 feat(lipid-search): add LipidSearch source and lp_lipid_search layer

Add LipidSearchSource(), which parses LipidSearch result files - both 4.2
and 5.2, auto-detected - into an xcms-style peak table. The per-sample
Area/Height/RT/observed-m/z columns are reshaped into one row per
lipid/sample, rejected lipids are dropped unless keep_rejected = TRUE, and
lipid ions reported at several retention times get distinct plot labels.
Chromatograms are drawn with the new lp_lipid_search() layer, whose
lipids_query can reference the lipid annotations (class, sub_class, grade,
adduct, lipid_rank, ...).

Because 5.2 exports carry no raw-file names, their samples are keyed s1,
s2, ... from the OrgMeanArea[...] columns; sample_paths can be named with
those keys or matched positionally, while 4.2 keeps basename matching. The
sample list comes from sample_paths rather than from the result file, so a
supplied path the file never declares is still a full sample - every
queried lipid is extracted there using its consensus m/z and RT window, it
simply has no reported peak to highlight.

The per-compound extraction loop is now shared with the Compound Discoverer
scripting-node source via create_compound_chromatograms(), along with the
compound ranking and column-resolution helpers. Bumps the package version
to 1.1.6.

Closes #31.
 

 ci: stop leaning on bioconductor.org more than needed (#138)

* ci: stop leaning on bioconductor.org more than needed

On 2026-07-25 bioconductor.org served 504s for over an hour. 'Set BiocVersion'
took 23 minutes on Linux and 53 on macOS, and BiocCheck failed outright while
fetching its deprecated-package list, so a green branch looked broken.

Four changes, none of which trade away what the matrix actually verifies:

- push runs are limited to master. A commit on a branch with an open PR used to
  run the whole matrix twice on the same SHA, once per event.
- superseded pull request runs are cancelled; master runs are not, since they
  deploy pkgdown and push to Bioconductor.
- 'Set BiocVersion' is skipped on the Linux container, which is already pinned
  to devel; a cheap assertion takes its place so image drift still surfaces.
- BiocCheck's BiocFileCache directory is cached between runs. Cold, its fetch of
  meat-index.dcf is a bfcadd() and fatal when the host is down; warm, the failed
  refresh is survivable and the stored copy is used. That list changes rarely.

A BioC_mirror escape hatch is wired to an empty 'bioc_mirror' env variable.
Mirrors answered in under a second while the main host timed out, but they sync
daily and this package tracks devel, so it stays off until it is wanted.

Related: #124

* ci: brace the Bioc version check so Rscript parses the else branch

* ci: take BiocCheck off bioconductor.org for the deprecation lookup

The deprecated-package check is the one BiocCheck step that reaches the host,
pulling checkResults//bioc-LATEST/meat-index.dcf through BiocFileCache. That
endpoint served 504s for hours on both 2026-07-25 and 2026-07-26 while the rest of
bioconductor.org answered in under a second, and a cold-cache bfcadd() against it
is fatal - it failed every job on all three systems, in runs whose R CMD check had
already passed with 166 tests.

Warming the cache only narrowed the window, since the first run of the day still
has to reach the host, so drop the two cache steps in favour of switching the check
off: it reports whether the package is deprecated in Bioc, which igvShiny is not,
and the official build farm runs the full BiocCheck regardless.

* ci: stop the macOS and Windows jobs rebuilding the world every run

Set BiocVersion called BiocManager::install() with no pkgs, which defaults to
update = TRUE - "bring every installed package up to this version's repositories".
Bioc devel publishes no macOS or Windows binaries, so each run recompiled the whole
dependency tree from source: 52 minutes of an 84-minute job on 2026-07-25, on both
systems, in a run that was otherwise healthy. The restored 261 MB package cache was
being thrown away immediately after it was restored.

The step only needs to point BiocManager at the right release; the dependencies this
package actually needs come from the two install passes below it. </pre>
    </div>
  
    

      Package: igvShiny

      Commit: 7a002943a9606eb37e2ec15bafe1ca07b0830fdd

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

      Date: 2026-07-26 07:35:08 +0200

      Commit message:


	  
		
 ci: require the macOS and Windows jobs to pass (M3) (#136)

The matrix carried allow-failure on macOS and Windows since the R 4.5/4.6
version mismatch was mistaken for shinytest2 flakiness. That root cause was
fixed in #123 (r: '4.6' on both), and the jobs have since run green — the last
12 consecutive check-bioc runs (2026-07-25, 6 distinct SHAs, push and
pull_request) succeeded on the full matrix, with mac/win producing a complete
BiocCheck 0 ERROR / 0 WARNING / 2 NOTES.

Dropping the flags makes 'CI green on Linux, macOS and Windows' an enforced
condition rather than a reported one, which is the M3 deliverable.

Related: #129 
    
  
    

      Package: GSABenchmark

      Commit: 2e7d1881054aa925a96a28c0a95be62f864385e7

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-07-26 12:32:06 +0800

      Commit message:


	  
		
 Bumped version
 
    
  
    

      Package: GSABenchmark

      Commit: 1c7aaa19d32b43129973459c3f7864e538497495

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-07-26 12:31:32 +0800

      Commit message:


	  
		
 Edited description
 
    
  
    

      Package: CSOA

      Commit: 0ca54521078826e3a03090ebb6d1c3d23a81f604

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-07-26 11:20:42 +0800

      Commit message:


	  
		
 Bumped version
 
    
  
    

      Package: CSOA

      Commit: ac7b1e74b199a6e762fa65aa2194e47c5401bbd1

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-07-26 11:20:11 +0800

      Commit message:


	  
		
 Corrected vignette date
 
    
  
    

      Package: fishash

      Commit: 2454c9575df9b63f0c09fcb34b1fb8928d1b95d4

      Author:  Jack Kamm <jackkamm@gmail.com> 

      Date: 2026-07-25 19:48:37 -0700

      Commit message:


	  
		
 Remove unnecessary Suggests that I missed in last commit
 
    
  
    

      Package: fishash

      Commit: 45824552ec732d7635c48d2b32229a8920cccc70

      Author:  Jack Kamm <jackkamm@gmail.com> 

      Date: 2026-07-25 19:05:08 -0700

      Commit message:


	  
		
 Revise vignette: fix typo, add guards if missing Suggested packages
 
    
  
    

      Package: marinerData

      Commit: 706b79815fede82d897ae5b6cd34b8e2a9984e32

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 15:41:10 -0400

      Commit message:


	  
		
 Document the (m)cool accessors

Adding the four rows to metadata.csv makes .onLoad create four new accessor
functions, and R CMD check flagged all four as undocumented code objects --
a WARNING that would have appeared on the Bioconductor build report.

Each accessor here gets its own roxygen block in zzz.R and a matching Rd,
following the pattern already used for the .hic and BEDPE accessors. Rd files
were written to match rather than regenerated: this package records
RoxygenNote 7.2.3 and the available roxygen2 is 8.0.0, which would have
rewritten every Rd in the package.

R CMD check is now Status: OK, with 13/13 tests passing.
 
    
  
    

      Package: marinerData

      Commit: 5aea2c518db1f0678f21b93c2c605749660b7420

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 15:00:21 -0400

      Commit message:


	  
		
 Merge Bioconductor devel and add the (m)cool records

The .cool/.mcool ExperimentHub records that Sarah Parker added in April 2024
were only ever pushed to GitHub, so no released marinerData exposes them.
mariner's cooler support has the same history, and issue #35 on that repo is
the visible consequence.

GitHub main was 12 commits ahead and 14 behind Bioconductor devel, whose only
commits since RELEASE_3_18 were the automated version bumps. The sole
conflict was the version: main had never moved off 0.99.12 while Bioconductor
had reached 1.13.0. Resolved to 1.13.1 and the NEWS heading corrected to
match, since it still carried the old 0.99.12 number.

The four data files are already archived at
https://doi.org/10.5281/zenodo.10906240 and the records use
Location_Prefix "https://zenodo.org/" with DispatchClass "FilePath", the same
pattern as all twelve records Bioconductor already serves for this package.
Nothing needs uploading; the hub only stores metadata pointing at the DOI.
 
    
  
    

      Package: marinerData

      Commit: 08822a8c16c71fc4d9ac1327e67ca66019fd8517

      Author:  Sarah Parker <57263711+sarmapar@users.noreply.github.com> 

      Date: 2024-04-26 14:52:31 -0500

      Commit message:


	  
		
 Merge pull request #4 from sarmapar/main

Corrected RDataPath links 
    
  
    

      Package: marinerData

      Commit: 22fabac523b6ea793032d6862a04bf79d3fe53bd

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-26 15:51:03 -0400

      Commit message:


	  
		
 Corrected RDataPath links
 
    
  
    

      Package: marinerData

      Commit: c9b2b15671201a0cf8c5debe0867ed516fd4210c

      Author:  Sarah Parker <57263711+sarmapar@users.noreply.github.com> 

      Date: 2024-04-12 11:42:49 -0500

      Commit message:


	  
		
 Merge pull request #3 from sarmapar/main

Updating RDataClass 
    
  
    

      Package: marinerData

      Commit: 8de9bc844c0fe45feae63e0fb78b5d9887a51b23

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-12 12:41:59 -0400

      Commit message:


	  
		
 Updating RDataClass
 
    
  
    

      Package: marinerData

      Commit: f8a0ed1f9dc5fe0a44e3ccf4c313d0f7b1e56a96

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-12 12:40:06 -0400

      Commit message:


	  
		
 Updated RDataClass
 
    
  
    

      Package: marinerData

      Commit: beeb708f013736965717d3c627f79fd2c17c9e5b

      Author:  Sarah Parker <57263711+sarmapar@users.noreply.github.com> 

      Date: 2024-04-11 10:14:45 -0500

      Commit message:


	  
		
 Merge pull request #2 from sarmapar/main

Correcting BiocVersion for new files 
    
  
    

      Package: marinerData

      Commit: 10d5a316d64923e8076e51189de34ce3e44d6cef

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-11 11:13:40 -0400

      Commit message:


	  
		
 Making new metadata csv
 
    
  
    

      Package: marinerData

      Commit: d7a6d241c11cb4afb9d5971615f1b751605f50d0

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-11 11:06:38 -0400

      Commit message:


	  
		
 Correcting BiocVersion
 
    
  
    

      Package: marinerData

      Commit: 5f5f1107e463bef689c9ea24737838455954ce50

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-11 11:04:20 -0400

      Commit message:


	  
		
 updating BioC version
 
    
  
    

      Package: marinerData

      Commit: bf5bc33734435c3ffc367c3ff979b2afe9ff35bb

      Author:  Sarah Parker <57263711+sarmapar@users.noreply.github.com> 

      Date: 2024-04-10 13:10:12 -0500

      Commit message:


	  
		
 Merge pull request #1 from sarmapar/main

Adding (m)cool files 
    
  
    

      Package: marinerData

      Commit: de4281143687e939a321241f46f648b43fcdee93

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-10 14:09:10 -0400

      Commit message:


	  
		
 Bumping package version and updating news
 
    
  
    

      Package: marinerData

      Commit: 92ded17dba6dc9e0993fa07118b0e7de9977f0c4

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-10 14:08:55 -0400

      Commit message:


	  
		
 Adding (m)cool files
 
    
  
    

      Package: mariner

      Commit: 91f71090fbbc591af8145d4c9a020d1b7b184c47

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 15:30:02 -0400

      Commit message:


	  
		
 Correct the note on why cooler fixtures are synthetic

The ExperimentHub records for marinerData's .cool/.mcool files do exist --
EH9511 through EH9514, pointing at doi:10.5281/zenodo.10906240. I had stated
they were never published, which was wrong.

The actual gap is narrower: marinerData builds its accessors in .onLoad from
inst/extdata/metadata.csv, and those four rows were never pushed to
Bioconductor. So the data is served but unreachable through the documented
API, and the accessors the branch's tests called do not exist in any
installable marinerData.

The reason for using synthetic fixtures is unchanged, and does not actually
depend on that: they keep R CMD check off the network and let the tests
assert on known counts.
 
    
  
    

      Package: mariner

      Commit: 75d2fb88bf01ecea02b05ef51131432813ac1b16

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 15:20:34 -0400

      Commit message:


	  
		
 Fix the pkgdown site build

The merge broke `pkgdown::build_site()`, which would have surfaced when
deploying gh-pages rather than in R CMD check.

_pkgdown.yml keeps a hand-curated reference index, and pkgdown treats any
documented topic missing from it as an error. The four exported cooler
functions were absent, so the build aborted; had it not, they would have been
missing from the reference page entirely. They now appear under a "Cooler
files" subtitle beside pullHicPixels/pullHicMatrices.

.checkIfCool() also lacked @noRd, so it generated man/dot-checkIfCool.Rd --
the only dot-*.Rd in the package, and a public help page for an internal
function. Every other internal helper here uses @noRd, including the sibling
cooler helpers, so this follows suit and the Rd is removed.
 
    
  
    

      Package: mariner

      Commit: 68fc9f9ec22b78e7e52b1aaad63dbdd556172ba1

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 15:02:18 -0400

      Commit message:


	  
		
 Move the cooler section ahead of the pulling walkthroughs

Placing it after the strawr chunk split that discussion from the paragraph
explaining the missing 'chr' prefix, which reads as commentary on
readHicChroms() output and has to follow it. File-format support also belongs
before the walkthroughs rather than partway through one.
 
    
  
    

      Package: mariner

      Commit: 3ee8dc8c4eb62dfacc7d0f162985259d5a92bf1f

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 15:01:11 -0400

      Commit message:


	  
		
 Avoid an implicit header reference in the vignette

Pandoc's implicit_header_references would resolve [Using .cool and .mcool
files], but if the dialect ever changes it degrades to literal brackets in
the rendered page rather than failing loudly. Refer to the section by name
instead.
 
    
  
    

      Package: mariner

      Commit: c50932ca3afcb66028c68be7ec3ffb063e8f0a07

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 14:58:34 -0400

      Commit message:


	  
		
 Document cooler support

Issue #35 asked for the package and the paper to agree, and half of that is
documentation: nothing in the vignette or the pullHic* help said cooler files
were usable at all.

Adds a "Using .cool and .mcool files" section to the vignette covering
automatic format detection, the readCool* counterparts to the strawr
inspection functions, the "observed"-only and no-mixing restrictions, and the
differing normalization conventions. Examples there are not evaluated,
because marinerData's cooler files are on Zenodo but not yet published to
ExperimentHub.

Updates pullHicPixels() and pullHicMatrices() to say they accept cooler
files, and points `norm` at readCoolNormTypes(). Man pages were edited to
match rather than regenerated: the available roxygen2 is 8.0.0 against this
package's RoxygenNote 7.3.3, and regenerating would rewrite every Rd file.
 
    
  
    

      Package: mariner

      Commit: de7ca1d0ff51fe2dfa7ee5b4065e7b6a53b95fa2

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 14:58:25 -0400

      Commit message:


	  
		
 Apply cooler balancing weights by multiplication

cooler defines the balanced value as A_ij * w_i * w_j -- its `weight` column
holds multiplicative biases. coolStraw() was dividing by them, so every
"BALANCE" result was wrong by a factor of (w_i * w_j)^2 relative to what
cooler itself reports for the same file.

The other branch still divides, and that is deliberate rather than an
oversight left half-fixed. Normalizations other than BALANCE are read from
like-named bin columns, which in practice are juicer vectors carried into
cooler files by converters such as hic2cool. Juicer's convention is divisive,
so dividing there keeps those values consistent with strawr::straw(). The
distinction is now documented on coolStraw() and in the vignette.

The existing test asserted the divisive result, so it was updated alongside;
it had been written against the implementation rather than against cooler.
 
    
  
    

      Package: mariner

      Commit: 646573ebeae7c1aca1a9eaf89e5ad22a788e3ee1

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 14:52:11 -0400

      Commit message:


	  
		
 Test cooler support against synthetic fixtures

The branch's cooler tests called marinerData accessors for .cool/.mcool
example files. Those files are archived on Zenodo (10.5281/zenodo.10906240)
but the ExperimentHub records were never published to Bioconductor, so the
accessors do not exist in any installable marinerData and every one of those
tests failed to even load.

Rather than block on publishing those records, build small cooler files
locally with rhdf5 in helper-coolFixtures.R. This keeps R CMD check free of
network access -- the real .mcool is 55 MB -- and lets the tests assert on
counts we chose ourselves. That matters: the branch's tests only checked that
cooler output agreed with .hic output for square on-diagonal queries, which
is the one shape where both bugs fixed in the previous commit cancel out.

Cooler coverage now lives in test_useCool.R alongside R/methods-useCool.R,
and covers file-type detection, the metadata readers, eight query shapes
including off-diagonal and interchromosomal, balancing weights, cool/mcool
agreement, multi-resolution mcool, and argument validation. The .hic tests in
test_pullHic.R are unchanged; only the cooler sections were removed from it.
 
    
  
    

      Package: mariner

      Commit: 6497fb9ace015743c6861122c301c599c9863c27

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 14:49:00 -0400

      Commit message:


	  
		
 Fix two bin-range bugs in coolStraw()

Both found by testing against synthetic cooler files with known contents.
Neither was caught before, because the branch's only tests compared cooler
output against .hic output for square on-diagonal queries, which is the one
shape where both bugs happen to cancel out.

Queries ending at or past the end of a chromosome errored with "argument of
length 0". end1bin was resolved with which(bin_starts == end), but the last
bin of a chromosome starts one binsize before the chromosome end, so nothing
matched. Now clamped to the final bin via .coolBinId().

More seriously, the pixel range for the requested rows ended at
bin_offsets[end1bin+1]+1, which is the *first* pixel of the last row bin
rather than the last. Every pixel in that row was dropped except one. For a
square on-diagonal query the only in-range pixel of the last row is the
diagonal element, which is exactly the one retained, so the results looked
correct. For off-diagonal or interchromosomal queries an entire row of the
matrix went missing and the function returned silently wrong counts. The
range now ends at bin_offsets[end1bin+2].
 
    
  
    

      Package: mariner

      Commit: e68fffe67ef8eb4a9845c66c51fb5a546dfe05e1

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 14:42:58 -0400

      Commit message:


	  
		
 Bump to 1.13.1 and add NEWS entry for cooler support

Note NEWS.md had not been updated since 1.2.1, so there is a gap between
that entry and this one. Backfilling the intervening releases is left
alone here rather than reconstructed from git log.
 
    
  
    

      Package: mariner

      Commit: bfa48e4635619dbfbf75328921dac54f92e42849

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 14:42:19 -0400

      Commit message:


	  
		
 Fix defects carried over from the cool-integration branch

* The mixed .cool/.mcool test built imat_mixedCool then asserted against
  imat_cool, so mixed file input was never actually verified. This was
  preserved through the merge deliberately; fixing it here keeps the defect
  visible in history.

* Four abort() calls in coolStraw() passed their "i" hint as a second argument
  to abort() rather than inside c(). rlang treats that as a data field, so
  every one of those hints was silently dropped and users got a bare error
  with no guidance on what to do next.

* The chr2loc format check reported "chr1loc=..." in its error message.

* readCoolNormTypes() documented a `resolutions` parameter but the formal is
  `resolution`. Corrected in both the roxygen block and the generated Rd.
 
    
  
    

      Package: mariner

      Commit: 18716a336e553c675bf317386440a26e088137ff

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 14:41:03 -0400

      Commit message:


	  
		
 Make cool support installable

The cool-integration branch was never brought to an installable state, which
is a large part of why it sat unmerged. Three defects, each fatal on its own:

* DESCRIPTION specifies Collate, and methods-useCool.R was not listed. R only
  sources the files named there, so none of the cool code was loaded at
  install time and R CMD check errors on the unlisted file.

* stringr was called and imported in NAMESPACE but never declared in
  DESCRIPTION, which is a check ERROR. It was used in only three places, so
  replace them with base strsplit() rather than take on a new dependency. The
  str_extract import was already dead and is dropped.

* dplyr::pull() was called in .checkIfCool() without an import; NAMESPACE only
  brings in dplyr::mutate. This is the first function reached by every cooler
  call, so it failed immediately. Replaced with base `$` subsetting.
 
    
  
    

      Package: mariner

      Commit: 8a89d79c90a09cd29aec4d96ead7f60d84b13c58

      Author:  Eric Davis <ericscottdavis@outlook.com> 

      Date: 2026-07-25 14:37:09 -0400

      Commit message:


	  
		
 Merge branch 'cool-integration' into cool-integration-2026

Brings in .cool/.mcool support originally written by Sarah Parker in
April 2024 (origin/cool-integration, 4 commits) onto current Bioconductor
devel (1.13.0). The work was never merged or pushed to Bioconductor, which
is why no released version of mariner has the cooler support described in
the paper. See issues #35 and #33.

The only conflict was tests/testthat/test_pullHic.R: devel reformatted the
file (4-space indent, multi-line call style) while the branch appended
tests in the older 2-space style. Resolved by keeping devel's formatting
and re-applying the branch's additions in that style. NAMESPACE and
R/methods-pullHic.R merged cleanly.

The merged test for mixed .cool/.mcool input asserts against imat_cool
rather than the imat_mixedCool it builds. That defect is preserved here
and fixed in a follow-up commit so it stays visible in history.

This merge alone does not install: methods-useCool.R is missing from
Collate, stringr is undeclared, and dplyr::pull is unimported. Those are
addressed next.
 
    
  
    

      Package: mariner

      Commit: 523f0f0139ce2f0729a2e509138633821e929754

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-22 16:33:01 -0400

      Commit message:


	  
		
 export straw-like functions for cool files
 
    
  
    

      Package: mariner

      Commit: db6a698cac5e8ea01a7d080413d3517ead9029f3

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-22 16:32:38 -0400

      Commit message:


	  
		
 new imports and exports for cool fxns
 
    
  
    

      Package: mariner

      Commit: 91ba88f59131bb3b7dded085fabe440868206541

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-22 16:30:45 -0400

      Commit message:


	  
		
 Testing cool functions
 
    
  
    

      Package: mariner

      Commit: c3b26ec3865f23f30cb72b56d826a050648c303b

      Author:  Sarah Parker <smp3800@gmail.com> 

      Date: 2024-04-22 16:26:10 -0400

      Commit message:


	  
		
 Pulling counts from cool files
 
    
  
    

      Package: amplican

      Commit: 7a947f10ed84294debc65a543779e85af9ba8719

      Author:  JokingHero <kornel.labun@gmail.com> 

      Date: 2026-07-25 21:18:47 +0200

      Commit message:


	  
		
 fix NA reading, rare case
 
    
  
    

      Package: OSCA.advanced

      Commit: c136f4d23eb52f75cb04e41a78bef41e060f06a0

      Author:  lgeistlinger <ludwig.geistlinger@gmail.com> 

      Date: 2026-07-25 13:33:36 -0400

      Commit message:


	  
		
 merge upstream changes
 
    
  
    

      Package: OSCA.advanced

      Commit: 06225560116192a4679c557c05887593050cc705

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2026-04-27 13:35:40 +0100

      Commit message:


	  
		
 Version bump
 
    
  
    

      Package: OSCA.advanced

      Commit: b1d3d37f5f529695974ceef24fc7bac190b8a6c3

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2026-04-27 13:30:02 +0100

      Commit message:


	  
		
 Remove density reddims
 
    
  
    

      Package: GSVAdata

      Commit: 96cffff0143c1503f869c08f0a9ed65efcc39b95

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

      Date: 2026-07-25 18:11:42 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: GSVAdata

      Commit: 459f1c4664dd2100b8bcd77676be8250164ecb6a

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

      Date: 2026-07-25 18:11:11 +0200

      Commit message:


	  
		
 Added gene sets derived from the snRNA-seq data from Tran et al. (2021) and the corresponding script generating them
 
    
  
    

      Package: TSENAT

      Commit: 9322fed5dd909d40e6203e55d5c90a3ee25c5ead

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-25 16:39:24 +0200

      Commit message:


	  
		
 Increase test coverage
 
    
  
    

      Package: igvShiny

      Commit: 9e7db0b0be6b0fadbc3a14244026a387bd0b9a43

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

      Date: 2026-07-25 17:11:48 +0200

      Commit message:


	  
		
 docs: add a getting-started vignette (M4) (#135)

* docs: add a getting-started vignette (M4)

The package shipped one vignette, an overview written around
parseAndValidateGenomeSpec. It never showed a complete app, a track loaded
from a data.frame, or how the browser reports its position back to R — the
three things a new user needs first.

This vignette goes install -> running app -> own data, and documents the
parts of the API that are easy to get wrong from the reference docs alone:

- the region is read asynchronously; getGenomicRegion() sends a request and
  the answer arrives as the currentGenomicRegion. input
- the From URL loaders are fetched by the user's browser, so CORS applies
  where download.file() would have worked
- inside a module the loaders take ns("igv"), because they address the HTML
  element rather than the input
- unrecognised startup track keys are dropped with a warning

Also a short troubleshooting section for the failure modes that produce a
blank browser rather than an error: a 404 on the genome, chromosome naming
mismatches, and loaders failing silently because they are one-way messages.

Renders clean under BiocStyle. The module section links issue #134 rather
than documenting the hard-coded "igv-" prefix as intended behaviour.

* docs: drop the stray width argument from the vignette's fluidPage

fluidPage() has no width parameter; the value was carried over from the
overview vignette and htmltools would have rendered it as a width attribute
on the page div. Copy in a getting-started document should be code someone
can paste.

* docs: keep the vignette under 80 characters per line

CI came back green but with 3 BiocCheck NOTES against master's 2: the new
vignette added lines over 80 characters. Two hg38 URLs assembled with
paste0, one call broken across lines, one table cell shortened and the
demo link moved to a reference definition.

Renders unchanged. </pre>
    </div>
  
    

      Package: igvShiny

      Commit: 33298b0d2db4623175052c4fcb60a5bcfd8193be

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

      Date: 2026-07-25 16:59:00 +0200

      Commit message:


	  
		
 chore: configure CodeRabbit and check external assets on a schedule (#115) (#133)

* chore: configure CodeRabbit and check external assets on a schedule (#115)

Automated review changed underneath us when Gemini Code Assist shut down;
CodeRabbit replaced it running on defaults. Configure it, and take the one
job an AI reviewer is structurally unable to do and give it to a script.

- .coderabbit.yaml: profile assertive (the default CHILL produced zero
  inline comments on #114, with no way to tell correct silence from not
  looking), vendored igv.js and generated man/NAMESPACE filtered out of
  review, and path instructions carrying the conventions a diff cannot
  show — the R/JS allowlist bridge, the pinned igv.js version, the local
  httpuv fixtures, and the gDRstyle NEWS linter rules.
- .github/pull_request_template.md: a "Related: #NNN" field. Our PRs avoid
  "Fixes #NNN" on purpose, which silently disabled CodeRabbit's linked-issue
  and out-of-scope checks; this restores them without auto-closing issues.
- .github/scripts/check-asset-urls.sh plus a weekly workflow: HEAD-request
  every external genome, index and demo track URL the package points at.
  The test suite serves its fixtures locally by design, so a dead upstream
  asset is invisible to it — #107 reached us as a user bug report instead.
  URLs are scraped from the sources rather than listed, so the check cannot
  drift from what the code requests; only run-time composed URLs are listed.
- AGENTS.md: what automated review is expected to catch, and what it is not.

The first run is already red: the tair10 and rhos assets on gladki.pl,
the hg19 gencode annotation on igv.broadinstitute.org (403), and the
igv.org.demo GWAS sample (404) are all gone.

* chore: address CodeRabbit review on #133

- exit when cd to the repo root fails, instead of scraping the caller's
  directory and reporting whatever it happens to find
- run the check on pull requests that touch R/, inst/demos/, vignettes/ or
  igvShiny.js, so a dead URL surfaces before merge rather than on Monday.
  PR runs report in the job summary but do not fail the build: the assets
  that are already dead are not that PR's doing, and a check that is red
  for everyone gets ignored
- drop issues:write to the job that needs it and stop the checkout
  persisting credentials
- comment nothing when a tracking issue is already open, rather than
  appending the same table every week
- reword the igvShiny.js review instruction: the vendored library is out of
  review scope, so ask the author to confirm a config key against the
  pinned version rather than implying the reviewer can read it

Also cover the three ribosomal-RNA-gene fixtures the overview vignette
assembles from a base URL.

Not applied: the PR template keeps a bare "Related: #" placeholder.
"Related: #NNN" left unedited would read as a reference to issue 0. 
    
  
    

      Package: igvShiny

      Commit: 5f68d2f53913843485527664392056163ee6fa4e

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

      Date: 2026-07-25 15:24:03 +0200

      Commit message:


	  
		
 fix: keep the tracks resource path in step with the tracks directory (#132)

addResourcePath("tracks", get_tracks_dir()) ran once, in .onLoad, which
pins the served directory for the life of the process. The default tracks
directory lives under tempdir(), and tempdir() is not guaranteed to stay
put: when it moves, loadGFF3TrackFromLocalData() and friends write into
the new directory while shiny still serves the old one, so igv.js gets a
404 for a file that exists on disk and the track never renders.

.tracksDir() re-points the resource path whenever it has drifted, and
every write site goes through it. Measured before the fix: the local GFF3
track never rendered (>180s, against 1.6s for the remote one).

The test for that track was skipped off CI with a comment blaming slow
headless rendering; it is a 404, so the assertion is back and runs
everywhere. The remote ENCODE bigWig assertion moves to its own test with
an explicit skip(): the browser refuses that fetch outright (status 0),
which is neither a slow render nor a dead host. 
    
  
    

      Package: TSENAT

      Commit: 9bdd86aa729daff133b18bbe305fa45959c5870f

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-25 14:50:37 +0200

      Commit message:


	  
		
 Upgrade version
 
    
  
    

      Package: TSENAT

      Commit: 841cc4697cbe7d7e98d57ab63533ee2ecbfb501e

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-07-25 14:49:12 +0200

      Commit message:


	  
		
 Merge branch 'stable' into devel 
    
  
    

      Package: TSENAT

      Commit: 368190fc8205d5387c94902495ac366f7ffe18c3

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-07-25 14:39:55 +0200

      Commit message:


	  
		
 TSENAT 1.0.0 Release: Increase coverage (#58)

* Fix issues

* Skip tests

* Fix issues

* Fix tests

* Add skip_on_bioc

* Bioconductor submission review

* Increase test coverage

* Fix codefactor style

* Fix tests in Windows and increase coverage

* Bug fixes

* Fix tests

* Fix addtional bugs

* Fix statistical bugs

* Fix rendering issue

* Fix rendering issue

* Fix identified bugs

* Split files

* Increase test coverage

* Fix documentation issues

* Change version

* Remove innecesary files

* Restore bug_report.md issue template

* Fix version

* Fix formatR

* Fix test

* FIx version

* Increase coverage

* Increase coverage

* Increase coverage

* Add tests 
    
  
    

      Package: TSENAT

      Commit: cc9923a163f3c6d8dada91e6f56463da3ae37c8b

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-07-25 01:14:09 +0200

      Commit message:


	  
		
 TSENAT 1.0.0 Release (#57)

What's New

Aligned Rank Transform (ART) is now the default for calculate_rank_transform(). Powered by the ARTool package (Kay et al. 2021), ART correctly handles non-parametric interaction testing by stripping main effects before ranking — a known limitation of classical rank-transform methods. The Conover-Iman Rank Transform remains available via method='rt'.
18+  
    
  
    

      Package: TSENAT

      Commit: a0e50ceea219aacec7fe9c0e680f45c005dc89c7

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 20:25:04 +0200

      Commit message:


	  
		
 Harden silent-failure paths across the TSENAT R workflow and document audit findings (#55)

This patch addresses a set of high-risk silent-recovery behaviors identified during a source review of the R package code. The goal was to make the analysis workflow more fail-fast, transparent, and reproducible.

Included review-driven changes

-     Hardened assay resolution so invalid or malformed assay references now raise an explicit error instead of silently falling back to assay 1.
-     Removed in-place mutation from the TSENATAnalysis() constructor by copying the incoming SummarizedExperiment before adding metadata.
-     Tightened orchestration error handling so critical pipeline steps now stop on failure instead of continuing with partial state and only issuing a warning.
-     Removed the SAIT wrapper’s tryCatch() fallback that converted genuine model/setup failures into warning-only empty result objects.
-     Removed the lower-level SAIT fitting fallback that downgraded fitting errors to an empty data.frame().
-     Added a regression test to confirm the SAIT wrapper now fails fast on invalid method input.
-     Hardened auto_detect_column() so invalid default_fallback values now return NULL instead of silently accepting unavailable column names.
-     Tightened calculate_jis() column auto-detection so missing condition_col, gene_col, or isoform_col now raise explicit errors instead of falling back to an incorrect default.
-     Hardened calculate_sait() parameter resolution so missing condition_col now fails fast with a clear message.
-     Added explicit validation to plot_expression() and plot_sait() so missing/undetectable condition_col stops execution immediately rather than proceeding with bad state.
-     Added regression coverage verifying auto_detect_column() ignores an unavailable default_fallback.
-     Fixed the .detect_jis_columns() test fixture so it removes colData safely without relying on unsupported in-place mutation.
-     Tightened the Storey q-value helper in westfall_young_permutation.R:295-314 so it now computes ordered Storey q-values directly from explicitly sorted p-values, then enforces monotonicity with a cumulative correction and keeps a robust lower bound to avoid nonsensical q-value results. 
    
  
    

      Package: TSENAT

      Commit: 51292977f121ea38d9b83f2c19f2813a91733c39

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-25 14:45:30 +0200

      Commit message:


	  
		
 Fix version: 0.99.30 (Bioconductor pre-release numbering)
 
    
  
    

      Package: TSENAT

      Commit: 58e0cc793df13be186ba1746c98ad214261d8f2d

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-25 13:47:53 +0200

      Commit message:


	  
		
 Add tests
 
    
  
    

      Package: TSENAT

      Commit: e6e038fd62fd14a9c4c857f2be2326c42a65eda2

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-25 02:47:51 +0200

      Commit message:


	  
		
 Increase coverage
 
    
  
    

      Package: TSENAT

      Commit: 4e50eb0aa9bba5041e1a20c411549421072921a5

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-25 02:43:26 +0200

      Commit message:


	  
		
 Increase coverage
 
    
  
    

      Package: TSENAT

      Commit: 6658f067cdf6c2c695d54579e63f6a615310bb92

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-25 01:49:26 +0200

      Commit message:


	  
		
 Increase coverage
 
    
  
    

      Package: TSENAT

      Commit: e33cd9d6bc145190f5da1bd43bcb12fe60bc41fa

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 23:59:52 +0200

      Commit message:


	  
		
 FIx version
 
    
  
    

      Package: TSENAT

      Commit: 8159e2b87a334dae916f5dd7d757577e12058851

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 23:52:19 +0200

      Commit message:


	  
		
 Fix test
 
    
  
    

      Package: TSENAT

      Commit: 7d18400cc4cf19ad042e16fff8d4a86c78ba31c1

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 23:44:41 +0200

      Commit message:


	  
		
 Fix formatR
 
    
  
    

      Package: TSENAT

      Commit: 83427a871dc1a09dfc3b20f38d01f97cd5d26634

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 23:07:21 +0200

      Commit message:


	  
		
 Fix version
 
    
  
    

      Package: TSENAT

      Commit: bb22991555cf182083359cba3749462e8fb2631a

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 22:51:25 +0200

      Commit message:


	  
		
 Restore bug_report.md issue template
 
    
  
    

      Package: TSENAT

      Commit: 8030fdff47cd84eb9574e1be88483a80806ef6cb

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 22:49:17 +0200

      Commit message:


	  
		
 Remove innecesary files
 
    
  
    

      Package: TSENAT

      Commit: ea52b834f7c34563398da248083cbaa074c4744d

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 17:37:30 +0200

      Commit message:


	  
		
 Change version
 
    
  
    

      Package: TSENAT

      Commit: 9b85189b2670cca67c1a4c210fee1222cb7969a4

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 17:36:45 +0200

      Commit message:


	  
		
 Fix documentation issues
 
    
  
    

      Package: TSENAT

      Commit: 2d580857f619943f7915211028567dd6259f896a

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 16:35:05 +0200

      Commit message:


	  
		
 Increase test coverage
 
    
  
    

      Package: TSENAT

      Commit: f44514d9c9836f1e9bc056a35a4c9325fc20d01a

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 14:54:52 +0200

      Commit message:


	  
		
 Split files
 
    
  
    

      Package: TSENAT

      Commit: a8323147d914afad5690cd696343c185938135ae

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 14:35:50 +0200

      Commit message:


	  
		
 Fix identified bugs
 
    
  
    

      Package: TSENAT

      Commit: 589ed4bd5dcba58c5017be218d1bfabe59637a20

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 14:04:32 +0200

      Commit message:


	  
		
 Fix rendering issue
 
    
  
    

      Package: TSENAT

      Commit: 40e42a0408c973b6226bdad0a4f25b148b0d20c9

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 14:03:48 +0200

      Commit message:


	  
		
 Fix rendering issue
 
    
  
    

      Package: TSENAT

      Commit: 76ec4be6310ff59719a4a58146ba052369f2aac5

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 13:45:06 +0200

      Commit message:


	  
		
 Fix statistical bugs
 
    
  
    

      Package: TSENAT

      Commit: d7f500b09b690936842c3c6ffe219965420a8d89

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 13:32:32 +0200

      Commit message:


	  
		
 Fix addtional bugs
 
    
  
    

      Package: TSENAT

      Commit: fb43eb091214d7954d57c68cf18651ca038f787a

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 13:01:31 +0200

      Commit message:


	  
		
 Fix tests
 
    
  
    

      Package: TSENAT

      Commit: 831aab585c435269627780f1f3de6a36b00b2576

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-24 04:09:39 +0200

      Commit message:


	  
		
 Bug fixes
 
    
  
    

      Package: TSENAT

      Commit: f74c3a9870ad87dc5de5555e23e25bdfdb5d2d07

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-22 21:36:29 +0200

      Commit message:


	  
		
 Fix tests in Windows and increase coverage
 
    
  
    

      Package: TSENAT

      Commit: 9c025b41bec21134de2a4efc03bc0b8ed7d19e39

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-05-20 21:04:50 +0200

      Commit message:


	  
		
 Fix codefactor style
 
    
  
    

      Package: TSENAT

      Commit: 80c187534933eb498acfba6bcc6f3fe0ab10106c

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-05-20 20:58:21 +0200

      Commit message:


	  
		
 Increase test coverage
 
    
  
    

      Package: TSENAT

      Commit: 8a29a8a970cf2932b2e474622f3da56f792af6a2

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-05-20 18:48:30 +0200

      Commit message:


	  
		
 Bioconductor submission review
 
    
  
    

      Package: TSENAT

      Commit: 50239389cc86d032f5f71efb2d983ae7a8ca1a4d

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-05-05 18:04:44 +0200

      Commit message:


	  
		
 Add skip_on_bioc
 
    
  
    

      Package: TSENAT

      Commit: f58a13672d81af402f4faf3ab9482b78768972a7

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-05-05 14:49:50 +0200

      Commit message:


	  
		
 Fix tests
 
    
  
    

      Package: TSENAT

      Commit: 900a80bc57f95de8e6a4b413db0f9e16fd54900e

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-05-05 05:01:02 +0200

      Commit message:


	  
		
 Fix issues
 
    
  
    

      Package: TSENAT

      Commit: a5c42c0cee86ad21a0c05d688acb500fc3ec61b7

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-05-05 03:04:20 +0200

      Commit message:


	  
		
 Skip tests
 
    
  
    

      Package: TSENAT

      Commit: b6c47aac1cd98123ebdab69993b9e332f78cbae6

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-05-05 02:39:21 +0200

      Commit message:


	  
		
 Fix issues
 
    
  
    

      Package: igvShiny

      Commit: c27690d6f689a37a695974f05817a0a5832877da

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

      Date: 2026-07-25 12:17:08 +0200

      Commit message:


	  
		
 fix: build igvShiny() outside a shiny session (#128) (#131)

* fix: build igvShiny() outside a shiny session (#128)

igvShiny() read the module namespace off the current reactive domain
unconditionally, so calling it from a script or a vignette hit
NULL$ns("") and died with 'attempt to apply non-function'. The JS side
concatenates moduleNS with the event name (moduleNamespace() in
inst/htmlwidgets/igvShiny.js), so the no-module case is the empty
string.

* style: keep the new comment under 80 characters (BiocCheck) 
    
  
    

      Package: igvShiny

      Commit: e0cab7dfe9d0045f5ee0a4bed92a32593611402f

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

      Date: 2026-07-25 09:52:57 +0200

      Commit message:


	  
		
 fix: harden trackConfig/tracks input validation (CodeRabbit on #127) (#130)

* fix: reject NA/empty names and unusable urls in the input sanitizers

Two edge cases caught by CodeRabbit review on #127, both verified:

- .sanitizeAndMergeOptions: any(names(userOptions) == "") evaluates to NA when
  a name is NA, so the guard errored ('missing value where TRUE/FALSE needed')
  instead of warning and returning baseOptions. anyNA() added, matching the
  sibling .sanitizeTracks guard.

- .sanitizeTracks: is.null(track[["url"]]) only caught NULL, so NA, "",
  character(0) and non-character urls passed through and reached igv.js as
  broken startup tracks. Now requires a non-empty scalar character url.

Adds test-sanitizer-validation.R covering both (pure functions, no session).

Version 1.9.11 + NEWS.

* test: cover multi-valued and missing track url (CodeRabbit on #130)

Adds the length(url) != 1L branch (a url that is a character vector) and the
missing-url-field case, both of which drop the entry with the same warning.

* style: use whitelisted imperative verbs in NEWS entries 
    
  
    

      Package: SeqArray

      Commit: 49fb7f23a913354441e32099708c55746286840e

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-07-25 02:24:08 -0500

      Commit message:


	  
		
 fixes
 
    
  
    

      Package: Voyager

      Commit: 25d880e1c269c3df59023f08e52d1bca9db4f71b

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2026-07-24 19:45:05 -0400

      Commit message:


	  
		
 Removed deprecated functions from scran and scater
 
    
  
    

      Package: Voyager

      Commit: 71b7c356e17c068472faae1c59958d8b6e6db054

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2026-07-22 22:28:14 -0400

      Commit message:


	  
		
 Updates to ggplo2 binning that is visible but not consequential
 
    
  
    

      Package: Voyager

      Commit: b75af3d262d92a6ff075ffc3171ffc261a30f2c4

      Author:  Lambda Moses <dlu2@caltech.edu> 

      Date: 2026-07-22 22:27:41 -0400

      Commit message:


	  
		
 Last change broke colDataUnivariate
 
    
  
    

      Package: drugTargetInteractions

      Commit: d036d77685ef9ac6e556313b4ca7be3bd4ba191e

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

      Date: 2026-07-24 16:06:05 -0700

      Commit message:


	  
		
 raised version number
 
    
  
    

      Package: drugTargetInteractions

      Commit: becc2a67ac027465f84ecc8077ab83092e60609a

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

      Date: 2026-07-24 16:00:39 -0700

      Commit message:


	  
		
 Add @noRd to internal dot-prefixed functions to stop generating their man pages

NAMESPACE exports only 54 functions, but nothing told roxygen2 to skip
the ~91 internal dot-prefixed helpers, so they each got their own
dot-*.Rd page. Added @noRd to every roxygen block documenting one of
these (93 blocks, 91 distinct man pages after two @rdname groupings).

Also unwrapped \link{.internalFn} cross-references in 8 exported
functions' own docs (getChemblDrugTarget, getOpenTargetsDrugs,
buildBroadRepurposingHubDb, broadRepurposingHubAnnot, queryDrugTargets,
combineDrugTargets, downloadHgncTable, buildUnichemDb) to plain
\code{.internalFn}, since those Rd link targets no longer exist -
R CMD check's Rd cross-reference warning caught this.

NAMESPACE untouched (hand-maintained, no export changes). 55 exported
.Rd pages unaffected in content. Full test suite: 179 pass, 0 fail,
same 1 pre-existing unrelated warning. R CMD check: same baseline
(vignette-not-prebuilt warnings from --no-build-vignettes, the
long-standing create_time/setNames NOTE); the long-standing
gtoPdbStripHtml.Rd brace-escaping NOTE is gone since that page no
longer exists. The 1 ERROR seen locally (missing EnsDb.Hsapiens.v86)
is a pre-existing Suggests package not installed on this machine,
unrelated to this change.
 
    
  
    

      Package: igvShiny

      Commit: bac3eb1ed6871d3b5efcae39de5c0704e28ea412

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

      Date: 2026-07-24 23:11:07 +0200

      Commit message:


	  
		
 test: unit-test the track loaders, 16% -> 92% coverage (M3) (#129)

* ci: enable the covr coverage step and report the total on every Linux build

The step existed but was dead twice over: run_covr was 'false' and the
condition required refs/heads/devel, while this repo develops on master.

Coverage now runs on every Linux build (pushes and PRs) so a regression is
visible in the diff rather than at the end of M3. The Codecov upload is
guarded on CODECOV_TOKEN being present - without the secret the job prints
the summary and moves on instead of failing.

Baseline measured locally at 16.1% (94/583 expressions). R/igvShiny.R is at
0% because the shinytest2 tests run the app in a separate process, which covr
cannot instrument; that file holds 440 of the 583 expressions.

Version 1.9.11 + NEWS.

* test: cover the track loaders with a fake Shiny session

Every loader ends in session$sendCustomMessage(), so a recording fake session
exercises them without a browser. This matters twice over: the shinytest2
tests run the app in a separate process, which covr cannot instrument, and the
R->JS payload is exactly what regressed in #36, #105 and #116 with nothing
outside a browser to catch it.

Also replaces the two tests that reached out to gladki.pl with a local httpuv
static server over inst/extdata. The http code path (httr::HEAD, http_error)
is still tested for real, but a slow or throttled third-party host can no
longer turn CI red on an unrelated commit - which is what happened on run
30121014760.

Coverage: 16.1% -> 67.5% overall, R/igvShiny.R 0% -> 68.1%.

* test: cover GWASTrack display/show and the widget constructor

Takes coverage past the M3 target: 72.8% -> 84.6% overall, R/igvShiny.R to
84.0% and R/GWASTrack.R to 91.4%.

igvShiny() reads the module namespace off the current reactive domain, so the
widget tests run inside a MockShinySession. Worth noting: outside any domain
the call dies with 'attempt to apply non-function', because
getDefaultReactiveDomain() returns NULL and NULL$ns is not callable. Left
as-is here - in an app the constructor always runs inside a session - but it
does block building a widget from a plain script.

Version 1.9.12 + NEWS. 
    
  
    

      Package: igvShiny

      Commit: 19ce14a779a7969f27d4da112e9a9fc7f46d780d

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

      Date: 2026-07-24 22:38:22 +0200

      Commit message:


	  
		
 style: clear the BiocCheck line-length NOTE (M1) (#127)

* style: wrap over-long source lines, keep paste() out of condition signals

Clear the BiocCheck line-length NOTE (25 lines > 80 chars in R/igvShiny.R,
the last blocker for the M1 acceptance criterion of <=2 NOTEs).

Wrapping the two multi-line warnings first traded that NOTE for a new one
('Avoid the use of paste in condition signals'), so the message strings are
now assembled into a local variable before being passed to warning(). The
emitted text is byte-identical to before.

Also ignore the local *.BiocCheck/ output folder, which BiocCheck drops into
the package directory on every local run and otherwise shows up as an ERROR
on the next run.

Version 1.9.10 + NEWS.

* docs: shorten NEWS entries to satisfy gDRstyle::lintNewsEntries

The devel linter accepts only a fixed list of imperative verbs; 'Build' and
'Ignore' are not on it, so switch to 'Move' and 'Exclude' and keep every
bullet on a single line. 
    
  
    

      Package: Pirat

      Commit: 115ce1c1a8a3321cf69300ee12a08cecf67d9662

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2026-07-24 13:17:00 -0700

      Commit message:


	  
		
 Add CITATION upstream
 
    
  
    

      Package: igvShiny

      Commit: 1454847dea68341979e0a93c6bc45ed14021b058

      Author:  Mateusz <gladkiimateusz@gmail.com> 

      Date: 2026-07-24 20:46:21 +0200

      Commit message:


	  
		
 feat: bundle igv.js 3.8.4 (minified), fix locuschange for 3.x (#116) (#125)

Swap the bundled igv.js from 2.13.1 to 3.8.4, using the minified UMD build
(igv-3.8.4.min.js). igvShiny.yaml points at it and declares the real bundled
version instead of the long-stale 1.4.5.

Adapt the locuschange handler to the 3.x payload: the callback now receives
the referenceFrameList; read the first frame and rebuild the same comma-free
"chr:start-end" string currentGenomicRegion has always emitted, guarding the
whole-genome "all" view (the old raw start/end were meaningless there).

Adapt the shinytest2 tests to 3.x: igv.js 3.x renders the browser inside a
shadow root, so the track DOM is no longer in the element's light-DOM HTML.
The helper now polls shadowRoot.innerHTML instead of get_html(). Two
assertions (remote ENCODE bigWig, local biotype-coloured GFF3) render
reliably locally but are flaky in headless CI under 3.x's fetch-before-render
behaviour, so they run off CI only.

Scope stays narrow (version bump + locuschange + the test changes it forces);
the lib/ cleanup, rn6 via twoBit, and the #114 patch removal follow in a
separate PR. 
    
  
    

      Package: immunoClust

      Commit: f1d31c0d3f23334cced133b84b3d23819b444817

      Author:  Till Sörensen <till-antoni.soerensen@charite.de> 

      Date: 2026-07-24 16:10:26 +0200

      Commit message:


	  
		
 added accessor ICL_bias
 
    
  
    

      Package: immunoClust

      Commit: 9ac35b49104796c9ba07f330bafd42332ec7ec15

      Author:  Till Sörensen <till-antoni.soerensen@charite.de> 

      Date: 2026-05-05 09:18:01 +0200

      Commit message:


	  
		
 minor bugfix
 
    
  
    

      Package: immunoClust

      Commit: 339d078e3989c6d18343177d164cbb719cc2922b

      Author:  Till Sörensen <till-antoni.soerensen@charite.de> 

      Date: 2026-04-30 16:27:03 +0200

      Commit message:


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

      Package: immunoClust

      Commit: 56d9333ccecd91036464e8804a4c0ecf354cda48

      Author:  Till Sörensen <till-antoni.soerensen@charite.de> 

      Date: 2026-04-30 16:24:31 +0200

      Commit message:


	  
		
 code cleaing
 
    
  
    

      Package: immunoClust

      Commit: aef5c5249e03dff42acbfa243f450fe994870916

      Author:  Till Sörensen <till-antoni.soerensen@charite.de> 

      Date: 2026-01-12 11:43:25 +0100

      Commit message:


	  
		
 minor
 
    
  
    

      Package: immunoClust

      Commit: 6fa739f986ad55b00e7ff6a799596687b9db7e69

      Author:  Till Sörensen <till-antoni.soerensen@charite.de> 

      Date: 2026-01-12 11:42:02 +0100

      Commit message:


	  
		
 added method meta.Mstep
 
    
  
    

      Package: spatialLIBD

      Commit: 94b68c69aeea6417ba7599edd723a11e02ee9682

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-07-24 09:53:12 -0400

      Commit message:


	  
		
 v1.25.2 -- fix colors on app at the layer-level tab
 
    
  
    

      Package: Rarr

      Commit: a1370094e7f0b77470c8e4a7df32f787e83574d9

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 14:23:28 +0200

      Commit message:


	  
		
 Add comment and tests about spec deviations
 
    
  
  


</div>

</div>