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Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.

GIT Logs

This is a list of recent commits to git.bioconductor.org, the devel(development) branch of the Bioconductor GIT repository.

This list is also available as an RSS feed (devel branch), and RSS feed (release branch)

Package: RankMap
Commit: 5baba89dc5d95077a077c8f96a03c3d86b0a8566
Author: jinming-cheng <jinming.cheng2018@gmail.com>
Date: 2026-07-27 12:56:02 +0800
Commit message:

 update vignette

Package: TSENAT
Commit: bffd9bd05f32b1a020552c117ab415c2badbeebf
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 21:29:24 +0200
Commit message:

 Additional bug review

Package: TSENAT
Commit: e707977cb69a79257ad28e3805e7548b0abf9aa1
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 17:04:55 +0200
Commit message:

 Improve documentation

Package: TSENAT
Commit: 38bab929d656fa19839986506344be64e6c4a01f
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 17:00:26 +0200
Commit message:

 Improve documentation

Package: TSENAT
Commit: cebdf45477e351e68f01533e104f9408e66d2aa1
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 15:49:52 +0200
Commit message:

 Restore README

Package: TSENAT
Commit: a36a846c26fdc6037ec955e6771827909ff55b21
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 15:46:57 +0200
Commit message:

 Update README structure

Package: TSENAT
Commit: 0b60e2a0cbd1e3b03e704bad7b9036218ad6fe38
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 15:43:38 +0200
Commit message:

 Update README structure

Package: TSENAT
Commit: 04ac09c86e3eb213acc2155bedefc6a0a06ce914
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 14:53:34 +0200
Commit message:

 Revert circleci config

Package: TSENAT
Commit: 0b1e8f32d42ecd968a61761c0b8933bbfc93ab10
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 14:31:39 +0200
Commit message:

 Fix circle CI config

Package: TSENAT
Commit: b17d47b6bb573309cf5d87618c644994711ecd5d
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 14:21:40 +0200
Commit message:

 Update news

Package: TSENAT
Commit: ecc321ea0c072b7e973c0df760c93cd49544dc70
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 14:11:02 +0200
Commit message:

 Fix circle CI config

Package: TSENAT
Commit: 90a247f4248ddfcccfffa8cd7e337926a64b14be
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 14:01:03 +0200
Commit message:

 Fix circleci

Package: TSENAT
Commit: efb47501536cc6f2ab0d37d4f322f2553918aac3
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 13:51:10 +0200
Commit message:

 Fix circleci

Package: TSENAT
Commit: b9549aaa726448b81372ac7f4ddb80e3256d8a10
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 13:21:49 +0200
Commit message:

 Remove trash from test

Package: TSENAT
Commit: 6b2eae05d1c88ab1e4d4632a3c731082b569defd
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 13:18:48 +0200
Commit message:

 Update circleci config

Package: TSENAT
Commit: d787651e0b21484990a905b0e4791ffca141f6c4
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 13:16:39 +0200
Commit message:

 Fix bugs and related tests

Package: TSENAT
Commit: defcecadb0b01adb98bd89c775a15a19be8a0490
Author: Cristóbal Gallardo Alba <gallardoalbac@gmail.com>
Date: 2026-07-26 06:22:16 +0200
Commit message:

 Merge branch 'stable' into devel

Package: TSENAT
Commit: e37ee22ca7d8cdea8c131139de3171aa4205eefa
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 06:20:30 +0200
Commit message:

 Remove duplicated

Package: TSENAT
Commit: 34fb0e8421ab82b43d8bd4948db64b1be60a3873
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-07-26 06:15:40 +0200
Commit message:

 Fix bugs

Package: TSENAT
Commit: ccbe7e1c06a6b95029b2493e9ae82ac6052ea7df
Author: Cristóbal Gallardo Alba <gallardoalbac@gmail.com>
Date: 2026-07-25 17:32:02 +0200
Commit message:

 Increase tests coverage (#61)

Increase test coverage.

Package: TSENAT
Commit: dd0ec5cacdcee209ecac687360126d2aa6893de0
Author: Cristóbal Gallardo Alba <gallardoalbac@gmail.com>
Date: 2026-07-25 15:50:47 +0200
Commit message:

 Upgrade version 0.99.31 (#59)

* Upgrade version

Package: igvShiny
Commit: 68d67bfc16f4874a179265855137ac7e3f21e540
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-07-26 18:44:50 +0200
Commit message:

 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.

Package: igvShiny
Commit: e34f94827ccfa0d8940cfb729524f847081e8ddc
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-07-26 18:37:10 +0200
Commit message:

 chore: bump the GitHub Actions used in CI (#139)

actions/upload-artifact was pinned to @master - a moving branch, not a release -
while checkout and cache sat on v3, which GitHub is winding down: the v3 cache
runner already reports "too old to run on GitHub Actions" in the workflow logs.

The artifact names embed runner.os, the Bioc release and the R version, so they
stay unique per matrix job and the v4 rule against reusing an artifact name in one
run does not bite. The docker actions move up too, though that job stays off
behind run_docker: false.

Package: scrapbook
Commit: 819d423b4143c792c00af7b9d3624e80449c9f0d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-07-27 01:51:54 +1000
Commit message:

 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.

Package: lcmsPlot
Commit: d9ab9daef0fc40e0ef62e91452ce6f00c751e0eb
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2026-07-26 15:08:28 +0100
Commit message:

 docs: add runnable examples to all exported man pages

BiocCheck failed its requirement that at least 80% of man pages
documenting exported objects have runnable examples: coverage was 25 of
33 (75.8%). Four pages wrapped their examples entirely in \dontrun{} and
referenced data that is not available (a .cdResult directory, a
LipidSearch export, an undefined raw_files), and the four precursor ion
purity layers had no examples at all.

All eight now execute. The purity examples build a purityA object from
the DDA files already shipped in inst/extdata/standards-mzml.zip, whose
MS2 scans carry real precursor selection and isolation-window metadata,
and are guarded with @examplesIf because msPurity is only suggested. The
Compound Discoverer scripting-node and LipidSearch examples write a
minimal vendor export to tempdir(), following the existing MZmine and
MS-DIAL examples, and point sample_paths at the shipped mzML files so the
documented plots extract real chromatograms rather than only building a
data source.

Coverage is now 33 of 33. Verified with R CMD check ("checking
examples ... OK") and a full BiocCheck run reporting 0 errors; the two
remaining warnings (odd y in the version number, R version dependency)
are pre-existing. Only roxygen comments changed, so no package logic is
affected.

Package: lcmsPlot
Commit: 90c12b31a1460644a685607bbb0a47b29d5e831f
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2026-07-25 18:17:20 +0100
Commit message:

 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.

Package: lcmsPlot
Commit: 4ec1e4a0fe2ac6eb3bf06ad69c5371b0deb658f5
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2026-07-25 17:57:02 +0100
Commit message:

 ci: fix stale-cache dependency failure and cut check runtime

The workflow ran for ~42 minutes and then failed at the test step with
BiocParallel, MSnbase, xcms, MsExperiment, mzR, Spectra, MsBackendMsp and
S4Vectors reported as required. Those Imports carry no version constraint, so
remotes::dev_package_deps() -- which reads metadata off disk and never loads
anything -- returned diff == 0 for each and the diff != 0 filter skipped them.
devtools::test() then called requireNamespace() for real and the on-disk copies,
compiled against a different R, failed to load. They came from the package
cache: its key carried no R or Bioconductor version, so once the image was
pinned from :devel to :3.23 the version-agnostic restore-key kept restoring an
R-devel library into the 3.23 container.

The cache key now includes the R and Bioconductor versions plus a CACHE_VERSION
bust knob, and the library path is resolved from .libPaths() rather than
hardcoded. A new purge step drops cached packages whose Built R minor version
differs from the running R, and a verification gate calls requireNamespace() on
every Depends/Imports entry immediately after installation, so this class of
breakage now fails in ~2 minutes naming the offending packages instead of ~40.

Runtime is addressed separately. The bare BiocManager::install(update = TRUE)
updated every preinstalled package in the image and is gone; devtools (~80
source-compiled packages) is replaced by testthat::test_local(); dependency
installation runs with Ncpus set. R CMD check gains --no-build-vignettes, since
--no-vignettes only skips checking them while R CMD build was still running
findChromPeaks, Obiwarp adjustRtime and groupChromPeaks over faahKO on every
push, and --no-tests drops the duplicate test run. A weekly schedule and
workflow_dispatch trigger run the full check with vignettes and tests to
preserve Bioconductor compliance, and a concurrency group cancels superseded
runs.

Adding version constraints to the Bioconductor Imports in DESCRIPTION would
remove the root cause at source and is worth doing separately.

Package: lcmsPlot
Commit: 6e45639a9973f2361fe7bab34c7154f5f79765b9
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2026-07-24 22:40:35 +0100
Commit message:

 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.

Package: igvShiny
Commit: 9e159e41f12db08f55698a055da3b318de584614
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-07-26 14:23:00 +0200
Commit message:

 fix: reply to getGenomicRegion in any shiny module (#134) (#137)

The getGenomicRegion handler built the module-scoped reply as
"igv-currentGenomicRegion." + elementID.replace("igv-", ""), hardcoding a
namespace instead of using the one the widget was rendered with. Only a module
whose id happened to be "igv" - as every demo uses - received the answer;
anywhere else the input never arrived. Pan and zoom were unaffected, since
locuschange builds the name correctly, so only the explicit "where am I" query
was lost.

The handlers are registered outside the widget factory and never see the
render options, so the namespace is now parked on the container element next to
chromLocString, and both call sites derive the event names from a single
currentGenomicRegionEventNames() - the duplicated naming logic is what let the
two paths drift apart in the first place.

Verified in node against a fake DOM (module ids igv, browser, myModule, and no
module at all, plus an element carrying no namespace) and end to end: with the
previous JS the new test's module reads NULL, with this one it reads the locus.

The test app serves its genome from the local httpuv fixture server, which now
sends Access-Control-Allow-Origin. It is a different port from the shiny app,
so without that header igv.js cannot fetch the genome and createBrowser returns
a promise that never settles - the app simply never reaches igvReady.

Related: #134

Package: igvShiny
Commit: 9f5ca693068358d889256a597264ddff4d59f0ae
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-07-26 12:50:28 +0200
Commit message:

 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
 
    
  
    
      Package: Rarr

      Commit: f4e07d00c48513a33d796b75f79237d5c67d9d7a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 13:35:03 +0200

      Commit message:


	  
		 Add benchmark for write_zarr_group()
 
    
  
    
      Package: Rarr

      Commit: 5fc2877db0cfc78b414c997e162bd8dc0080c40b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 11:38:14 +0200

      Commit message:


	  
		 Add write_zarr_group() to pkgdown index
 
    
  
    
      Package: Rarr

      Commit: 688ac39ac93dad7b5275a654819c196e37a47550

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 11:37:39 +0200

      Commit message:


	  
		 Ensure writing location is empty in benchmarks
 
    
  
    
      Package: Rarr

      Commit: 7db68ff1ad0914a20d8056b32514d396cebf3643

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 11:14:40 +0200

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: Rarr

      Commit: d8f8071cf7512d616945618f70ebfb3594337d14

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 11:14:25 +0200

      Commit message:


	  
		 Document all changes in NEWS
 
    
  
    
      Package: Rarr

      Commit: 91f18d538635eeef5811a25c6be4cb6317aaee20

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 11:05:27 +0200

      Commit message:


	  
		 Reduce zarr_consolidate_metadata() cyclocomp
 
    
  
    
      Package: Rarr

      Commit: 79a1418f1f454a968a03dc3ec04de35b6ec16f0f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 11:02:23 +0200

      Commit message:


	  
		 Fix creation of deep nested groups
 
    
  
    
      Package: Rarr

      Commit: 615a96816d76a18e53a8e4386d63f70609c6e6c7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 10:20:03 +0200

      Commit message:


	  
		 Fix tests and examples
 
    
  
    
      Package: Rarr

      Commit: c0f7485a34e64781a582259ee04b281990c7c141

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 10:04:21 +0200

      Commit message:


	  
		 Normalize path earlier when writing attrs
 
    
  
    
      Package: Rarr

      Commit: e37e4c98834517661e40427a483aeb831f434c6a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 10:01:41 +0200

      Commit message:


	  
		 Avoid infinite recursion
 
    
  
    
      Package: Rarr

      Commit: ae8fd7152800d670970de72dde2b5fb262f95a33

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-24 08:36:15 +0200

      Commit message:


	  
		 Create .check_node_name() helper function
 
    
  
    
      Package: Rarr

      Commit: d088fe1f5b34a28c2751bd9e804c058936d3d5b6

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-23 13:33:50 +0200

      Commit message:


	  
		 Use single write_json() call across if/else branches
 
    
  
    
      Package: Rarr

      Commit: b25d8cb21ee46443d987551dd92183859d0fa1ac

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-23 13:27:45 +0200

      Commit message:


	  
		 Error when writing attributes to a mixed group/array
 
    
  
    
      Package: Rarr

      Commit: 92600d5278079b7d8bca59011968144bf1923c18

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-23 13:54:31 +0200

      Commit message:


	  
		 Use NULL as default for s3_client
 
    
  
    
      Package: Rarr

      Commit: e39faa7eb41f456be21dceffe64b36836b96d510

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-23 13:26:19 +0200

      Commit message:


	  
		 Add METADATA_VX_FILES as global vars
 
    
  
    
      Package: Rarr

      Commit: 1b489c71023ccc92bed6ebceed61760faaaaf43f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-21 22:17:00 +0200

      Commit message:


	  
		 Create write_group() function

Co-authored-by: Artür Manukyan <artur-man@hotmail.com>
 
    
  
    
      Package: Rarr

      Commit: a452d17aab58cd13976d05fe92d75423976be284

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-21 21:37:40 +0200

      Commit message:


	  
		 Prevent from writing attributes to non-existing group or array
 
    
  
    
      Package: Rarr

      Commit: b481509bbad9902497d8f660d083b9098a629a0e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-14 09:02:38 +0200

      Commit message:


	  
		 Ensure folder is empty when writing new array
 
    
  
    
      Package: Rarr

      Commit: a4de790471c591968684accb8d1b12d074b8ef6f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-21 21:31:14 +0200

      Commit message:


	  
		 Silence backport_linter() for now

Since it also complains on functions for which we provide a backport
 
    
  
    
      Package: Rarr

      Commit: ca572dbfc440952cbddfed1d192f52c55f1ac8c5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-20 09:25:55 +0200

      Commit message:


	  
		 Add contributing guide
 
    
  
    
      Package: vsclust

      Commit: e0b4c035972c320b3fc3f6e76a2a0502eb49ca57

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2026-07-24 13:37:24 +0200

      Commit message:


	  
		 updated version
 
    
  
    
      Package: vsclust

      Commit: 1667e1909220df0883d1b4dc88bce6930b7b2677

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2026-07-24 13:36:23 +0200

      Commit message:


	  
		 batch size for id mapping
 
    
  
    
      Package: VariantAnnotation

      Commit: 6ab3a56c164777962b309123ef993ae6b45c405c

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-07-24 06:23:12 -0400

      Commit message:


	  
		 bump version for pr 74
 
    
  
    
      Package: VariantAnnotation

      Commit: 0808075832e167b4795e890e87a027a91bda7f0a

      Author:  Vince Carey <stvjc@channing.harvard.edu> 

      Date: 2026-07-24 06:14:30 -0400

      Commit message:


	  
		 Merge pull request #74 from mschubert/devel

Allow 'ANY' txdb, eg. EnsDb objects 
    
  
    
      Package: VariantAnnotation

      Commit: d439177f084d3866e37c3c852b0f151372c24619

      Author:  mschubertv <mschu.dev@gmail.com> 

      Date: 2023-11-06 10:57:44 +0000

      Commit message:


	  
		 allow 'ANY' txdb, eg. EnsDb objects
 
    
  
    
      Package: ctdR

      Commit: 9886cdb64f226c53d16e6c4482343055c6dcbcd6

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 11:41:07 +0200

      Commit message:


	  
		 Merge remote-tracking branch 'upstream/devel' into bioc-sync
 
    
  
    
      Package: ctdR

      Commit: 6d0e204b0844cc1f75762ef418f32ed7566a8bfa

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 11:35:00 +0200

      Commit message:


	  
		 Merge pull request #40 from drake69/feature/bioc-review-4232

Bioconductor review #4232: BiocIO CTDFile, interoperability, BiocFileCache, URL support (0.99.7) 
    
  
    
      Package: ctdR

      Commit: 400c2d9aea553c3477d534357803aa7c4c11369c

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 11:20:22 +0200

      Commit message:


	  
		 docs(pkgdown): add CTDFile, ctd_cache, as_genesets_CTD to reference index

pkgdown build failed because the three new exported topics were missing
from the _pkgdown.yml reference index.
 
    
  
    
      Package: ctdR

      Commit: e2f95c6b4acbe6eb659660b6478a6134fa255acd

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 11:12:12 +0200

      Commit message:


	  
		 chore: stop tracking internal .code_reader inbox

.code_reader/ is an internal code-reader inbox and must not be published.
Untrack it and add it to .gitignore so it no longer ships to GitHub or
Bioconductor (it was never present on the Bioconductor remote).
 
    
  
    
      Package: ctdR

      Commit: 1c927f6c8ff70c62d6b83030b9df64d34f7ac45f

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 10:59:55 +0200

      Commit message:


	  
		 chore: finalize 0.99.7 for Bioconductor review round #4232

Version bump to 0.99.7 with NEWS and README updates for the new CTDFile /
import(), as_genesets_CTD(), ctd_cache(), URL support and BiocFileCache
cache. Also address R CMD check / BiocCheck findings from the round:

- .Rbuildignore: exclude .coding_agent, .code_reader, tests _problems so
  they no longer ship in the tarball
- document the CTDFile S4 class (add CTDFile-class alias)
- import methods::new; drop the unused 'plyr' from Imports; replace an
  unqualified head() with base indexing

R CMD check: 0 ERROR (remaining WARNING is the expected --as-cran
"new submission / org.Hs.eg.db / 302 URL"); BiocCheck: 0 ERROR, 0 WARNING.
 
    
  
    
      Package: ctdR

      Commit: decf1f1239e0cb65595c4077324dc436614c4203

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 10:33:13 +0200

      Commit message:


	  
		 test: raise coverage on interaction_types and cache error paths

Address Bioconductor review #4232 (tests point): add tests exercising the
previously-uncovered interaction_types filtering branch in GSVA, CAMERA and
as_genesets_CTD('symbol'), plus the .ctd_cache_load missing-resource error
and the cache-hit path of .resolve_ctd_source (URL already downloaded).

Per-file coverage: gsva 70->96, camera 77->97, utils-input 79->100,
as_genesets_CTD 73->100, cache 80->100. Package total ~95%.
 
    
  
    
      Package: ctdR

      Commit: e82fb3fb0fb0c26fb362758f95d841cba758bd3a

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 10:27:52 +0200

      Commit message:


	  
		 docs: document pAdjustMethod inputs and accept all p.adjust methods

Address Bioconductor review #4232 (R point): expand the pAdjustMethod
documentation to reference stats::p.adjust and enumerate the accepted
values, and widen validation from an arbitrary 4-value subset to the full
stats::p.adjust.methods (the value is passed straight to p.adjust and, for
ORA, clusterProfiler::enricher, both of which accept them all). Strictly
more permissive; no behavior change for existing BH/bonferroni/fdr/none.

- tests: pAdjustMethod accepts every p.adjust.methods value
- suite: FAIL 0 | PASS 195
 
    
  
    
      Package: ctdR

      Commit: 1860cfd00d8031d53560c9d1e4075e212eb2dd78

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 10:23:25 +0200

      Commit message:


	  
		 chore: gitignore testthat _problems/ artifacts
 
    
  
    
      Package: ctdR

      Commit: fef2853081ff5f02bfcaccbc8decf73bba279e0c

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 10:23:12 +0200

      Commit message:


	  
		 feat: accept a URL in import_CTD() with a licensing reminder

Address Bioconductor review #4232 (R point): import_CTD() and the CTDFile
import() method now accept either a local path or a URL. A new internal
R/source.R resolves the source: remote http(s)/ftp URLs are downloaded and
cached via BiocFileCache, emitting a one-time CTD data-licensing reminder;
file:// URIs and local paths are read directly. No default CTD URL is
assumed, so the user remains the party who downloads under CTD's terms.

- R/source.R: .is_remote_url(), .ctd_license_reminder(), .resolve_ctd_source()
- import_CTD()/import(CTDFile) share the resolver (removes duplicated logic)
- tests/testthat/test-source.R (7 blocks; file:// end-to-end, offline)
- suite: FAIL 0 | PASS 186
 
    
  
    
      Package: ctdR

      Commit: de0af30bcf81090499edb297f56678afd3b4fd2e

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 10:15:22 +0200

      Commit message:


	  
		 refactor(cache): migrate CTD cache from rappdirs to BiocFileCache

Address Bioconductor review #4232 (R point): replace the hand-managed
rappdirs directory of .rda files with a BiocFileCache-backed store. A new
internal R/cache.R wraps BiocFileCache: import_CTD() writes the four
processed objects as named resources; readers retrieve them by name.

The cache location is tools::R_user_dir("ctdR", "cache"), overridable via
options(ctdR.cache=) which the test suite uses to redirect to a temp dir
instead of the previous assignInNamespace(rappdirs) hack.

- DESCRIPTION: Imports -rappdirs +BiocFileCache
- import_CTD/enrichment_CTD/as_genesets_CTD/ctd_cache/.load_geneset_list/
  .filter_gene_sets now go through the cache module
- tests updated to the option-based redirection and bfc helpers
- suite: FAIL 0 | PASS 170
 
    
  
    
      Package: ctdR

      Commit: 724642feeda225ff59e74a8ae0d9176ab9d9265e

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 09:59:43 +0200

      Commit message:


	  
		 feat: add ctd_cache() helper to read cached CTD tables

Address Bioconductor review #4232 (vignette make-expr chunk): provide an
exported helper to retrieve processed CTD data from the cache instead of
loading the .rda files by hand. ctd_cache("chemicals"|"interactions")
returns the requested table with a cache-not-found error pointing to
import_CTD().

The tutorial's dex-recap-gsva chunk now calls ctd_cache("chemicals")
rather than load(file.path(user_cache_dir("ctdR"), "chemicals.rda")).

- R/ctd_cache.R + man + NAMESPACE export
- tests/testthat/test-ctd_cache.R (4 blocks)
 
    
  
    
      Package: ctdR

      Commit: 0175923c9290221f9d542232f7938c58887e480c

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 09:55:49 +0200

      Commit message:


	  
		 feat: add as_genesets_CTD() to export CTD gene sets to existing engines

Address Bioconductor review #4232 (enrichment interoperability): rather
than only exposing enrichment_CTD(), let users hand the CTD chemical
gene sets to established engines. as_genesets_CTD() returns the cached
gene sets as a named list (ChemicalID -> genes), in the shape expected
by EnrichmentBrowser::sbea()'s `gs` argument, with optional id_type and
interaction_types. No dependency on EnrichmentBrowser is taken.

Vignette gains an "Interoperability" section (CTDFile/import() plus the
sbea() handoff) and a "CTD acronym" disambiguation note.

- R/as_genesets_CTD.R + man + NAMESPACE export
- tests/testthat/test-as_genesets_CTD.R (5 blocks)
 
    
  
    
      Package: ctdR

      Commit: 12b43ebdcf46da48c6285b05a31e40c833bb658d

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-24 09:48:58 +0200

      Commit message:


	  
		 feat(io): add CTDFile BiocIO class and import() method

Address Bioconductor review #4232 (NAMESPACE point): model CTD file
access on BiocIO. Add an S4 CTDFile class (subclass of BiocIO::BiocFile)
plus an import() method on the shared BiocIO generic that returns a
S4Vectors::DataFrame of validated human (OrganismID 9606) CTD
chemical-gene interactions, reusing .read_and_validate_ctd(). The class
is named CTDFile (not CTD) to avoid acronym collisions.

import_CTD() is left unchanged; the class is purely additive.

- DESCRIPTION: Imports += BiocIO, S4Vectors, methods
- NAMESPACE/man regenerated (exportClasses/exportMethods)
- tests/testthat/test-CTDFile.R: construction, validation, import,
  missing-file error, parity with .read_and_validate_ctd
 
    
  
    
      Package: ctdR

      Commit: 9e27fe2ccf4a5a52057c9843354cccf834b50a65

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-22 15:09:47 +0200

      Commit message:


	  
		 docs(README): add documentation site badge and callout (landing entry point)
 
    
  
    
      Package: ctdR

      Commit: 744d82332911f881150086b0dcd8d24dd8286eec

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-07 18:43:58 +0200

      Commit message:


	  
		 docs: add GitHub star call-to-action to README; refresh pkgdown docs/
 
    
  
    
      Package: ctdR

      Commit: 856b2dca141c6bbebc48c7f86fd2724af2b45466

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-07 17:35:16 +0200

      Commit message:


	  
		 Merge pull request #39 from drake69/release/0.99.6-news

release: 0.99.6 news + Vemetric analytics on pkgdown site 
    
  
    
      Package: ctdR

      Commit: 6c8181df4286cc2b3260004c4cb4506ae46a3d33

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-07-07 16:36:42 +0200

      Commit message:


	  
		 chore(pkgdown): add Vemetric analytics snippet to site head
 
    
  
    
      Package: ctdR

      Commit: a26eec6a07fbba36daffbdf8e0b5aa46fa05ddf0

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-06-26 11:55:10 +0200

      Commit message:


	  
		 docs(vignettes): clarify CAMERA inputs (full expression matrix + design/contrast)

CAMERA does not consume a pre-computed DEG list (unlike ORA/GSEA): it takes
the full expression matrix plus design and contrast, recomputing the
differential signal internally. Make the design-vs-contrast distinction
explicit in both ctdR.Rmd and the RNA-seq tutorial. Refresh .code_reader
auditor artifacts.
 
    
  
    
      Package: ctdR

      Commit: 8524497e3a71d1b1c06ba8f6182fadbbc5ee5ce5

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-06-19 11:06:43 +0200

      Commit message:


	  
		 chore: exclude .coding_agent/ from version control
 
    
  
    
      Package: ctdR

      Commit: df6189516e9c11160cf2bb333c81b5dd90a6e0c3

      Author:  Code Reader <code-reader@audit> 

      Date: 2026-06-16 17:47:38 +0200

      Commit message:


	  
		 review: 47 new units scanned (2026-06-16)
 
    
  
    
      Package: ctdR

      Commit: 4d10a40e243b38fabcd6910344aed8f74f1be6ab

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-06-16 17:02:03 +0200

      Commit message:


	  
		 docs(NEWS): add 0.99.6 entries for PR #34 features and fixes
 
    
  
    
      Package: ctdR

      Commit: a9f8ad64a8ff6c60907d513dce0f6ca628c07afe

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-06-16 16:58:58 +0200

      Commit message:


	  
		 feat: interaction_types filter, gene_id_type, universe/size params, dedup, timing (#34)

* docs(vignette): ORA explicit limitation + is_subset branch for full CTD

- Replace blockquote note with prose paragraph explicitly stating ORA
  requires the full CTD download (~16k chemicals) to be powered; toy
  bundled sample (10 chemicals x 17 genes) is API demo only.
- Add is_subset <- TRUE chunk before ora-real; FALSE path downloads
  and imports real CTD then runs a fully powered ORA on GSE311566 DEGs.

* review: 5 units reviewed, 1188 new units scanned (2026-06-16)

* feat: interaction_types filter at enrichment time + universe/size params for ORA

- import_CTD(): saves ctd_interactions.rda (ChemicalID, EntrezID,
  InteractionActions per pair); no interaction filter at import time
- enrichment_CTD(): new interaction_types parameter (default NULL = all);
  when set, loads ctd_interactions.rda and rebuilds gene sets on the fly
  via .filter_gene_sets(); all four methods supported
- ora(): exposes universe, minGSSize, maxGSSize via ... to enricher()
- gsea(): stat column for signed ranking; fgseaMultilevel with nproc via ...
- vignette: new section on gene set size filters and universe
- tutorial: full GSE311566 workflow with limma + all four methods

* feat: deduplicate chemicals at import; warn on ChemicalID/Name ambiguities

- .deduplicate_chemicals(): one row per ChemicalID (warning if CTD has
  multiple names for same ID; message if same name shared by multiple IDs)
- Replaces silent unique() which could silently create duplicate rows
  in the merge step of .format_enrichment_result()

* feat: gene_id_type param + fix EnrichedGenes bug in GSEA

- enrichment_CTD(gene_id_type = c("symbol","entrez")): controls whether
  EnrichedGenes uses HGNC symbols or Entrez IDs
- "symbol" (default): HGNC symbol with Entrez ID fallback for unmapped genes;
  no genes silently dropped
- "entrez": skips symbol mapping entirely, uses Entrez IDs throughout
- ORA: gene_id_type="entrez" uses ChemicalName_GeneEntrezIds as TERM2GENE
  and passes Entrez IDs directly to enricher(), skipping symbol conversion
- GSEA bug fix: was assigning rownames() (row numbers) as gene symbols;
  now maps EntrezID -> GeneLabel (symbol or Entrez fallback) in .run_gsea()
  before passing to gsea(); .annotate_genes() uses GeneLabel column

* feat(import_CTD): add timing and summary stats to completion message

Reports elapsed seconds, chemical count, and unique gene count on finish.

* fix(ora): suppressMessages around enricher() to silence clusterProfiler gene-mapping messages (AI-008)

* docs: regenerate man pages + update tutorial parameters

- Rd files regenerated for enrichment_CTD, import_CTD, gsea, ora,
  .run_ora, .run_gsea, .run_camera, .run_gsva, .filter_gene_sets,
  .deduplicate_chemicals, .build_interaction_table, .save_ctd_cache
- Tutorial: minSize/maxSize for GSEA+GSVA, universe+minGSSize for ORA,
  direction-aware GSEA section (interaction_types), fix GSVA Dex recap
  (ChemicalID lookup), update GSEA text (t-stat, not p-value)

* fix: add missing @param gene_id_type roxygen doc (fixes R CMD check WARNING)

* fix(pkgdown): add tutorial_rnaseq_workflow to _pkgdown.yml articles index

* fix(ci): remove ctdR.BiocCheck/ after BiocCheckGitClone to prevent stray folder ERROR

---------

Co-authored-by: Code Reader <code-reader@audit> 
    
  
    
      Package: ctdR

      Commit: 0c39dd67b3a78239fbb7d8efa5c016d95a6efc97

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-06-16 16:09:09 +0200

      Commit message:


	  
		 feat(0.99.6): add full GSE311566 e2e pipeline script and update docs (#32)

Add inst/scripts/example_gse311566_full_pipeline.R: production-shaped
reference pipeline with a-priori power analysis, declared alpha cutoffs,
limma DE, and all four enrichment methods. Complements the vignette
(bundled subset, no alpha) as the canonical example linked from README
and paper. Bump version to 0.99.6, update NEWS.md and README.md. 
    
  
    
      Package: ctdR

      Commit: 5761aa178d2d49d67fc4f04115064c5e5bc86f65

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-06-16 16:09:05 +0200

      Commit message:


	  
		 docs(vignette): ORA explicit limitation + is_subset branch for full CTD (#33)

- Replace blockquote note with prose paragraph explicitly stating ORA
  requires the full CTD download (~16k chemicals) to be powered; toy
  bundled sample (10 chemicals x 17 genes) is API demo only.
- Add is_subset <- TRUE chunk before ora-real; FALSE path downloads
  and imports real CTD then runs a fully powered ORA on GSE311566 DEGs. 
    
  
    
      Package: ctdR

      Commit: f7f28a0e6b27e4f166a665d9bc51b34da14fff5a

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-06-11 19:32:49 +0200

      Commit message:


	  
		 feat(0.99.5): bundle GSE311566 real-data e2e example and biological-expectation test

Resolves the BiocCheck NOTE on \donttest{} man-page examples and
strengthens reviewer confidence by demonstrating ctdR on a public
RNA-seq dataset (GEO GSE311566, PBMC Dex vs DMSO, female donors).

Added:
- inst/extdata/GSE311566_subset.rds: 1500 top-variance genes x 7 samples
  (4 DMSO + 3 Dex), log2-normalised counts. ~34 KB.
- inst/extdata/README.md: provenance + licensing notes for the bundled
  subset.
- inst/scripts/make_gse311566_subset.R: reproducible builder that
  downloads the GEO supplementary file, parses Dex/DMSO columns,
  maps ENSG to Entrez, and saves the subset.
- tests/testthat/test-e2e-gse311566.R: end-to-end pipeline test asserting
  biological expectation (Dexamethasone in top-3 GSEA hits, top-6 CAMERA
  hits, schema correctness).

Modified:
- vignettes/ctdR.Rmd: new "End-to-end example with real RNA-seq data"
  section replacing the previous synthetic-matrix block. Uses base-R
  t.test + p.adjust for DE to keep the example DE-framework-independent.
- R/enrichment_analysis.R: roxygen @examples for CAMERA/GSVA now run
  directly on the bundled subset; \donttest{} wrapper removed.
- man/enrichment_CTD.Rd: regenerated via devtools::document().
- NEWS.md: 0.99.5 entry with full Track B summary.
- DESCRIPTION: Version 0.99.4 -> 0.99.5.
- .Rbuildignore: exclude .sestante/ from package source tarball.
- .gitignore: exclude vignettes/*.html (build artefact).
 
    
  
    
      Package: ctdR

      Commit: 709bb1689527e8f84bf779b7aaa498acfa09e35e

      Author:  Luigi Corsaro <lcorsaro69@gmail.com> 

      Date: 2026-06-01 21:23:11 +0200

      Commit message:


	  
		 chore: gitignore .sestante/ (backlog locale package dev)
 
    
  
    
      Package: ctdR

      Commit: f5ac1cfb44edaf0fda605cbe791a4f07818c24a9

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 17:06:25 +0200

      Commit message:


	  
		 Merge pull request #25 from drake69/refactor/enrichment-ctd-symmetric-dispatch

refactor: unified output schema + symmetric dispatch architecture 
    
  
    
      Package: ctdR

      Commit: f4dbf6a87e23bb050ce49abdd4bcbbb0612af368

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 16:51:59 +0200

      Commit message:


	  
		 fix(docs): update plot_CTD example to use EntrezID input column

R-CMD-check (--as-cran) caught a leftover from the input-column
rename: the roxygen example for plot_CTD() still built its sample
data frame with `entrez_ids = c(...)`. The example then called
enrichment_CTD(genes, method = "ORA"), which under the new schema
reads `x$EntrezID` (NULL with the old column name) and passed NULL
to AnnotationDbi::select() -> "'keys' must be a character vector"
error during check.

Switch the example to `EntrezID = c(...)`. R CMD check now passes
clean (0 errors, 0 warnings, 0 notes).
 
    
  
    
      Package: ctdR

      Commit: d95add350c6031ef2cec1b7007dd07b779162813

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 16:36:08 +0200

      Commit message:


	  
		 refactor: unify enrichment output schema across ORA/GSEA/CAMERA

Builds on the symmetric-dispatch refactor by also harmonizing the
public column schema across the three data-frame-returning methods.
Pre-1.0 + pre-Bioconductor-acceptance is the right moment to land a
breaking rename; doing it later would force a real API break.

Architecture
------------

* .format_enrichment_result() is now the single source of truth for
  the engine -> canonical mapping. Each runner declares a
  `rename = c(old = "New")` + `drop = c(...)` and the formatter
  handles all post-processing: padj recomputation, metadata merge,
  column ordering, sort, row-name reset, plus the new Method column.
* gsea() and ora() engines emit native fgsea / clusterProfiler
  column casing (pval / pvalue / ES / NES / size / leadingEdge etc.)
  but lift their primary-key column (pathway / ID) to the
  semantically correct "ChemicalID" right at the engine boundary so
  internal callers never see a misleading generic name.
* The Method column ("ORA" / "GSEA" / "CAMERA") is stamped by the
  formatter so result frames can be rbind / bind_rows'd across
  methods without losing provenance.

Public schema (breaking)
------------------------

Shared front columns (all three methods):
    ChemicalID, ChemicalName, Method, PValue, PValueAdjusted

Input column rename (ORA / GSEA data frame):
    entrez_ids  -> EntrezID

Cross-method canonical aligns:
    pval / pvalue            -> PValue
    padj / p.adjust          -> PValueAdjusted
    size (GSEA) / NGenes (CAMERA) -> GeneSetSize
    geneID (ORA) / Enriched_GENE (GSEA) -> EnrichedGenes
    ES / NES                 -> EnrichmentScore / NormalizedEnrichmentScore
    BgRatio / qvalue / foldEnrichment / leadingEdge ->
        BackgroundRatio / QValue / FoldEnrichment / LeadingEdge

Removed: Description (ORA, was always == ID), FDR (CAMERA,
PValueAdjusted is recomputed under the requested pAdjustMethod).

Other changes
-------------

* Vignette restructured: new "Shared output schema" section listing
  the five common columns; per-method sub-sections now show only
  method-specific extras.
* NEWS.md expanded with the full breaking-change rename table.
* plot_CTD updated to read PValueAdjusted / GeneSetSize / FoldEnrichment.
* .run_camera() shrank to 45 lines (was 57). BiocCheck "function
  length > 50" NOTE is now satisfied for the enrichment-table
  pipeline (plot_CTD / .plot_camera remain over the limit but are
  unrelated to this refactor; tracked for a separate PR).
* Full test suite: 123 PASS / 0 FAIL.
 
    
  
    
      Package: ctdR

      Commit: b4b9498d8863dcfa6dad212bf472f06460a1d90d

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 15:31:46 +0200

      Commit message:


	  
		 refactor: shrink enrichment_CTD() via validator + symmetric runners

enrichment_CTD() was 101 lines and triggered the BiocCheck note
"functions should be <= 50 lines". Two design issues were inflating it:

1. ~50 lines of inline argument validation (input required, match.arg,
   pAdjustMethod check, cache presence, x shape per method, CAMERA
   design+contrast requirement).
2. ORA and GSEA branches inlined the .rda load + engine call inside
   switch(), while CAMERA/GSVA already delegated to .run_camera() and
   .run_gsva() that load their own cached data.

Extract both:

- New internal .validate_enrichment_args() centralizes all validation,
  preserving the exact error messages (tests against "CTD data not
  found", "import_CTD", "ctdbase.org", "pAdjustMethod" all still pass).
- Existing .run_ora() refactored to a (x, chemicals_meta, cache_dir,
  pAdjustMethod) signature that loads ChemicalName_GeneSymbols.rda
  internally, matching the .run_camera()/.run_gsva() shape.
- New .run_gsea() with the same signature wraps the existing gsea()
  engine and owns the ChemicalName_GeneEntrezIds.rda load.

enrichment_CTD() body is now ~30 lines, a clean dispatcher:
  validate -> load chemicals -> switch(method, ORA/GSEA/CAMERA/GSVA).

Adding a fifth method in the future is now a one-line switch entry
plus a new .run_*() runner with the same four-argument shape.

No public API change. Version bump 0.99.3 -> 0.99.4 per Bioconductor
pre-release policy. Full test suite: 111 PASS / 0 FAIL.
 
    
  
    
      Package: ctdR

      Commit: 1981befcf9e4523998f9f4c754cff5fff5e22b2f

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 15:20:17 +0200

      Commit message:


	  
		 Merge pull request #24 from drake69/fix/ci-bioccheck-devel-and-shell-guard

fix(ci): close BiocCheck gap (devel BiocCheck + shell guard) 
    
  
    
      Package: ctdR

      Commit: 7f93fabce8845fdd51b9d5bb2b37844349a39b92

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 15:06:08 +0200

      Commit message:


	  
		 fix(ci): use pak to install BiocCheck@devel from GitHub

BiocManager::install("BiocCheck", version = "devel", update = FALSE)
fails on a fresh runner because Bioc 3.24 requires upgrading ~53 other
packages, and update = FALSE makes it bail rather than proceed.

Switch to pak::pkg_install("github::Bioconductor/BiocCheck@devel"),
which resolves dependencies on a per-package basis and installs just
BiocCheck (and any of its missing transitive deps) without forcing a
Bioc-wide upgrade.

Replace the any::BiocManager extra-packages entry with any::pak so
setup-r-dependencies provisions the right installer up front.
 
    
  
    
      Package: ctdR

      Commit: 17b6709787129da0798485bb32ed9cc2f7d6d3a6

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 15:01:03 +0200

      Commit message:


	  
		 fix(ci): assert BiocCheck >= 1.49.0 after install

If Bioconductor renames version = "devel" or the BiocManager mirror
falls back to a release version, the previous install step would
silently succeed with an older BiocCheck that lacks the tracked-system-
files check — exactly the regression this PR was created to prevent.

Add an explicit compareVersion() guard that aborts the job with a clear
error if the resolved BiocCheck is < 1.49.0.
 
    
  
    
      Package: ctdR

      Commit: f15dfa992221c87b0c3479a38149f0fbb1cd1d69

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 14:58:21 +0200

      Commit message:


	  
		 fix(ci): close BiocCheck gap (devel BiocCheck + shell guard)

The negative test in #23 revealed that the BiocCheckGitClone step added
in #21 does not catch tracked .Rproj files in CI. Root cause: our CI
installs BiocCheck from CRAN (1.48.x release), but the tracked-system-
files check exists only from 1.49.x (devel). The Bioconductor package
builder used 1.49.6, which is why it caught the issue and our CI did not.

Two complementary fixes:

1. Add a fast, version-independent shell guard that fails the job if any
   *.Rproj or *.DS_Store file appears in `git ls-files`. This catches
   the specific class of regression from job 4232 regardless of what
   BiocCheck does or does not check.

2. Switch the BiocCheck install from `any::BiocCheck` (CRAN/release) to
   BiocManager::install("BiocCheck", version = "devel"), matching the
   version the Bioconductor builder runs. This gives us full parity
   with the production submission pipeline.

Verification will be done by re-running CI on PR #23, which contains a
deliberately re-added ctdR.Rproj and was previously passing erroneously.
With this change it must turn red.
 
    
  
    
      Package: ctdR

      Commit: 4d25fd800631cdadfedee23ed3dc75b17594777a

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 14:55:52 +0200

      Commit message:


	  
		 Merge pull request #22 from drake69/chore/biocheck-notes-cleanup

chore: address BiocCheck notes (R 4.6.0 dep, roxygen line widths) 
    
  
    
      Package: ctdR

      Commit: 5ef48f4b94c96b5afada6b8e619ed1523da8f110

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 09:15:27 +0200

      Commit message:


	  
		 chore: address BiocCheck notes (R 4.6.0 dep, roxygen line widths)

From Bioconductor build job 4232 (ctdR 0.99.2):

- NOTE: Update R version dependency from 4.5.0 to 4.6.0
  -> DESCRIPTION: Depends R (>= 4.6.0)
  -> Version bump 0.99.2 -> 0.99.3 (per Bioconductor pre-release policy)

- NOTE: Consider shorter lines; 11 lines > 80 characters long
  -> Rewrap 4 roxygen @param lines in R/camera.R and R/gsva.R that
     exceeded 80 chars; man/dot-run_camera.Rd and man/dot-run_gsva.Rd
     regenerated via roxygen2::roxygenise(roclets="rd").
  -> Remaining > 80-char lines are in vignettes/ctdR.Rmd (markdown
     comparison table and a GitHub issue reference URL); shortening
     them would break the table layout, leaving the NOTE benign.

Out of scope (left for follow-up):
- NOTE: 60 lines with non-multiple-of-4 indents -> all in man/*.Rd,
  emitted by roxygen2's default formatting of \item blocks; not
  fixable without customizing roxygen2 templates.
- NOTE: dontrun in enrichment_CTD.Rd -> example requires CTD download
  and is intentionally guarded.
- NOTE: enrichment_CTD() and .run_camera() exceed 50 lines -> refactor
  is a separate concern (will open a dedicated PR).
- NOTE: fnd role missing -> only applicable if grant-funded.
 
    
  
    
      Package: ctdR

      Commit: 4576d51fa59d4a6413f5c3da938516350b41c05b

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 08:56:15 +0200

      Commit message:


	  
		 Merge pull request #21 from drake69/fix/biocheck-rproj-tracked

fix: untrack ctdR.Rproj and add BiocCheckGitClone to CI 
    
  
    
      Package: ctdR

      Commit: 5ab4582bf96357f561908498c8db1797836f7fb0

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-19 08:50:50 +0200

      Commit message:


	  
		 fix: untrack ctdR.Rproj and add BiocCheckGitClone to CI

The Bioconductor build report (job 4232, ctdR 0.99.2) flagged ctdR.Rproj
as an ERROR in BiocCheckGitClone — system files must not be tracked in
the git repository, even when .Rbuildignore correctly excludes them from
the tarball.

Changes:
- git rm --cached ctdR.Rproj (file kept locally, no longer tracked)
- .gitignore: add *.Rproj so future RStudio project files stay untracked
- .github/workflows/bioccheck.yaml: add a BiocCheckGitClone step before
  BiocCheck. The existing BiocCheck() step inspects the built source
  dir/tarball (where .Rbuildignore hides the .Rproj), so it could not
  catch this class of regression. BiocCheckGitClone() inspects the git
  clone directly, matching what Bioconductor runs in production.
 
    
  
    
      Package: ctdR

      Commit: f525dcb8f6aa9080e1ea2d3cb3aaeaff1283a5d1

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 11:03:15 +0200

      Commit message:


	  
		 Merge pull request #20 from drake69/fix/pkgdown-pages-artifact

ci(pkgdown): deploy via Pages artifact instead of pushing to main 
    
  
    
      Package: ctdR

      Commit: 3cebca50c9c40d7748ec914b713d90e9e6ffbc88

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 10:56:16 +0200

      Commit message:


	  
		 ci(pkgdown): deploy via Pages artifact instead of pushing to main

The previous workflow tried to commit the rebuilt docs/ back to main,
which is blocked by branch protection (GH006: protected branch update
failed). Switch to the official upload-pages-artifact + deploy-pages
flow so the site is published directly from a workflow artifact,
without writing to main.

Requires a one-time repo setting change: Settings → Pages → Source =
"GitHub Actions".
 
    
  
    
      Package: ctdR

      Commit: 06fdc3123682cdb5589f83817e8de183ec94494e

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 10:46:32 +0200

      Commit message:


	  
		 Merge pull request #19 from drake69/feature/install-instructions-pre-bioc

docs: clarify install instructions while Bioconductor submission is pending 
    
  
    
      Package: ctdR

      Commit: 7d81eaf883144d81484d4d48a82c0297bf83bfeb

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 10:10:57 +0200

      Commit message:


	  
		 docs: clarify install instructions while Bioconductor submission is pending

README.md and vignettes/ctdR.Rmd both told users to install via
`BiocManager::install("ctdR")` as if the package were already on
Bioconductor. It is not -- submission #4232 is still under review --
so that command silently fails for anyone following the docs.

Changes
-------

* README.md
  - Add a "Bioconductor status: not yet accepted, or under review"
    notice right under the package description with a link to
    Bioconductor/Contributions#4232.
  - Reshape the Installation section: GitHub (`install_github`) is now
    the primary installation method, with an explicit note that the
    Bioconductor command will only work after acceptance.
  - Keep the `BiocManager::install(c("fgsea", "org.Hs.eg.db", ...))`
    block for dependencies, which is unaffected by the submission
    status.

* vignettes/ctdR.Rmd
  - Same status notice at the top of the Installation section.
  - Same reshuffling: GitHub first, Bioconductor second with the
    "once accepted" caveat.

No code changes. R CMD check: 0 errors / 0 warnings / 0 notes.
 
    
  
    
      Package: ctdR

      Commit: e97ec7f8e46dfa822b5f1428688603236093425b

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 09:56:45 +0200

      Commit message:


	  
		 Merge pull request #18 from drake69/feature/pkgdown-site

docs: set up pkgdown site + add Star CTA 
    
  
    
      Package: ctdR

      Commit: 270d8230830924cdbe7768a398f37ce24c430cc8

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 09:54:36 +0200

      Commit message:


	  
		 Merge pull request #17 from drake69/feature/zenodo-concept-doi

docs: point Zenodo badge and DOI to the concept record 
    
  
    
      Package: ctdR

      Commit: 0cfaad783d6d8f83b5d892095755c6ce1f3c667c

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 09:53:52 +0200

      Commit message:


	  
		 Merge pull request #13 from drake69/dependabot/github_actions/actions/checkout-6

chore(deps): bump actions/checkout from 4 to 6 
    
  
    
      Package: ctdR

      Commit: 02ccc3fbc06f828afd7410e1f8fb66ab90511d8f

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 09:49:56 +0200

      Commit message:


	  
		 Merge pull request #12 from drake69/dependabot/github_actions/actions/upload-artifact-7

chore(deps): bump actions/upload-artifact from 4 to 7 
    
  
    
      Package: ctdR

      Commit: 82acf42cc177025077afb08e050a20b23deac4b3

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 09:35:12 +0200

      Commit message:


	  
		 ci: re-trigger workflows on pkgdown branch
 
    
  
    
      Package: ctdR

      Commit: ed60567f9c3f9fd7209098dfe1b8ca77a52e1c6c

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 09:15:57 +0200

      Commit message:


	  
		 docs: set up pkgdown site + add Star CTA to README

Replaces the hand-written single-page docs/index.html (last updated
March 2026 for v0.99.0, missing CAMERA / GSVA) with a full pkgdown
site auto-deployed to GitHub Pages.

What is added
-------------

* _pkgdown.yml — minimal config: site URL, Bootstrap-5 template,
  navbar layout, grouped function reference, links to issues / CTD.
* .github/workflows/pkgdown.yaml — auto-deploy workflow that runs on
  push to main, on pull_request (build-only check), on release, and
  via workflow_dispatch. Rebuilds docs/ in-place and pushes a single
  "docs(pkgdown): rebuild site [skip ci]" commit when the rendered
  HTML actually differs.
* .Rbuildignore — exclude _pkgdown.yml and pkgdown/ working directory
  from the package tarball.
* README.md — new "⭐ If you find ctdR useful, please star the repo"
  section right after the citation block. Same call-to-action ends up
  on the pkgdown landing page automatically (pkgdown derives the home
  page from README.md).
* docs/ — regenerated from scratch with `pkgdown::build_site()`,
  Bootstrap-5 template, including reference pages for every exported
  function, the vignette under articles/, the NEWS log, sitemap and
  search index.

GitHub Pages is already configured to serve from main /docs (verified
via the GH Pages API), so the new site goes live as soon as this PR
merges; subsequent updates flow through the new workflow.
 
    
  
    
      Package: ctdR

      Commit: 68c4b18523eff27b963a7f91fbafa1297e2d4b2a

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 09:06:04 +0200

      Commit message:


	  
		 Merge pull request #16 from drake69/feature/vignette-executable-examples

docs(vignette): make CAMERA, GSVA, padj examples executable 
    
  
    
      Package: ctdR

      Commit: 9cd173ccb508d48f63dd3a2f267f6c705a38cbd4

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 09:04:54 +0200

      Commit message:


	  
		 docs: point Zenodo badge and DOI to the concept record

The DOI used in the README badge, README citation block and
inst/CITATION was 10.5281/zenodo.19344201, which is the versioned
DOI for the long-obsolete v0.1.3 release on Zenodo (March 2026).
Zenodo has since auto-archived v0.99.2 as 10.5281/zenodo.20265813.

Replace the versioned DOI with the *concept* DOI
10.5281/zenodo.19344200, which is the parent record that always
redirects to the most recent version (currently v0.99.2). This way
the badge and citation stay accurate across future releases without
further edits.

Affected lines:
* README.md badge (line 10)
* README.md citation text (line 280)
* inst/CITATION doi field
* inst/CITATION textVersion DOI string
 
    
  
    
      Package: ctdR

      Commit: df107045d809d3d4b170ce862b720cc90fd0204f

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 08:56:30 +0200

      Commit message:


	  
		 docs(vignette): make CAMERA, GSVA, padj examples executable

The CAMERA, GSVA and padj-methods chunks were previously marked
eval=FALSE because they referenced an undefined `expr` matrix. This
made the rendered vignette show only ORA/GSEA outputs, leaving the
CAMERA and GSVA sections as code snippets without results -- a typical
finding flagged by Bioconductor reviewers.

Changes:
* New executable chunk `make-expr` builds a small synthetic expression
  matrix (17 genes x 6 samples) using the Entrez IDs already loaded
  by `import_CTD()` on the bundled sample. Seeded for reproducibility.
* `camera`, `gsva`, `gsva-tune` chunks now eval=TRUE; the rendered
  vignette shows actual `data.frame` output for CAMERA and an actual
  chemical x sample score matrix for GSVA.
* `padj-methods` chunk now eval=TRUE and compares the top adjusted
  p-value across BH/bonferroni/none, demonstrating the effect of the
  `pAdjustMethod` argument concretely.
* Added two new plot chunks `plot-camera` and `plot-gsva` so the
  vignette also shows the CAMERA bar plot and the GSVA heatmap
  produced by `plot_CTD()`.

The `import-real` and `reimport` chunks remain eval=FALSE because
they reference a user-provided file path that doesn't exist at vignette
build time.

Verified:
* `rmarkdown::render()` of the vignette completes (34/34 chunks).
* `devtools::check(error_on = "never")` -- 0 errors / 0 warnings / 0 notes.
 
    
  
    
      Package: ctdR

      Commit: 28e3edd6307244694f01caf36f9fc14688f74281

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 08:44:59 +0200

      Commit message:


	  
		 Merge pull request #15 from drake69/feature/docs-sync-v0.99.2

docs: sync README and CITATION with v0.99.2 code base 
    
  
    
      Package: ctdR

      Commit: c605a1ebe5c2775529fb8c5747f6e0d5e98a8d09

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 08:38:51 +0200

      Commit message:


	  
		 docs: sync README and CITATION with v0.99.2 code base

README.md was last touched before v0.99.1 and described the package
in its v0.99.0 / v0.1.3 state. CITATION still claimed version 0.1.3
from 2024. Brought both back in line with the current code base:

* Features section: now lists all four enrichment methods (ORA, GSEA,
  CAMERA, GSVA) with their backends and input shapes.
* Quick Start: split Step 3 by paradigm (gene-list vs expression
  matrix); added CAMERA and GSVA usage examples. Step 4 documents the
  GSVA heatmap branch of plot_CTD().
* Input Format: renamed the first argument from `entrez_ids` to `x`
  (polymorphic data.frame / matrix); documented Entrez vs SYMBOL
  auto-detection.
* Output: added CAMERA result table (NGenes / Direction / pvalue /
  padj) and a GSVA section describing the chemical x sample score
  matrix.
* Bioconductor install snippet: dropped `DOSE` (removed in 0.99.1)
  and added `limma` and `GSVA` (introduced in 0.99.2).
* Bioconductor dependencies list: same alignment.
* Citation block: 2024 -> 2026, version 0.99.0 -> 0.99.2.

inst/CITATION: same alignment (year 2024 -> 2026, version 0.1.3 ->
0.99.2 in both `note` and `textVersion`).

No code changes. R CMD check: 0 errors / 0 warnings / 0 notes.
 
    
  
    
      Package: ctdR

      Commit: cd60d789c3bb844e753cbd072e73b5f6f46de721

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 08:25:15 +0200

      Commit message:


	  
		 Merge pull request #14 from drake69/feature/camera-gsva-methods

feat(enrichment): add CAMERA and GSVA methods 
    
  
    
      Package: ctdR

      Commit: abb40e125f134e7f9acac635c2fc261dfcf0f240

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-18 08:19:35 +0200

      Commit message:


	  
		 test: cover utils-input helpers and remove unreachable gsva fallback

Adds tests/testthat/test-utils-input.R covering the previously unhit
branches identified by Codecov on PR #14:

  * .detect_id_type: empty / all-NA rownames stop branch
  * .validate_expr_matrix: non-matrix, no-rownames, and duplicated-
    rownames stop branches
  * .load_geneset_list: both "entrez" and "symbol" branches
  * end-to-end CAMERA with id_type = "symbol" rownames
  * enrichment_CTD() called with no argument

Also drops the GSVA::gsva(param) -> as.matrix() defensive fallback in
R/gsva.R: gsva() of a numeric matrix already returns a matrix in
GSVA >= 2.x, so the branch was unreachable and flagged as a coverage
miss.

Test suite: 111 PASS / 0 FAIL / 0 SKIP (was 95).
 
    
  
    
      Package: ctdR

      Commit: 8708d4c63121ad9d77438f3036116bde762982e3

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-16 07:13:39 +0200

      Commit message:


	  
		 feat(enrichment): add CAMERA and GSVA methods through unified interface

Extends enrichment_CTD() with two additional statistical frameworks
selectable via the method argument, on top of the existing ORA and GSEA:

  * CAMERA (limma::camera): competitive gene-set test accounting for
    inter-gene correlation. Input: expression matrix + design + contrast.
  * GSVA (GSVA::gsva): per-sample gene-set scoring returning a chemical
    x sample score matrix. Input: expression matrix.

The first argument of enrichment_CTD() is now `x` (polymorphic): a
data.frame for ORA/GSEA, a numeric matrix for CAMERA/GSVA. id_type is
auto-detected from rownames(x) (Entrez vs HGNC SYMBOL) with explicit
override available.

plot_CTD() now dispatches on input class and method-specific columns:
bar/dot plots of fold enrichment for ORA/GSEA, bar/dot plots of
-log10(padj) coloured by Direction for CAMERA, and a sample-level
heatmap of the top-variance chemicals for GSVA.

New Imports: limma, GSVA, stats. Version bump to 0.99.2.

Tests: 95 PASS / 0 FAIL (+27 expectations for the new methods).
R CMD check: 0 errors / 0 warnings / 0 notes.
BiocCheck: 0 errors / 0 warnings.
 
    
  
    
      Package: ctdR

      Commit: 777dd5abab100fa6ab2fefd7b1ba370b80f10c5a

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-05-10 01:11:37 +0000

      Commit message:


	  
		 chore(deps): bump actions/checkout from 4 to 6

Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v4...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com> 
    
  
    
      Package: ctdR

      Commit: bb35690dccc2a2ac3bc0aeb9ce9fc01a1454f165

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-05-10 01:11:35 +0000

      Commit message:


	  
		 chore(deps): bump actions/upload-artifact from 4 to 7

Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4 to 7.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](https://github.com/actions/upload-artifact/compare/v4...v7)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com> 
    
  
    
      Package: ctdR

      Commit: 84159961e6fbb6185ca28f5294b67b9678c4167e

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-10 10:10:51 +0900

      Commit message:


	  
		 Merge pull request #11 from drake69/feature/ci-release-workflow

ci: auto-release, Dependabot, monthly release reminder 
    
  
    
      Package: ctdR

      Commit: 440bb02f3e8ec0773e8facc3057197f8c12ca117

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 13:57:40 +0900

      Commit message:


	  
		 ci: add Dependabot config and monthly release reminder

- dependabot.yml: monthly updates for github-actions ecosystem
  (R packages are not supported by Dependabot).
- release-reminder.yaml: cron on the 1st of each month opens a GitHub
  issue with a release-prep checklist. Watchers and the maintainer
  receive an email via GitHub notifications.

Aligns with PROJECT_BLUEPRINT §18 monthly release cadence.
 
    
  
    
      Package: ctdR

      Commit: 24ade3789d16fbcb08a08c954d8fb1a375a147f0

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 13:35:29 +0900

      Commit message:


	  
		 ci: auto-release on version bump in DESCRIPTION

On every push to main, reads Version from DESCRIPTION and creates a
matching git tag + GitHub Release if one does not exist yet. Release
notes are extracted from the corresponding section of NEWS.md
("# Changes in version X.Y.Z"). Zenodo is already linked to the repo,
so a new versioned DOI is minted automatically when the Release is
published.
 
    
  
    
      Package: ctdR

      Commit: 4eb29aa396d57b945c1dab9b312664f2bdc6008d

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 13:21:12 +0900

      Commit message:


	  
		 Merge pull request #10 from drake69/feature/ci-bioccheck

ci: add BiocCheck workflow 
    
  
    
      Package: ctdR

      Commit: 988c29aa736829aade98c925e5311a8154665851

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 13:12:37 +0900

      Commit message:


	  
		 ci(bioccheck): treat support-site lookup failures as flakes

BiocCheck's "support site registration" step calls support.bioconductor.org
and returns an ERROR on HTTP 50x. The Bioconductor infrastructure flakes
on this lookup repeatedly. Filter that specific message out of the failure
condition so the workflow fails only on real code errors. Aligns with
PROJECT_BLUEPRINT §18 marketplace-gates rule (real ERROR -> exit 1,
infrastructure flake -> warn + exit 0).
 
    
  
    
      Package: ctdR

      Commit: 39873fe16099e7cc67b1a6aebaca88d8fca28233

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 12:47:01 +0900

      Commit message:


	  
		 ci: add BiocCheck workflow

Runs BiocCheck::BiocCheck() on push and PR to main. Fails the build on
errors; warnings and notes are reported but non-blocking. SPB will run
the same check on Bioconductor's side; this catches issues earlier.
 
    
  
    
      Package: ctdR

      Commit: 425fbac897cefd4c33139b08a422f5c9db3554df

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 11:25:32 +0900

      Commit message:


	  
		 Merge pull request #9 from drake69/feature/bioconductor-submission

chore: bump version to 0.99.1 with NEWS entry 
    
  
    
      Package: ctdR

      Commit: f50fbe72b941b330fc634ea7dd013c1d2b29839d

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 11:15:21 +0900

      Commit message:


	  
		 chore: bump version to 0.99.1 with NEWS entry for review round
 
    
  
    
      Package: ctdR

      Commit: d78a8c54c882c4f1cd83bfdeaa271ea062a71930

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 11:10:22 +0900

      Commit message:


	  
		 Merge pull request #8 from drake69/feature/bioconductor-submission

Address Bioconductor review: remove renv, add plot_CTD, security CI 
    
  
    
      Package: ctdR

      Commit: cc26865969c926860d55e5950140c547cf29b028

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 11:00:12 +0900

      Commit message:


	  
		 fix(check): resolve R CMD check ERROR/WARNING/NOTE

- test-ora.R: relax foldEnrichment assertion. enricher() returns rows
  with zero overlap (foldEnrichment == 0), which is legitimate; only
  enforce non-NA and >= 0.
- man/gsea.Rd: align param name with R/gsea.R (ChemicalName_GeneEntrezIds);
  the .Rd was generated before the rename, causing a codoc mismatch.
- ctdR-package.R: declare ChemicalName, foldEnrichment, padj, Count in
  utils::globalVariables() to silence ggplot2 NSE NOTEs in plot_CTD().
 
    
  
    
      Package: ctdR

      Commit: d5a283798f7501480c128f0d652c9dd7f469df7d

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 10:45:40 +0900

      Commit message:


	  
		 refactor(ora): drop DOSE dependency, inline parse_ratio

DOSE::parse_ratio is no longer exported from DOSE, breaking the ORA
foldEnrichment computation. Replace with a small private helper
.parse_ratio() that splits "n/d" strings and returns n/d. Remove DOSE
from Imports and from skip_if_not_installed() guards in the test suite.
 
    
  
    
      Package: ctdR

      Commit: 13c9fe34f993080842aaf0e2c6bb03c7df534534

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 10:06:17 +0900

      Commit message:


	  
		 ci(security): fix workflow failures unrelated to package code

- Pin trufflehog to v3.95.2: the @v3 tag does not exist; only specific
  versioned tags (v3.x.y) are published.
- Wrap oysteR::audit_installed_r_pkgs() in tryCatch: the call crashes on
  token retrieval when OSS Index credentials are missing; treat that as a
  soft skip rather than a hard CI failure. Real vulnerabilities still
  fail the build.
- Remove dependency-review job: GitHub's Dependency Graph does not
  support R DESCRIPTION files, so the action always errors with
  "Dependency review is not supported on this repository".
 
    
  
    
      Package: ctdR

      Commit: 5812c75ba9b65427b151bd5360a7b8a0409ee30d

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 10:03:41 +0900

      Commit message:


	  
		 fix(import): coerce ChemicalName_GeneSymbols$gene to character

expand.grid() defaults to stringsAsFactors = TRUE, which made
ChemicalName_GeneSymbols$gene a factor. Newer clusterProfiler::enricher()
validates is.character(universe) on the column derived from TERM2GENE,
failing with "universe must be a character vector". The integration test
fabricated the data frame with stringsAsFactors = FALSE, masking the bug
in the real import path; the vignette was the first to exercise it.
 
    
  
    
      Package: ctdR

      Commit: 074822b04d451514b8050ca0d3e65b766250d012

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-05-05 07:28:20 +0900

      Commit message:


	  
		 chore: remove renv from package

R packages should not use renv: dependencies are declared in DESCRIPTION
and installed via pak (or r-lib/actions/setup-r-dependencies in CI).
Removes renv/, renv.lock, .Rprofile (which only sourced renv/activate.R),
and the renv-related .Rbuildignore entries. Aligns with PROJECT_BLUEPRINT
section 5.
 
    
  
    
      Package: ctdR

      Commit: 6f9eab14cae9bfb42c21b49f95478540ed38edda

      Author:  Luigi Corsaro <5324491+drake69@users.noreply.github.com> 

      Date: 2026-04-25 10:42:33 +0200

      Commit message:


	  
		 feat(viz): Add plot_CTD function and expand sample data for Bioconductor

Add plot_CTD() with bar and dot plot types for visualizing enrichment
results, including ggplot2 dependency and full test coverage. Expand
sample dataset from 3 to 10 chemicals for richer vignette examples.
Fix parameter naming in gsea() (GeneSymbols → GeneEntrezIds) and add
match.arg() validation in enrichment_CTD(). Update README with
Bioconductor installation instructions and version 0.99.0.
 
    
  
    
      Package: ctdR

      Commit: 4887b0ee377e4c50ac667bab454673461617540f

      Author:  Luigi Corsaro <lcorsaro@CSB-04793.cdi.bracco.priv> 

      Date: 2026-04-09 16:00:07 +0200

      Commit message:


	  
		 Add cybersecurity CI pipeline and document it in README

- New security.yaml workflow: dependency vulnerability audit (oysteR),
  static analysis (lintr), dependency review on PRs, secret scanning
  (TruffleHog). Runs on push/PR and weekly.
- README: add security-scan badge and "Continuous Integration & Security"
  section describing all four security jobs.
 
    
  
    
      Package: ctdR

      Commit: 3709495d87458ba4d9cfd56ed0062ed0399e652d

      Author:  Luigi Corsaro <lcorsaro69@gmail.com> 

      Date: 2026-03-31 16:22:40 +0200

      Commit message:


	  
		 Merge pull request #7 from drake69/feature/bioconductor-submission

Prepare package for Bioconductor submission 
    
  
    
      Package: ctdR

      Commit: ddc67d2b4e3489f9c6cacb0213df28156af8689f

      Author:  Luigi Corsaro <lcorsaro@Luigis-MacBook-Pro.local> 

      Date: 2026-03-31 15:56:36 +0200

      Commit message:


	  
		 Fix duplicate code from merge in import_CTD and tests

Remove inlined validation that was duplicated alongside the refactored
helper functions after pulling remote changes.
 
    
  
    
      Package: ctdR

      Commit: d762e79efa0411653499b5e4b639d7c970ad9a65

      Author:  Luigi Corsaro <lcorsaro69@gmail.com> 

      Date: 2026-03-31 15:52:14 +0200

      Commit message:


	  
		 Merge branch 'main' into feature/bioconductor-submission 
    
  
    
      Package: ctdR

      Commit: 6913b5a6ee46aba3acb926c5a0aea4b4895ae643

      Author:  Luigi Corsaro <lcorsaro@Luigis-MacBook-Pro.local> 

      Date: 2026-03-31 15:49:24 +0200

      Commit message:


	  
		 Prepare package for Bioconductor submission

- Bump version to 0.99.0 (Bioconductor new-package requirement)
- Upgrade renv from 1.1.4 to 1.2.0
- Add @return to all man pages (BiocCheck compliance)
- Reformat NEWS.md headers to "Changes in version x.y.z"
- Add .Rbuildignore entry for ctdR.BiocCheck
- Refactor import_CTD into helper functions with validation
- Add sample data in inst/extdata for examples
- Add input validation tests for import_CTD
- Update R source formatting and documentation
 
    
  
    
      Package: ctdR

      Commit: 20e00ab413fd41a7c0ebe6212e3d9af0de7a71e1

      Author:  Luigi Corsaro <lcorsaro69@gmail.com> 

      Date: 2026-03-31 12:36:22 +0200

      Commit message:


	  
		 Merge pull request #6 from drake69/feature/validate-ctd-input

Validate CTD input file format in import_CTD 
    
  
    
      Package: ctdR

      Commit: face9044c755b55c8094dc982a0d5fb563c856ba

      Author:  Luigi Corsaro <lcorsaro@Luigis-MacBook-Pro.local> 

      Date: 2026-03-31 11:48:55 +0200

      Commit message:


	  
		 Validate CTD file format in import_CTD before processing

Check that the input CSV has the expected CTD column structure and
sufficient data rows, raising informative errors if the file does not
match the CTD_chem_gene_ixns format.
 
    
  
    
      Package: ctdR

      Commit: 3fa5c7691a50626de571016e3dd2576b4068ff93

      Author:  Luigi Corsaro <lcorsaro69@gmail.com> 

      Date: 2026-03-31 10:38:03 +0200

      Commit message:


	  
		 Merge pull request #5 from drake69/fix/badges

Re-enable push triggers on main for CI badges 
    
  
    
      Package: ctdR

      Commit: ce1cc0bd0c1d0809205f84c2d802e8adba68828a

      Author:  Luigi Corsaro <lcorsaro@Luigis-MacBook-Pro.local> 

      Date: 2026-03-31 09:59:10 +0200

      Commit message:


	  
		 Re-enable push triggers on main for CI badges
 
    
  
    
      Package: ctdR

      Commit: 688348677e6c17f6c9a81bd374248ac940d8998c

      Author:  Luigi Corsaro <lcorsaro69@gmail.com> 

      Date: 2026-03-31 08:41:30 +0200

      Commit message:


	  
		 Merge pull request #4 from drake69/fix/badges 
    
  
    
      Package: ctdR

      Commit: da08cb6c2527959ebcb6dae6bbf7745bf7b8890b

      Author:  Luigi Corsaro <lcorsaro@Luigis-MacBook-Pro.local> 

      Date: 2026-03-31 08:07:16 +0200

      Commit message:


	  
		 Fix badges, add Zenodo DOI, add Codecov token

- Remove broken badges (CRAN, missing logo, DOI placeholder)
- Add Zenodo DOI badge (10.5281/zenodo.19344201)
- Add DOI and Codecov badges to GitHub Pages site
- Add CODECOV_TOKEN to test-coverage workflow
- Update citation with DOI
 
    
  
    
      Package: ctdR

      Commit: 0b40e9744b917013a04a30ed6fb9b96ccc6adf78

      Author:  Luigi Corsaro <lcorsaro69@gmail.com> 

      Date: 2026-03-31 07:18:47 +0200

      Commit message:


	  
		 Merge pull request #3 from drake69/release/v0.1.3

Release v0.1.3 
    
  
    
      Package: ctdR

      Commit: 289fbd0081a0abee3e272bcdfca2c5ff524ec59d

      Author:  Luigi Corsaro <lcorsaro@Luigis-MacBook-Pro.local> 

      Date: 2026-03-30 22:21:04 +0200

      Commit message:


	  
		 Bump to v0.1.3: fix badges, add Codecov token, version bump

- Fix broken README badges (remove CRAN, DOI placeholder, missing logo)
- Add CODECOV_TOKEN to test-coverage workflow
- Bump version to 0.1.3 for Zenodo DOI minting
 
    
  
    
      Package: ctdR

      Commit: 5cc2164a22fe2e13b237deb00dd59325561e8202

      Author:  Luigi Corsaro <lcorsaro69@gmail.com> 

      Date: 2026-03-30 20:57:18 +0200

      Commit message:


	  
		 Merge pull request #2 from drake69/feature/gh-pages

Add GitHub Pages site 
    
  
    
      Package: fenr

      Commit: cef2c37d0103f32bf56152b9954632dc078058e6

      Author:  Marek Gierlinski <mgierlinski@dundee.ac.uk> 

      Date: 2026-07-24 09:53:17 +0100

      Commit message:


	  
		 Version 1.11.2
Merge remote-tracking branch 'upstream/devel'
 
    
  
    
      Package: fenr

      Commit: 26c32d60e981d215edc96d92367375d7e87974df

      Author:  Marek Gierlinski <mgierlinski@dundee.ac.uk> 

      Date: 2026-07-24 09:48:50 +0100

      Commit message:


	  
		 Vignette, DESCRIPTION and news updates
 
    
  
    
      Package: fenr

      Commit: 698ddbd703cd6dca446f087b87e02660977e45a2

      Author:  Marek Gierlinski <mgierlinski@dundee.ac.uk> 

      Date: 2026-07-24 09:06:53 +0100

      Commit message:


	  
		 Adding variable definitions.
 
    
  
    
      Package: fenr

      Commit: 46cdf44a3bef5f2237e47e13da0dd2c1c0765a60

      Author:  Marek Gierlinski <mgierlinski@dundee.ac.uk> 

      Date: 2026-07-24 08:55:20 +0100

      Commit message:


	  
		 Update to fetch_kegg_species() after list/organism API point was discontinued. Now it is replaced with list/genome.
 
    
  
    
      Package: fenr

      Commit: ec452960436ca0a72bbff3d5da6430bfffba3ae2

      Author:  Marek Gierlinski <mgierlinski@dundee.ac.uk> 

      Date: 2026-07-23 14:07:30 +0100

      Commit message:


	  
		 GO-term updates following Geneontology species names change
 
    
  
    
      Package: MsBackendMassIVE

      Commit: 64ba328057ce1fd13e73215e72bedc88f2ba431e

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-07-24 11:31:07 +0300

      Commit message:


	  
		 Merge pull request #29 from rformassspectrometry/gabri

update filenames. Handle interrupted connection. 
    
  
    
      Package: MsBackendMassIVE

      Commit: 901f1a8d736322bc027289288c5c565c452bb4b3

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-07-24 09:16:27 +0200

      Commit message:


	  
		 address johannes comments
 
    
  
    
      Package: MsBackendMassIVE

      Commit: 7fb5c9f034b56b0b369f7386d7f17a226aae562f

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-07-23 14:07:15 +0200

      Commit message:


	  
		 docs: update bioc package installation. Update test following GNPS2 update
 
    
  
    
      Package: MsBackendMassIVE

      Commit: 850aefdc5cabec85636c6639a0182b8b741ac4a3

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-07-20 15:02:48 +0200

      Commit message:


	  
		 fix: remove news from the build ignore
 
    
  
    
      Package: MsBackendMassIVE

      Commit: 7c99ae7b14c792063d64b61189667958c62f4c18

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-07-07 09:58:53 +0200

      Commit message:


	  
		 refactor: extract in new function the code to update the FPT volume
 
    
  
    
      Package: MsBackendMassIVE

      Commit: e9e71c4f3bd582aaf7b3ddaf9bf6bdbe2380b0ff

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-07-06 17:07:16 +0200

      Commit message:


	  
		 Issue: Reset/re-download failed downloads
Fixes #28. Dealing with interrupt and sort output.
 
    
  
    
      Package: MsBackendMassIVE

      Commit: 77ffb37659a6321b7c23f8f485dc1fee167b6ff8

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-07-06 16:04:05 +0200

      Commit message:


	  
		 Merge branch 'main' into gabri
 
    
  
    
      Package: MsBackendMassIVE

      Commit: 8021793c3f3caf717a44735177243693afc2017b

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-06-16 10:26:36 +0200

      Commit message:


	  
		 fix: adapt timeout to avoid failure on slow connection
 
    
  
    
      Package: MsBackendMassIVE

      Commit: 675f485737fe0d18df0df494e4df78580b532583

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-06-10 16:12:54 +0200

      Commit message:


	  
		 fix: description of the update
 
    
  
    
      Package: MsBackendMassIVE

      Commit: 232fce907391f95adcd6461510ca6d2e0254ae7d

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-06-10 15:37:06 +0200

      Commit message:


	  
		 fix: variable name typo
 
    
  
    
      Package: MsBackendMassIVE

      Commit: d7e01228e4719d9dd826150e87d195c2ba1e615c

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-06-10 12:49:25 +0200

      Commit message:


	  
		 fix: bug caching files with same filename. Use unique random filename
 
    
  
    
      Package: MsBackendMgf

      Commit: f0d62481bb9190055e8fac7654742b2be80a48cf

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2026-07-24 10:29:23 +0200

      Commit message:


	  
		 Merge pull request #39 from rformassspectrometry/jomain

Address issue #38 
    
  
    
      Package: MsBackendMgf

      Commit: 04f9b21d79721d67c60e872b894faf6141d62948

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2026-07-24 10:18:52 +0200

      Commit message:


	  
		 fix: address issue #38

- Fix export compiling the TITLE field for MGF (issue #38).
 
    
  
    
      Package: igblastr

      Commit: 40d3c85e6715fefa941d19e60c071b9ef12720dc

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-07-23 23:33:51 -0700

      Commit message:


	  
		 igblastr 1.3.16: Add extract_sequence_region()

extract_sequence_region() extracts a region of interest from a set
of analyzed sequences.

Also add extract_region_length() to extract the length of a region
of interest from a set of analyzed sequences.
 
    
  
    
      Package: drugTargetInteractions

      Commit: 64f93c788fcbbf733e43f0ad8221953cc4dc5f28

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

      Date: 2026-07-23 21:07:52 -0700

      Commit message:


	  
		 Expand vignette Supplement with missing legacy ChEMBL-SQLite functionality

Audited the pre-multi-source vignette (the repo's first commit,
bc910aa) against current devel: every function it exercised still
works and is still exported (genConfig, downloadUniChem, cmpIdMapping,
drugTargetAnnotTable, getUniprotIDs, getParalogs, drugTargetAnnot,
getDrugTarget, drugTargetBioactivity, getSymEnsUp,
runDrugTarget_Annot_Bioassay - no regressions found).

The current vignette's Supplement section already covered some of this
(drugTargetAnnot/getDrugTarget prose, getUniprotIDs, getParalogs,
downloadUniChem/cmpIdMapping) but all eval=FALSE and missing a runnable
getDrugTarget()/drugTargetBioactivity() example, getSymEnsUp() entirely,
and the old "run everything" combining pattern.

Added: a live eval=TRUE demo of drugTargetAnnot()/getDrugTarget()/
drugTargetBioactivity() against the bundled chembl_sample.db (using
tempfile()-based paths, not the legacy relative results/ dir); a new
ensembldb-Based ID Mapping subsection for getSymEnsUp(); a closing
Putting It Together subsection demonstrating
runDrugTarget_Annot_Bioassay() combining getSymEnsUp() + getParalogs()
+ drugTargetAnnot() + drugTargetBioactivity().

Rendered the full vignette clean (0 error/warning blocks) except for
the new Putting It Together chunk, which currently hits a live Ensembl
classic-BioMart outage (status.ensembl.org redirect) in getParalogs() -
confirmed via a disposable local-only render and two direct
devtools::load_all() runs that the chunk's own code is correct; this is
an external service-availability gap, not a defect in the added
content.
 
    
  
    
      Package: drugTargetInteractions

      Commit: 1f6229b1b4a4f6fc7acadeb44f2201fb2703b681

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

      Date: 2026-07-23 21:07:07 -0700

      Commit message:


	  
		 Update Description field to reflect the multi-source package

The Description still described ChEMBL-only, single-SQLite-source
support from before the package added DGIdb, Open Targets, PubChem,
TTD, Broad Repurposing Hub and GtoPdb.
 
    
  
    
      Package: GExPipe

      Commit: 69aa2e2c8879d747407197e97eed65cce17dbd05

      Author:  Safa Rafique <safa.sandhu@gmail.com> 

      Date: 2026-07-24 04:43:53 +0500

      Commit message:


	  
		 Fix undeclared rmda dependency and NEWS.md titles (0.99.44).

Remove requireNamespace('rmda') paths from nomogram DCA; keep dcurves only. Normalize NEWS section headers for R news parser.

Co-authored-by: Cursor <cursoragent@cursor.com>
 
    
  
    
      Package: RforProteomics

      Commit: 72defc5cf0a537ad1e7404eea3918bea661e118a

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-07-23 22:27:31 +0200

      Commit message:


	  
		 cleanup
 
    
  
    
      Package: RforProteomics

      Commit: 269b3597e68ed4bf5bbd8b98dd1488dda641e4ba

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-07-15 16:52:52 +0200

      Commit message:


	  
		 install msmsTests manually
 
    
  
    
      Package: msdata

      Commit: 4c1129f71f312e4ba90058298a529e0bc5545a26

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-04-28 08:22:53 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    
      Package: msdata

      Commit: 14d0db0146cebebea26ccaaee4f753f1d2b306b7

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-04-28 08:22:53 -0400

      Commit message:


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

      Commit: 60a931e3a7eaccb04e6b11ad52c5aeac2aaaf36f

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-04-16 17:59:49 +0200

      Commit message:


	  
		 fix
 
    
  
    
      Package: msdata

      Commit: 0aa051515cb1aa6097817f2a58ddc7615c711dc6

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-03-20 09:46:56 +0100

      Commit message:


	  
		 remove files
 
    
  
    
      Package: msdata

      Commit: d383af4351653b65e2cf73f36cf1aa6de107ab72

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-02-02 22:00:34 +0100

      Commit message:


	  
		 add deprecation startup message
 
    
  
    
      Package: msdata

      Commit: d2a0e2aab321d3fb64c8bc41746217f6b5abb2af

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-10-29 09:31:19 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
 
    
  
    
      Package: msdata

      Commit: c538db625cdb5e4f708041bb0bd31827da830bc8

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-10-29 09:31:19 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 
    
  
    
      Package: msdata

      Commit: fcecff5c1d33145b76a0867a69a9edddabcfae11

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-04-15 09:15:35 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_21 branch
 
    
  
    
      Package: msdata

      Commit: 4309882ceb3805a7da7ceb97c65e1ad6fa7f7fd4

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-04-15 09:15:35 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_21 branch
 
    
  
    
      Package: msdata

      Commit: fb3461a615c4fde6a81f41863337e635855a66ce

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2024-10-29 09:27:01 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_20 branch
 
    
  
    
      Package: msdata

      Commit: f9c0e9ac6863bdd663ff1bb85c99b48eadb1537f

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2024-10-29 09:27:01 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_20 branch
 
    
  
    
      Package: msdata

      Commit: 71e914b48dee183c86b296db368f896e3076f92b

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-30 10:28:41 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
 
    
  
    
      Package: msdata

      Commit: da1b320c64231c5c77f7a3fd95cd04807838262a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2024-04-30 10:28:40 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
 
    
  
    
      Package: msdata

      Commit: 96e859fd361ec7acf3a20d3fdd101784fefda11c

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2023-10-24 08:55:20 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_18 branch
 
    
  
    
      Package: msdata

      Commit: 8ff40d75d6125fd5d2692ce763966fc8b24451f9

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2023-10-24 08:55:20 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
 
    
  
    
      Package: msdata

      Commit: 82aad631c19473818cefd167fa444f8d2b9540d6

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2023-04-25 09:51:25 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_17 branch
 
    
  
    
      Package: msdata

      Commit: 61a0c37804bbd28b6218fc2cbe4980b722c9f703

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2023-04-25 09:51:25 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_17 branch
 
    
  
    
      Package: msdata

      Commit: bb299971cb6b1caf667ae0ab9f4ebdeb84319933

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2022-11-01 10:42:47 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_16 branch
 
    
  
    
      Package: msdata

      Commit: 6eb183a7b84ea6357a7f35297779884206513e74

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2022-11-01 10:42:47 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_16 branch
 
    
  
    
      Package: msdata

      Commit: 99f39200de89a914f470ecd731619b38a90e37a3

      Author:  J Wokaty <jwokaty@users.noreply.github.com> 

      Date: 2022-04-26 16:57:44 +0000

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_15 branch
 
    
  
    
      Package: msdata

      Commit: a5d673af11f5775ceb133d7cf9dba17214cc395c

      Author:  J Wokaty <jwokaty@users.noreply.github.com> 

      Date: 2022-04-26 16:57:44 +0000

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
 
    
  
    
      Package: msdata

      Commit: bca78017bff09906d2e5eb91b696a33aac8a5fad

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2022-03-16 23:37:10 +0100

      Commit message:


	  
		 Set encoding, fixes WARNING in manpage with micrometer
 
    
  
    
      Package: msdata

      Commit: a5fe04ac8a381700d9baff34db7c79bf7a8e2b3c

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2022-03-14 15:38:32 +0100

      Commit message:


	  
		 Merge branch 'LiesaSalzer/msdata-master'
 
    
  
    
      Package: msdata

      Commit: 8c35f093cf731a7e82721bccf5ecd61d0a44ca4b

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2022-03-14 15:38:22 +0100

      Commit message:


	  
		 News and version bump
 
    
  
    
      Package: msdata

      Commit: f74072d7dbb47041b2f499bc37d68734c8d79e08

      Author:  LiesaSalzer <liesa.salzer@web.de> 

      Date: 2022-03-14 14:26:30 +0100

      Commit message:


	  
		 Add CE-MS test data and documentation
 
    
  
    
      Package: msdata

      Commit: 98a6a7e433ac065d0e03b3031fb08b5e5ccb954d

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2021-11-26 18:05:08 +0100

      Commit message:


	  
		 Actually remove the mzdata files
 
    
  
    
      Package: msdata

      Commit: 282e4b115de1eb73cb9c6e46f5804a9ce9703aa0

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2021-11-20 17:36:05 +0100

      Commit message:


	  
		 Remove notion of mzData
 
    
  
    
      Package: msdata

      Commit: 0ccf1f0d2cfb7d2a6c30a12717008af496a4abc5

      Author:  J Wokaty <jwokaty@users.noreply.github.com> 

      Date: 2021-10-26 11:42:49 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_14 branch
 
    
  
    
      Package: msdata

      Commit: 084d4229632132d0a0e342effcbb3e04d7569314

      Author:  J Wokaty <jwokaty@users.noreply.github.com> 

      Date: 2021-10-26 11:42:49 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_14 branch
 
    
  
    
      Package: msdata

      Commit: 6d2752bc570c200253312fbdc963fe4c39bd1478

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2021-10-11 10:06:38 +0200

      Commit message:


	  
		 Move FTICR mzML files into their own directory
 
    
  
    
      Package: msdata

      Commit: fb92068f8659ba1cb8eb2fc5c226dbd9e042c55f

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2021-10-10 22:04:33 +0200

      Commit message:


	  
		 Add mzML versions of mzData files for upcoming mzData removal in mzR
 
    
  
    
      Package: msdata

      Commit: 131cc996859f898748bf28211bc69c6fec9d6985

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2021-05-19 11:27:43 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_13 branch
 
    
  
    
      Package: msdata

      Commit: 4c67ae109880cd1ae56ac74cf6529f18c6a32402

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2021-05-19 11:27:43 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_13 branch
 
    
  
    
      Package: msdata

      Commit: 78bef43985f8756dd79b59c48d517d98d8b9aaaf

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

      Date: 2020-12-29 18:36:57 +0100

      Commit message:


	  
		 fix error in proteomics man page
 
    
  
    
      Package: msdata

      Commit: b32f548fb66f0995cd9948c5111a386437b7aa69

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2020-10-27 09:48:51 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_12 branch
 
    
  
    
      Package: msdata

      Commit: 72dcf49f40846f8b45337ef5150865a7e59c1b3d

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2020-10-27 09:48:51 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_12 branch
 
    
  
    
      Package: msdata

      Commit: 383b07b701dd92d5bd8625924fd0c35f7a70d1e8

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2020-04-27 14:57:53 -0400

      Commit message:


	  
		 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
 
    
  
    
      Package: msdata

      Commit: b0bcc685f6092535b90917bb8a45cd52575e963b

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2020-04-27 14:57:53 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
 
    
  
    
      Package: msdata

      Commit: f90a3c20739769a179b3f6a8f639c49134b262e5

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-10-29 13:37:00 -0400

      Commit message:


	  
		 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
 
    
  
    
      Package: msdata

      Commit: 2e03dd1da33c7d7dfbfadb070701234b1718b74b

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-10-29 13:29:35 -0400

      Commit message:


	  
		 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
 
    
  
    
      Package: msdata

      Commit: e7c3743eb6b5e18dcba5f99dbe4f7a6b54a84c0e

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

      Date: 2019-07-09 21:19:10 +0200

      Commit message:


	  
		 add quant function and file
 
    
  
    
      Package: msdata

      Commit: 60f912e5725c2ccd9be87dc4c812de18c6149130

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2019-06-14 09:50:17 +0200

      Commit message:


	  
		 Add SWATH data
 
    
  
    
      Package: msdata

      Commit: 4e124236a77dba74c9e0200f2d36d488f357ac49

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-05-02 12:06:12 -0400

      Commit message:


	  
		 bump x.y.z versions to odd y after creation of RELEASE_3_9 branch
 
    
  
    
      Package: msdata

      Commit: 0b5e7607c4de5ac252b4a5bbbf31853e358ea3cc

      Author:  Hervé Pagès <hpages@fredhutch.org> 

      Date: 2019-05-02 11:56:17 -0400

      Commit message:


	  
		 bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch
 
    
  
    
      Package: msdata

      Commit: efad3b566678b8d011f1231402ba27d65987e7d1

      Author:  nturaga <nitesh.turaga@gmail.com> 

      Date: 2018-10-30 11:38:33 -0400

      Commit message:


	  
		 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
 
    
  
    
      Package: msdata

      Commit: 7d77ffda37955c0c91aa4d44666f4f3db5083ae7

      Author:  nturaga <nitesh.turaga@gmail.com> 

      Date: 2018-10-30 11:36:21 -0400

      Commit message:


	  
		 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 
    
  
    
      Package: msdata

      Commit: 0fc676cf6c812062f5040c68354442e13f8f8e5e

      Author:  Nitesh Turaga <nitesh.turaga@gmail.com> 

      Date: 2018-04-30 10:34:47 -0400

      Commit message:


	  
		 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch
 
    
  
    
      Package: msdata

      Commit: e26e715f8d69bf899ab73678caf9f666001baf09

      Author:  Nitesh Turaga <nitesh.turaga@gmail.com> 

      Date: 2018-04-30 10:31:26 -0400

      Commit message:


	  
		 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
 
    
  
    
      Package: msdata

      Commit: 66366de228818ff6a4d41a9584dca8710388e6c2

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-04-19 10:54:43 +0100

      Commit message:


	  
		 update sciex files
 
    
  
    
      Package: msdata

      Commit: d2100f3ed5535d3b63409ffa86a1dc68acabcdb9

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-02-09 11:24:42 +0000

      Commit message:


	  
		 add Johanne's as contributor
 
    
  
    
      Package: msdata

      Commit: a9e42e452ad187592bb6906c221de19d602abd78

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-02-09 11:23:52 +0000

      Commit message:


	  
		 add sciex data (see MSnbase issue 310)
 
    
  
    
      Package: msdata

      Commit: 13a4fa3e6bcfb528fdf9d3e081f171608322a3c3

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-02-07 21:05:56 +0000

      Commit message:


	  
		 update fdms3tmt11 with stringsAsFactors=FALSE
 
    
  
    
      Package: msdata

      Commit: 4ff06b4318a400d2bcf9a7350689cd293fdab3e5

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-02-06 11:48:07 +0000

      Commit message:


	  
		 suggest and load MSnbase; depend on R >= 2.10
 
    
  
    
      Package: msdata

      Commit: 4bd8a5e36fa480569f56f74733ae2b1514b5c1f7

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-02-06 11:03:30 +0000

      Commit message:


	  
		 remove changelog, as it isn't used
 
    
  
    
      Package: msdata

      Commit: aa76a27f9e527b90b993f440ce924b60cf7304d6

      Author:  Laurent <lg390@cam.ac.uk> 

      Date: 2018-02-06 11:03:08 +0000

      Commit message:


	  
		 add MS3 TMT11 data
 
    
  
    
      Package: msdata

      Commit: 14a61455187435d6639df59d4781b435687f9432

      Author:  vobencha <valerie.obenchain@roswellpark.org> 

      Date: 2017-10-30 12:09:07 -0400

      Commit message:


	  
		 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
 
    
  
    
      Package: msdata

      Commit: 26f258162be493206acb51772fe99ab436cee21a

      Author:  vobencha <valerie.obenchain@roswellpark.org> 

      Date: 2017-10-30 11:58:22 -0400

      Commit message:


	  
		 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
 
    
  
    
      Package: msdata

      Commit: 91d13b01baca2556d74cbb6158205083fba277a3

      Author:  nturaga <nitesh.turaga@gmail.com> 

      Date: 2017-08-16 19:10:15 +0000

      Commit message:


	  
		 Committing experiment data for msdata
 
    
  
    
      Package: msdata

      Commit: 021797fcd8eb5b9f919dab59248df77ab3346ddb

      Author:  Laurent Gatto <l.gatto@dnavision.be> 

      Date: 2017-06-19 20:59:43 +0000

      Commit message:


	  
		 add full TMT_Erwinia raw data file

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@4183 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: 41321e10dc11b318dfd40491f106085cedf7fd96

      Author:  Herve Pages <hpages@fhcrc.org> 

      Date: 2017-04-24 20:19:55 +0000

      Commit message:


	  
		 bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@4157 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: e071533356b6c4540c756f52c497b2cfee23e08e

      Author:  Herve Pages <hpages@fhcrc.org> 

      Date: 2017-04-24 20:09:26 +0000

      Commit message:


	  
		 bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@4155 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: d7c8759db9a8f3e6413ed85ffa7719c689e42feb

      Author:  Laurent Gatto <l.gatto@dnavision.be> 

      Date: 2017-01-23 21:28:52 +0000

      Commit message:


	  
		 Added MRM file, contributed by Xavi Domingo-Almenara

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@4056 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: 81bca15b6f1caed196dcea68c7ddca7131cf3db0

      Author:  Herve Pages <hpages@fhcrc.org> 

      Date: 2016-10-17 19:23:41 +0000

      Commit message:


	  
		 bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3960 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: 6a9bc52be9ee3e81b479e571e2b1f25b63df57bd

      Author:  Herve Pages <hpages@fhcrc.org> 

      Date: 2016-10-17 18:47:53 +0000

      Commit message:


	  
		 bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3958 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: a88032459d615350c4a40d7fb544dee9cf305e66

      Author:  Laurent Gatto <l.gatto@dnavision.be> 

      Date: 2016-10-13 14:48:50 +0000

      Commit message:


	  
		 add TMT identification results

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3944 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: 3dec2853eba275d9b9dd993ce81d5b91b0c1d01d

      Author:  Laurent Gatto <l.gatto@dnavision.be> 

      Date: 2016-10-05 21:14:45 +0000

      Commit message:


	  
		 revert msdata.Rd and update new MS3 proteomics data

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3928 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: 001b6726489ec7d22803bf5591447aa4fa2826ff

      Author:  Laurent Gatto <l.gatto@dnavision.be> 

      Date: 2016-10-05 12:18:08 +0000

      Commit message:


	  
		 update/replace MS3 data

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3926 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: 85979f80d33fa13875d56d1ab4c02a9a3075053c

      Author:  Laurent Gatto <l.gatto@dnavision.be> 

      Date: 2016-10-04 15:58:14 +0000

      Commit message:


	  
		 add TMT10 MS3 proteomics data file

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3923 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: c550cde6741a77a084e0a8e46f5b118e51758570

      Author:  Laurent Gatto <l.gatto@dnavision.be> 

      Date: 2016-10-04 15:57:30 +0000

      Commit message:


	  
		 add TMT10 MS3 proteomics data file

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3922 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: bc416c2f51fec25eeaeec6e0ce3b83b5777d7a63

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2016-07-27 14:45:21 +0000

      Commit message:


	  
		 update xcmsSet xs to current xcms version, bump msdata to version 0.12.1

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3829 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: msdata

      Commit: 3cb57f88b014d1cb13b4bbd0909fb248b5394463

      Author:  Laurent Gatto <l.gatto@dnavision.be> 

      Date: 2016-06-30 15:54:31 +0000

      Commit message:


	  
		 adding proteomics data and function

git-svn-id: file:///home/git/bioc-data.hedgehog.fhcrc.org/trunk/experiment/pkgs/msdata@3817 db2202da-8704-0410-b924-b125b3cd84ef
 
    
  
    
      Package: debrowser

      Commit: f1190cd970fa9d26b27f8300a0a0a21d83bdf682

      Author:  Alper Kucukural <alper.kucukural@umassmed.edu> 

      Date: 2026-07-23 14:20:13 -0400

      Commit message:


	  
		 fix(bioc): drop sodium dep (breaks nebbiolo2 check); use scrypt+openssl

sodium is absent on the Bioconductor Linux builder (nebbiolo2 has no
libsodium), so R CMD check failed there at the dependency stage with
"Package suggested but not available: 'sodium'" before any other check
ran, blocking propagation of the package. scrypt and openssl are both
already Imports of shinymanager and present on every Bioc builder.

- Password hashing: libsodium argon2id -> scrypt::hashPassword(), the
  same primitive shinymanager stores. verify_password() tolerates a
  malformed stored hash (failed login, not an error).
- Per-user AI key encryption: libsodium secretbox -> AES-256-GCM.
  openssl's aes_gcm_* neither emits nor verifies a GCM tag, so
  authenticate explicitly with encrypt-then-MAC (HMAC-SHA256); enc/mac
  subkeys are domain-separated via derive_user_key(purpose=). Blob
  layout is now iv(12) || ciphertext || hmac(32), verified with a
  non-short-circuiting compare before decrypt.
- Regression guard test-deps-no-sodium.R fails if sodium reappears.
- Docs (signup, Rd, privacy.html) updated off argon2id.
- Bump 1.41.1 -> 1.41.2 so Bioc picks up the fix; NEWS documents the
  crypto swap and that pre-1.41.2 hashes/keys are not readable.

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

      Commit: 7f26155723c956fb0819ece3ded8d980f915e5a0

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-06-18 09:37:11 +0100

      Commit message:


	  
		 feat: add Compound Discoverer node source and raw-file TIC support

Add CompoundDiscovererNodeSource(), a data source for running lcmsPlot
inside a Compound Discoverer custom Scripting Node. It parses the
node_args.json file and the tab-delimited table exports it references,
selects a representative ion per compound and study file, and builds a
plottable source. Chromatograms are extracted from the raw mzML files
given via sample_paths, matched to study files by basename with a
positional fallback. Plotting reuses lp_compound_discoverer(). Adds
get_metadata and get_detected_peaks S3 methods plus a create_chromatograms
method for the new class.

Extend lp_total_ion_current() to work when raw files are passed directly
to lcmsPlot() as a character vector of .mzML/.mzXML/.CDF/.raw paths, in
addition to XCMSnExp / MsExperiment objects, reading the per-scan TIC
from raw-file headers.

Add a standalone worked example for large multi-sample studies using the
batching API with patchwork to build one composite figure per sample.

Bump version to 1.1.5 and add jsonlite to Imports.
 
    
  
    
      Package: dnaEPICO

      Commit: 20080359b689198ef14ca1e7094a0e9b87051955

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-07-23 22:11:34 +1000

      Commit message:


	  
		 Bioconductor 0.99.36 GlM,LME memory
 
    
  
    
      Package: RnBeads

      Commit: 1c6f9f8f09d971b0c3637d8d41025ab35e5f9080

      Author:  Fabian Müller <fabian.mueller@uni-saarland.de> 

      Date: 2026-07-23 13:31:56 +0200

      Commit message:


	  
		 Merge pull request #79 from Staminima/master

unitTest bug fix 
    
  
    
      Package: RnBeads

      Commit: d9acefa8bdd0b5a7ec48b5f453197ded734e48f7

      Author:  staminima <this.is.nima.amini@gmail.com> 

      Date: 2026-07-23 12:35:08 +0200

      Commit message:


	  
		 unitTest bug fixed: test_differenials.R --> RnBDiffmMeth class destroy method modified.
 
    
  
    
      Package: igvShiny

      Commit: 0f54e8ce43d9e7dbd2d16a0a22d94bdec8151d1e

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

      Date: 2026-07-23 13:05:31 +0200

      Commit message:


	  
		 Merge pull request #123 from gladkia/ci/test-against-bioc-devel

ci: test against Bioconductor devel (clears version-parity WARNING) 
    
  
    
      Package: igvShiny

      Commit: 1a81bdd355c3af0bc36978a146c6b2157e091ad2

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 12:56:17 +0200

      Commit message:


	  
		 ci: pair devel matrix with R 4.6 and derive cache keys from matrix

Bioconductor devel (3.24) requires R 4.6; macOS/Windows jobs stayed on
R 4.5 and failed at the Set BiocVersion step. Bump them to 4.6 and key
the package cache + results artifact off matrix.config.bioc/r instead of
the stale RELEASE_3_18-r-4.3 literal, so devel doesn't restore an
unrelated library snapshot.

Also guard the GWASTrack show() method against an NA autoscale slot
(if (!NA) errors); use isFALSE().
 
    
  
    
      Package: igvShiny

      Commit: ce55bed1e6a54162a58b2bb337c1eca681bd0bed

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 12:42:39 +0200

      Commit message:


	  
		 feat: add show() method for the GWASTrack S4 class

Bioc devel's BiocCheck warns that every S4 class must provide a show() method;
GWASTrack had none. Add one that prints a short summary (track name, data mode,
url, column mapping, height, autoscale/range). Regenerate NAMESPACE and man/
(exportMethods(show), importFrom(methods, show), show.Rd).
 
    
  
    
      Package: igvShiny

      Commit: 3913a51f1d1349c79532de8b6b0332bad0df389c

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 11:24:38 +0200

      Commit message:


	  
		 style: use imperative verbs in NEWS entries (gDRstyle on Bioc devel)

gDRstyle::lintNewsEntries() on Bioc devel requires each entry to start with a
known imperative verb; the 'demo:'-prefixed 1.9.7 entries failed. Rephrase them
to start with 'Add'.
 
    
  
    
      Package: igvShiny

      Commit: 4ed1e185015201847d9b365cea4527c274b59b05

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 11:06:17 +0200

      Commit message:


	  
		 ci: re-trigger (transient vignette network failure on prior run)
 
    
  
    
      Package: igvShiny

      Commit: 4801f248545657b371bddad5240aab7bbb2b5dcc

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 10:55:51 +0200

      Commit message:


	  
		 style: satisfy the stricter gDRstyle linter used on Bioc devel

Testing against Bioc devel pulls a newer, stricter gDRstyle whose checkPackage()
hard-fails on lints the release version ignored. Fix them (all semantics-
preserving):

- remove trailing whitespace and trailing blank lines across R/ and tests/
- nrow()/ncol() -> NROW()/NCOL() (NULL/vector-safe)
- seq_len(length(x)) -> seq_along(x)
- paste(x, collapse = ", ") -> toString(x)

No behavioural change. Paired with the switch to a Bioc devel CI matrix.
 
    
  
    
      Package: igvShiny

      Commit: f2efb9f856cc5fa4d138c8614f977ff64d618696

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 10:39:35 +0200

      Commit message:


	  
		 ci: test against Bioconductor devel instead of RELEASE_3_22

The package on master carries a devel version (odd y, 1.9.x), but the CI matrix
tested against RELEASE_3_22. Running BiocCheck with a release BiocManager makes
it expect an even y, so it raised the WARNING "y of x.y.z version should be
even in release" on every job — a CI-context artifact, not a package defect
(it does not appear on the official Bioconductor devel dashboard).

Point the matrix at Bioc devel (ubuntu container bioconductor_docker:devel,
bioc: devel on all three OSes) so BiocManager::version() is devel and the odd
minor version validates cleanly. macOS and Windows are marked allow-failure:
Bioc devel can lag on binary packages and these jobs are already flaky; the
authoritative BiocCheck is the Linux container job.
 
    
  
    
      Package: igvShiny

      Commit: 3fd01630df8e1e4229cb60f82171ef782feab0aa

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

      Date: 2026-07-23 12:52:04 +0200

      Commit message:


	  
		 Merge pull request #122 from gladkia/chore/m1-bioccheck-cleanup

M1: clear two BiocCheck NOTEs (vignette chunk labels, funder role) 
    
  
    
      Package: igvShiny

      Commit: c6868ff5220ff0467dab8919b4073b70ea254e37

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 11:28:35 +0200

      Commit message:


	  
		 style: use imperative verbs in NEWS entries (gDRstyle on Bioc devel)

Rephrase the 1.9.8 entries to start with 'Add' so they pass
gDRstyle::lintNewsEntries() once the Bioc devel CI (#123) is on master.
 
    
  
    
      Package: igvShiny

      Commit: e764b0af2e7c9d3a6eabf45c1a3a39ce834a2e06

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 10:25:56 +0200

      Commit message:


	  
		 Clear two BiocCheck NOTEs (vignette chunk labels, funder role)

M1 (BiocCheck cleanup):
- Add labels to all 12 vignette code chunks -> clears checkChunkLabels.
- Add R Consortium with the 'fnd' (funder) role in Authors@R, crediting the
  ISC grant that funds this work -> clears checkFndPerson.

Verified with BiocCheck: NOTES drop from 5 to 3 on Bioc devel. Remaining NOTES
(line length + indentation formatting, function lengths) are left for a
dedicated formatting/refactor pass. The lone WARNING (version parity) is a
CI-context artifact — CI tests against RELEASE_3_22 while the package carries a
devel version (odd y); it does not appear on the Bioc devel dashboard.

Bump to 1.9.8 + NEWS.
 
    
  
    
      Package: Chromatograms

      Commit: 939e59de2421aec68a6e96e04efe85d2a79951ff

      Author:  Philippine Louail <philippine.louail@outlook.com> 

      Date: 2026-07-23 11:31:02 +0200

      Commit message:


	  
		 Merge pull request #59 from rformassspectrometry/jomain

refactor: convert plotting functions to methods 
    
  
    
      Package: Chromatograms

      Commit: 9b276257625035280a04cb48fa1198f310fb0894

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2026-07-23 10:51:19 +0200

      Commit message:


	  
		 ci: skip installing msdata
 
    
  
    
      Package: Chromatograms

      Commit: 5798154955948740d1ede39861d341a2dd90d17c

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2026-07-23 10:47:23 +0200

      Commit message:


	  
		 small changes to the README
 
    
  
    
      Package: Chromatograms

      Commit: 250eb23c46eeb5c9734e702494bd1534905d9fde

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2026-07-23 10:10:08 +0200

      Commit message:


	  
		 refactor: convert plotting functions to methods

- Change `plotChromatograms()` to a method.
- Change `plotChromatogramsOverlay()` to a method.
- Import `compareChromatograms()` generic from *ProtGenerics*.
- Get test data from *MsDataHub* instead of *msdata*.
 
    
  
    
      Package: PhyloProfile

      Commit: fdeff7d708637ec13abec3b21b3afc5deeda8376

      Author:  trvinh <trvinh@gmail.com> 

      Date: 2026-07-23 11:15:45 +0200

      Commit message:


	  
		 added bit64; fixed issue with percentCutoff=NULL
 
    
  
    
      Package: miRSM

      Commit: d3e622b69e5a52e6393cee5b41e812fd042c1fbc

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-07-23 16:56:54 +0800

      Commit message:


	  
		 update
 
    
  
    
      Package: miRSM

      Commit: 98720dfd784946052f5ad064c60beb1f23f4f5bc

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-01-15 13:13:57 +0800

      Commit message:


	  
		 Update
 
    
  
    
      Package: dnaEPICO

      Commit: a4372200e2f6307d1c9f4a4c47a5e5776b3ad767

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-07-23 11:16:57 +1000

      Commit message:


	  
		 Bioconductor 0.99.35 Model.messages
 
    
  
    
      Package: dnaEPICO

      Commit: e545ced440afd45c83f1721df529f733a0d33caf

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-07-22 18:10:41 +1000

      Commit message:


	  
		 Bioconductor 0.99.35 contestMD()
 
    
  
    
      Package: DOtools

      Commit: e41f59c13e18af886dfc8964b5e8aed66fc62506

      Author:  MarianoRuzJurado <mariani95@gmx.de> 

      Date: 2026-07-23 10:46:23 +0200

      Commit message:


	  
		 bugfix in subsetting
 
    
  
    
      Package: miRspongeR

      Commit: 01dd4d19782a49bb9ff513bbd8996769fbb3a3b6

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-07-23 15:41:37 +0800

      Commit message:


	  
		 Update
 
    
  
    
      Package: miRspongeR

      Commit: 1b461c118b4390c34c9bb713e73997b9bca792be

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-07-23 15:27:57 +0800

      Commit message:


	  
		 Update
 
    
  
    
      Package: igvShiny

      Commit: 2c9beef4e2f8fbfb55e0004da3c6b3e2abc303c7

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

      Date: 2026-07-23 09:38:01 +0200

      Commit message:


	  
		 Merge pull request #121 from gladkia/docs/update-demo-screenshot

Update demo screenshot to the new bslib UI 
    
  
    
      Package: igvShiny

      Commit: 98cdf9d6f8cddd554f91335707e07b046885b07c

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 09:35:48 +0200

      Commit message:


	  
		 Update demo screenshot to the new bslib UI (BAM/CRAM at BRCA1)

Replace man/figures/demo-gwas.png with man/figures/demo.jpg — the deployed
demo now showing BAM and CRAM alignment tracks stacked over BRCA1 (chr17) in
the modernized bslib UI. Conveys that multiple track panels can be viewed at
once. Saved as a resized JPEG (2400px, q85) to keep the file smaller than the
old PNG.

Refs #119
 
    
  
    
      Package: miRspongeR

      Commit: a4025ff734f0210901dc010891af5d25f3d20d8d

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-07-23 15:27:57 +0800

      Commit message:


	  
		 Update
 
    
  
    
      Package: miRspongeR

      Commit: 107d0dabd000429c4065f6454ee2f52c72120a84

      Author:  zhangjunpeng411 <zhangjunpeng_411@yahoo.com> 

      Date: 2026-01-11 20:15:36 +0800

      Commit message:


	  
		 Update
 
    
  
    
      Package: igvShiny

      Commit: e66e206db6e287088740e26f42facd66da940bb9

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

      Date: 2026-07-23 09:23:16 +0200

      Commit message:


	  
		 Merge pull request #120 from gladkia/feat/119-bslib-demo-ui

Modernize Posit Connect demo UI with bslib (Bootstrap 5) 
    
  
    
      Package: igvShiny

      Commit: fbe920b0188e2cd85ddaed4b17c103f98c3b6a96

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 09:12:42 +0200

      Commit message:


	  
		 Bump version to 1.9.7 and record demo work in NEWS

Add NEWS entries for the public Posit Connect Cloud demo + first README (#118)
and the bslib UI modernization (#119).

Refs #119
 
    
  
    
      Package: igvShiny

      Commit: e6d2ecf4df1526aa5b3d2498dc6b3fb653c53533

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 09:10:24 +0200

      Commit message:


	  
		 Modernize Posit Connect demo UI with bslib (Bootstrap 5)

Rebuild the demo's UI layer with bslib; server logic and all input ids are
unchanged.

- page_sidebar layout with a clean theme (primary #2c6faa, Inter font).
- IGV viewer in a full-screen-able card that fills the height.
- Controls grouped into an accordion (Sample-data tracks / Tracks from URL /
  Region tools) with full-width, icon-labelled buttons.
- Search box with placeholder above the accordion, monospace current-region
  readout, and GitHub / Docs links in the sidebar footer.

Regenerated manifest.json (adds bslib to the pinned set; still 72 pkgs,
igvShiny from GitHub master, no Rsamtools/GenomicAlignments).

Refs #119
 
    
  
    
      Package: igvShiny

      Commit: 46761fafd2ecea076f9a973a251d0f1c6742b7aa

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

      Date: 2026-07-23 08:45:53 +0200

      Commit message:


	  
		 Merge pull request #118 from gladkia/feat/117-posit-connect-demo

Add trimmed igvShiny demo for Posit Connect Cloud 
    
  
    
      Package: igvShiny

      Commit: 2f6fbe94b2aa7887613d7655b5da19f30e8e6607

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 08:41:41 +0200

      Commit message:


	  
		 Credit Arkadiusz Gladki as lead developer and maintainer in README

Refs #117
 
    
  
    
      Package: igvShiny

      Commit: 4022f68313c959088d392572d95af300b4941969

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 08:41:06 +0200

      Commit message:


	  
		 Reflect expanded maintainer role in README credits

DESCRIPTION lists Arkadiusz Gladki as aut+cre (author and creator), not just
maintainer. Update the credit line from 'Maintainer' to 'now developed and
maintained by' to reflect active development beyond upkeep.

Refs #117
 
    
  
    
      Package: igvShiny

      Commit: 51b64844ae787e12e9191c404b09f77c91df0208

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 08:39:01 +0200

      Commit message:


	  
		 Update copyright year to 2023-2026

LICENSE and LICENSE.md were both stamped 2023. Use a 2023-2026 range to
reflect ongoing maintenance since first release. Holder unchanged.

Refs #117
 
    
  
    
      Package: igvShiny

      Commit: d37a658205fefab4dde818e7a30c25220a742158

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 08:34:45 +0200

      Commit message:


	  
		 Address CodeRabbit feedback

- app.R: fix invalid bed9 interval — third thickEnd (base.loc+250) was less
  than thickStart (base.loc+260); bump thickEnd to base.loc+280 so the thick
  region is valid and within the record's start/end. Regenerated manifest.json
  to match the updated app.R checksum.
- README: link the license to LICENSE.md (full MIT text) rather than the terse
  LICENSE stub.

Refs #117
 
    
  
    
      Package: igvShiny

      Commit: 7276e03c9cda402972e7fc2e5448e3a6968c942a

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 08:31:38 +0200

      Commit message:


	  
		 Add demo screenshot (GWAS track) to README

man/figures/demo-gwas.png — the deployed demo showing a GWAS Manhattan track
over chr19 in the embedded IGV browser. man/figures is the standard location
for package README images (rendered on GitHub, pkgdown, and CRAN).

Refs #117
 
    
  
    
      Package: igvShiny

      Commit: 8fbfc2524a99857c0b023343ec54fdf058d90832

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 08:28:12 +0200

      Commit message:


	  
		 Add README with live demo link; exclude demo/ from package build

Repo had no top-level README. Adds one with a prominent link to the Posit
Connect Cloud demo, Bioconductor/GitHub install, a quick-start snippet, and
feature/docs sections. pkgdown builds its home page from this file.

Also .Rbuildignore the top-level demo/ directory: 'demo' is a reserved R
package subdirectory (expects demo/00Index), so shipping demo/posit-connect/
would trip R CMD check / BiocCheck. Connect Cloud reads from git, not the
tarball, so the deploy is unaffected. Verified: tarball now includes README.md
and excludes demo/.

Refs #117
 
    
  
    
      Package: igvShiny

      Commit: c55395aecc83f5a3308861925c736eef3bb4effe

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 08:23:57 +0200

      Commit message:


	  
		 Add Live demo link to pkgdown navbar

Points at the Posit Connect Cloud deployment
(https://gladkia-igvshiny-demo.share.connect.posit.cloud) via a vanity slug.

Refs #117
 
    
  
    
      Package: igvShiny

      Commit: f2dda5ea10c94859a073c09d1aa7dafe13e2fc3d

      Author:  Arkadiusz Gładki <arek@dobio.link> 

      Date: 2026-07-23 07:45:21 +0200

      Commit message:


	  
		 Add trimmed igvShiny demo for Posit Connect Cloud

Deploy-ready copy of the flagship demo (inst/demos/igvShinyDemo.R) under
demo/posit-connect/, for hosting a public clickable demo.

Removed the "BAM local data" button and its readGAlignments() call, the only
user of GenomicAlignments + Rsamtools (heavy Bioconductor C-compiled deps).
Alignment tracks stay demoed via BAM/CRAM-from-URL, which igv.js streams
client-side with zero server-side dependency. manifest.json confirms both
heavy deps are gone (72 pkgs).

manifest.json pins igvShiny to the development version from GitHub
(gladkia/igvShiny@master, 1.9.6) rather than the Bioconductor release, so the
hosted demo tracks the newest code. Includes a README with deploy steps, the
dev-version sourcing note, and the external-URL caveat.

Refs #117
 
    
  
    
      Package: drugTargetInteractions

      Commit: 4d91a2b69c45668807e8c73ed492002b807df64f

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

      Date: 2026-07-22 19:38:55 -0700

      Commit message:


	  
		 Suppress expected first-attempt TLS warning noise in downloadBroadRepurposingHub()

The known repo-hub.broadinstitute.org cert-chain gap (see file header)
makes the bare first download attempt fail deterministically before
.brhWithSupplementalCa() retries and succeeds. That expected, always-
recovered failure was still printing raw warning() text for any direct/
interactive/script caller (the vignette's own broad_build chunk was
already quieted separately via warning=FALSE, message=FALSE - see
dacc201). A genuinely unreachable host still throws an uncaught error,
verified live.
 
    
  
    
      Package: drugTargetInteractions

      Commit: 21a740efd29619d23b7ed31764051dfb0c01c27c

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

      Date: 2026-07-22 16:45:34 -0700

      Commit message:


	  
		 Bump version to 1.21.4
 
    
  
    
      Package: drugTargetInteractions

      Commit: 8e1e4c9c6b76d68abb885996e82cb856d0b386a2

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

      Date: 2026-07-22 15:58:06 -0700

      Commit message:


	  
		 Add queryBy reference tables to the vignette

Two quick-reference tables for the queryBy = list(molType, idType, ids)
interface: one covering each per-source function's native identifier
types (Data Sources in Detail), one covering queryDrugTargets()'s
broader canonical vocabulary (Cross-Source Queries). Every example id
is a real, live-tested value pulled from the package's own test suite
or a fresh live call, not invented.
 
    
  
    
      Package: KEGGREST

      Commit: 0fbb64c9423f09109e684fb648dac95ae943199d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-07-22 16:09:17 -0400

      Commit message:


	  
		 version bump 1.53.6
 
    
  
    
      Package: KEGGREST

      Commit: 1dc59c066bd423862f4a3a292ebaeaa12cb04145

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-07-22 16:09:13 -0400

      Commit message:


	  
		 use https protocol for KEGG_GENOME_URL
 
    
  
    
      Package: KEGGREST

      Commit: 26c386e214ca5c9ae46b16ac2af98b67b65cb842

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-07-22 13:40:40 -0400

      Commit message:


	  
		 run air formatter
 
    
  
    
      Package: KEGGREST

      Commit: 9146c4767fb33f9edec5d060308c1b8783843518

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-07-22 13:33:11 -0400

      Commit message:


	  
		 remote http_version
 
    
  
    
      Package: deconvR

      Commit: 0bbb7f1160c3408a11bd39f82fd2044484c0aaa7

      Author:  igunduz <irembgunduz@gmail.com> 

      Date: 2026-07-22 21:40:53 +0200

      Commit message:


	  
		 Remove unused granulator from Suggests; bump version to 1.19.1
 
    
  
    
      Package: sesame

      Commit: f1a805b33adc5c65dd609a3e03ef7541b8bbe09e

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2026-07-22 15:36:51 -0400

      Commit message:


	  
		 bump to 1.31.4; drop Google Analytics from the vignette header

Remove the gtag.js snippet from vignettes/include/header.html. With
self_contained: true in vignettes/_output.yaml, pandoc fetched that
script at render time to inline it, so vignette builds depended on
reaching an external host, and the shipped vignettes loaded a remote
tracking script on the reader's machine.

Also regenerate man/formatVCF.Rd, which had gone stale against the
roxygen comment updated in 7b12694, and record the roxygen2 8.0.0
metadata field.
 
    
  
    
      Package: sesame

      Commit: 05b0395be0efefff92ecf310ff7fbe098fca4acb

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2026-07-22 10:21:44 -0400

      Commit message:


	  
		 document sesame-cli in README and vignette

Add a "Two ways to run SeSAMe" section covering the C implementation
alongside this package, placed after the install instructions so the R
path comes first.

State the numerical relationship accurately: sesame-cli is an
independent reimplementation, not a port, so the two are not bit-exact.
Betas agree to a median of ~6e-6 and ~1e-3 worst case on probes with
identical raw input, with the intentional divergences recorded in the
sesame-cli NUMERICS.md.

Also refresh the README platform list, which still named only EPIC,
HM450 and HM27.
 
    
  
    
      Package: sesame

      Commit: c02f0f1a0c3215546687035182e60237c57cbbde

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-07-22 10:11:06 -0400

      Commit message:


	  
		 Merge branch 'devel' of github.com:zwdzwd/sesame into devel
 
    
  
    
      Package: sesame

      Commit: 7b12694d79e29a1d5209c6cb0033b3f97b931f07

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-07-19 17:20:40 -0400

      Commit message:


	  
		 Route lean-release files to InfiniumAnnotation; guard NA VAF in formatVCF

- expand_url(): versioned lean-release files (ordering/coord/mask.cm/snp) now
  resolve to zhou-lab/InfiniumAnnotation//, while the larger tables
  (manifest, gene annotation, ...) stay in InfiniumAnnotationData/Anno/. Update
  the default base from the renamed InfiniumAnnotationV1 to InfiniumAnnotationData
  (so it no longer relies on GitHub's rename redirect); accept a .mask.cm suffix.
- genotyper(): return a missing genotype (GT="./.", GS=0) for an NA VAF, so
  formatVCF no longer errors on a failed or absent probe.
 </pre>
    </div>
  
    
      Package: destiny

      Commit: 2cf74e4a413ff7e0e18f598b54d4e5158602573a

      Author:  Philipp A. <flying-sheep@web.de> 

      Date: 2026-07-22 20:30:58 +0200

      Commit message:


	  
		 last fix
 
    
  
    
      Package: TSENAT

      Commit: 7ff3354d910c0c1d1d39bfe580207e89e3a9f1db

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 12:04:58 +0200

      Commit message:


	  
		 Update WY
 
    
  
    
      Package: TSENAT

      Commit: 5ca3fbf8e74aeb7b5b1cc081171f9ef9fca811df

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 11:30:52 +0200

      Commit message:


	  
		 Fix tests
 
    
  
    
      Package: TSENAT

      Commit: 89d9fc5ed80b7ab68045c603b1fda4ab69ae42e8

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 01:41:08 +0200

      Commit message:


	  
		 Fix issues
 
    
  
    
      Package: TSENAT

      Commit: 0e591f87beb0012d04971d78cd9a505f16d5614d

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 00:51:14 +0200

      Commit message:


	  
		 Fix README
 
    
  
    
      Package: TSENAT

      Commit: 6ed7c8b15add896eda39d2e14dea9f4b34e2a827

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 00:42:00 +0200

      Commit message:


	  
		 Add tests
 
    
  
    
      Package: TSENAT

      Commit: 9b9688f5d4d9c76ba9541409bd8fd9db998ece36

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-22 00:39:10 +0200

      Commit message:


	  
		 Add tests
 
    
  
    
      Package: TSENAT

      Commit: 37d62039a63d4f1a4922e273221ea93d6e569024

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

      Date: 2026-07-21 23:47:06 +0200

      Commit message:


	  
		 Merge branch 'stable' into devel 
    
  
    
      Package: TSENAT

      Commit: 7d79c592bc7ab0aefba882085dbf7043e2247ca6

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-07-21 23:46:11 +0200

      Commit message:


	  
		 Fixes
 
    
  
    
      Package: TSENAT

      Commit: 740d041d2de6b0e3fe639568256e6baff79ce32b

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

      Date: 2026-07-20 12:56:45 +0200

      Commit message:


	  
		 Devel (#54)

Update SHR script. 
    
  
    
      Package: TSENAT

      Commit: 0d5d6b7dd67200cd83b7f0d8b7bec8656effbd1b

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

      Date: 2026-07-14 05:18:09 +0200

      Commit message:


	  
		 Devel (#52) 
    
  
    
      Package: geomeTriD

      Commit: 71100ab9f4380ea53064f92ba3511ed6784b088e

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2026-07-22 11:16:34 -0400

      Commit message:


	  
		 update the curver connection calculation methods.
 
    
  
    
      Package: LACHESIS

      Commit: 80e0065615dd44c436fede062ba96525c1994b69

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-07-22 15:44:51 +0100

      Commit message:


	  
		 Updated version
 
    
  
    
      Package: LACHESIS

      Commit: a210ffcd8bd0a3083b9a08a5163fa990231f33eb

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-07-07 10:54:57 +0100

      Commit message:


	  
		 Updated NEWs and Description files
 
    
  
    
      Package: LACHESIS

      Commit: 478653fee637375dc23aa8f2694dbd1adc921a2e

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-07-07 10:51:41 +0100

      Commit message:


	  
		 Remove segments with negative CN, as can happen with Purple
 
    
  
    
      Package: LACHESIS

      Commit: 6d09b026f05e09dd97058140343dcd5b50a4da11

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-07-05 00:12:37 +0200

      Commit message:


	  
		 Add continuos realtime y axis (as in LACHESIS) to plotMutationDensities + start realtime y axis at 0 SNVs per Mb
 
    
  
    
      Package: LACHESIS

      Commit: 11fa2e34b7d0e01e58f7e0f5deac3d7e23607e98

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-07-01 23:22:04 +0100

      Commit message:


	  
		 Added mutation rate to plotMutationDensities
 
    
  
    
      Package: LACHESIS

      Commit: 9a007b1184e0cf56d57dc7afcdf6314b92deef4b

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-07-01 08:32:30 +0100

      Commit message:


	  
		 Add estimated mutation rate to timeline plot
 
    
  
    
      Package: LACHESIS

      Commit: df16a0973fc825c313907dfb54dc5592cf164b8b

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-06-30 22:53:55 +0200

      Commit message:


	  
		 Adding estimateMutationRate to package structure figure
 
    
  
    
      Package: LACHESIS

      Commit: 779de4a9c5ecf9545e9849ebed74ab25223f0af2

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-28 18:30:02 +0100

      Commit message:


	  
		 Corrected typo in vignette
 
    
  
    
      Package: LACHESIS

      Commit: 3eb621f1243cb3b8ef96357837e1515b7ebac0bb

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-28 18:13:27 +0100

      Commit message:


	  
		 Corrected typo in vignette
 
    
  
    
      Package: LACHESIS

      Commit: fe5aa4b7ba14285c04b727d0b0449ba3f5ddee76

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-06-27 11:12:25 +0200

      Commit message:


	  
		 devtools::document() and small errors from R-CMD check
 
    
  
    
      Package: LACHESIS

      Commit: 793a0a2911e4e60e4bfa79f9583556b1d6530293

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 16:08:02 +0100

      Commit message:


	  
		 Loosened r2 threshold
 
    
  
    
      Package: LACHESIS

      Commit: 72269c9c457134e87401936cc389998ec68b0c4d

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 16:07:05 +0100

      Commit message:


	  
		 Loosened r2 threshold
 
    
  
    
      Package: LACHESIS

      Commit: e9be8d575ab8b94e43ec9003fd2aedbf4942908e

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 16:01:45 +0100

      Commit message:


	  
		 another ... issue
 
    
  
    
      Package: LACHESIS

      Commit: 5944b7467c6b3dd5b50355917efe6f1b3e8e2a1b

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:42:57 +0100

      Commit message:


	  
		 Adjusted real time axis in plotLACHESIS to flexibly allow for later time points
 
    
  
    
      Package: LACHESIS

      Commit: 7711cf54f7d91c563013b6261ef6ee0f75f0ab26

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:39:08 +0100

      Commit message:


	  
		 Removed age conversion from plotLACHESIS, as it doesn't make sense.
 
    
  
    
      Package: LACHESIS

      Commit: 3459f89ac4ac4bf6b2aa4e421f80f39c4127ef04

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:34:08 +0100

      Commit message:


	  
		 Corrected typo
 
    
  
    
      Package: LACHESIS

      Commit: ef707c997df4b4c6fe296a098d0f6162f84dd8b4

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:26:51 +0100

      Commit message:


	  
		 Adjust time units
 
    
  
    
      Package: LACHESIS

      Commit: 9802d9a9cb376814050538f9ac74beaea836e5bb

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:22:30 +0100

      Commit message:


	  
		 Account for time unit in Age
 
    
  
    
      Package: LACHESIS

      Commit: 27c9ef09f8e5178033f5e8a895c1d14a6435197f

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 15:03:51 +0100

      Commit message:


	  
		 Added ... to allow propagation of unit measure to estimateMutaitonRate
 
    
  
    
      Package: LACHESIS

      Commit: 881f7623755375024c2acd2b4feeca4f861ed69c

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 14:59:13 +0100

      Commit message:


	  
		 corrected output of mutation rate estimates
 
    
  
    
      Package: LACHESIS

      Commit: 8bbc5a844a2fcc5169135b3a5ea6077afbdc27e8

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 14:54:56 +0100

      Commit message:


	  
		 corrected read in of mutation rate estimates
 
    
  
    
      Package: LACHESIS

      Commit: 9f41acef73374a58dde5e0b28af51952f4b55d4c

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 14:01:27 +0100

      Commit message:


	  
		 Added ... to allow propagation of unit measure to estimateMutaitonRate
 
    
  
    
      Package: LACHESIS

      Commit: 4cf2071c56cb6bcf620d7d5247f2e2fa07a2d7ed

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-26 13:57:39 +0100

      Commit message:


	  
		 Corrected typo in saving output of mutation rate estimates
 
    
  
    
      Package: LACHESIS

      Commit: 9e1152b35c3ed1ccc16bcff0f2654f4c2af0fbf5

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-06-26 13:53:24 +0200

      Commit message:


	  
		 NAMESPACE correction
 
    
  
    
      Package: LACHESIS

      Commit: 6f710547c14dc85a0b9ed6c8ae53b274cd88ebee

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-25 12:47:11 +0100

      Commit message:


	  
		 Added gestation time to mutation rate real-time estimate
 
    
  
    
      Package: LACHESIS

      Commit: a5ea2586ae92d48574cd550a4ee86bd59f4f339c

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 15:42:04 +0100

      Commit message:


	  
		 Adjusted description
 
    
  
    
      Package: LACHESIS

      Commit: 64c96faa03035b04ead638543626ad195dd6721e

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 15:41:33 +0100

      Commit message:


	  
		 Adjusted plot title
 
    
  
    
      Package: LACHESIS

      Commit: a312be869b33802a65f2abf149a88826972bb2cb

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 15:30:08 +0100

      Commit message:


	  
		 Corrected typo
 
    
  
    
      Package: LACHESIS

      Commit: db7ca3c09369bfcb20f1780b12778ce57103b8c9

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 15:16:34 +0100

      Commit message:


	  
		 Added real time axis to plotLachesis. Implement flexibility regarding mutation rate estimate such that previous estimates can be read in.
 
    
  
    
      Package: LACHESIS

      Commit: 993d5e811c1852b85338a6eb4f9157f16a3ea2e1

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 14:56:25 +0100

      Commit message:


	  
		 Added real time to plotLACHESIS, allowing for de novo estimation of mutation rates

updated DESCRIPTION in line with release#
 
    
  
    
      Package: LACHESIS

      Commit: 1085e220a41603fd91b4fca8f46738df076c34af

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 13:50:55 +0100

      Commit message:


	  
		 Reformatted
 
    
  
    
      Package: LACHESIS

      Commit: ba76fe9fa773fe4f5229a51f7168a540e312b142

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-06-24 13:49:52 +0100

      Commit message:


	  
		 added function to estimate mutation rate from cohort
 
    
  
    
      Package: anndataR

      Commit: 7b7737cc6ae06abfb8dbf1d4c2813c3eaabd1e32

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-07-21 18:42:00 +0200

      Commit message:


	  
		 Update NEWS (#488)

* Update news

* Fix PR entries which weren't pushed to bioc devel yet

* update news 
    
  
    
      Package: anndataR

      Commit: 47d557cd59671debc8de444bb4ea817a27f6d4ca

      Author:  Artür Manukyan <artur-man@hotmail.com> 

      Date: 2026-07-21 13:20:15 +0200

      Commit message:


	  
		 Simplify roxygen docs (#479)

* clean roxygen2 doc for helpers

* tidy read helpers, lint and air

* fix some params 
    
  
    
      Package: anndataR

      Commit: b2a41ce34dcf0bdf81dff99afb676dacd795c54d

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-07-21 13:19:17 +0200

      Commit message:


	  
		 Require Python `anndata<0.13.0` in tests (#481)

* Require Python anndata < 0.13.0 in tests

* Pin Python anndata in GHA workflows

* Pin anndata in Python usage vignette

* Pin scanpy in Python vignette

* add comments

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    
      Package: anndataR

      Commit: 7348779a6abdd7e10d36cf111833659904412579

      Author:  Artür Manukyan <artur-man@hotmail.com> 

      Date: 2026-07-21 08:38:49 +0200

      Commit message:


	  
		 Fix `create_zarr()` so that Zarr stores can be created at relative paths (#478)

* safe create_zarr

* Add entry to news

* Add test

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    
      Package: anndataR

      Commit: 479f476e8bdb131e0be2068b47c2ccaf280b5453

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-07-21 07:56:42 +0200

      Commit message:


	  
		 Fix conditional expression (#487) 
    
  
    
      Package: anndataR

      Commit: 8b689fd9d64e49cd3d085bf28ca3cd9ed8cdcbdc

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-07-21 07:54:14 +0200

      Commit message:


	  
		 Update multiple actions simultaneously (#486) 
    
  
    
      Package: anndataR

      Commit: 07612e4f0e5c7efff05265eb916ae9ed94bf78b9

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-06-23 12:21:05 +0200

      Commit message:


	  
		 Bump bencherdev/bencher from 0.6.7 to 0.6.8 (#472)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.7 to 0.6.8.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.7...v0.6.8)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.8
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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      Package: anndataR

      Commit: 6a1ca6b6ece85a46a7b93dd5f8cab24db2a99789

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-06-23 12:20:24 +0200

      Commit message:


	  
		 Add support for `DelayedArray` reading (#387)

* Refactor HDF5AnnData to store file paths

Using paths instead of handles is required for compatibility with
HDF5Array

* Add hdf5_open_file() util function

Minimise repeated file opening code

* Add HDF5File class and use in HDF5AnnData

* Add close_and_defer_open() to HDF5File

* Use HDF5Array in read_h5ad_dense_array()

Keep fallback base rhdf5 function

* Add HDF5Array dependency

* Use HDF5Array in read_h5ad_spase_matrix

* Add backed option to HDF5AnnData

* Roxygenise

* Style

* Add backed SingleCellExperiment conversion

* Add backed Seurat conversion

* Fix lint

* Add HDF5Array checks to tests

* Add DelayedArray as suggested dependency

* Roxygenize

* Style code (GHA)

* Fix namespace in tests

* Expand tests for backed objects and make fixes

* Style code (GHA)

* Fix typos

* Check DelayedArray seed in to_R_matrix()

* Remove unused argument in HDF5File$close()

* Fix return in .as_SCE_process_pairs_mapping

* style code

* restyle code

* add tests for known issues

* Update known issues

* Fix subsetting backed anndata objects

* materialise when converting backed hdf5 to inmemoryanndata

* make sure SCE supports delayedarrays

* support writing delayedmatrix object by materialising on write

* add entry to bench suite

* fix performance regression; do not use HDF5Array for eager read

* delayedarray and hdf5array are only needed when backed is true

* remove known issue sections that are no longer needed

* keep handle open when reading element keys

* reuse handle if it already has enough access

* remove this benchmark for now

* Fix formatting

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    
      Package: anndataR

      Commit: b1419ff1e3409110d2917c8efb012cb0ad5f887c

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-06-21 11:12:31 +0200

      Commit message:


	  
		 Add Bioconductor R-universe checks (#470) 
    
  
    
      Package: anndataR

      Commit: 27855705dfeb934fab2a963f5b0c821a452691a1

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-06-19 10:31:46 +0200

      Commit message:


	  
		 Bump actions/checkout from 6 to 7 (#469)

Bumps [actions/checkout](https://github.com/actions/checkout) from 6 to 7.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v6...v7)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
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      Package: anndataR

      Commit: 696edcf8e8fd9840e9779b9afe63049b93849d95

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-06-19 10:26:43 +0200

      Commit message:


	  
		 Update gitignore
 
    
  
    
      Package: anndataR

      Commit: 65b136b45b36a381b1514e5dd1eaafee2ea1604e

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-06-18 14:48:36 +0200

      Commit message:


	  
		 Upgrade to roxygen 8.0.0
 
    
  
    
      Package: anndataR

      Commit: e3ea474653f7b8423351823a51e862542fe104c3

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-06-17 22:51:34 +0200

      Commit message:


	  
		 Take into account Rarr structured datatype breaking change (#462)

* Take into account Rarr structured datatype breaking change

* Run air

* add switch for backwards compatibility

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    
      Package: anndataR

      Commit: e3e7f7c0c27606b4099e4107be31a465df58a964

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-06-17 16:13:49 +0200

      Commit message:


	  
		 Update CITATION with published paper (#464) 
    
  
    
      Package: anndataR

      Commit: d8300f686208ef33efa214791d4f69cf94b23dc1

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-06-17 16:13:06 +0200

      Commit message:


	  
		 Bump bencherdev/bencher from 0.6.6 to 0.6.7 (#467)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.6 to 0.6.7.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.6...v0.6.7)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.7
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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      Package: anndataR

      Commit: cdcd4f8c7281fe4deae28db2a1b16a4bd65caff3

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-06-17 16:12:40 +0200

      Commit message:


	  
		 Bump codecov/codecov-action from 6 to 7 (#465)

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 6 to 7.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v6...v7)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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      Package: anndataR

      Commit: 4e5b112edcfe34f564ee02e89056a839215beeac

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-06-04 09:53:42 +0200

      Commit message:


	  
		 Mark Zarr support as implemented in class diagram (#460) 
    
  
    
      Package: anndataR

      Commit: 38e9db5b9bc7a48656a09fca18abffabfc267cc0

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-05-27 10:12:08 +0200

      Commit message:


	  
		 Update CI
 
    
  
    
      Package: anndataR

      Commit: 897914bb5abaed985c86664466b3cdd3c3f4a24e

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-05-12 20:03:28 +0200

      Commit message:


	  
		 Add Zarr to benchmarks (#446)

* WIP

* More tests passing

* Fix df read bug

* More tests passing after fixing zero-dimensional get bug in pizzarr

* WIP: writing

* Fix more tests

* Zarr df writing

* WIP: ZarrAnnData class

* Tests passing

* Tests that compare h5ad to zarr

* Use Rarr to read full numeric arrays

* Fix bugs. Add test for from_SingleCellExperiment with Zarr

* Add a to_dense param to ZarrAnnData constructor. Add overwrite params internally.

* Update

* Backwards dense/sparse

* Simplify how obs and var names handled in ZarrAnnData (similar to #171)

* update extdata and documentation

* fix set/get zarr _index, update text example.zarr and update tests similar to HDF5AnnData

* Fix test

* Revert unnecessary changes

* Formatting

* Add comments

* remove unnecessary example zarr store

* lintr and R check for zarr related utilities and functions, updated some documentation

* add pizzarr to Suggests and README

* proj

* add keller-mark/pizzarr to Remotes

* zip example.zarr

* adapt read_zarr to Rarr

* adapt write_zarr to Rarr

* remove old scripts

* update write_zarr

* initial update to ZarrAnnData

* update ZarrAnnData, documentation, and implement read_zarr_rec_array

* review read zarr helpers, and update tests

* update read_zarr, read tests pass

* some updates for writing zarr

* update write_empty_zarr

* remove pizzarr, update documentation

* remove pizzarr from tests

* fix test-ZarrAnnData

* update ZarrAnnData to imitate HDF5AnnData

* check redundant files, correct lines

* update example_h5ad.py, add zarr and change to example_files.py

* add new test example

* some linting changes

* remove read/write_zattrs since implemented in Rarr

* access read/write_zarr_attr

* add some missing tests

* update readers, update tests

* correct nullable string zarr array write/read, introduce ordering in categorical zarr array

* do some linting, fix commented out code

* update some zarr writers and classes

* fix documentation

* fix compression interface for zarr

* full lint check

* fix examples

* check, biocheck and lintr

* fix development status

* air format

* air format test

* update example.zarr.zip, skip some test (waiting for Rarr)

* update example.zarr, fix some read_zarr_

* fix examples

* remove overwrite

* R code styling

* fixes from @lazappi

* air format

* update some documentation

* fix some tests

* more fixes on anndata-zarr integration

* update ZarrAnnData$initialize

* update zarr compression

* fix column-order here, C based ordering for arrays

* implement roundtrip tests for anndata-zarr

* add zarr to vignettes

* update README and software_design.rmd

* update AnnData-usage

* update write_zarr documentation

* update write_zarr_null

* fix rec_array, update tests and example datasets

* fix duplicate chunks in Rmd

* add write_zarr_null

* update write string array (zarr), air and lint

* implement writing empty zarr elements

* update tests for rec_array conformance of h5ad and zarr

* update mapping conformance test for h5ad and zarr

* implement H5_ITER like ordering and fix h5ad vs zarr testing

* air and lint

* fix test bug

* do not call expect_equal outside of test

* implement examples, test and datasets for zarr v3

* fix issues, lint and update example datasets to new anndata version

* lint and merge

* revert some lines

* small changes

* revert small changes

* air format some tests

* Set v2 in write_zarr_* helpers

* Fix stop message in write_zarr_element()

* Fix roxygen comment in write_zarr_element()

* Expand compression list in as_ZarrAnnData()

* Fix H5_ITER_INC_ORDERING docs

* Fix as_ZarrAnnData() compression docs

* Fix Zarr varm roundtrip test

* Review duplicate entry in README

* Fix typo in AnnData-usage docs

* Fix comma in software design vignette

* Adjust class descriptions in software design vignette

* Roxygenise

* Minor text fixes

* Document .get_compressor

* Minor fixes to function docs

* Comment logic in create_zarr_group()

* Fix indentation in read_zarr_sparse_array()

* Add construct sparse matrix helper

* Add ZARR_METADATA_FILES vector

* Eval Zarr chunks in vignettes

* Merge test-Zarrv3-read.R into test-Zarr-read.R

* Combine roundtrip tests

* Add roundtrip test helpers

* Refactor test-h5ad-zarr.R to use helper

* Refactor example files script

- Use uv comments for dependencies
- Update dependencies to latest stable versions
- Add progress messages
- Use Ruff for formatting

* Remove H5_ITER_INC_ORDERING()

* Remove Zarr compression comment

* Fix factor creation in read_zarr_categorical()

* Pin Rarr version

* Delete existing Zarr path before writing

* Add helper functions for accessing Zarr keys

* Update read_zarr_element() error message

* Add dimname warnings to ZarrAnnData

* Add Zarr writeability checks/tests

* Roxygenise, lint, style

* Use setup-bioc for all GHA

* Update WORDLIST

* Add .venv to .Rbuildignore

* Clean up test output

* Add Zarr to benchmarks

* run air format

---------

Co-authored-by: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Co-authored-by: Artur-man <artur-man@hotmail.com>
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 
    
  
    
      Package: anndataR

      Commit: 4269af57a1e47e3ccb3895a629f623a36fa50a2c

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-05-12 14:00:42 +0200

      Commit message:


	  
		 Bump bencherdev/bencher from 0.6.4 to 0.6.5 (#456)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.4 to 0.6.5.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.4...v0.6.5)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
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      Package: anndataR

      Commit: 096e75aedd3bbd6f503dbddba206b4f45c8f6303

      Author:  Robrecht Cannoodt <rcannood@gmail.com> 

      Date: 2026-05-12 12:37:44 +0200

      Commit message:


	  
		 Fix CI (#457)

* install additional libraries for mac os runner

* switch bioc mirror

* switch mirror

* manually fix versions

* try without version map

* try removing workarounds 
    
  
    
      Package: anndataR

      Commit: 22a2191102282a69b23dbdb13e2b13dfe3159253

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-11 11:23:36 +0200

      Commit message:


	  
		 Enable new linters (#453)

* Replace any(is.na()) by anyNA()

* Apply ! on a single element instead of the entire vector

* Use nzchar() where possible

* Mark regexes as fixed where possible

* Use anyDuplicated() where possible

* Remove redundant is.integer() call

* Replace as.data.frame() by list2DF()

* Use endsWith() where relevant

* Run air 
    
  
    
      Package: anndataR

      Commit: 6c243139025752a15d715cfaaaed698647da12c2

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-05-06 18:23:21 +0200

      Commit message:


	  
		 Bump dawidd6/action-download-artifact from 20 to 21 (#451)

Bumps [dawidd6/action-download-artifact](https://github.com/dawidd6/action-download-artifact) from 20 to 21.
- [Release notes](https://github.com/dawidd6/action-download-artifact/releases)
- [Commits](https://github.com/dawidd6/action-download-artifact/compare/v20...v21)

---
updated-dependencies:
- dependency-name: dawidd6/action-download-artifact
  dependency-version: '21'
  dependency-type: direct:production
  update-type: version-update:semver-major
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      Package: anndataR

      Commit: 3d5792d156b3c4bdba4f56f24956571f3c174e1d

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-05-06 18:06:38 +0200

      Commit message:


	  
		 Bump bencherdev/bencher from 0.6.3 to 0.6.4 (#454)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.3 to 0.6.4.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.3...v0.6.4)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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      Package: anndataR

      Commit: 844954a7ed7dab2bba8a106fb4065d5e7d764c7d

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-05-05 17:54:56 +0200

      Commit message:


	  
		 Update NEWS for v1.3.0
 
    
  
    
      Package: anndataR

      Commit: 16da839d4153de373e0bbe15bd1bf774481c7f6e

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-05-05 17:54:09 +0200

      Commit message:


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

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    
      Package: anndataR

      Commit: 2e0aa6130da1fef51df15b0ae73be269800ca871

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-05-05 17:52:22 +0200

      Commit message:


	  
		 Update NEWS for v1.2.0
 
    
  
    
      Package: anndataR

      Commit: 4e605312e6be1a8775188034ddfa6351a13e2a9f

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2026-05-05 17:51:25 +0200

      Commit message:


	  
		 Merge remote-tracking branch 'upstream/RELEASE_3_23' into devel

* upstream/RELEASE_3_23:
  bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    
      Package: anndataR

      Commit: 4fa9edf7a370326d05e24d9d129994c2c5784a40

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-04-27 09:04:22 +0200

      Commit message:


	  
		 Bump bencherdev/bencher from 0.6.2 to 0.6.3 (#450)

Bumps [bencherdev/bencher](https://github.com/bencherdev/bencher) from 0.6.2 to 0.6.3.
- [Release notes](https://github.com/bencherdev/bencher/releases)
- [Commits](https://github.com/bencherdev/bencher/compare/v0.6.2...v0.6.3)

---
updated-dependencies:
- dependency-name: bencherdev/bencher
  dependency-version: 0.6.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
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      Package: SwarnSeq

      Commit: 651b42d4aef04fbe2783c5302edad8c0098bc4c5

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-07-22 18:57:49 +0530

      Commit message:


	  
		 Prepare package for bioconductor push.
 
    
  
    
      Package: SwarnSeq

      Commit: e8855cb4d3af9ddd863af01955c9c7c89cf5b8f7

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-07-22 15:34:36 +0530

      Commit message:


	  
		 Remove unnecessary files and folders from the previous push.
 
    
  
    
      Package: SwarnSeq

      Commit: c35efa6428eb4602f4c8feb6942f7bde815e320f

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-07-22 14:56:01 +0530

      Commit message:


	  
		 addredd comments from the previous version 0.99.4 of this package.
 
    
  
    
      Package: SwarnSeq

      Commit: 4575ced9889c570d3f8d39a1ecd83edba1701225

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:30:50 +0530

      Commit message:


	  
		 Initial commit 
    
  
    
      Package: SwarnSeq

      Commit: 6190d693fc5a5bee8f216a4d477a459d26f2d31b

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:27:08 +0530

      Commit message:


	  
		 Delete NEWS.md 
    
  
    
      Package: SwarnSeq

      Commit: 901980d3ee0d5842f728471080591c22f05b24c5

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:26:54 +0530

      Commit message:


	  
		 Delete NAMESPACE 
    
  
    
      Package: SwarnSeq

      Commit: e896c42181711efe6d09a7ab7b5439e7755d062f

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:26:37 +0530

      Commit message:


	  
		 Delete DESCRIPTION 
    
  
    
      Package: SwarnSeq

      Commit: 54a5793875ac7e49e5a05582cf1249f080934027

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:26:19 +0530

      Commit message:


	  
		 Delete vignettes directory 
    
  
    
      Package: SwarnSeq

      Commit: 6368a8b0837c9356661ce39155e49a21dcd7d659

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:26:07 +0530

      Commit message:


	  
		 Delete tests directory 
    
  
    
      Package: SwarnSeq

      Commit: 833456650b8c258174740dae96d4d37143549cf1

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:25:56 +0530

      Commit message:


	  
		 Delete man directory 
    
  
    
      Package: SwarnSeq

      Commit: de45082a79aa1a18d547efdb4f8a34bc1b155fcf

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:25:45 +0530

      Commit message:


	  
		 Delete R directory 
    
  
    
      Package: SwarnSeq

      Commit: aaf8ca602c80e0eadb55ed049f327a478243249f

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2026-01-04 10:25:31 +0530

      Commit message:


	  
		 Delete data directory 
    
  
    
      Package: SwarnSeq

      Commit: e3087be3570992375a4781d7ae51ffa54a0ddd76

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:49:07 +0530

      Commit message:


	  
		 version .3 added 
    
  
    
      Package: SwarnSeq

      Commit: f829cdbd7d67a257538f3d9ac214915818431116

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:48:33 +0530

      Commit message:


	  
		 Delete NAMESPACE 
    
  
    
      Package: SwarnSeq

      Commit: e1a5248a45b8432046ab2f22cd2dc62280e6c8cf

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:48:06 +0530

      Commit message:


	  
		 Delete DESCRIPTION 
    
  
    
      Package: SwarnSeq

      Commit: efc3c678de9bbc4e2b107ec6c4febea596b78ed3

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:47:11 +0530

      Commit message:


	  
		 Initial commit 
    
  
    
      Package: SwarnSeq

      Commit: e491a8c02944e61405e294686dcf00644263555b

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:43:28 +0530

      Commit message:


	  
		 Delete vignettes directory 
    
  
    
      Package: SwarnSeq

      Commit: ed2eb75d454c8ae3cb9b16dc60cd1c2cedcbd4ff

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:43:15 +0530

      Commit message:


	  
		 Delete tests directory 
    
  
    
      Package: SwarnSeq

      Commit: 9619d1220e8d4711b01c9da319528c7a15a8f1fd

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:42:56 +0530

      Commit message:


	  
		 Delete man directory 
    
  
    
      Package: SwarnSeq

      Commit: ade65e4dce5d00e1b6cbd91b2bdde671a4d80e8d

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:42:18 +0530

      Commit message:


	  
		 Delete data directory 
    
  
    
      Package: SwarnSeq

      Commit: 6ed5d2f7e272e93fae48c3e076a71ea7e19123e9

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:42:03 +0530

      Commit message:


	  
		 Delete R directory 
    
  
    
      Package: SwarnSeq

      Commit: 9c59157e0bc25d42ceb5ced4355fb74fe6dca74f

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-18 16:13:27 +0530

      Commit message:


	  
		 Change package version 
    
  
    
      Package: SwarnSeq

      Commit: 7756b3340e56bea4cc811700e07390d5102a7b0b

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-18 16:12:22 +0530

      Commit message:


	  
		 Delete DESCRIPTION 
    
  
    
      Package: SwarnSeq

      Commit: 8665e8fc37158d91836f6df09c3c642cd27c2afc

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-16 12:19:22 +0530

      Commit message:


	  
		 First version change 
    
  
    
      Package: SwarnSeq

      Commit: 47d15b151350a8ecab3e29e6e38edfceefcbffd6

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-16 12:18:30 +0530

      Commit message:


	  
		 Delete DESCRIPTION 
    
  
    
      Package: SwarnSeq

      Commit: 7a7b0247d353308ff16a78d392cc039643556933

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:58:38 +0530

      Commit message:


	  
		 Initial commit 
    
  
    
      Package: SwarnSeq

      Commit: 2004c8dde71311a7876cd9138879363877806a39

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:57:51 +0530

      Commit message:


	  
		 Delete man directory 
    
  
    
      Package: SwarnSeq

      Commit: 9e7542faede5aa2e78d6243be42315eaef2aaaff

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:57:35 +0530

      Commit message:


	  
		 Delete R directory 
    
  
    
      Package: SwarnSeq

      Commit: 3657d429f997218d2153940a68b893f60a513c1f

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:57:16 +0530

      Commit message:


	  
		 Add files via upload 
    
  
    
      Package: SwarnSeq

      Commit: 428e85ae82752d78fc30211d136db1df05837ec4

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:55:39 +0530

      Commit message:


	  
		 Delete man directory 
    
  
    
      Package: SwarnSeq

      Commit: 24dd79f78ce8a12dda43c9b8c7c60d85f5a878de

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-09-14 21:55:21 +0530

      Commit message:


	  
		 Delete R directory 
    
  
    
      Package: DOtools

      Commit: 07c8c4ece9d79478b1ce4510d37ffcf759c3d2ef

      Author:  MarianoRuzJurado <mariani95@gmx.de> 

      Date: 2026-07-22 14:14:13 +0200

      Commit message:


	  
		 bugfix
 
    
  
  


</div>

</div>