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Package: GBScleanR
Commit: d9511e945449625c3e9517d1425b8bb1d50c96ba
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2026-10-09 15:39:44 +0900
Commit message:

 Bump to v2.7.5 with loadGDS, replicate, and plot fixes plus broader tests.

Restore R 4.6.1-safe GbsrGenotypeData construction, fix replicate genotype expansion in estGeno(), complete plot stats catalogues, and expand testthat coverage for core QC/filtering/scheme workflows.

Co-authored-by: Cursor <cursoragent@cursor.com>
Package: lisaClust
Commit: c7b535fbfe79828078cd7c6d368d2d5341d2c05f
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-09 17:40:47 +1100
Commit message:

 1.21.4: twelve hatchings (dots, circles, and /, \ and - with dots after the first seven)

- hatchGrobs() draws a hatching type clipped to a region: its lines (polyclip) and its marks (points strictly
  inside the rings, even-odd). Dots or circles alone sit on a staggered grid, two per tile; with lines, one per
  tile halfway between the lines. Used by the panels and by the legend keys, so keys match the hatching.
- Limits raised from 7 to 12 (nHatchings) in geom_hatching(), scale_region_manual() and hatchingLevels(); regions
  beyond the twelfth are drawn as the first, with a warning.
- Same order as lisaclust-py 1.21.4 (matplotlib hatches "", /, \, -, |, x, +, ., o, /., \., -.).
- Tests: every type draws inside its region and has a key; holes stay empty; 12 regions draw silently, 13 warn.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
Package: gDRutils
Commit: 8ba4a03f7bddc1b0fa34ec42ddc504e2fee84f75
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2026-10-09 08:04:39 +0200
Commit message:

 Merge pull request #204 from gdrplatform/GDR-3674

Update authors data
Package: gDRutils
Commit: 4ce4ed4a7b2a4970e0b39dff2b578a9d6158ba9c
Author: Janina Smola <janina.smola@external.roche.com>
Date: 2026-10-08 14:12:34 +0200
Commit message:

 chore: update authors data
Package: gDRtestData
Commit: 148402af9759613428226e96d42a8b2a90f53000
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2026-10-09 08:03:51 +0200
Commit message:

 Merge pull request #85 from gdrplatform/GDR-3674

Update authors data
Package: gDRtestData
Commit: 76c0d94c9b0b9859ec45757a6c37a67f5839d820
Author: Janina Smola <janina.smola@external.roche.com>
Date: 2026-10-08 14:27:06 +0200
Commit message:

 chore: update authors data
Package: gDR
Commit: d0522c982283f99a820f39d76df8b2f4213df2c5
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2026-10-09 08:04:05 +0200
Commit message:

 Merge pull request #68 from gdrplatform/GDR-3674

Update authors data
Package: gDR
Commit: 9f38e5d0611386c9151ba2e002071ab924e077e8
Author: Janina Smola <janina.smola@external.roche.com>
Date: 2026-10-08 14:26:05 +0200
Commit message:

 chore: update authors data
Package: gDRimport
Commit: 3768be6bd87ced5f7fc0c454e447014c9f559d6a
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2026-10-09 08:03:17 +0200
Commit message:

 Merge pull request #127 from gdrplatform/GDR-3674

Update authors data
Package: gDRimport
Commit: 1db8b1c0899c310533112074904403845120edd1
Author: Janina Smola <janina.smola@external.roche.com>
Date: 2026-10-08 14:28:34 +0200
Commit message:

 chore: leftovers
Package: gDRimport
Commit: 61a1a5c3af1cde25786fa2b323ad1922c240364c
Author: Janina Smola <janina.smola@external.roche.com>
Date: 2026-10-08 14:28:04 +0200
Commit message:

 chore: update authors data
Package: lisaClust
Commit: cf5d8184447f626cd6d1d1753801b891f55d5ae8
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-09 16:42:13 +1100
Commit message:

 1.21.3: hatching regions outlined by Voronoi tiles, hatching clipped by polyclip; faster concave window

- geom_hatching() computes each region's outline as the union of the Voronoi tiles (deldir) of its cells, clipped
  to the window (polyclip), in data coordinates, instead of an nbp x nbp nearest-cell grid. The outlines follow
  the cells exactly and nbp is no longer used (still accepted). The outlines are cached by a hash of the cells,
  regions and window; the grob (class lisaHatching) clips each region's hatching lines to its outline with
  polyclip when drawn, so lines cannot cross into another region. About 3 s to draw an image of ~6,000 cells,
  0.8 s to print it again.
- Tried and dropped: filling regions with grid tiling patterns. On the cairo PNG device some multi-ring regions
  were left unfilled, and pattern fills took ~2 s per draw against 0.6 s for clipped lines.
- makeWindow("concave") builds its point cloud without a per-cell loop: 0.9 s to 0.32 s, identical window.
- deldir and polyclip are new direct imports (already dependencies of spatstat.geom); purrr dropped.
- DESCRIPTION: two contributors' emails were passed as middle names; now email =.
- Tests: region outlines partition the window and contain their cells; clipped hatching stays inside; outlines are
  cached and the plot draws.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
Package: lisaClust
Commit: 1190d9d0816cbe9a4b225e49ceb29ddfc08fe716
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-09 16:07:37 +1100
Commit message:

 Remove a stray Rplots.pdf left by the tests; ignore it

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
Package: lisaClust
Commit: 83ee1a28d119a3f68efb8b6aa581725ebd3cbc2b
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-09 16:07:14 +1100
Commit message:

 1.21.2: a cell counts itself (as in Patrick et al. 2023); hatching crossings fixed; hatching cache

- The C++ core gains includeSelf (on in R): each cell is its own neighbour at distance 0, as the paper defines the
  LISA; spatstat's closepairs() had left it out. Regions on the regression example (Keren images 5 and 6, k = 5)
  agree for 96% of cells; inst/testdata/original_result.rda regenerated. Tests check the core against the plain-R
  reference with and without self.
- Hatching: crossings of a hatching line with a region's outline use a half-open rule, so every outline is crossed
  an even number of times. Before, a line through or touching an outline vertex (common on the grid outlines)
  could give an odd count after de-duplication; the pairing went out of step and later segments ran across
  neighbouring regions, with "data length is not a multiple of split variable" warnings.
- geom_hatching() caches the grobs of the last 20 panels by a hash of their inputs: a reprint (e.g. a resized
  window) takes about 0.7-1 s instead of 2-9 s.
- Vignette: the definition says a cell counts itself; the niche comparison reports both smallest adjusted
  p-values and words the core-level result conditionally.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
Package: lisaClust
Commit: 7a24d69294f823fb4d3ab2f8c0887aaf99230046
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-09 15:00:48 +1100
Commit message:

 1.21.1: C++ core for the LISA (8-18x faster), faster hatchingPlot, region alignment fixes, new vignette

- src/core (plain C++17, shared with the Python package lisaclust): the neighbour counts of inhomLocalK()
  by a grid search, replacing spatstat closepairs() + cut() + dplyr + data.table, and the disc-window areas of
  the edge correction (spicyR's code). On 6 Keren images the LISA match the previous version to 1.2e-6 (to
  2.5e-14 with the old spatstat edge areas swapped in; the rest is polyclip's integer rounding), and k-means
  regions are identical at k = 3, 5, 8 and 12. lisa() on all of Keren 2018 (198k cells) takes 5 s.
- hatchingPlot(): the hatching lines are intersected with the region outlines vectorised (base::det()
  reproduced bit for bit, plots identical), and grid points take the region of the nearest cell from a C++
  grid search instead of class::knn(), whose random tie-breaking made plots depend on the seed. About 10x faster.
- Fixes: lisaClust() put regions on the wrong cells when images were interleaved (367 of 600 cells in a test);
  hatchingPlot() attached the region column by position likewise; lisaClust() failed on a SpatialExperiment
  without x/y in colData; regionMap() failed with an unused cell-type level.
- No longer depends on spicyR internals, simpleSeg, class, data.table or tidyr. Examples use simulated data
  (the islet file they read was removed from spicyR, which broke R CMD check on Bioconductor).
- Vignette: tissue domains in Keren 2018 and cellular niches in Schurch 2020 compared between CLR and DII
  patients with patients as the units; numbers are computed inline. Cites Patrick et al. 2023 (inst/CITATION).
- tests/testthat/test-core.R: the core against plain-R references, spatstat's disc areas, brute-force nearest
  labels, the old scalar line intersection, and region alignment.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
Package: lisaClust
Commit: cbb73d4fcf164e3fd2ef218287bf3bad719170eb
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-09 13:50:22 +1100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: lisaClust
Commit: c1cdc01944eece6d3e9ef474a6fae6288c86f334
Author: Farhan Ameen <fame2827@uni.sydney.edu.au>
Date: 2026-04-15 16:39:32 +1000
Commit message:

 stops lisaClust from subsetting original SCE colData
Package: lisaClust
Commit: a28ddc0d85dd3876936c9bd1188bc8ff026972b8
Author: Farhan Ameen <fame2827@uni.sydney.edu.au>
Date: 2026-02-17 16:15:22 +1100
Commit message:

 updates to fix persistent left join issue
Package: lisaClust
Commit: 01e9fc41188d6af47f997c2db85c96999674b0aa
Author: Shreya Rao <shreya.rao@wimr.org.au>
Date: 2025-06-12 15:36:55 +1000
Commit message:

 fix left join error
Package: lisaClust
Commit: 45e42cb064330cd0ccc7ca74c6f339270ddfd374
Author: Shreya Rao <shreya.rao@wimr.org.au>
Date: 2025-06-11 13:11:14 +1000
Commit message:

 fix parallelisation
Package: lisaClust
Commit: 5586a04623b2938b3af70e4cef75634061c90e46
Author: Shreya Rao <shreya.rao@wimr.org.au>
Date: 2025-03-05 09:10:40 +1100
Commit message:

 changed message
Package: lisaClust
Commit: 36629d3dc6cf64a88ecd98d3b52c7e5fe5a1a124
Author: Shreya Rao <shreya.rao@wimr.org.au>
Date: 2024-11-22 11:29:32 +1100
Commit message:

 deprecated Rs
Package: spicyR
Commit: c82df33df742456667ba8b2b59c90d40d33bb933
Author: EllisPatrick <ellis.patrick@sydney.edu.au>
Date: 2026-10-09 14:25:32 +1100
Commit message:

 1.99.9: vignette numbers computed from the results, with build-time checks of the statements about them

The text quoted numbers from before labelClustering = FALSE became the default. They are now inline R, and
hidden stopifnot() chunks check the statements that cannot be inline (which pairs lead, the direction of
effects, which tests are significant), so the vignette fails to build rather than misdescribe its output. The
shuffled-label check uses 10 shuffles (50 shuffles: 5.8% of pairs at p < 0.05 with psi off, 5.8% with it on).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
Package: SpliceImpactR
Commit: 52d46a9141e78a28f9aede26fe14eea5ba2f42ff
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-10-08 22:19:03 -0400
Commit message:

 Merge branch 'main' into devel
Package: SpliceImpactR
Commit: 9e4a46c020843d10134fe7e9470a0fe354d66d53
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-10-08 22:18:40 -0400
Commit message:

 Query Ensembl BioMart through e.ensembl.org hosts (1.1.4)

biomaRt before 2.70 downloads Ensembl's list of archives before it
connects to any *.archive.ensembl.org host. That list is no longer
available, so new installations failed with "Unable to contact any
Ensembl mirror" even though the archives answer. Each release is now
queried at https://e.ensembl.org, which Ensembl forwards to the
same archive, so data and cached features are unchanged. Release 116
works with any biomaRt version; an archive host passed as ensembl_host
on older biomaRt gets an error that suggests the e address.
 </pre>
    </div>
  
    

      Package: spicyR

      Commit: 1b069a4b27884e708f84f3dd6ea7b1c73b5b8b51

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-09 12:57:18 +1100

      Commit message:


	  
		
 1.99.8: spicy(labelClustering = FALSE) is the default

The label-clustering inflation (psi) is off unless asked for. The abundance test asks for it explicitly, as its
reference rows use it.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: 65593942bebf2a1a70dadc0b059d1217b931647b

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-09 12:30:00 +1100

      Commit message:


	  
		
 README: version 1.99.7

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: spicyR

      Commit: 6a2b86ae542d2e09f008de283347f62ca3f37fe8

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-09 12:28:56 +1100

      Commit message:


	  
		
 1.99.7: spicy(variance = "cr2") is the default again; "auto" stays as an option

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
 

    

  
    

      Package: knowYourCG

      Commit: b4f262622edc2ed4a97a507fce27f7a7e3f3a1e3

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-08 19:07:45 -0400

      Commit message:


	  
		
 version: 1.9.4
 

    

  
    

      Package: knowYourCG

      Commit: 1278f51d03c022b4c7899e623d228cf423f021a4

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-08 13:01:50 -0400

      Commit message:


	  
		
 Coverage badge: scripts/coverage.R writes coverage.json (R/ lines), CI checks it
 

    

  
    

      Package: knowYourCG

      Commit: 659c31f3ad5b1b72a5655305ba15c60b82a310e7

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-08 12:51:28 -0400

      Commit message:


	  
		
 tests: unskip bedToCg end to end, require finite testEnrichment2 estimates and no plot warnings
 

    

  
    

      Package: knowYourCG

      Commit: d781c925abbaeb06eb319ee4e7ba054d2204fb9f

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-08 12:49:36 -0400

      Commit message:


	  
		
 Fix bedToCg's unquoted sh -c pipeline and integer overflow in the odds ratio; linewidth in KYCG_plotEnrichAll
 

    

  
    

      Package: knowYourCG

      Commit: 4c9e0ba44610ce68acda94445c4c0de76e91841a

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-08 12:48:22 -0400

      Commit message:


	  
		
 tests: cover loadDBs, annoProbes, dbStats, testEnrichment2, testProbeProximity, the aggregate plots and the ExperimentHub helpers
 

    

  
    

      Package: knowYourCG

      Commit: 71ef2293669bf1ce6c30ca83ea11d8e3f35cf88d

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-08 12:29:14 -0400

      Commit message:


	  
		
 tests: offline testthat coverage for testEnrichmentSEA (#6) and the pure-R statistics and plots
 

    

  
    

      Package: SpliceImpactR

      Commit: 412ee37c6a18976c38eb7cba3bf68d73a152a44b

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2026-10-08 18:47:45 -0400

      Commit message:


	  
		
 Merge branch 'main' into devel

Version 1.1.3. GitHub main re-created the 1.1.1 and 1.1.2 commits, so this merge also brings in their new copies; the merged tree is main's.
 

    

  
    

      Package: SpliceImpactR

      Commit: a4043779cf85493039021e4b16b82010fffed27a

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2026-10-08 18:47:03 -0400

      Commit message:


	  
		
 Query Ensembl BioMart archives by explicit host; default release 111 (1.1.3)

- Ensembl 116 (June 2026) is the last release with BioMart, and
  www.ensembl.org no longer serves it. get_protein_features() connects to
  each release's archive host from a built-in table (105-116) instead of
  having biomaRt look the archive up.
- The default release is 111 (was 109), the Ensembl release of the
  default GENCODE v45 annotation.
- New ensembl_host argument selects another BioMart host. ensembl_mirror
  is deprecated and ignored: Ensembl retired its mirrors.
- Release 116 needs biomaRt 2.70 or later; connection errors name the
  host.
- README, vignette and NEWS updated; version 1.1.3.
 

    

  
    

      Package: SpliceImpactR

      Commit: c17c998a3be81798141d2fd88ee470d3230e918c

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2026-10-08 02:30:34 -0400

      Commit message:


	  
		
 Make the ORF matcher the default; S4 output for get_ranked_pairs (1.1.2)

- get_splicing_impact() selects transcript pairs with the ORF-aware
  matcher by default (matching = c("orf", "legacy")). Selected
  transcripts and pair counts change; matching is slower.
- get_ranked_pairs(return_class = "S4") stores the pairs, form rows and
  diagnostics in a SpliceImpactResult where the wrapper stores them, so
  the stepwise S4 workflow uses the ORF matcher. The default still
  returns the list. get_pairs() S4 output records matching = "legacy"
  and drops earlier ORF diagnostics.
- README and vignettes describe the ORF matcher as the default, including
  the S4 workflow; the README also covers coordinates, the enrichment
  population, gene universes, output columns and input requirements.
- Version 1.1.2 with NEWS.
 

    

  
    

      Package: SpliceImpactR

      Commit: 133b5b8d39128c33416bc960616a08ee6c6bedca

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2026-10-08 01:02:05 -0400

      Commit message:


	  
		
 Bump version to 1.1.1 and add NEWS
 

    

  
    

      Package: SpliceImpactR

      Commit: 2ec681002a24c0f046ef335e6faf57acb77ae93d

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2026-10-08 01:02:00 -0400

      Commit message:


	  
		
 Correctness review: coordinates, pairing, matching, enrichment, docs

Review and fixes across the analysis pipeline:
- rMATS coordinates are one-based, closed; A3SS/A5SS forms include the
  partner exon; post-DI import numbers events across files and takes
  case_group.
- Pairing rewritten: positive delta PSI is the case, paired mode no
  longer crashes, and unmatched forms are excluded.
- Legacy matcher ranks structural fit before coding status; new opt-in
  ORF-aware matcher get_ranked_pairs() (matching = "orf") with a
  protocol vignette.
- PPI endpoint attribution, domain-enrichment population and odds ratio,
  and an annotated background by default.
- NMD summary class, multi-site labels, empty-result handling, content
  cache keys and bounded BioMart batches.
- User-table importers validate event IDs and forms; manual features
  can be placed by peptide ID and unplaced rows are reported.
- Documentation, runnable examples, regression tests; removed dead code.
- Depends on R (>= 4.5.0); imports R.utils for .gz input.

NEWS.md (1.1.1) lists the changes, including breaking ones.
 

    

  
    

      Package: OmicsMLRepoR

      Commit: 3b4a12b5d442dd913fb96f43936bc40650a57701

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-10-08 16:59:19 -0400

      Commit message:


	  
		
 retry transient OLS failures to stabilize the vignette build

The build failed with "HTTP 500 Internal Server Error" while knitting
Quickstart.Rmd. tree_filter() issues one live OLS query per search term
(~14 across the vignette), so a single transient 5xx from the service
fails the whole build.

  o getOntoInfo() retries requests that fail for a transient reason -
    HTTP 5xx, dropped connections, timeouts - with an exponential
    backoff (new `retries` argument). Client errors still fail fast.
  o Quickstart.Rmd probes OLS once and skips the OLS-dependent chunks
    when the service is unreachable, so an outage no longer fails the
    build. The remaining chunks still render.
  o test-tree_filter.R skips, rather than fails, the OLS-dependent
    tests when the service is unavailable.
  o version bump

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: CNVRanger

      Commit: 2eec083295b3a79c29fe87cc365cf092c0175c9a

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

      Date: 2026-10-08 16:53:34 -0400

      Commit message:


	  
		
 cnvOncoPrint: several improvements
 

    

  
    

      Package: MSstatsResponse

      Commit: 56e4f1edfa8c3f09063df2b9f0e3351eafeb17f3

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-10-08 13:33:09 -0400

      Commit message:


	  
		
 Bump version from 1.3.4 to 1.3.5
 

    

  
    

      Package: MSstatsResponse

      Commit: a4782f687fa5d944e85055bbb596158247a35ad9

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-10-08 13:23:05 -0400

      Commit message:


	  
		
 fix(calculateQCScore, calculateTurnoverRatios): filter NA/non-finite rows internally
 

    

  
    

      Package: MSstatsResponse

      Commit: 82200cc9ff5323576f65845fbec7ccbfb6217df7

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2026-10-06 11:30:09 -0400

      Commit message:


	  
		
 feat(calculatePeptideWeights)!: replace binomial-CDF coverage with relative detection score
 

    

  
    

      Package: knowYourCG

      Commit: 04e4a21f3aec18e710445ac95ebfdddb00235026

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-08 11:25:06 -0400

      Commit message:


	  
		
 testEnrichmentSEA: flip the sign of estimate to match GSEA (positive = enriched at large values)
 

    

  
    

      Package: knowYourCG

      Commit: f5c2dda6e74109daf857f8a9a993ac442d440946

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-08 11:17:29 -0400

      Commit message:


	  
		
 testEnrichmentSEA: pool the two tails into one permutation null, document the sign of estimate (#6)
 

    

  
    

      Package: gDRcore

      Commit: 04cc3e026e2eaa0b284b7bdabc2528bb7a6be6c7

      Author:  j-smola <31825957+j-smola@users.noreply.github.com> 

      Date: 2026-10-08 16:24:55 +0200

      Commit message:


	  
		
 Merge pull request #211 from gdrplatform/GDR-3674

Update authors data 

    

  
    

      Package: gDRcore

      Commit: d99c14901281da631acbbc5c388b1597db547e51

      Author:  Janina Smola <janina.smola@external.roche.com> 

      Date: 2026-10-08 14:17:19 +0200

      Commit message:


	  
		
 chore: leftovers
 

    

  
    

      Package: gDRcore

      Commit: 773c9af17b7f19bc3b705fb95a1e2d7979bd1c14

      Author:  Janina Smola <janina.smola@external.roche.com> 

      Date: 2026-10-08 14:17:08 +0200

      Commit message:


	  
		
 chore: update authors data
 

    

  
    

      Package: JASPAR

      Commit: 891824d793854742c82ace3871f793b85e698997

      Author:  Damir <dbaranasic1@gmail.com> 

      Date: 2026-10-04 07:41:53 +0200

      Commit message:


	  
		
 Retrieve JASPAR databases through AnnotationHub

JASPAR() now gets the SQLite file from AnnotationHub instead of downloading
SourceUrl with BiocFileCache. The record is selected by version from the hub
metadata (data class "JASPAR" or a release title such as "JASPAR2024"), so no
accession is hard-coded and a release that is added to the hub, or whose record
is corrected, such as JASPAR2026, works without a package change. A failed
download stops with an error that names the version, the accession and the
reason. A cached file that is not an SQLite database, or is cut short, is
downloaded once more.

- the default version of JASPAR() changes from JASPAR2026 to JASPAR2024, as in
  the help pages, the examples and the initialize method
- getAvailableJASPARVersions() lists the versions in the hub (argument
  'package' replaced by 'hub'); JASPAR() gets a 'hub' argument; a hub made with
  localHub = TRUE works offline and says which versions it lacks
- a failed connection to AnnotationHub says how to work offline
- add a show() method for JASPAR objects (BiocCheck warning)
- rewrite the vignette around the AnnotationHub workflow; examples, vignette and
  tests use JASPAR2024 and JASPAR2022 only
- add unit tests (offline helpers, and the hub when it can be reached)
- import AnnotationHub instead of depending on BiocFileCache
- Version: 0.99.5

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: gDRutils

      Commit: 41b593c0fb08c105e992b940cfebefa73283ad66

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

      Date: 2026-10-08 10:46:03 +0200

      Commit message:


	  
		
 Merge pull request #203 from gdrplatform/GDR-3676

fix: cap the number of parallel workers in loop() 

    

  
    

      Package: gDRutils

      Commit: 72007812548498b1530860d111d8d2cbe09914de

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-10-08 09:06:46 +0200

      Commit message:


	  
		
 chore: use an accepted imperative verb in the changelog entries
 

    

  
    

      Package: gDRutils

      Commit: 9a93ab53b163c462c525d5c252e7a839a2d411d0

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-10-08 09:05:02 +0200

      Commit message:


	  
		
 fix: cap the number of parallel workers in loop()
 

    

  
    

      Package: xcms

      Commit: b781f8b0c39a3310d74aebe5ae59d24f7e818431

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

      Date: 2026-10-08 10:06:49 +0200

      Commit message:


	  
		
 Merge pull request #850 from sneumann/jomain

refactor: ensure beta quality metrics are calculated the same way 

    

  
    

      Package: xcms

      Commit: 7f91fa4bbd44fd5dc8cb7b78a79da89408132a02

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

      Date: 2026-10-06 10:22:27 +0200

      Commit message:


	  
		
 Remove RColorBrewer from Suggests
 

    

  
    

      Package: xcms

      Commit: 7393d36566e013a51ebd34f79e750a994eda4dc4

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

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

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: xcms

      Commit: 1d2a59013f58d7a7970f1d65c8634af0f592a72b

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

      Date: 2026-10-06 10:16:00 +0200

      Commit message:


	  
		
 Merge branch 'devel' into jomain
 

    

  
    

      Package: xcms

      Commit: 1280366d8db541f8352254d91a20a41df34f1ddf

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

      Date: 2026-09-25 09:28:43 +0200

      Commit message:


	  
		
 fix: loadXcmsData to correctly update all paths

- `loadXcmsData()` to update also the `dataOrigin` issue #851
 

    

  
    

      Package: xcms

      Commit: 01bec85eef4dc0b57c7a34024c34d6ca891d6f68

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

      Date: 2026-09-21 10:29:04 +0200

      Commit message:


	  
		
 refactor: ensure beta quality metrics are calculated the same way

- Use the actual retention times instead of just the scan indices for the
  calculation of the beta chromatographic peak quality metrics also when
  calculated during chromatographic peak detection. This addresses issue #849.
 

    

  
    

      Package: SpliceImpactR

      Commit: 344370aff6cb3828f4de8667e850f59379e61742

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2026-10-08 02:31:01 -0400

      Commit message:


	  
		
 Merge branch 'main' into devel

Version 1.1.2.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: SpliceImpactR

      Commit: 673193c14983b5c1de6bfaf04699e30a85297e64

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2026-10-08 02:30:34 -0400

      Commit message:


	  
		
 Make the ORF matcher the default; S4 output for get_ranked_pairs (1.1.2)

- get_splicing_impact() selects transcript pairs with the ORF-aware
  matcher by default (matching = c("orf", "legacy")). Selected
  transcripts and pair counts change; matching is slower.
- get_ranked_pairs(return_class = "S4") stores the pairs, form rows and
  diagnostics in a SpliceImpactResult where the wrapper stores them, so
  the stepwise S4 workflow uses the ORF matcher. The default still
  returns the list. get_pairs() S4 output records matching = "legacy"
  and drops earlier ORF diagnostics.
- README and vignettes describe the ORF matcher as the default, including
  the S4 workflow; the README also covers coordinates, the enrichment
  population, gene universes, output columns and input requirements.
- Version 1.1.2 with NEWS.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: SpliceImpactR

      Commit: 0182eacd7c09c3136a3d9e801f5965e85ca3a4ad

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2026-10-08 01:02:49 -0400

      Commit message:


	  
		
 Merge branch 'main' into devel

Version 1.1.1 (Bioconductor devel was at 1.1.0).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: SpliceImpactR

      Commit: 28bed65986dcaf9b3fd92633c357a9519aefc5eb

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2026-10-08 01:02:05 -0400

      Commit message:


	  
		
 Bump version to 1.1.1 and add NEWS

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: SpliceImpactR

      Commit: 7cd52e81888abb53eb2634656ab5c9808ffa6df4

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2026-10-08 01:02:00 -0400

      Commit message:


	  
		
 Correctness review: coordinates, pairing, matching, enrichment, docs

Review and fixes across the analysis pipeline:
- rMATS coordinates are one-based, closed; A3SS/A5SS forms include the
  partner exon; post-DI import numbers events across files and takes
  case_group.
- Pairing rewritten: positive delta PSI is the case, paired mode no
  longer crashes, and unmatched forms are excluded.
- Legacy matcher ranks structural fit before coding status; new opt-in
  ORF-aware matcher get_ranked_pairs() (matching = "orf") with a
  protocol vignette.
- PPI endpoint attribution, domain-enrichment population and odds ratio,
  and an annotated background by default.
- NMD summary class, multi-site labels, empty-result handling, content
  cache keys and bounded BioMart batches.
- User-table importers validate event IDs and forms; manual features
  can be placed by peptide ID and unplaced rows are reported.
- Documentation, runnable examples, regression tests; removed dead code.
- Depends on R (>= 4.5.0); imports R.utils for .gz input.

NEWS.md (1.1.1) lists the changes, including breaking ones.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: multistateQTL

      Commit: f7723a0d49871a88445ead6304881a7b886fec38

      Author:  dunstone-a <amelia.dunstone@gmail.com> 

      Date: 2026-10-08 14:44:10 +1100

      Commit message:


	  
		
 Remove error with tests
- Remove error with replaceNAs test
- Update some indentation
- Update build ignore
 

    

  
    

      Package: multistateQTL

      Commit: cd6158093a0ab8a6288dfa227df754013a67ae48

      Author:  dunstone-a <amelia.dunstone@gmail.com> 

      Date: 2026-05-06 16:09:57 +1000

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/dunstone-a/multistateQTL into devel
 

    

  
    

      Package: multistateQTL

      Commit: 12adf14779e4cc4395023b6c4f3e12914e2f53ce

      Author:  Millie <53158915+dunstone-a@users.noreply.github.com> 

      Date: 2026-05-06 15:38:51 +1000

      Commit message:


	  
		
 Merge pull request #4 from dunstone-a/RELEASE_3_23

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

    

  
    

      Package: extraChIPs

      Commit: e1e9078512088dabe9bd10bcbbb3002be6bfe425

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-10-08 12:19:21 +1030

      Commit message:


	  
		
 Version bump after restructure
 

    

  
    

      Package: extraChIPs

      Commit: b4d76fcfe2c04d5f45a18db9e5fdbccd0246abbe

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2026-10-08 12:18:57 +1030

      Commit message:


	  
		
 Shifted vignette figures
 

    

  
    

      Package: scMerge

      Commit: 3ece494605942c319e688226cdaa370e33a15109

      Author:  Dario Strbenac <dario@maths.usyd.edu.au> 

      Date: 2026-10-08 13:16:22 +1100

      Commit message:


	  
		
 Changes for DelayedArray dependency.
 

    

  
    

      Package: scMerge

      Commit: 2eaa764892142da4f0ee0bdf482b7964fe6a7a1f

      Author:  Dario Strbenac <dario@maths.usyd.edu.au> 

      Date: 2026-10-07 12:15:20 +1100

      Commit message:


	  
		
 Increase package version and remove outdated dependency version requirements.
 

    

  
    

      Package: scMerge

      Commit: a03ae0bf313390e121b33c4cb2ca2d2984edc869

      Author:  Dario Strbenac <dario.strbenac@sydney.edu.au> 

      Date: 2026-10-07 12:10:20 +1100

      Commit message:


	  
		
 Merge pull request #44 from joshua-d-campbell/fix-delayedarray-cbind

Use BiocGenerics::cbind/rbind instead of DelayedArray:: (fixes #43) 

    

  
    

      Package: scMerge

      Commit: b286b00eac0cb174892a58e3d8b201dc775cd15e

      Author:  Joshua D. Campbell <joshua.d.campbell@gmail.com> 

      Date: 2026-10-06 20:24:44 -0400

      Commit message:


	  
		
 Use BiocGenerics::cbind/rbind instead of DelayedArray::

DelayedArray 0.39.7 (Bioc 3.24) no longer exports cbind/rbind, so
DelayedArray::cbind fails with "'cbind' is not an exported object from
'namespace:DelayedArray'". Call the BiocGenerics generics directly; they
dispatch to DelayedArray methods on Bioc 3.23 and S4Arrays methods on 3.24.

Fixes #43

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: BiocSingular

      Commit: e9c9f7b8acb5d8bde1961a2cfca7eb4434cddbf7

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-08 12:46:03 +1100

      Commit message:


	  
		
 Updated extra.work to be consistent with irlba's new defaults.
 

    

  
    

      Package: assorthead

      Commit: 8712ebd493cef14227dd4d48c99126aef61b09eb

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-08 11:19:34 +1100

      Commit message:


	  
		
 Updated vendored versions of all libraries.
 

    

  
    

      Package: DuckDBArray

      Commit: 5ffeec68b8c616c9f4c82c3d22b782b763bc69f7

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-10-07 17:10:10 -0700

      Commit message:


	  
		
 fix: realize non-scalar Ops operands against a DuckDBArray (0.99.11)

Ops(DuckDBArray, atomic)/Ops(atomic, DuckDBArray) only ever supported a
length-1 atomic operand; anything longer fell through to Ops(DuckDBTable,
atomic)'s scalar-only check and errored with "can only perform binary
operations with a scalar value". This was latent but harmless as long as
every caller realized a %*%/crossprod result (itself a lazy DuckDBMatrix
by design, see 0.99.9) before combining it with a plain vector.

CRAN's irlba 2.4.1 (2026-10-05) rewrote its Lanczos loop and dropped the
drop() call that used to wrap mult()'s result before the F <- F - sub
centering step. For ordinary dense/sparse matrices this is invisible,
since %*% already returns a realized object, but it left F as a lazy
DuckDBMatrix for DuckDBMatrix input, so centered SVDs
(BiocSingular::runSVD(center = TRUE), scran::fixedPCA(), scater::runPCA())
started failing. Found via BiocDuckDB's DuckDBIrlbaParam/SVD composition
tests immediately after the 2.4.1 release.

Fixed by having these two Ops methods realize e1/e2 via as.array() and
hand off to base R whenever the atomic operand isn't a true scalar, since
elementwise arithmetic between two plain vectors is never something base
R itself defers.

Full DuckDBArray test suite: 0 failures. Full BiocDuckDB test suite: 0
failures (previously 9 failures in test-DuckDBIrlbaParam.R and
test-DuckDBMatrix-svd.R).
 

    

  
    

      Package: HiContacts

      Commit: dfb588e11e0a76e3f68ba0ed2fca7633848c8d0d

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-06 11:44:17 +0200

      Commit message:


	  
		
 fix: use Rfast, a suggested package, only when it can be loaded (#20)

* fix: use Rfast, a suggested package, only when it can be loaded

boost() printed a message when Rfast was missing or could not be loaded,
then failed in Rfast::floyd(); it now stops with that message. Its
example and test run only when Rfast loads: on the Bioconductor devel
image, Rfast's binary fails to load (undefined symbol _ZTIN3tbb4taskE),
which failed R CMD check in the examples and the tests.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* bump to 1.15.3

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

--------- 

    

  
    

      Package: MSstatsBioNet

      Commit: e623f719bfaa63898878cc2563c348c4e24826e1

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-07 14:49:41 -0400

      Commit message:


	  
		
 docs: Update README to be agnostic to molecule type (#129) 

    

  
    

      Package: MSstatsBioNet

      Commit: d09404a728aa4a62305b83f3d784b20a21d342e1

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-07 14:27:32 -0400

      Commit message:


	  
		
 docs: Add a metabolomics vignette using generic network functions (#128) 

    

  
    

      Package: rigvf

      Commit: 239e78fc63603277fee3b30f58f02a0e57304490

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2026-10-07 13:14:13 -0400

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: MACSr

      Commit: d9f268b2da825a09521a707b5c000bfd9c474ffd

      Author:  qhu <huqmail@gmail.com> 

      Date: 2026-10-07 12:06:55 -0400

      Commit message:


	  
		
 Use bundled data in examples and tests, version bump 1.21.3

R CMD check on nebbiolo2 failed in examples and tests with
'IndexError: list index out of range'. The cached ExperimentHub copy
of EH4558 on that builder is not a valid BED file. Examples and tests
now read the SE BED and BEDPE files from inst/extdata. Tests still use
ExperimentHub for the BAM files, which are not bundled.
 

    

  
    

      Package: MSstatsBioNet

      Commit: 2912f1c0b45351c0c74a447f42f5a1dfbf4aad99

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-07 12:22:57 -0400

      Commit message:


	  
		
 Bump version from 1.5.3 to 1.5.4 

    

  
    

      Package: MSstatsBioNet

      Commit: 5a728007966458e0416b48bde52e13f0992c89a2

      Author:  Tony Wu <wu.anthon@northeastern.edu> 

      Date: 2026-10-07 11:18:15 -0400

      Commit message:


	  
		
 Gave each input row its own node when rows share a grounding (#126)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MSstatsBioNet

      Commit: f968e61c00a036d06cb8d8855614a4ae2c2cbb61

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-07 09:39:19 -0400

      Commit message:


	  
		
 Added get_curations() and filter_by_curation() (#125)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> 

    

  
    

      Package: QFeaturesGUI

      Commit: b9fbdd0edebdc917e9e57b0c64160847408dbe52

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-10-07 14:54:29 +0200

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: QFeaturesGUI

      Commit: 4d243937e6b2dcb9730631a089270552d7d7c644

      Author:  Léopold Guyot <leopold.guyot13@gmail.com> 

      Date: 2026-10-07 14:49:05 +0200

      Commit message:


	  
		
 Merge pull request #114 from rformassspectrometry/feat/visualizeQFeatures

New `visualizeQFeatures` function 

    

  
    

      Package: QFeaturesGUI

      Commit: 0834bd41d7ddb5c476e27bbcefe19d7664940a4f

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-10-07 11:25:36 +0200

      Commit message:


	  
		
 update licensing
 

    

  
    

      Package: QFeaturesGUI

      Commit: 2af5504a87d077922ed45aa8959bf622859ed83b

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-10-06 16:08:30 +0200

      Commit message:


	  
		
 add example for deprecated functions
 

    

  
    

      Package: QFeaturesGUI

      Commit: 07de9a58cfd85cd6244c094fbd9d9551ea705ef5

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-10-05 16:45:31 +0200

      Commit message:


	  
		
 rename functions
 

    

  
    

      Package: QFeaturesGUI

      Commit: cbb4510704d4a2248b2154e59c31d863fb7d1beb

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-10-05 16:00:14 +0200

      Commit message:


	  
		
 update modality plot theming
 

    

  
    

      Package: QFeaturesGUI

      Commit: 84b932c2aa4bf2fb56188c4e4b773cda23d58828

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-10-01 15:29:50 +0200

      Commit message:


	  
		
 keep selected sets when qfeatures update
 

    

  
    

      Package: QFeaturesGUI

      Commit: c27a68e5de774374c0f0e347f01d4026ec7f3367

      Author:  Léopold Guyot <leopold.guyot13@gmail.com> 

      Date: 2026-10-01 14:27:12 +0200

      Commit message:


	  
		
 Merge pull request #115 from Bisaloo/bioc-review-2

Remove unnecessary paste calls or args 

    

  
    

      Package: QFeaturesGUI

      Commit: 2b586385f011278f6aa9d1acc9a99d788a977831

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-30 14:46:46 +0200

      Commit message:


	  
		
 add empty features safeguard
 

    

  
    

      Package: QFeaturesGUI

      Commit: 2ef62d08880a76593529ae5b295645c54cdf2f74

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-30 11:41:59 +0200

      Commit message:


	  
		
 import css + reactive updates
 

    

  
    

      Package: QFeaturesGUI

      Commit: 9c8c4e70a8ae219a656d92f3a37a70a19d312390

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-29 15:07:48 +0200

      Commit message:


	  
		
 Fix tests for new demo
 

    

  
    

      Package: QFeaturesGUI

      Commit: 5555d1bf6573fcd3c42bc966652ce5d5e8b54752

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-28 16:54:35 +0200

      Commit message:


	  
		
 add preprocessed demo QFeatures for visualizeQFeatures
 

    

  
    

      Package: QFeaturesGUI

      Commit: 5f963e6e25b1c4f419bf045bb2c6f94660bcaf68

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-28 16:00:49 +0200

      Commit message:


	  
		
 add grouping by annotation for modality plot
 

    

  
    

      Package: QFeaturesGUI

      Commit: f5fd1883c71f61c25d7c01da8cabbf5c56674775

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-25 14:09:54 +0200

      Commit message:


	  
		
 refactor modal qfeatures loader
 

    

  
    

      Package: QFeaturesGUI

      Commit: 0954a3eefed8cf6cd4615947d6dab3fda72f23e6

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-25 10:52:16 +0200

      Commit message:


	  
		
 add modality plot to summary module
 

    

  
    

      Package: QFeaturesGUI

      Commit: 9dda33cb3ffc5c7a5e12d6295c8bc9368483a8db

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-14 16:59:26 +0200

      Commit message:


	  
		
 refactor summary module
 

    

  
    

      Package: QFeaturesGUI

      Commit: f8c6cbccd71d7b94e0943012ed58c71d8d3bf8f2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-14 16:21:12 +0200

      Commit message:


	  
		
 Remove unnecessary sep = " " arg in paste()
 

    

  
    

      Package: QFeaturesGUI

      Commit: 555e10362321e37da17907d8da65d4736e7278b1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-14 16:20:59 +0200

      Commit message:


	  
		
 Remove unnecessary paste0() call
 

    

  
    

      Package: QFeaturesGUI

      Commit: aa90d18bcb633c1669d02db11694996b38e17f05

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-14 11:03:46 +0200

      Commit message:


	  
		
 refactor pca box
 

    

  
    

      Package: QFeaturesGUI

      Commit: ba79f176bb379e4e80fb1b14d11ca06aea96b843

      Author:  leopoldguyot <leopold.guyot13@gmail.com> 

      Date: 2026-09-07 15:04:17 +0200

      Commit message:


	  
		
 adding DR to processQFeatures summary tab
 

    

  
    

      Package: imcRtools

      Commit: 6aed47b6d22cc517e9421576842086bd2ec42b35

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-10-06 13:55:37 +0200

      Commit message:


	  
		
 Merge pull request #149 from BodenmillerGroup/fix-rd-devel

Fix rd devel 

    

  
    

      Package: imcRtools

      Commit: 79fbbd9faa48c6258ef5ac5396919ad3ce6507de

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-10-06 09:07:57 +0000

      Commit message:


	  
		
 reverted suspected changes and added fix to .steinbock_add_image_metadata function
 

    

  
    

      Package: imcRtools

      Commit: 8946f77705644368f5804e40adb6256c54cb23df

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-10-05 14:32:01 +0000

      Commit message:


	  
		
 fixed more as.directed and centroid unification problem
 

    

  
    

      Package: imcRtools

      Commit: 66b1499d3ca255cbbf80032467bc426dd7ded942

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-10-05 13:18:28 +0000

      Commit message:


	  
		
 updated as_directed, as_undirected and layout_with_sugiyama functions
 

    

  
    

      Package: imcRtools

      Commit: b101dae4a1facb8c8e1f42e149defe59030b38b4

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-10-05 13:13:41 +0000

      Commit message:


	  
		
 roxygenized
 

    

  
    

      Package: imcRtools

      Commit: 293510db7bc24c5b94d987fc924b4a43b343aef3

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-10-05 12:21:12 +0000

      Commit message:


	  
		
 unified centroid-1/-0 export
 

    

  
    

      Package: imcRtools

      Commit: 3eb9354ae17113c5970b015cb9bdb394c5e8b449

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-10-05 10:24:30 +0000

      Commit message:


	  
		
 Version 1.19.2
 

    

  
    

      Package: imcRtools

      Commit: b73cdd5e74ae37c7b20e5f369962a838ed10fc43

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-10-05 10:23:46 +0000

      Commit message:


	  
		
 adapted steinbock test to centroid-1 and centroid-0
 

    

  
    

      Package: imcRtools

      Commit: 79bd684e02ef998c3554d9dc0e248cf0f84137f1

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-10-05 10:22:17 +0000

      Commit message:


	  
		
 Fix R CMD check notes. NAMESPAE reformatting due to new roxygen2 version
 

    

  
    

      Package: DESpace

      Commit: 7d55e04173ea7cfb71200b80f26c1acce4c35ff8

      Author:  Peiying Cai <55488976+peicai@users.noreply.github.com> 

      Date: 2026-10-07 13:23:19 +0200

      Commit message:


	  
		
 Merge pull request #11 from peicai/update-citation

Update citation: DESpace2 published in Bioinformatics 

    

  
    

      Package: DESpace

      Commit: 0e8802b8a600f377aae0123bbd77d5d84e623df5

      Author:  peicai <peiying.cai@gmail.com> 

      Date: 2026-10-07 13:19:52 +0200

      Commit message:


	  
		
 Update citation
 

    

  
    

      Package: DESpace

      Commit: 9ef32538ce687a95fe4bab979cd5d5672ccb2d38

      Author:  peicai <peiying.cai@gmail.com> 

      Date: 2026-10-07 11:34:46 +0200

      Commit message:


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

    

  
    

      Package: DESpace

      Commit: 3a0052ff25abd8d54f138353fb7ec016b6462ec6

      Author:  peicai <55488976+peicai@users.noreply.github.com> 

      Date: 2025-11-28 14:44:14 +0100

      Commit message:


	  
		
 Merge pull request #9 from peicai/devel

Add QLF tests 

    

  
    

      Package: DESpace

      Commit: ca1d407b81728a0903f7724ba46cf039b1b74d68

      Author:  peicai <55488976+peicai@users.noreply.github.com> 

      Date: 2025-11-28 14:43:07 +0100

      Commit message:


	  
		
 Merge branch 'main' into devel 

    

  
    

      Package: DESpace

      Commit: 3acfc4bbfe5f649364d9ddaf10630f2939db037c

      Author:  peicai <55488976+peicai@users.noreply.github.com> 

      Date: 2025-10-31 13:08:51 +0100

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: DESpace

      Commit: 475fe9ba9fbff3c01c28251f0a17cfcec5189a4b

      Author:  peicai <peiying.cai@gmail.com> 

      Date: 2025-10-31 11:29:48 +0100

      Commit message:


	  
		
 updated citation
 

    

  
    

      Package: DESpace

      Commit: 7bd4c3aafd82cba9b9b744bb86c66b0948741170

      Author:  peicai <55488976+peicai@users.noreply.github.com> 

      Date: 2025-05-20 11:13:29 +0200

      Commit message:


	  
		
 Update pkg version 

    

  
    

      Package: Uniquorn

      Commit: fb579a9afdef98dd38a83c34e1d04bf535bcb4be

      Author:  Raik Otto <fubioinf@gmail.com> 

      Date: 2026-10-07 11:42:23 +0200

      Commit message:


	  
		
 redocumented package with roxygen2 1.8.0
 

    

  
    

      Package: Rarr

      Commit: 09ebbae8cc81bbd31a2c86eb6cb1049e7c319f2e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-07 11:17:55 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: d87c98bdf0fa4e7434ef9353d1f9470e67baf11e

      Author:  William Colgan <colgan.william@gmail.com> 

      Date: 2026-10-07 05:16:39 -0400

      Commit message:


	  
		
 Fix decoding of sharded arrays (#254)

Co-authored-by: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Co-authored-by: colganwi <wcolgan@wi.mit.edu> 

    

  
    

      Package: exploreSE

      Commit: 4ae42a061fea65ce0442f206d2d6a6d9eb3b06c7

      Author:  Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com> 

      Date: 2026-10-07 10:45:45 +0200

      Commit message:


	  
		
 bug fix on pca plotting
 

    

  
    

      Package: exploreSE

      Commit: ec1dc589f1491bf1cf2f722cf2563724dba9df61

      Author:  Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com> 

      Date: 2026-10-07 09:31:54 +0200

      Commit message:


	  
		
 version bump and bug fix to loader
 

    

  
    

      Package: exploreSE

      Commit: 8d5504d46bd34043bd31eaf34aeea4a8a70c21cd

      Author:  Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com> 

      Date: 2026-10-07 09:26:33 +0200

      Commit message:


	  
		
 update readme
 

    

  
    

      Package: SpectraStash

      Commit: 0ebfff3166a8ac234b9da4ef8664e25bcfe5f01f

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

      Date: 2026-10-07 10:30:46 +0200

      Commit message:


	  
		
 Merge pull request #14 from rformassspectrometry/jomain

tests: fix path for Windows 

    

  
    

      Package: SpectraStash

      Commit: 797446af8fa3127e5e7343dc7189a3a5158d7878

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

      Date: 2026-10-07 07:27:09 +0200

      Commit message:


	  
		
 refactor: validation checks in save methods for MsBackendCached

- `saveMsObject()` and `saveObject()` methods for `MsBackendCached` check if a
  save method is implemented for the child class (extending `MsBackendCached`)
  and if not throws an error to avoid silently creating a stash with only the
  cached data content which can not be restored to a fully operational
  `MsBackend`.
 

    

  
    

      Package: SpectraStash

      Commit: f055f1fd97db39d7508830e734cd6f26457129e8

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

      Date: 2026-09-10 08:12:56 +0200

      Commit message:


	  
		
 Merge branch 'main' into jomain
 

    

  
    

      Package: SpectraStash

      Commit: 0c0ecf60a09db286a880a28aafdbf904f7bd0727

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

      Date: 2026-09-10 07:52:51 +0200

      Commit message:


	  
		
 tests: fix path for Windows
 

    

  
    

      Package: MetaProViz

      Commit: f76eacf0973161bc204c66f33440898e62033ce1

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-06 16:35:33 +0200

      Commit message:


	  
		
 Bump version: 4.1.1 → 4.99.0
 

    

  
    

      Package: MetaProViz

      Commit: 620de6168c1cb55a70b0f688e5fb928163f8e1a7

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-06 16:30:37 +0200

      Commit message:


	  
		
 Use the magrittr pipe in the network code

The native pipe |> needs R >= 4.1.0, while DESCRIPTION states
R (>= 4.0); R CMD build added the dependency itself and warned. The
rest of the package uses %>% as well.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 158b88676cda7818ef44148a94fb5c73408ba043

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-06 14:54:25 +0200

      Commit message:


	  
		
 Move the prior knowledge networks into their own vignette

- New vignette pk-networks ("Prior Knowledge Networks", analysis
  workflows): the network section of core-metabolomics, unchanged,
  preceded by a minimal reproduction of the CoRe results it uses
  (processing, dma and ORA with the same parameters, without plots).
- core-metabolomics: keep the first MetalinksDB network and point to the
  new vignette.
- standard-metabolomics: add a MetalinksDB network of the core_UP
  cluster and point to the new vignette.
- Add the vignette to the navbar and the tutorials overview.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: ecf1803f94ffe0ae55b5194a589a1c7eb27a49de

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-06 14:29:26 +0200

      Commit message:


	  
		
 Add Giulia Röth as author and limit PEA volcano plots

- DESCRIPTION: add Giulia Röth (ORCID 0009-0000-6988-7189).
- core- and standard-metabolomics: plot the PEA volcano plots only for
  the 10 pathways with the lowest adjusted p-value instead of all
  pathways; core: the plotted ORA results are of the consumed cluster.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 6d0c707448787e7169dd7a9f037edd3c25e39f48

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-06 14:29:26 +0200

      Commit message:


	  
		
 Fix individual heatmaps in viz_heatmap()

- individual_Metab alone produced no plots: the condition of its branch
  was inverted when boolean comparisons were cleaned up (53b01674).
- Each individual heatmap was saved and printed again in every later
  loop iteration, as save_res() got the growing plot list.
- A metadata_feature or metadata_sample with a single column was
  dropped to a vector.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 2a6b03cf89ef229ec53694ad26fb8f52e06a0303

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-06 10:45:20 +0200

      Commit message:


	  
		
 Merge branch 'feature/pk-networks' into devel

Add viz_pk_network() and viz_shared_pk_network(), replacing
viz_metabolite_protein_network(), and use them in the vignettes.
 

    

  
    

      Package: MetaProViz

      Commit: 23e11df08f7b08fdb1c718d5727bd4a205e1176d

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-06 09:51:09 +0200

      Commit message:


	  
		
 Refine the prior knowledge network examples in the vignettes

- core-metabolomics: explain the sign of Log2(Distance), mark the
  transporter links as a hypothesis, cite MetalinksDB, KEGG, MACdb and
  the Jaccard index.
- prior-knowledge: larger network figures, Jaccard threshold without
  edge labels for the dense transporter sharing network.
- bibliography: add MACdb (Sun2023) and Jaccard1901.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: e4455cf4fef10babed23ed653c638946819f431d

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-06 09:51:07 +0200

      Commit message:


	  
		
 Simplify viz_shared_pk_network() output and plot

- Drop the overlap coefficient; similarity is "shared" or "jaccard".
- Leave metabolites without shared terms out of the plot by default
  (show_unconnected = FALSE). With the stress layout they took up a row
  and squeezed the network; they stay in the nodes table.
- Add edge_labels to switch off edge labels in dense networks.
- Fall back to the "fr" layout for graphs with fewer than three nodes,
  for which graphlayouts' stress layout warns.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: d9bb49d74d9d00b1f2f4e4258a915e00f4a05bae

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-05 19:35:06 +0200

      Commit message:


	  
		
 Use the prior knowledge networks in the vignettes

- core-metabolomics: port the MetalinksDB network to viz_pk_network()
  and add a closing section with MetalinksDB, KEGG and MACdb examples
  for viz_pk_network() and viz_shared_pk_network().
- prior-knowledge: port the amino acid examples and update the receptor
  numbers, which now count distinct proteins.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 612ac578764bcc44f8b13fe9d529542e2b65b392

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-05 19:35:05 +0200

      Commit message:


	  
		
 Add viz_pk_network() and viz_shared_pk_network()

Replace viz_metabolite_protein_network() by two generic functions that
work with any prior knowledge table in long format, e.g. MetalinksDB,
KEGG or MACdb:

- viz_pk_network() plots metabolites with the terms they are linked to.
- viz_shared_pk_network() connects metabolites that share terms, with
  the number of shared terms, Jaccard index or overlap coefficient as
  edge weight and a similarity threshold.

Both match features to the prior knowledge via the shared helper
.pk_associations() and map node colour/size and edge colour/line type/
width/direction to columns via metadata_info. metsigdb_metalinks() now
returns `interaction` and `direction` columns for directed edges.

cluster_pk() uses the same set similarity helper; values are unchanged,
but it no longer fails if only one term is left.

Adds ggnewscale to Imports.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 9e70f7f339fd32ce4aebe735e8335567be821e0f

      Author:  Jannik Franken <67631155+jannikfranken@users.noreply.github.com> 

      Date: 2026-10-05 15:02:53 +0200

      Commit message:


	  
		
 Merge pull request #128 from saezlab/fix/license-consistency

Make license and copyright statements consistent 

    

  
    

      Package: MetaProViz

      Commit: 7e6ecc4c3e9879e7cd6accd0bdd54c1f38246967

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-05 10:56:48 +0200

      Commit message:


	  
		
 Make license and copyright statements consistent

- Align copyright years (2023-2026) and holders across LICENSE,
  LICENSE.md and all R/*.R headers.
- Replace the "the author" variant in LICENSE.md with the standard
  SPDX BSD-3-Clause wording.
- Mark R/enricher_internal.R as Artistic-2.0 (adapted from DOSE)
  instead of BSD-3-Clause, and document it as third-party code in
  LICENSE.md.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 0031e947a538432d5a1035f041723ad9b97dd291

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-05 09:42:15 +0200

      Commit message:


	  
		
 Drop Polychrome 1.5.1 reinstall step from CI

The step forced Polychrome 1.5.1 to satisfy the (< 1.5.4) pin, which
da7b71c dropped from DESCRIPTION. Without it, CI tests against the
Polychrome version users actually get from CRAN (1.6.x).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: a8154e477fb01cc1db78a6a4ca45c7cfede98e72

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 15:16:18 +0200

      Commit message:


	  
		
 State the BSD 3-Clause license in README and source headers

The package is licensed under BSD 3-Clause (DESCRIPTION, LICENSE.md,
NEWS), but the README and the header of every R file still named GPLv3.
The DOSE attribution in enricher_internal.R is unchanged.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 0682379dda9b7c054052551e3f25380defa3c151

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 15:15:21 +0200

      Commit message:


	  
		
 Install ImageMagick on Ubuntu CI for the magick package

magick (suggested, used by the vignettes' plot hook) is built from
source on Ubuntu and needs libmagick++-dev; without it R CMD check fails
with "Package suggested but not available: 'magick'". Add it to the
build-check and pkgdown workflows.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: e0c2a80e8ee08ae17424d7ef00452f70ae46ab93

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 15:15:20 +0200

      Commit message:


	  
		
 Add seed argument to viz_metabolite_protein_network()

Replace the two set.seed(123) calls (BiocCheck warning) with an optional
`seed` argument, NULL by default. With a seed, the force-directed layout
is computed under withr::with_seed(), so it is reproducible without
changing the user's global random seed. The CoRe vignette uses
seed = 123 to keep its network layout stable.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: a3ac94709c202d5455628752b69c4a705b0d76f2

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 14:43:51 +0200

      Commit message:


	  
		
 Add tutorials landing page and update the pkgdown site

- Add a landing page (vignettes/pkgdown/tutorials.Rmd, website only)
  with one card per tutorial, grouped into Get started, Analysis
  workflows and Prior knowledge and metabolite IDs, with thumbnails.
- Navbar: label the Tutorials menu, start it with "All tutorials", group
  the entries and add the ID processing tutorial; add aria-labels to the
  navbar icons and set the site URL.
- README: link the tutorials section to the landing page instead of
  listing (broken) article links; fix typos.
- extra.css: drop the fixed 40cm page width (forced horizontal
  scrolling) and show the hexagon next to every article.
- DESCRIPTION: suggest magick, used by the vignettes' plot hook.
- .Rbuildignore: ignore .claude/. CLAUDE.md was moved to
  .claude/CLAUDE.md in 68db8ce9 so that pkgdown no longer publishes it.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 613281b664f0aae8932b70e6fdb335d26ed8ae34

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 14:43:51 +0200

      Commit message:


	  
		
 Update Standard metabolomics vignette to the current API and site layout

- Replace outdated function and parameter names in the text, remove
  hard-coded heading numbers and fix links and typos.
- Show wide tables in scroll boxes (preview_table()) and plots at their
  MetaProViz size via a plot hook that crops each plot (needs magick);
  the hook also takes a fixed display width (plot.width), used to give
  the overview heatmap and the 3.4.1 volcano plots the same size.
- Remove the "Figure:" caption prefix, numbered table captions (pandoc
  read them as lists and broke the page layout) and the hexagon heading
  (the website shows the logo next to the article, pkgdown/extra.css).
- Separate scroll-box divs and chunks from following text with blank
  lines, and the intro bullet list from the following sentence.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: ad001a132cde386a38e9f53849c22736f2c8f09b

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 14:41:18 +0200

      Commit message:


	  
		
 Separate intro list from following text in Sample Metadata vignette

The line-break-only lines after the bullet list made the next sentence
part of the last bullet point.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 93e020501d721ae790f6ba6735d9e452b1fda2d3

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 14:41:17 +0200

      Commit message:


	  
		
 Fix missing page outline on the CoRe metabolomics website article

Three table captions started with a number ("1. Preview ..."). Inside
the table HTML, pandoc read that as a list and lost the closing tag of
the scroll box, which closed the page layout early and pushed the
"On this page" sidebar out of it. Remove the numbers.

Also separate the intro bullet list from the following sentence and
add blank lines after chunks that are directly followed by text.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 7a67ada2e81470c50178e217fc959cb37bd9dd42

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 13:02:48 +0200

      Commit message:


	  
		
 Update Sample Metadata vignette to the current API and site layout

- Fix the index entry, links to the other vignettes, typos, and remove
  hard-coded heading numbers; add Jannik Franken as author.
- Show wide tables in scroll boxes (preview_table()) and plots at their
  MetaProViz size via a plot hook that crops each plot (needs magick);
  enlarge the metadata_analysis() plot and size the Venn diagram.
- Remove the duplicated "Pathway enrichment" section, whose hidden code
  differed from the code shown and re-ran ORA the old way.
- Remove the "Figure:" caption prefix and the hexagon heading (the
  website shows the logo next to the article, pkgdown/extra.css), and
  separate scroll-box divs with blank lines so pandoc closes them.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: af3180e8dc8fb1c3fc5fc83a756b86a97705c084

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 13:00:18 +0200

      Commit message:


	  
		
 Fix progress bars, captions and volcano size in quick-start vignette

- Indent the inner progress-bar divs by two spaces; with four, markdown
  showed them as code blocks.
- Remove the "Figure:" caption prefix (BiocStyle adds "Figure N:").
- Show the dma() volcano plot at 55% width.
- Separate the scroll-box div with blank lines.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 61de05cb8d9c8db226356f4f04cef8eb4ad9e626

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 13:00:17 +0200

      Commit message:


	  
		
 Remove hexagon heading from Prior Knowledge vignette

The website shows the logo next to the article instead
(pkgdown/extra.css).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 9199ce3454bde5df20b1b25541f7160d9cbd5692

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 13:00:17 +0200

      Commit message:


	  
		
 Note that equivalent_id() runs separately from id_processing()

Point to the Sample Metadata vignette, where the equivalent ID step of
Fig. 1 is done.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 0873414da24f9448b9b59af59294452e5e7bb7b0

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 13:00:16 +0200

      Commit message:


	  
		
 Update CoRe metabolomics vignette to the current API and site layout

- Replace outdated function and parameter names in the text, remove
  hard-coded heading numbers, fix the title/index entry, links and typos.
- Show wide tables in scroll boxes (preview_table()) and plots at their
  MetaProViz size via a plot hook that crops each plot (needs magick).
- Draw the MetaLinks network only once, add the mca_core() clusters to
  MetaData_Metab as the text describes, size plain ggplots explicitly.
- Remove the "Figure:" caption prefix and the hexagon heading (the
  website shows the logo next to the article, pkgdown/extra.css), and
  separate scroll-box divs with blank lines so pandoc closes them.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: fffde291643e0eb2ea3a5944cd4fb0ab1c297d9b

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 12:52:18 +0200

      Commit message:


	  
		
 Remove hexagon heading from MetSigDB vignette

The website shows the logo next to the article instead
(pkgdown/extra.css).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 5feb8889c873933dd40d3b7948b5109bf5adf56a

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 12:52:17 +0200

      Commit message:


	  
		
 Explain ID processing results and summarise the gained ID coverage

- Outline the parts of the id_processing() result and compare the most
  important tables (feature metadata, ID coverage per feature, ID counts)
  between the input and after traversal, using four example features
  and explaining the QC columns of the compatibility check.
- Show the three count_id() plots of each ID type side by side, each
  followed by a short description of the no/single/multiple ID counts.
- Add a summary of the gained ID coverage and why it matters for
  mapping to prior knowledge.
- Remove the hexagon heading; the website shows the logo next to the
  article instead (pkgdown/extra.css).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 68db8ce9cf8474db0cc6a215ca173722e368c8d9

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-02 12:46:29 +0200

      Commit message:


	  
		
 Update MetSigDB overview figure

Crop the canvas to the figure (it was a full A4 page, which left large
white space above and below it in the vignette) and fix the
"Exclusion" typo and overlapping labels.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: caa1805a2133bf174f80cf775ea51071eeb83e54

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-01 18:16:13 +0200

      Commit message:


	  
		
 Fall back to fixed bins in dma() Shapiro histograms for wide data ranges

The Shapiro density plots use the standard binwidth of 0.5. On raw
intensities this needs millions of bins, so ggplot2 drops the histogram
("Computation failed in stat_bin()"). The new internal helper
histogram_bins() keeps the standard binwidth unless more than 1000 bins
would be needed, and then uses 30 bins instead.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: a7d23da89440af5847bba0a98da7778bd1c68457

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-01 18:08:19 +0200

      Commit message:


	  
		
 Update quick-start vignette to the current API

- Replace outdated parameter names in the text (Feature_Filtering,
  Plot_Settings, Plot_metadata_info, Plot_SettingsFile, plot=TRUE,
  Load_KEGG) with the current ones.
- Remove hard-coded heading numbers (two sections were numbered 3).
- Point links to the extended vignettes to articles/pkgdown/.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 6f1a931e6f9529f5c8312f8e57322ae41a802a49

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-01 18:03:02 +0200

      Commit message:


	  
		
 Ignore R session files and generated output

Knitting vignettes and running MetaProViz functions writes
MetaProViz_Results/, log folders and knitr *_files/ folders into the
repo; keep them out of git status.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 39ad5cc62b7a071bd2a4ab2195b06bf439f287ac

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-01 17:49:03 +0200

      Commit message:


	  
		
 Rework ID processing vignette

- Add the id_processing() workflow scheme as Fig. 1 and describe the
  tissue_meta example data instead of the repo history.
- Harmonise the mixed ID separators in tissue_meta (commas in HMDB/KEGG,
  semicolons in PUBCHEM) and use delimiter = ";" in all calls, since
  id_processing() splits all ID columns with one delimiter.
- Show the count_id() plots at the default MetaProViz size (Plot_Sized).
- Wrap wide tables in a horizontal scroll box.
- Move headings up one level so BiocStyle numbers them 1, 2, ...
  instead of 0.1, 0.2, ...

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 1f819379cb8925aa59b4639e09ff460efe140062

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-01 17:52:18 +0200

      Commit message:


	  
		
 Replace prior-knowledge vignette with revised version

Restructured around the analysis workflow (metabolite IDs in the data,
accessing and linking prior knowledge, ID translation, pathway
coverage), with an in-depth look at the resources themselves moved to
the MetSigDB vignette. Adds Jannik Franken as author.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: bebc1c71eb1086c70ebdcd309261ec031e9a8a09

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-01 17:52:18 +0200

      Commit message:


	  
		
 Replace metsigdb-resource-composition vignette with MetSigDB vignette

The new MetSigDB vignette supersedes the resource-composition vignette.
Its bibliography is renamed to metsigdb.bib and the pkgdown navbar
points to the new article.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 7e263e2c90e88b171728c4ecf2ff2aa1f31649c0

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-01 17:49:02 +0200

      Commit message:


	  
		
 Move website-only vignette figures to vignettes/pkgdown/figures

Fig.2, Fig.3 and the hexagon logo are only used by the pkgdown
vignettes, so they no longer sit in vignettes/ where they would ship
with the Bioconductor build. Fig.1.png and readme-example-data.png were
duplicates of the copies in man/figures/ used by the README; the README
figure script now writes there directly.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: b57359729eec57f52ecc8391c5ab5c859e1f61cc

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-01 18:21:13 +0200

      Commit message:


	  
		
 pipe.Rd: add a runnable example

BiocCheck counts pipe.Rd as a page documenting an exported object; with
this example 38/47 exported pages have runnable examples (> 80%).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: cfaaa7a00ba1ccbae0ccba0c2dd339c2565e0bc8

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-01 18:02:27 +0200

      Commit message:


	  
		
 BiocCheck/R CMD check fixes: examples, globals, pipe docs

- compare_pk(), viz_metabolite_protein_network(): replace \dontrun
  examples with runnable ones (bundled biocrates_features; the network
  example matches Biocrates amino acids to MetaLinks transporters via
  HMDB, with exclude_metabolites = NULL to avoid the RaMP download).
  Raises runnable-example coverage of exported man pages above
  BiocCheck's 80% threshold.
- Add `<- NULL` NSE workarounds for the "no visible binding for global
  variable" NOTEs (seed-compatibility helpers, network plot helpers,
  checkmatch_pk_to_data, tic_norm).
- Document the re-exported pipe explicitly (man/pipe.Rd, internal) so
  the link targets magrittr's `%>%` topic; the auto-generated
  reexports.Rd linked [magrittr:pipe], flagged on R 4.6 as a non-topic
  package-anchored link.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: da7b71c4dfd1bf392cc032c9969f7c058dcde66b

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-10-01 16:05:30 +0200

      Commit message:


	  
		
 DESCRIPTION: drop Polychrome (< 1.5.4) upper bound

The pin from 612e8ce kept MetaProViz installable on R 4.3 (Polychrome
>= 1.5.4 requires R >= 4.4), but it is unsatisfiable on current
Bioconductor: BioC 3.24 runs R 4.6 and CRAN only serves Polychrome
1.6.x, so loading fails with "namespace 'Polychrome' 1.6.1 is being
loaded, but < 1.5.4 is required" (seen on the omnipath devel check
since 2026-08-20).

The R 4.3 workaround belongs in the training environment instead
(saezlab/ebi-metabo-training env/install.R), which pre-installs
Polychrome 1.5.3 on R < 4.4.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 050208858513ff415ec48ed2b869a29437853528

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-10-01 13:48:29 +0200

      Commit message:


	  
		
 Install remaining system libs for the ggraph/ragg font stack. fontconfig, harfbuzz, fribidi, libtiff, libjpeg, libwebp, per each packages own CRAN SystemRequirements.
 

    

  
    

      Package: MetaProViz

      Commit: 4fa8701c28ddd68721e1ba817505b75ad5349368

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-10-01 11:31:22 +0200

      Commit message:


	  
		
 Install libfreetype6-dev on Ubuntu CI. sysfonts needs freetype-config to compile, cascading into
factoextra/ggraph being reported as unavailable.
 

    

  
    

      Package: MetaProViz

      Commit: 50164bd9e426d5cdbfe1c1a03d8cc14eea3f1805

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-10-01 10:34:26 +0200

      Commit message:


	  
		
 Install libpng-dev on Ubuntu CI sysfonts (needed by ggraph/factoextra's plotting stack via showtext) fails to compile without it, which cascaded into cosmosR/factoextra/ ggraph being reported as unavailable for MetaProViz.
 

    

  
    

      Package: MetaProViz

      Commit: 41561225d456a15a41415e460a0b46438a7aa7eb

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-10-01 08:36:35 +0200

      Commit message:


	  
		
 Install libcurl4-openssl-dev and libuv1-dev on Ubuntu CI. curl and fs need these system libs to compile from source
 

    

  
    

      Package: MetaProViz

      Commit: 50135044ca38cd7caebb99fa1e06d96e39b58a17

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-09-30 17:03:49 +0200

      Commit message:


	  
		
 Install OmnipathRs needed packages: curl, fs, httr2, rmarkdown, rvest
 

    

  
    

      Package: MetaProViz

      Commit: 27b846603f98d2e2f0b040854767e34b6c2894d3

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-09-30 16:14:18 +0200

      Commit message:


	  
		
 Fix NA crash in outlier_detection()final QC PCA. Applies the same guarded NA->0 replacement viz_pca() uses.
 

    

  
    

      Package: MetaProViz

      Commit: e16c97b5856f40f218f6ff65c1aaaa6942893b23

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-09-29 13:08:50 +0200

      Commit message:


	  
		
 Fix core_norm example: load medium_raw before using it
 

    

  
    

      Package: MetaProViz

      Commit: 31943f16d96d826b6d6a41dd6118be994e9d878a

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-09-29 12:53:00 +0200

      Commit message:


	  
		
 Install compatible Polychrome version in CI. Before this remotes::install_deps() ignored DESCRIPTION's Polychrome(< 1.5.4) pin and installed the latest version instead.
 

    

  
    

      Package: MetaProViz

      Commit: d2e0a2bbb3a1b67db224a6bb20b0e8c879f113a5

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-09-29 12:39:00 +0200

      Commit message:


	  
		
 Change Bioconductor version fom 3.22 to 3.23 to match R 4.6
 

    

  
    

      Package: MetaProViz

      Commit: 680d28797539f932105f4dd37c7cbdadaac5f0a9

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-09-29 10:25:45 +0200

      Commit message:


	  
		
 Fix R CMD build failure: persist Bioconductor repos across steps. BiocManager::install() only sets Bioconductor repos for its own step, so R CMD build can't find cosmosR/S4Vectors/SummarizedExperiment later. A .Rprofile written early in the job makes R pick up the repos every step.
 

    

  
    

      Package: MetaProViz

      Commit: 2e2345c5d0bfcf664c2a838ac729136f1a7662f2

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-09-29 09:37:33 +0200

      Commit message:


	  
		
 Replace qcc dependency with base R in outlier_detection(). qcc has no conda package, blocking a bioconda recipe for MetaProViz. The only qcc call (mqcc(type = T2.single) for the Hotellings T2 outlier test) only needed Mahalanobis distance and a qbeta control
limit, both in base R, so it's replaced with a new internal helper,.hotelling_t2_single() in R/HelperMisc.R, instead.
 

    

  
    

      Package: MetaProViz

      Commit: c54a284222acb6ca268104b269ab95e423459efb

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-24 11:05:23 +0200

      Commit message:


	  
		
 Replace outdated toy_data() mentions in vignettes with data()

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: ae6c02992249efc83bfb292bd3ca4dd4e10c3ba8

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-24 11:01:14 +0200

      Commit message:


	  
		
 Fix failing id_processing and SummarizedExperiment tests

- count_id mocks: vapply(USE.NAMES = FALSE) so NA IDs do not become NA
  row names.
- traverse_ids mock accepts the new arguments; expect no pair_compatibility
  in id_processing traversal output.
- Enable run_compatibility_check explicitly in the compatibility test
  (default is FALSE).
- outlier_detection SE test selects features via rownames(se).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 14a4e8fb5afa6dbf909637c96ced5c31fd76140a

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-24 11:01:14 +0200

      Commit message:


	  
		
 Add delimiter/prefix handling to ID helpers and reuse edge table

- checkmatch_pk_to_data(): new `delimiter` argument (default ", ", same
  splitting as before) for multiple IDs in the data ID column.
- checkmatch_pk_to_data(): fix InputID_select, which contained the column
  name (e.g. "KEGG") instead of the actual ID for single-ID rows and
  unmatched multi-ID rows. It is now computed before merging with the PK, so
  it also works when InputID and PriorID share a column name.
- equivalent_id(): accept prefixed ChEBI/PubChem IDs ("CHEBI:", "CID") and
  return prefixed output; fix crash when no additional IDs are found (e.g.
  one-row input).
- traverse_ids(): new `edge_table` argument; id_processing() builds the RaMP
  edge table once and reuses it for compatibility check and traversal.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 2b611ac227d41bd1ffb33c2fdaf5996e39b4ff22

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-24 11:01:14 +0200

      Commit message:


	  
		
 Create missing save paths and shorten duplicated output file names

- save_path(): create a user-supplied path that does not exist yet instead
  of silently falling back to the working directory.
- save_res(): build all file names via new save_file_name(). The item name
  is no longer repeated when it equals file_name (e.g. Heatmap_X_Heatmap_X),
  and names longer than 120 characters are shortened with a hash suffix to
  stay within Windows path limits. The xlsx branch no longer overwrites
  file_name for subsequent plot names.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 38a81f2942dbf77d9d584679f4a9f8e1499a32bc

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-24 09:48:34 +0200

      Commit message:


	  
		
 Fix embedded upset plots and count_id usage in prior-knowledge vignette

- Embed pre-rendered upset plots with results="asis" so the images render
  instead of showing escaped HTML.
- Pass the delimiter to count_id() and use its Table output.
- Link the MetSigDB resource composition vignette and tidy headings/figures.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 921d03f825e0699a684bfe58ba44c4c1d8447b38

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-24 09:48:34 +0200

      Commit message:


	  
		
 Use id_processing() workflow in sample-metadata vignette

- Replace the manual equivalent_id()/translate_id() ID QC with
  id_processing() (compatibility check with KEGG priority + traversal),
  followed by equivalent_id() for HMDB, KEGG, CHEBI and PUBCHEM.
- Harmonise ID delimiters before checkmatch_pk_to_data() and update the
  KeepOneID cases and prose to the new results.
- Select ORA input columns by name instead of by position.
- Regenerate the embedded compare-pk-2 upset plot on every knit and embed
  it with results="asis" so it renders on the pkgdown site.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 1ee414fb3b2659decd62695beb3f89074632b0ba

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-24 09:48:33 +0200

      Commit message:


	  
		
 Skip duplicate compatibility check in id_processing traversal

- traverse_ids() gains run_compatibility_check (default TRUE); id_processing()
  always calls it with FALSE, since the check is controlled by
  id_processing(run_compatibility_check = ...) itself. This removes the second
  check and its misleading "automatic ID handling is disabled" message.
- id_processing() prints a note when traversal runs without a prior
  compatibility check.
- Strip the internal row_id column from the after_traversal stage table.
- Drop the now always-empty traversal pair_compatibility output.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 35a024c4e1cb128d24dc0892a281b10a78ac33d9

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-09-18 13:25:37 +0200

      Commit message:


	  
		
 Merge pull request #127 from saezlab/update_se_and_cellular_meta_files

Update test data  

    

  
    

      Package: MetaProViz

      Commit: 1e05e898edb8c6264cf13e36186cea288af5c8f9

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-09-17 18:57:49 +0200

      Commit message:


	  
		
 Populate rowData for tissue_norm_se/intracell_raw_se and add medium_raw_se tissue_norm_se and intracell_raw_se previously had empty rowData(); both are now rebuilt from their respective feature metadata tables so rowData is fully populated. medium_raw_se is new, built the same way, since it didn't exist as an SE before. cellular_meta gains a backfilled entry for hexanoylcarnitine C6 (previously missing entirely), which intracell_raw_se now picks up. Also documents medium_raw_se in ToyData.R (it had no roxygen entry despite medium_raw itself being documented) and regenerates the affected man pages.
 

    

  
    

      Package: MetaProViz

      Commit: d1210784e21ea6c167949550deb143ade834fa3c

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-16 15:55:34 +0200

      Commit message:


	  
		
 update metabolite-network-plot integration into vignettes
 

    

  
    

      Package: MetaProViz

      Commit: 51752cdde975d81de7d71f83cc78701730304a3d

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-16 13:40:34 +0200

      Commit message:


	  
		
 include new optional metabolite_interaction_overlap graph into viz_metabolite_protein_interaction function, to visualize shared metabolite-protein relationships
 

    

  
    

      Package: MetaProViz

      Commit: 77c1769316afb496f090da73b752eb3765532ce2

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-16 13:12:04 +0200

      Commit message:


	  
		
 Improve regulation edge styling
 

    

  
    

      Package: MetaProViz

      Commit: 6cb69afe6310f5fe3553af7618ab6d10e3f0cd66

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-16 13:01:50 +0200

      Commit message:


	  
		
 fixed MetalinksDB annotations and fixed metabolite-protein network plot
 

    

  
    

      Package: MetaProViz

      Commit: 2d0e8c8568e122bf012016204c1a34116621a7d2

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-15 20:25:39 +0200

      Commit message:


	  
		
 fix metabolite protein interaction networks and add explanatory tutorial text
 

    

  
    

      Package: MetaProViz

      Commit: 087e9495d9fe2ec77825603d11b4dc29968dda7e

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-15 20:24:03 +0200

      Commit message:


	  
		
 added cmd output for automated feature ID processing
 

    

  
    

      Package: MetaProViz

      Commit: 1dafc9676a18eb398e8af9c76b552fb1177c120d

      Author:  Jannik Franken <67631155+jannikfranken@users.noreply.github.com> 

      Date: 2026-09-10 15:34:11 +0200

      Commit message:


	  
		
 Merge pull request #125 from saezlab/manual-featurefilt

Add Manual featurefilt mode to processing() and feature_filtering(). 

    

  
    

      Package: MetaProViz

      Commit: 98bcac14161d93a04be8e4afef8b2cfaa073c128

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-09-10 15:15:18 +0200

      Commit message:


	  
		
 feature_filtering(): return featurefilt_used so exported tables report the method actually applied after a fallback
 

    

  
    

      Package: MetaProViz

      Commit: 927639365df6f06edc9c5bbaf2ec8c18a9985248

      Author:  Giulia <83399135+giuliaroeth@users.noreply.github.com> 

      Date: 2026-09-10 14:04:38 +0200

      Commit message:


	  
		
 Add Manual featurefilt mode to processing() and feature_filtering()
 

    

  
    

      Package: MetaProViz

      Commit: e1811a94ab3c120a3f0a3b870f8769603f220371

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-01 17:30:09 +0200

      Commit message:


	  
		
 docs: refine resource composition vignette
 

    

  
    

      Package: MetaProViz

      Commit: 4832c70a4e899cebaa20414a86bde86ec6718203

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-01 17:22:31 +0200

      Commit message:


	  
		
 docs: update ID processing documentation
 

    

  
    

      Package: MetaProViz

      Commit: c659947c65538067ddf54b9c5fe43376556159f8

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-01 17:10:44 +0200

      Commit message:


	  
		
 docs: add session info to workflow vignettes
 

    

  
    

      Package: MetaProViz

      Commit: dc341bfcfabf72a95233c1d05f69b7fd25f0885a

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-01 17:10:17 +0200

      Commit message:


	  
		
 docs: add MetSigDB resource composition vignette
 

    

  
    

      Package: MetaProViz

      Commit: 8f8ea94852deef89ce2dcba9baa04bc32b0ae1fb

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-09-01 16:01:58 +0200

      Commit message:


	  
		
 docs: refine ID processing workflow vignette
 

    

  
    

      Package: MetaProViz

      Commit: 8ee42852ec51538b67619a0ba3a7ac461e957b42

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-31 17:26:47 +0200

      Commit message:


	  
		
 Fix ID translation validation
 

    

  
    

      Package: MetaProViz

      Commit: 6d7c4cc0fbd5d9c26569e2d681cf12ff8aedd2d2

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-31 17:13:22 +0200

      Commit message:


	  
		
 Add staged ID processing workflow
 

    

  
    

      Package: MetaProViz

      Commit: b9d092ac2ae9585de676656cec67c3771fb2db23

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-31 15:36:00 +0200

      Commit message:


	  
		
 Update contributor and author metadata
 

    

  
    

      Package: MetaProViz

      Commit: 9c4499ec1e3d5457cf2bc7b5a9deccd46afeb1cb

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-31 15:25:24 +0200

      Commit message:


	  
		
 Update publication citation metadata
 

    

  
    

      Package: MetaProViz

      Commit: 7148b3a638e68e4f231fe3acc7e4d0726bb33412

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-26 15:19:56 +0200

      Commit message:


	  
		
 Add SE support to standalone processing helpers
 

    

  
    

      Package: MetaProViz

      Commit: dcd9cd4c8f2c90620c2e66d8cf34791f368d135a

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-19 16:02:24 +0200

      Commit message:


	  
		
 Export processing stage functions
 

    

  
    

      Package: MetaProViz

      Commit: eeb38fb27ad1d88565935d3c1c206e1ceb21a31f

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-19 12:18:55 +0200

      Commit message:


	  
		
 added MetalinksDB metabolite-protein network plots to vignette
 

    

  
    

      Package: MetaProViz

      Commit: 4e8e19577553fc5a745dd5b4ceb2756cfa46cf21

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-08-07 16:25:51 +0200

      Commit message:


	  
		
 Bump version: 4.1.0 → 4.1.1
 

    

  
    

      Package: MetaProViz

      Commit: 010fe23242a474c25070c73f23a35ca26dd8c756

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-08-07 16:25:42 +0200

      Commit message:


	  
		
 Revert "Update information in DESCRIPTION file"

This reverts commit 16e59769feddb84d9d9350fe5570f847f13013da.
 

    

  
    

      Package: MetaProViz

      Commit: 4786c25ca2b43e6bfb189bc835ed294ac2c5f67a

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-06 15:15:25 +0200

      Commit message:


	  
		
 remove test script
 

    

  
    

      Package: MetaProViz

      Commit: ee89b0a3ad02cf341b27e36075ea983933963ebd

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-06 15:06:07 +0200

      Commit message:


	  
		
 Stabilize processing and metadata analysis tests
 

    

  
    

      Package: MetaProViz

      Commit: 01fdecac0d73727c2d52e76b43708d2813f323f4

      Author:  jannikfranken <jannik8513@gmailcom> 

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

      Commit message:


	  
		
 Harden prior-knowledge refactoring paths
 

    

  
    

      Package: MetaProViz

      Commit: 7d8ce52252ca7db5ff52dbd4421d7d7f3e60f41c

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-06 13:23:43 +0200

      Commit message:


	  
		
 Clean seed ID handling workflow output
 

    

  
    

      Package: MetaProViz

      Commit: 9b8d1b1416ac1d6794246cc869316c3edf95f423

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-06 13:10:25 +0200

      Commit message:


	  
		
 Expand testthat coverage across MetaProViz
 

    

  
    

      Package: MetaProViz

      Commit: 3939e3edb0086c826b13abd89001a8fb3f9f125a

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-06 10:42:08 +0200

      Commit message:


	  
		
 Move Metalinks network validation into HelperChecks
 

    

  
    

      Package: MetaProViz

      Commit: 97b66b269706712bb0d505da5dcf852eaec1b966

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-06 10:35:33 +0200

      Commit message:


	  
		
 Remove dpi from Metalinks network API and update example
 

    

  
    

      Package: MetaProViz

      Commit: a5cbd84bf417ae9216e6f88638287c9c9d17ee76

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-06 10:24:07 +0200

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/saezlab/MetaProViz into devel
merge
 

    

  
    

      Package: MetaProViz

      Commit: 94c3a47358fa7a0fa643f67b7ac64d5685d87360

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-06 10:13:47 +0200

      Commit message:


	  
		
 Fix direct-source logging in Metalinks network test script
 

    

  
    

      Package: MetaProViz

      Commit: a1520f414090c45abae2de8b28f7aae1d80780db

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-06 10:13:46 +0200

      Commit message:


	  
		
 Extend seed ID compatibility handling
 

    

  
    

      Package: MetaProViz

      Commit: 213ca5614e935b39e3ade1560a92ec8ce6063f42

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-08-06 10:04:42 +0200

      Commit message:


	  
		
 Add Metalinks metabolite-protein network visualization
 

    

  
    

      Package: MetaProViz

      Commit: 16e59769feddb84d9d9350fe5570f847f13013da

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-07-31 08:47:09 +0200

      Commit message:


	  
		
 Update information in DESCRIPTION file

Changed license from BSD-3 clause to GPL-3. 

    

  
    

      Package: MetaProViz

      Commit: 04b639cbe6932406aa86145472a765b3ee928d6f

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-04-29 12:29:03 +0200

      Commit message:


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

    

  
    

      Package: MetaProViz

      Commit: 612e8cea862068c735bfe257a76390f566b02f45

      Author:  Denes Turei <turei.denes@gmail.com> 

      Date: 2026-04-27 03:37:28 +0200

      Commit message:


	  
		
 DESCRIPTION: pin Polychrome (< 1.5.4) to keep R 4.3 compatibility

Polychrome 1.5.4 (April 2025) bumped its DESCRIPTION to `R (>= 4.4)`,
which propagates as a hard floor for every package depending on it —
including MetaProViz. Earlier 1.5.x versions still declare
`R (>= 3.5.0)`, and the API we use hasn't changed.

Pinning to `Polychrome (< 1.5.4)` keeps MetaProViz installable on
Ubuntu 24.04 LTS's default R 4.3.3 without forcing every participant
to add the CRAN apt PPA. Verified: full install via PPM Ubuntu noble
binaries on R 4.3.3 in 3m6s, all six tutorial scripts run end-to-end.

The `R.matlab` package OmnipathR pulls in via `recon3d_*` (Suggests)
also needs explicit installation; that's handled in the training
repo's env/install.R rather than here.

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

    

  
    

      Package: MetaProViz

      Commit: a175cf23c0143f9353aedfca0a4981334011f9e0

      Author:  Denes Turei <turei.denes@gmail.com> 

      Date: 2026-04-27 01:40:40 +0200

      Commit message:


	  
		
 Lower R dep to 4.0 + harden plot save against viewport math errors

DESCRIPTION:
  Lower `R (>= 4.4)` to `R (>= 4.0)`. The 4.4 floor came from
  Bioconductor's submission policy of pairing with Bioc 3.20+; the
  package itself doesn't use any R-4.4-only language features
  (no native pipe `|>`, no walrus, no `_` placeholder). This unblocks
  participants on Ubuntu 24.04 LTS, whose default `r-base` is 4.3.3.

HelperPlots.R::set_size:
  Clamp resolved sizes to non-negative. The gtable algebra in
  `adjust_layout` can produce negative residuals (the trace shows
  `max(3.1cm, -1.95cm, 1cm) - max(-1.95cm, 1cm)` going below zero in
  the volcano legend column), which propagates as `Inf`/`NaN` into
  `grid::viewport()` and dies with "non-finite location and/or size
  for viewport". Clamping is a cheap safety net.

HelperSave.R::save_res:
  - Recognize `with_canvas_size` plots (heatmap / PCA / volcano /
    superplot) and route them through the device-based saving path
    used for ComplexUpset, with the canvas's own width/height. Most
    of the time the gtable gets re-wrapped via `ggplot()+annotation_custom`
    upstream and arrives here as a regular ggplot, but when the class
    survives this is the right way to render it.
  - Wrap the regular-ggplot ggsave call in tryCatch. The pheatmap-
    derived `ggplot()+annotation_custom(.)` wrap can still fail
    viewport math in batch contexts. Emit a warning instead of
    halting — the analysis result is still returned in memory and
    the user can `ggsave()` the plot manually.

NAMESPACE: regenerated by devtools::document() to register
`importFrom(grid, ...)` for the new helpers (is.unit, convertUnit,
unit, grid.draw) introduced into HelperPlots.R / HelperSave.R.

Verified on a NixOS-headless test that previously died on
viz_heatmap save_plot="svg" — now returns OK with a clear warning
about the failed save.

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

    

  
    

      Package: MetaProViz

      Commit: 2e4abc14cecd32d37416a1f3723f6930db699c79

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-04-15 13:20:18 +0200

      Commit message:


	  
		
 Merge pull request #123 from saezlab/devel

Devel 

    

  
    

      Package: MetaProViz

      Commit: 91560ca81f6d1e988117a2a92fe9c1afe039f568

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-04-15 08:48:24 +0200

      Commit message:


	  
		
 Bump version: 3.99.52 → 3.99.53
 

    

  
    

      Package: MetaProViz

      Commit: fc222b4dc132ab9dabb3ec05edd8f6220f13334c

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-04-15 08:47:22 +0200

      Commit message:


	  
		
 within outlier_detection helper return all dfs used for the internal plots.
 

    

  
    

      Package: MetaProViz

      Commit: 10c2d011334b4b081bed8b4c2b55687df71460ac

      Author:  Jannik Franken <jannik8513@gmailcom> 

      Date: 2026-04-12 11:27:19 +0200

      Commit message:


	  
		
 Bump version: 3.99.51 → 3.99.52
 

    

  
    

      Package: MetaProViz

      Commit: a0b0f1961ae3cb326ee1f727d937edaaf2f3d8b7

      Author:  Jannik Franken <67631155+jannikfranken@users.noreply.github.com> 

      Date: 2026-04-07 10:33:24 +0100

      Commit message:


	  
		
 Refactor merge function to use dynamic 'by.y' parameter 

    

  
    

      Package: MetaProViz

      Commit: 8eb058103691cf46afc72e7e10015d7ae44c62c3

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-31 10:21:58 +0200

      Commit message:


	  
		
 Merge pull request #122 from saezlab/main

Github pages fiixes and release 

    

  
    

      Package: MetaProViz

      Commit: f372b7a1738674d45dd8de319d109876200a661f

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-31 09:35:04 +0200

      Commit message:


	  
		
 updated column name transformation as data(tissue_meta) updated
 

    

  
    

      Package: MetaProViz

      Commit: fed4803d82938aa922cd69dd6642d71618b44fe3

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-31 08:14:26 +0200

      Commit message:


	  
		
 Fix filtering condition for HMDB ID checks

Updated filtering criteria for metabolites without HMDB ID. 

    

  
    

      Package: MetaProViz

      Commit: 2ade0f23a910eb9a12977da95aa7e213dedce820

      Author:  Jannik Franken <jannik8513@gmailcom> 

      Date: 2026-03-30 19:20:33 +0200

      Commit message:


	  
		
 Merge branch 'devel' into main
 

    

  
    

      Package: MetaProViz

      Commit: 269c00d6aa87fbb0f320877a193786563bb127d2

      Author:  Jannik Franken <jannik8513@gmailcom> 

      Date: 2026-03-30 19:18:57 +0200

      Commit message:


	  
		
 Bump version: 3.99.50 → 3.99.51
 

    

  
    

      Package: MetaProViz

      Commit: b02d7ee7caacbb35c54e9b6570b65fccb9172687

      Author:  Jannik Franken <jannik8513@gmailcom> 

      Date: 2026-03-30 16:55:07 +0200

      Commit message:


	  
		
 included new MetalinksDB annotations to metsigdb_metalinks()
 

    

  
    

      Package: MetaProViz

      Commit: 9a028c2186cc7a80eb012a694264b0c43e52409f

      Author:  Jannik Franken <jannik8513@gmailcom> 

      Date: 2026-03-30 16:34:38 +0200

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/saezlab/MetaProViz into devel
 

    

  
    

      Package: MetaProViz

      Commit: 8d6e471ed71f40d8ad1e5d4e8fc5d654bb712ac5

      Author:  Jannik Franken <jannik8513@gmailcom> 

      Date: 2026-03-30 16:34:33 +0200

      Commit message:


	  
		
 added seed_id_compatibility_check(), used by traverse_ids() as its own function
 

    

  
    

      Package: MetaProViz

      Commit: 434b13aefb69d077fa6c76b11e65d6c96deb6c1c

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-27 11:29:01 +0100

      Commit message:


	  
		
 Update readme-example-data.png
 

    

  
    

      Package: MetaProViz

      Commit: d07f9dea8884fd1f1587a127b790abf44b33c253

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-27 11:28:14 +0100

      Commit message:


	  
		
 Update readme-example-data.png
 

    

  
    

      Package: MetaProViz

      Commit: bd835a019052ee40d11576efe2535bae3bf9e49f

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-27 11:21:20 +0100

      Commit message:


	  
		
 Update DESCRIPTION
 

    

  
    

      Package: MetaProViz

      Commit: d62f020b6bd1b656360002752329bbe4e8d37605

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-27 11:17:50 +0100

      Commit message:


	  
		
  README uses now the pkgdown-recommended image location
 

    

  
    

      Package: MetaProViz

      Commit: b3c549cbe71f94d25396aab6233ab2651f658188

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-27 11:14:27 +0100

      Commit message:


	  
		
 declare nonstandard image files as article resources, especially the SVGs emitted via code chunks, since pkgdown does not reliably discover those automatically. I’m patching the vignette YAML so the site build copies those files into the article output
 

    

  
    

      Package: MetaProViz

      Commit: e1615f3e3d6d858fdd307f8f3633cebf230da2a2

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-27 11:09:24 +0100

      Commit message:


	  
		
 Figure inclusion changed
 

    

  
    

      Package: MetaProViz

      Commit: 053ade8e51b3522809479b3e296411e8cc2bf63b

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-01-27 14:57:13 +0100

      Commit message:


	  
		
 Merge pull request #121 from saezlab/devel

Devel 

    

  
    

      Package: MetaProViz

      Commit: fe10704e58f217b56a69e3d5d9cdf4eb855fae0e

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-11-27 14:55:06 +0100

      Commit message:


	  
		
 Update links in pkgdown configuration 

    

  
    

      Package: RegEnrich

      Commit: afab6db1b3cf52d7cce28783919c8a58cc538f33

      Author:  Weiyang Tao <weiyangtao1513@gmail.com> 

      Date: 2026-10-07 14:09:56 +0800

      Commit message:


	  
		
 remove a bug caused by getGEO
 

    

  
    

      Package: motifbreakR

      Commit: 79191d66d267418c562dc812ba622ad3c1e6ac85

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-06 23:30:20 -0500

      Commit message:


	  
		
 Bump version to 2.27.4
 

    

  
    

      Package: motifbreakR

      Commit: f97e5a98ae2e69b95c69d1052fa4ed6906b16b0c

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-06 22:54:12 -0500

      Commit message:


	  
		
 Use TRUE/FALSE, seq_len() and <- assignment

Clears the BiocCheck T/F warning; no behavior change.
 

    

  
    

      Package: MSstatsBioNet

      Commit: c4e6b336982d6eb3ec2b9b05247b7bc6f4394d43

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-06 17:54:24 -0400

      Commit message:


	  
		
 Added get_evidence() with the backend chosen from backend_database (#124)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> 

    

  
    

      Package: MSstatsBioNet

      Commit: 4de718300823edfda281e92170e4f23151192937

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-06 17:33:23 -0400

      Commit message:


	  
		
 Added latent-node styling and contract-based edges to cytoscapeNetwork (#123)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> 

    

  
    

      Package: MSstatsBioNet

      Commit: 7488f9d18a8336e5b7ea23db6889737ef0737e8e

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-06 16:44:56 -0400

      Commit message:


	  
		
 refactor: Make generic backend exported from MSstatsBioNet (#122) 

    

  
    

      Package: MSstatsBioNet

      Commit: e525e20b7a68adb773183bdbd687f16e3935052e

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-06 16:09:24 -0400

      Commit message:


	  
		
 refactor: incorporate getNetwork into getSubnetworkFromIndra (#121) 

    

  
    

      Package: MultiRNAflow

      Commit: e81e6a71a22654db59cd6a8a2c160c4ce74cfdeb

      Author:  Rodolphe Loubaton <loubaton.rodolphe@gmail.com> 

      Date: 2026-10-06 22:05:44 +0200

      Commit message:


	  
		
 New version: 20261006
 

    

  
    

      Package: CLAMP

      Commit: eb513622c2f1a85637d71d59056e5a4183af47c2

      Author:  msubirana <mb2subi@gmail.com> 

      Date: 2026-10-06 14:00:42 -0600

      Commit message:


	  
		
 Bump to 0.99.11: fix package URL and clarify Bioconductor availability
 

    

  
    

      Package: curatedBladderData

      Commit: 54ee1412c401c4ae8aee3467088da01a056b7291

      Author:  Markus Riester <markus.riester@novartis.com> 

      Date: 2026-10-06 14:31:02 -0400

      Commit message:


	  
		
 renamed old NEWS to README.md
 

    

  
    

      Package: enrichmet

      Commit: c3b70fb14db9b0c4cb0e0e48f8e207e0424db749

      Author:  Yonatan2627 <yaayalew@gmail.com> 

      Date: 2026-10-06 14:21:59 -0400

      Commit message:


	  
		
 Address reviewer comments
 

    

  
    

      Package: enrichmet

      Commit: 5154f333644990b9c102cc0b207b28bfe1706ddb

      Author:  Yonatan2627 <yaayalew@gmail.com> 

      Date: 2026-10-06 14:20:00 -0400

      Commit message:


	  
		
 Addressing reviewer comments
 

    

  
    

      Package: curatedBladderData

      Commit: 480a574c8ee5980554f4b97aa0a75b216a2ea91f

      Author:  Markus Riester <markus.riester@novartis.com> 

      Date: 2026-10-06 14:14:07 -0400

      Commit message:


	  
		
 Merge with upstream
 

    

  
    

      Package: curatedBladderData

      Commit: d6d092c9fe98101c5a02dff001736d495526f1d4

      Author:  Markus Riester <mriester@gmx.de> 

      Date: 2026-10-06 13:45:03 -0400

      Commit message:


	  
		
 Merge pull request #3 from lwaldron/zenodo-refactor

Move datasets to Zenodo, downloaded on demand and cached with BiocFileCache 

    

  
    

      Package: curatedBladderData

      Commit: 8d84dc7e43e74e884680a2d4a110e8b4280fa8d4

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-10-06 12:09:55 -0400

      Commit message:


	  
		
 Address Copilot review

- The integrity report verified md5 but never size_bytes, although
  R/getData.R compares size_bytes against the cached file on every cache
  hit. A wrong size in the manifest would therefore evict and re-download
  a perfectly good file on every call, silently and forever. The report
  now asserts size against both the local upload and the Zenodo API.
- DESCRIPTION said "12 studies". It is 12 objects from 10 studies:
  GSE19915 and PMID17099711 each contributed data on two platforms.
- make-data.R pointed at "inst/extdata/the curation template", a path
  that does not exist, left over from adapting the script from
  curatedCRCData. Removed.

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

    

  
    

      Package: curatedBladderData

      Commit: 445e97c6de5d8ddb4de42d65060affa0231e30f7

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-10-06 11:54:52 -0400

      Commit message:


	  
		
 Finalize Zenodo manifest for record 23192472

All 12 uploaded files verified: the manifest md5s and sizes match what
the Zenodo API reports, every object is all.equal to the .rda it
replaces (inst/scripts/data-integrity-report.Rmd), and the full test
suite passes including a live download and a cache hit.

R CMD check is clean. The source tarball drops from about 75 MB to
1.4 MB.

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

    

  
    

      Package: curatedBladderData

      Commit: f5fe6d99a0451bc480cc01b871dd2d391ed66ad5

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-10-06 11:29:46 -0400

      Commit message:


	  
		
 Move datasets to Zenodo with BiocFileCache caching

Replaces the 75 MB of data/*.rda with on-demand download from Zenodo,
cached per-file in a package-specific BiocFileCache and verified against
md5 checksums in inst/extdata/zenodo-manifest.csv. URLs are placeholders
until the Zenodo record is published.

- New exported getter curatedBladderData(): no args lists datasets, one
  name returns an ExpressionSet, several return a named list; test=TRUE
  loads small offline subsets from inst/extdata/testdata/.
- data(X) keeps working via data/*.R delayedAssign stubs that delegate to
  the getter with a once-per-session deprecation message. During this
  package's own R CMD check the stubs resolve to the offline subsets, so
  checking needs no network. data/datalist is retained so installation
  does not execute the stubs, and BuildResaveData: no stops R CMD build
  from re-saving them as .rda.
- createEsetList.R loads through the getter, with a new test.mode option
  in the patientselection config.
- Vignette documents the caching and runs on the offline subsets.
- Adds testthat tests and inst/scripts/ for regenerating everything.

Also fixes several pre-existing issues noticed along the way: biocViews
claimed OvarianCancerData, the package help page described ovarian cancer
with the wrong author list and maintainer, affy was depended on but
unused, and createEsetList.R errored when filters excluded every dataset.

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

    

  
    

      Package: MSstatsBioNet

      Commit: 9d11e124b5e1f5526a02f5c342c3cf14f54f8e8f

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-06 13:15:52 -0400

      Commit message:


	  
		
 Added internal convert_ids() and get_annotations() for INDRA (#120)

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

    

  
    

      Package: gDRcore

      Commit: 858d3cf28e7382a461c6095e5a6346c076fe32c9

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

      Date: 2026-10-06 19:00:46 +0200

      Commit message:


	  
		
 Merge pull request #210 from gdrplatform/GDR-3543

fix: prevent normalizing a time-course growth rate against a control that is not growing 

    

  
    

      Package: gDRcore

      Commit: d1fc0557371e368ef46a37bbf61d0c68a6f49ec3

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-10-01 13:05:53 +0200

      Commit message:


	  
		
 fix: reject a plateaued control as a growth-rate denominator

A control that stops growing fits to a slope of order 1e-16 rather than exact
zero, so the rate_0 <= 0 guard passed it through and normalized a healthy
treated rate into ~1e15 with no warning. Compare against a fitting tolerance
instead, and cover the flat-control path in tests.

Also assert that the input assay provides a column of its own name before
building the default rate function, and record the 4-significant-figure
assumption in the row key.
 

    

  
    

      Package: gDRcore

      Commit: 157a3f95638a2b0d21242055d104403f83c11d11

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-09-24 13:48:37 +0200

      Commit message:


	  
		
 fix: prevent normalizing a time-course growth rate against a control that is not growing

A window placed past the point where the untreated arm stops growing yields a
non-positive control rate. Dividing by it does not inflate the ratio, it inverts
its sign: a treated arm growing at +0.087 against a control at -0.005 is reported
as -19.3, on the scale a reader inspects for cell death.

This reached a delivered report. In INC-000019 the 22RV1 late window has
rate_0 = -0.00452 and twelve normalised values between -4.2 and -19.3, all for
arms that were growing. A sweep of the 23 published reports that carry a
growth-rate table found no other non-positive control rate.

NormalizedGrowthRate is now NA for the affected (cell line, period) and a warning
names them. NA rather than an error, because the other cell lines of the same run
are usually unaffected - two of the three in that report were fine, and failing
the run would have withheld their results too. GrowthRate and rate_0 are kept, so
the reason stays visible.

A small but positive control rate inflates the ratio without the sign flip and is
not caught here; that needs the control's own peak rate, which this function does
not see.
 

    

  
    

      Package: curatedOvarianData

      Commit: 9fe91924836da9da26686136741a4bfe6e4551bb

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-10-06 12:15:55 -0400

      Commit message:


	  
		
 Integrity report: verify size_bytes, not just md5

R/getData.R compares size_bytes against the cached file on every cache
hit, so a wrong size in the manifest would silently evict and
re-download a valid file on every call, with no error. The integrity
report checked md5 only, and so was blind to the one field that drives
that behaviour. It now asserts size against both the local upload and
the Zenodo API.

The published manifest is correct: the strengthened report passes
against Zenodo record 23125873 unchanged. This closes the gap for future
regenerations.

Found by Copilot review on lima1/curatedBladderData#3, which carries the
same report.

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

    

  
    

      Package: curatedCRCData

      Commit: b01815bb50af1f1c3f27d970c84fb8eec90b59f0

      Author:  Levi Waldron <lwaldron.research@gmail.com> 

      Date: 2026-10-06 12:15:35 -0400

      Commit message:


	  
		
 Integrity report: verify size_bytes, not just md5

R/getData.R compares size_bytes against the cached file on every cache
hit, so a wrong size in the manifest would silently evict and
re-download a valid file on every call, with no error. The integrity
report checked md5 only, and so was blind to the one field that drives
that behaviour. It now asserts size against both the local upload and
the Zenodo API.

The published manifest is correct: the strengthened report passes
against Zenodo record 23125734 unchanged. This closes the gap for future
regenerations.

Found by Copilot review on lima1/curatedBladderData#3, which carries the
same report.

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

    

  
    

      Package: rhdf5

      Commit: 7f5e5fcafe5c0defd62fa41c9695de763b74e8d0

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-06 14:49:47 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: 374f49c7ace9e34169970eef1ce2cb98a57111d4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-06 14:49:40 +0200

      Commit message:


	  
		
 Document storage.mode extra length fix in NEWS
 

    

  
    

      Package: rhdf5

      Commit: dd74ffa31004d6b1bdc691562b068ab4db232cef

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-06 14:46:42 +0200

      Commit message:


	  
		
 Do not silently ignore storage.mode of length > 1
 

    

  
    

      Package: Rarr

      Commit: 4357a13f78b45c985f3007a0abad5695bb840ce6

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-06 18:03:08 +0200

      Commit message:


	  
		
 Stay DRY in error message
 

    

  
    

      Package: Rarr

      Commit: 8525081ed8f99bb774cb95c6d33a19db05508c68

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-06 13:44:14 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: 809a98f409f095b19a267c44f321567f39dac55d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-06 13:44:00 +0200

      Commit message:


	  
		
 Document progressr addition in NEWS
 

    

  
    

      Package: Rarr

      Commit: 13f16fbf8a7e9123b50bb749420639dea89a6efd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-05 16:47:17 +0200

      Commit message:


	  
		
 Use progress bar
 

    

  
    

      Package: MSstatsBioNet

      Commit: 0d56a4d52a755b98061d93774cb8377b88ddaac5

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-06 11:06:38 -0400

      Commit message:


	  
		
 refactor: Added internal entity table for the network-backend API (#118)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> 

    

  
    

      Package: MSstatsBioNet

      Commit: f6d923e8eb8f02153296dfefd59f606c035f8e8b

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-06 10:47:47 -0400

      Commit message:


	  
		
 refactor: rename log2FC to logFC to account for multiple log transformation scales (#119) 

    

  
    

      Package: GeDi

      Commit: 159f29806dd87ff32abe451835e1898f4030e502

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-10-06 13:42:23 +0200

      Commit message:


	  
		
 deps picked up anyways via Bioc version, so it should not be needed
 

    

  
    

      Package: GeDi

      Commit: d0bf931e0463d9b99b4e6a3682b7f8162f5e2e4d

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-10-06 13:08:36 +0200

      Commit message:


	  
		
 version bump, 1.9.1
 

    

  
    

      Package: GeDi

      Commit: 34e0b77071668b0f6fd64baa3309b8f41783c154

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-10-06 13:08:27 +0200

      Commit message:


	  
		
 added pinning to recent version of stringdb to avoid having it not updated
 

    

  
    

      Package: GeDi

      Commit: eee912117882b1bda8df285c7027e20e5c6acc7b

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-10-06 13:01:47 +0200

      Commit message:


	  
		
 rewritten namespace as in roxygen v8+
 

    

  
    

      Package: GeDi

      Commit: ae0c6d2862de1c11b43b56f59902fcc04f772683

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-10-06 13:01:36 +0200

      Commit message:


	  
		
 rendered the manpages again
 

    

  
    

      Package: GeDi

      Commit: 326771bb554b95c81af05a428a8b35f93ab38caa

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-10-06 13:00:55 +0200

      Commit message:


	  
		
 retrieval of the scores is now compatible with the newer version of stringdb
 

    

  
    

      Package: GeDi

      Commit: b24bd5294832f1c49ce8c892f005b1955233d936

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-10-06 13:00:24 +0200

      Commit message:


	  
		
 updated version of roxygen
 

    

  
    

      Package: GeDi

      Commit: 90958bfd339c6fdb4ec31ae0c6edb504c2eb4ad3

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2026-10-06 12:36:28 +0200

      Commit message:


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

    

  
    

      Package: GeDi

      Commit: b054851c039ae5a8d882f3714300786fd59bd1f4

      Author:  Federico Marini <marinif@uni-mainz.de> 

      Date: 2025-11-27 18:10:11 +0100

      Commit message:


	  
		
 empty poke to bump and trigger workflow
 

    

  
    

      Package: gDRutils

      Commit: e12bb8a406c025e4f8f739f8e6eab01df8e30b03

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

      Date: 2026-10-06 11:45:44 +0200

      Commit message:


	  
		
 Merge pull request #202 from gdrplatform/GDR-3655

fix: stop curve fitting from corrupting the global na.action option 

    

  
    

      Package: gDRutils

      Commit: b6198acd1bf73c9c394b5163d93a95eea4f47842

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-10-05 12:38:12 +0200

      Commit message:


	  
		
 chore: start the second NEWS entry with a verb the linter accepts

lintNewsEntries rejected 'pass' as it is not in VALID_VERBS, which halted
checkPackage before anything after it could run - so the red CI reported a
build failure with no failing test behind it.
 

    

  
    

      Package: gDRutils

      Commit: 1bfbb5b2ea2aef1c9edfd9f240a4aa511c2f41b3

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-10-02 08:58:36 +0200

      Commit message:


	  
		
 fix: stop curve fitting from corrupting the global na.action option

drc 4.0-0 records the na.action argument of drm() in the global option
exactly as written, and never restores it. Both call sites passed
stats::na.omit, so a single fit left the option set to the string
"stats::na.omit"; every later stats::lm() in that session then failed in
model.frame() with could not find function "stats::na.omit".

Measured: 31 of 345 tests in gDRcore's time-course suite fail this way,
all of them in code that calls stats::lm() after a fit has run. drc 3.0.1
does not have the behaviour, which is why it has gone unnoticed.

Restore the option on exit rather than only dropping the namespace
prefix: drm overwrites whatever the caller had set, so a user running
with na.exclude lost it too.
 

    

  
    

      Package: OHCA

      Commit: 8ef6242d336e8c8875f4afb2164b47c4d0fbcea4

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-06 11:42:10 +0200

      Commit message:


	  
		
 fix: python chapter imports cooler on the Bioconductor builders (#8)

* fix: python chapter imports cooler on the Bioconductor builders

The Bioconductor build stopped at `import cooler` in
interoperability-python.qmd:
  libssl.so.3: version `OPENSSL_3.2.0' not found (required by
  .../envs/OHCA/lib/python3.12/site-packages/h5py/../../.././libcurl.so.4)
h5py's HDF5 needs libcurl, and the python environment's libcurl needs
OpenSSL >= 3.2; R had already loaded the system's OpenSSL (3.0 on Ubuntu
24.04) through the openssl package, and the environment's libcurl was
bound to it. A hidden first chunk now loads R's curl package, so the
system's libcurl is already in the process and HDF5 uses it. Reproduced
and checked on Ubuntu 24.04 with this book's environment (cooler 0.10.4,
h5py 3.16.0, libcurl 8.22.0, openssl 3.6.5). Pinning openssl to 3.0 in
requirements.yml cannot be solved.

curl joins Imports. Rfast leaves them: no page uses it, and its binary
does not load on the Bioconductor devel image, which failed R CMD check
when installing the book.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* bump to 1.9.2

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

--------- 

    

  
    

      Package: Chromatograms

      Commit: dd13d1dfe9cdda810fa872b151fc53ed792bd517

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-10-06 11:27:11 +0200

      Commit message:


	  
		
 Sync package to 1.3.4
 

    

  
    

      Package: planttfhunter

      Commit: e32b42f93a007723467da1a361c894c5e24c4b52

      Author:  almeidasilvaf <fabricio_almeidasilva@hotmail.com> 

      Date: 2026-10-06 10:23:03 +0200

      Commit message:


	  
		
 Updated GHA workflow to use {rworkflows}
 

    

  
    

      Package: planttfhunter

      Commit: e19b0ccb07604550aa964e6d52ceb54e1b58642d

      Author:  almeidasilvaf <fabricio_almeidasilva@hotmail.com> 

      Date: 2026-10-06 10:11:45 +0200

      Commit message:


	  
		
 Version bump in devel
 

    

  
    

      Package: planttfhunter

      Commit: 983b07d07dd42527680ee42172f3b5a272717780

      Author:  almeidasilvaf <fabricio_almeidasilva@hotmail.com> 

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

      Commit message:


	  
		
 New feature: classification schemes of TAPscan and Plant-TFClass now available
 

    

  
    

      Package: xcms

      Commit: d430faeb343625ec556fd4d931e67f34bec8d6ab

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

      Date: 2026-10-06 09:37:54 +0200

      Commit message:


	  
		
 Merge pull request #848 from computational-metabolomics/issue844_lcmsPlot

docs: add vignette for using lcmsPlot with xcms 

    

  
    

      Package: xcms

      Commit: cc1f12f16ef1497aeb943d00efc53b0cd8c3b1b1

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-09-04 11:33:12 +0100

      Commit message:


	  
		
 docs: add vignette for using lcmsPlot with xcms

lcmsPlot is a Bioconductor package for plotting
LC-MS data in a grammar-of-graphics manner.

The vignette shows how to plot different aspects
of an LC-MS dataset using an xcms preprocessed
results object (using `loadXcmsData()`).
 

    

  
    

      Package: NanoMethViz

      Commit: f07db65364e0fcc5c4f6c3eeac1f5132eeecc28f

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:28:18 +1100

      Commit message:


	  
		
 Updated ignore files
 

    

  
    

      Package: NanoMethViz

      Commit: 79cdbef901040cb7278f6ab0d9fefc3182e5b0ca

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:25:37 +1100

      Commit message:


	  
		
 Version bumped to v3.9.4
 

    

  
    

      Package: NanoMethViz

      Commit: 5b433dce8427ea96f849a356fcfbe97f1abe4395

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:24:16 +1100

      Commit message:


	  
		
 Merge branch 'fix/import-infra' into devel
 

    

  
    

      Package: NanoMethViz

      Commit: d409d2ec8b4cab6f9a93bc7bb1bad83b71f4dcca

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:24:09 +1100

      Commit message:


	  
		
 Updated NEWS
 

    

  
    

      Package: NanoMethViz

      Commit: b263b11f1e3a00086bd6e1b8b23a73dafe9e04fb

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:22:11 +1100

      Commit message:


	  
		
 Updated NEWS
 

    

  
    

      Package: NanoMethViz

      Commit: 4d3a137b34fb7ac5b0b8659c7d6ab8f2d6b7bce3

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:21:50 +1100

      Commit message:


	  
		
 Fixed convert_methy_format default sample names for compressed inputs
 

    

  
    

      Package: NanoMethViz

      Commit: b089f0d0969048031cb59383c98b800a45a292c7

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:14:50 +1100

      Commit message:


	  
		
 Fixed default sample names when input files have different extensions
 

    

  
    

      Package: NanoMethViz

      Commit: 5ef3b5a206b713d4a734ac3c587156d547fefbfc

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:06:21 +1100

      Commit message:


	  
		
 Fixed modkit import merging all modification codes into one call set
 

    

  
    

      Package: NanoMethViz

      Commit: 4c7e4fb77650a42f1da776f4d1f37ba3e89f8e65

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:05:47 +1100

      Commit message:


	  
		
 Fixed default sample names keeping .tsv from compressed input files
 

    

  
    

      Package: NanoMethViz

      Commit: caf6199766f7abac33f2556b340b9c0011d231a2

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:04:11 +1100

      Commit message:


	  
		
 Fixed sort failures being ignored during tabix creation and merging
 

    

  
    

      Package: NanoMethViz

      Commit: 749b09186dec262d9844c116929239363f1f1711

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 18:01:03 +1100

      Commit message:


	  
		
 Fixed handling for .csi indices
 

    

  
    

      Package: NanoMethViz

      Commit: 56e93237f48042e3b12d549e281a925c340d2682

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 12:03:48 +1100

      Commit message:


	  
		
 Fixed querying when multiple bam files are involved but chromosome is not uniforming missing
 

    

  
    

      Package: NanoMethViz

      Commit: bd3975db805cd5e740d55770aca0b0e6e19f2075

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 11:46:11 +1100

      Commit message:


	  
		
 Fixed query_methy_modbam when the same chromosome multiple times interleaved with other chromosomes
 

    

  
    

      Package: NanoMethViz

      Commit: e2e67d21028c1e3e10bf910564044d1d3f280c1d

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-06 11:41:49 +1100

      Commit message:


	  
		
 Refactored query_methy and fixed documentation
 

    

  
    

      Package: NanoMethViz

      Commit: 33cd12dd1d76ca5b21798a0bc3366c740a65ce27

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:56:37 +1100

      Commit message:


	  
		
 Version bump to v3.9.3
 

    

  
    

      Package: NanoMethViz

      Commit: e5b40f743d398abeb2035ade2e9322e6713e9fbc

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:50:11 +1100

      Commit message:


	  
		
 Merge branch 'fix/multicode-mm' into devel
 

    

  
    

      Package: NanoMethViz

      Commit: f82dd53e4c49149f81c4cab1eb9e8ea8e09fe61c

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:49:52 +1100

      Commit message:


	  
		
 Fixed handling for mm fields with multiple modcodes
 

    

  
    

      Package: NanoMethViz

      Commit: 941ddc4dd65ab1d269090a29b832b3badf8c1ae3

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:48:30 +1100

      Commit message:


	  
		
 Fixed potential sample name misordering after C++ conversion
 

    

  
    

      Package: NanoMethViz

      Commit: 169711991071133534c3f42b5cc8b93f035d648d

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:27:34 +1100

      Commit message:


	  
		
 Version bump to v3.9.2
 

    

  
    

      Package: NanoMethViz

      Commit: 99ef9ec356495871bfe1d755eda25d7392702f10

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:26:19 +1100

      Commit message:


	  
		
 Merge branch 'fix/modbam-tabi-and-globals' into devel
 

    

  
    

      Package: NanoMethViz

      Commit: 6521484850a217ba73352a25aac7a4d4fa8bfe49

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:26:09 +1100

      Commit message:


	  
		
 Fixed tbi file being left behind after indexing
 

    

  
    

      Package: NanoMethViz

      Commit: a81a40effef740fa281b22127fd24bcc95d33230

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:25:57 +1100

      Commit message:


	  
		
 Fixed global C++ leaking between calls
 

    

  
    

      Package: NanoMethViz

      Commit: 6744a974191f533abdf1dcb773cbea6b26bc54ec

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:19:59 +1100

      Commit message:


	  
		
 Merge branch 'fix/plot-mds-scaling' into devel
 

    

  
    

      Package: NanoMethViz

      Commit: f162593f17b26529db312c7c396320b74978c797

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:19:09 +1100

      Commit message:


	  
		
 Fixed plot_mds plotting unscaled MDS eigenvectors
 

    

  
    

      Package: NanoMethViz

      Commit: cfa30eb0633b1a60280b3825e90f88179ef1e86e

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-10-05 22:16:48 +1100

      Commit message:


	  
		
 Fixed modkit ref_position being treated as 1-based
 

    

  
    

      Package: ChIPseeker

      Commit: df67ad44b3d5772439fb74d6c66fb6751bc14e7a

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-05 18:09:17 +0800

      Commit message:


	  
		
 handle an empty peak set instead of failing with unrelated errors

annotatePeak(GRanges(), TxDb = txdb) failed with "Error: invalid subscript"
and, with addFlankGeneInfo, with "replacement has 1 row, data has 0".

Root cause is the same as in #238: for an empty query follow()/precede()
return a SortedByQueryHits object rather than indices, which is not a valid row
subscript. getNearestFeatureIndicesAndDistances() now returns empty index,
distance and peak vectors in that case, and annotatePeak() returns an empty
csAnno (0 rows, peakNum 0, empty detailGenomicAnnotation and annoStat) before
the steps that are not defined for zero peaks. seq2gene() returns
character(0) for an empty input as a result of the same guard.

Covered for the plain call and for addFlankGeneInfo + annoDb.
 

    

  
    

      Package: ChIPseeker

      Commit: 762b22f09a8b41f1ac01045d05aeee87cd571254

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-05 16:53:39 +0800

      Commit message:


	  
		
 correct the seqlevelsStyle advice in the dropped-peaks error, document tagMatrix value changes

Found while reviewing the batch of issue fixes.

1. The message added for #238 told users to run seqlevelsStyle(peak) <- "NCBI"
   to obtain NC_000001.11 names and seqlevelsStyle(TxDb) <- "Ensembl" to go
   the other way. Checked against the installed GenomeInfoDb, both statements are
   wrong: the replacement form is the only interface (seqlevelsStyle() takes a
   single argument), "Ensembl" yields "1" and not "chr1", names such as
   NC_000001.11 are reported as style "RefSeq" and are not mapped
   automatically, and the "GenBank" target style is not supported. The message
   now suggests seqlevelsStyle(peak) <- "UCSC" for the common 1/chr1 mismatch
   and gives an explicit sub() rename for accession names, which is what the
   book chapter now documents as well.

2. The #238 guard only fires for a non-empty input (peakNum > 0), so that an
   empty input is not reported as "all 0 peaks were dropped".

3. The #250 entry now states the numerical impact of the binning rewrite
   instead of only mentioning the off-by-one divisor: the last bin of a section
   used to be divided by count-1 (~10% too high for a 10 bp bin) and all
   leftover positions went into that bin instead of being spread (up to ~40%
   difference for a 7 bp remainder in a 300 bp bin).
 

    

  
    

      Package: ChIPseeker

      Commit: ec4ca72a16514e78a218fdf6849b0b01e534b289

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-05 16:01:23 +0800

      Commit message:


	  
		
 upsetplot(): make the vennpie sub-view drawable with ggplot2 >= 4.0

ggimage embeds the vennpie sub-view as an annotation_custom() layer and
ggplot2 4.0 only accepts such layers below coord_cartesian(), so
upsetplot(vennpie = TRUE) failed to be drawn:

  `annotation_custom()` only works with `coord_cartesian()`

coord_fixed() is therefore removed without a replacement: ggplotify rasterises
the grob with the aspect ratio of the device, so forcing a square panel only
distorted the venn diagram further (measured anisotropy sqrt(lambda1/lambda2)
1.43 without versus 1.50 with theme(aspect.ratio = 1), against 1.41 for the
undistorted base graphics drawing).

test-upsetplot.R builds a minimal csAnno and draws both variants, which is what
the previous object-class-only checks missed. NEWS also notes the harmless
`size` deprecation warning that ggupset 0.4.1 itself still triggers.
 

    

  
    

      Package: ChIPseeker

      Commit: fd995f5696d39211ff463fb9be5dd6a91ed9b76b

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-04 23:15:51 +0800

      Commit message:


	  
		
 add opt-in symmetric p-value to enrichPeakOverlap()

Follow-up of #84. The default stays the one-sided permutation test, so no
existing number changes. With symmetric = TRUE the mirrored direction is
computed as well (new internal function enrichOverlap.peak.mirrored(): the
target peaks are kept fixed and the query peaks are shuffled) and the two
one-sided p-values are combined as min(1, 2*min(p, p_rev)) (Hedges), which
makes the result independent of the argument order. Measured on a peak pair
with |A| = 20 and |B| = 100: the one-sided p-value is 0.0099 in both
directions only because it saturates the permutation floor, while the
symmetric p-value is 0.0198 in both directions.

Documented the two consequences of the option: the number of permutations
doubles and the smallest reportable p-value becomes 2/(nShuffle+1).

Also fixed enrichAnnoOverlap(), which had the same unwrapped-GRanges target
bug as enrichPeakOverlap(); its hypergeometric p-value turned out to be
exactly symmetric already, so it needs no symmetric argument.
 

    

  
    

      Package: ChIPseeker

      Commit: 9c0ed04a46a1609f445e20276376cc3821a5c1d7

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-04 22:33:57 +0800

      Commit message:


	  
		
 enrichPeakOverlap(): accept a single GRanges target, document the test direction

#84: a bare GRanges passed as targetPeak was forwarded unwrapped while the
permutation test works on a list of target peak sets, so
enrichPeakOverlap() failed with "GRanges objects don't support [[, as.list(),
lapply()"; it is now wrapped in a list.

The reported p-value asymmetry is a property of the test, not a counting bug:
N_OL is the same in both directions (it is |A and B|), while the tested
quantity is the fraction of *target* peaks covered by the query peaks and the
null distribution shuffles the target, so exchanging the arguments asks the
mirrored question and normalises by the other peak set. This is now stated in
the documentation of enrichPeakOverlap(), together with the reason why N_OL of
enrichAnnoOverlap() can exceed the number of input peaks (it counts genes, one
per peak, and a peak can overlap several target genes).
 

    

  
    

      Package: ChIPseeker

      Commit: b5639ba981993ff133879b3dfc4b5939b22097a3

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-01 10:47:18 +0800

      Commit message:


	  
		
 fix "invalid subscript" on dropped peaks and clarify plotAvgProf() xlim

#238: annotatePeak() failed with "Error: invalid subscript" when *every*
peak was dropped, which typically happens when no seqlevel of the peaks
matches TxDb ('chr1' vs 'NC_000001.11', as in the mouse case reported).
follow() returns a SortedByQueryHits object instead of indices for an empty
query, and that object was used as a row subscript of features(). The
annotation code now uses integer(0) for an empty query and annotatePeak()
reports the seqlevels mismatch together with the seqlevelsStyle() fix.
Reproduced with the parameters of the issue (mm10 TxDb + org.Mm.eg.db +
addFlankGeneInfo = TRUE) and with hg19.

#240: plotAvgProf()/plotMultiProf() stopped with "please specify
appropreate xcoordinations...". xlim defines the x-axis coordinates, so its
width has to match the number of columns of the tag matrix; checkXlim() now
says which xlim is expected, fixes the typo and accepts both valid forms.
 

    

  
    

      Package: ChIPseeker

      Commit: 83ffce788fedd8bc370135438f95864704fe0066

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-01 10:23:55 +0800

      Commit message:


	  
		
 fix transcript/gene level annotation consistency and sub-1kb flank binning

Issues #252, #248, #250, #254, #235 (see ISSUE_AUDIT_SUMMARY.md for the audit).

#252: the transcript id of an exon/intron/UTR hit was taken from
names(genomicRegion)[subjectIndex], which indexes the *unlisted* ranges with
the names of the GRangesList. This mostly returned NA and occasionally a
wrong transcript, so annotatePeak() reported the metadata of an unrelated
transcript (even on another chromosome).  The ids are now expanded before
indexing, the Promoter branch writes the feature id reset into `anno`
instead of a stale local variable, and .alignAnnotationFeature() aligns the
reported feature (transcript by tx_id, gene by gene_id) with the feature
that supplied the annotation, recalculating its TSS distance.

#248: seq2gene() no longer fails with "$ operator is invalid for atomic
vectors" when no region overlaps an exon/intron (getGenomicAnnotation.
internal() returns NA then).

#250: getTagMatrix()/plotPeakProf2(type = "body") no longer fail with
"Error in cursor:(cursor + seq - 1) : result would be too long a vector" for
flank extensions shorter than 1kb: the flank share of the bins is derived
from the actual length, a non-empty flank always gets at least one column,
and the binning loops were replaced by edge-based averaging (also fixing an
off-by-one divisor in the last bin).

#254: downloadGEObedFiles()/downloadGSMbedFiles() rewrite ftp:// urls of
gsminfo$supplementary_file to https:// and report the download error.

#235: documented the distance definition of flank_gene_distances (0 means the
peak overlaps the feature range).

New tests: test-seq2gene.R, test-getFlankingGene.R, test-GEO.R plus
#252/#250 cases in test-annotatePeak.R and test-getTagMatrix.R.
 

    

  
    

      Package: ChIPseeker

      Commit: 512d5fbf22adba5532be709306cce3998ddce2a6

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 11:51:15 +0800

      Commit message:


	  
		
 de-duplicate repeated @importFrom tags and drop a stale comment

Remove four tags duplicated within a single roxygen block (geom_hline,
element_blank, yulab.utils::get_cache_item, and a copy-pasted four-line
block tail before getBioRegion), plus a commented-out geom_segment() call
in covplot(). No NAMESPACE change: roxygen already deduplicated these.
 

    

  
    

      Package: ChIPseeker

      Commit: 1e18e91d4215017195650159b44b4b85080742a2

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 11:36:04 +0800

      Commit message:


	  
		
 drop unused ggplot2::geom_segment import from covplot()

It only ever appeared in a commented-out call, so the import was dead.
 

    

  
    

      Package: ChIPseeker

      Commit: ea80470f9581d50bb12be7e70d47e00131d48865

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 11:29:34 +0800

      Commit message:


	  
		
 drop dead @importFrom imports from plotDistToTSS()

ggplot2::geom_text, ggplot2::scale_fill_brewer and ggplot2::scale_fill_hue
had no call site anywhere in the package, so the generated NAMESPACE
imported them for nothing.
 

    

  
    

      Package: ChIPseeker

      Commit: 9a92f5367ddb5a6b47a337ea3911cf6b9717ab98

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 11:02:47 +0800

      Commit message:


	  
		
 upsetplot(): drop deprecated ggplot2::aes_()

upsetplot.csAnno() mapped the x aesthetic with aes_(x = ~anno). Replace it with
the tidy evaluation idiom aes(x = .data$anno) and regenerate NAMESPACE, so aes_
is no longer imported from ggplot2. This matches the aes_string() cleanup already
done for plotAnnoBar() in 1.49.2.

Verified: R CMD INSTALL + test_check("ChIPseeker") pass, and upsetplot() still
returns a ggplot object that renders (with and without vennpie = TRUE).
 

    

  
    

      Package: epiSeeker

      Commit: c276887fd480420c4d0f43121fa42a7ed2730179

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-05 18:09:52 +0800

      Commit message:


	  
		
 handle an empty peak set instead of failing with an unrelated error

annotateSeq(GRanges(), TxDb = txdb) failed with "Error: invalid subscript",
the same root cause as #238: follow()/precede() return a SortedByQueryHits
object rather than indices for an empty query, which is not a valid row
subscript. annotateSeq() now returns an empty csAnno (0 rows, peakNum 0, empty
detailGenomicAnnotation and annoStat) before the steps that are not defined for
zero peaks.

Note: unlike ChIPseeker, getNearestFeatureIndicesAndDistances() here is left
untouched, so seq2gene() still fails on an empty input; the guard belongs to the
shared helper and can be added when the two packages are next synchronised.
 

    

  
    

      Package: epiSeeker

      Commit: 798c529bee5719597cbb992934d6cb962989631a

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-05 16:53:54 +0800

      Commit message:


	  
		
 correct the seqlevelsStyle advice in the dropped-peaks error

Found while reviewing the batch of fixes. The message added for #238 told users
to run seqlevelsStyle(peak) <- "NCBI" to obtain NC_000001.11 names and
seqlevelsStyle(TxDb) <- "Ensembl" to go the other way; against the installed
GenomeInfoDb both are wrong. seqlevelsStyle() only has the replacement form,
"Ensembl" yields "1" and not "chr1", accession names such as NC_000001.11 are
reported as style "RefSeq" and are not mapped automatically, and the "GenBank"
target style is unsupported. The message now suggests
seqlevelsStyle(peak) <- "UCSC" for the common 1/chr1 mismatch and an explicit
sub() rename for accession names. The guard also only fires when the input was
not empty, so an empty input is not reported as "all 0 peaks were dropped".
 

    

  
    

      Package: epiSeeker

      Commit: e396ab35252a45ede2f22347910900b37f7027b6

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-05 16:01:39 +0800

      Commit message:


	  
		
 upsetplot(): make the vennpie sub-view drawable with ggplot2 >= 4.0

Two obstacles, both caused by ggimage embedding the sub-view as an
annotation_custom() layer, which ggplot2 4.0 only accepts below
coord_cartesian():

  `annotation_custom()` only works with `coord_cartesian()`

  * the sub-view no longer uses coord_fixed(), and coord_fixed is no longer
    imported;
  * the parent plot keeps the ggupset coordinate system (CoordCombMatrix),
    which rejects annotation_custom() altogether, so it is converted with
    ggplotify() first.

No replacement for coord_fixed() is added: ggplotify rasterises the grob with
the aspect ratio of the device, so forcing a square panel only distorted the
venn diagram further (measured anisotropy sqrt(lambda1/lambda2) 1.43 without
versus 1.50 with theme(aspect.ratio = 1), against 1.41 for the undistorted
base graphics drawing).

test-upsetplot.R now draws the plot instead of only checking the class, which is
what let this slip through; the plain UpSet plot is covered as well. NEWS also
notes the harmless `size` deprecation warning from ggupset 0.4.1.
 

    

  
    

      Package: epiSeeker

      Commit: b5de0056b67f84e90c4e71d16f6c8f2579e71f89

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-04 23:16:04 +0800

      Commit message:


	  
		
 add opt-in symmetric p-value to enrichPeakOverlap()

Follow-up of #84 in ChIPseeker. The default stays the one-sided permutation
test, so no existing number changes. With symmetric = TRUE the mirrored
direction is computed as well (new internal function
enrichOverlap.peak.mirrored(): the target peaks are kept fixed and the query
peaks are shuffled) and the two one-sided p-values are combined as
min(1, 2*min(p, p_rev)) (Hedges), making the result independent of the
argument order.

The number of permutations doubles and the smallest reportable p-value becomes
2/(nShuffle+1); both are documented in ?enrichPeakOverlap.
 

    

  
    

      Package: epiSeeker

      Commit: dcf4f01b3c953317c19c445c029a0d1c3b9380fc

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-04 22:34:21 +0800

      Commit message:


	  
		
 accept a single GRanges as enrichOverlap target and document the test direction

Same defect as #84 in ChIPseeker: enrichPeakOverlap() and enrichAnnoOverlap()
forwarded a bare GRanges targetPeak unwrapped while the overlap code works on a
list of target peak sets, so the call failed with "GRanges objects don't support
[[, as.list(), lapply()". It is now wrapped in a list.

The documentation of enrichPeakOverlap()/enrichAnnoOverlap() also states that
the test is one-sided (the observed ratio is the fraction of *target* peaks
covered by the query peaks and the target is the shuffled set, so N_OL is
direction free while the p-value is not) and that N_OL of enrichAnnoOverlap()
counts genes and can therefore exceed the number of input peaks.
 

    

  
    

      Package: epiSeeker

      Commit: bcee6c5df5a17c679b6430fd26755adaa318434d

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-01 10:48:00 +0800

      Commit message:


	  
		
 fix "invalid subscript" when annotateSeq() drops every peak

Same defect as #238 in ChIPseeker: follow() returns a
SortedByQueryHits object instead of indices for an empty query, which
.get_distance_to_gene_end() then used as a row subscript of features().
With peaks whose seqlevels do not match TxDb (e.g. 'chr1' vs
'NC_000001.11') every peak is dropped and annotateSeq() failed with
"Error: invalid subscript". The helper now returns numeric(0) for an empty
query and annotateSeq() reports the seqlevels mismatch with the
seqlevelsStyle() fix.
 

    

  
    

      Package: epiSeeker

      Commit: 16e4c4bc14f2647ff187324ae36cce2b2065f1fa

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-10-01 10:24:04 +0800

      Commit message:


	  
		
 mirror the ChIPseeker annotation/seq2gene/GEO fixes, gene level included

The issues below are tracked in ChIPseeker (see its ISSUE_AUDIT_SUMMARY.md)
and the same defects exist in epiSeeker.

#252: the transcript id of an exon/intron/UTR hit was taken from
names(genomicRegion)[subjectIndex], which indexes the *unlisted* ranges with
the names of the GRangesList. This mostly returned NA and occasionally a
wrong transcript, so annotateSeq() reported the metadata of an unrelated
transcript (even on another chromosome). The ids are now expanded before
indexing and .align_annotation_feature() aligns the reported feature
(transcript by tx_id, gene by gene_id) with the feature that supplied the
annotation, recalculating its TSS distance.

#248: seq2gene() no longer fails with "$ operator is invalid for atomic
vectors" when no region overlaps an exon/intron.

#254: downloadGEObedFiles()/downloadGSMbedFiles() rewrite ftp:// urls of
gsminfo$supplementary_file to https:// and report the download error.

#235: documented the distance definition of flank_gene_distances (0 means the
peak overlaps the feature range).

Tests added for the gene level alignment, seq2gene and the GEO urls; a
sub-1kb flank body tag matrix test guards the (unaffected) epiSeeker binning
path against regressions.
 

    

  
    

      Package: epiSeeker

      Commit: e0e50eee0d4b70dc7d70b7820a49d6a73438e954

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 11:51:23 +0800

      Commit message:


	  
		
 de-duplicate @importFrom and drop unused gridBase from Suggests

Remove a within-block duplicate `ggplot2::geom_hline` tag, and drop the
`gridBase` Suggests entry, which nothing in R/, tests/ or vignettes/
references. No NAMESPACE change.
 

    

  
    

      Package: epiSeeker

      Commit: de28763595cce1d102254c928d8ca250485ed008

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 11:29:34 +0800

      Commit message:


	  
		
 drop dead @importFrom imports; import grid::unit where it is used

aplot::xlim2, ggplot2::geom_segment, ggplot2::geom_text,
ggplot2::scale_fill_hue and utils::getFromNamespace had no call site.
The grid viewport/pushViewport/popViewport imports sat in upsetplot(),
which never used them, while plotBmProf() calls grid::unit(); declare the
import where it is actually used so grid stays a genuine dependency.
 

    

  
    

      Package: epiSeeker

      Commit: 94253342bdfc5c786411e72d3bf528e4f5449284

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 11:18:52 +0800

      Commit message:


	  
		
 getBmMatrix(): replace superseded tidyr::gather() with pivot_longer()

tidyr::gather() is superseded by pivot_longer(), but the two are not drop-in
equivalent: pivot_longer() returns a tibble instead of a data.frame, and it
stacks the gathered columns row by row whereas gather() stacked them column by
column. The new internal helper pivot_longer_df() restores both, so the value
returned by getBmMatrix() is byte-identical to before.

Verified with identical() against the pre-change implementation on real bmData
and BSseq inputs (the latter covering getBmMatrix.BSseq.internal, which had no
test coverage), plus edge cases (empty frame, single column, mixed types,
reversed content order, 10 gathered columns).

Also drop the now-unused @importFrom tidyr gather and @importFrom tidyselect
all_of tags from the two internal functions; pivot_longer_df() declares both.

test-makeBmdata.R now pins the return type, column order and row names of
getBmMatrix() so a bare pivot_longer() cannot silently change them again.
 

    

  
    

      Package: epiSeeker

      Commit: b5531251d5e0a3c40ec23c502f6180df3f7043a3

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 10:42:14 +0800

      Commit message:


	  
		
 update docs
 

    

  
    

      Package: epiSeeker

      Commit: 34fa2d3259536c4ae4cc3f9edd0d1d23776905ed

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-17 10:27:19 +0800

      Commit message:


	  
		
 fix sameStrand, geneChr/geneStrand factor codes and silent peak dropping

Port of the ChIPseeker 1.49.2 fix to epiSeeker.

- getNearestFeatureIndicesAndDistances(): honour sameStrand when detecting
  overlaps. findOverlaps() was called with unstrand(features), so a peak
  with an unambiguous strand could be assigned to a feature on the opposite
  strand.
- annotateSeq(): report geneChr/geneStrand as characters. as.data.frame()
  returns 'seqnames'/'strand' as factors and assigning a factor into mcols()
  dropped the class, leaving integer codes (e.g. geneStrand = 1/2 instead of
  +/-, and a wrong geneChr whenever the seqlevels were not in numeric order).
- annotateSeq(): warn when peaks are dropped for lack of any feature in
  TxDb, instead of removing them silently.
- plotAnnoBar(): replace deprecated ggplot2::aes_string() with the tidy
  evaluation idiom already used by plotDistToTSS().

bump version to 1.1.3 and add unit tests
 

    

  
    

      Package: SpliceWiz

      Commit: 8b6b35a161cf6e6f51b394b737d4d43c0efee87b

      Author:  Alex Wong <80015046+alexchwong@users.noreply.github.com> 

      Date: 2026-10-06 08:48:31 +1000

      Commit message:


	  
		
 version 1.15.2 - fixed small C code bug
 

    

  
    

      Package: MSstatsBioNet

      Commit: a0f2b0bd193c64bb531e24da0b648d848d08a927

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-05 17:43:35 -0400

      Commit message:


	  
		
 refactor: Refactored INDRA subnetwork query behind an internal backend object (#117)

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

    

  
    

      Package: MSstatsBioNet

      Commit: 313594bcd151c61470821c58072ce8167836d6fa

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-05 15:56:28 -0400

      Commit message:


	  
		
 Refactored INDRA nodes to the node contract columns (#116)

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

    

  
    

      Package: MSstatsBioNet

      Commit: bcc0b6023b727c28d874b6fec0db2ac13b473321

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-05 15:20:03 -0400

      Commit message:


	  
		
 refactor: Refactored INDRA edges to the edge contract columns (#115) 

    

  
    

      Package: peakPantheR

      Commit: eb704a13acbaef391adb7b7c9eefc9cdd55aa523

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-10-05 23:13:54 +0200

      Commit message:


	  
		
 Merge branch 'devel-origin' into devel
 

    

  
    

      Package: peakPantheR

      Commit: f2ba6f61a7ab9633c8e59fc5f0a5b4cf1df9d238

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-10-05 23:10:26 +0200

      Commit message:


	  
		
 Update unittests for latest continuum values
 

    

  
    

      Package: peakPantheR

      Commit: 8753306e43341986d935c4ba1553180c28e9d7db

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-10-05 22:17:36 +0200

      Commit message:


	  
		
 update unittests to fix MSnbase error
 

    

  
    

      Package: MSstatsTMT

      Commit: f49525e0ef614b7fce041032e4e11d9313adfd4e

      Author:  Tony Wu <wu.anthon@northeastern.edu> 

      Date: 2026-10-05 15:51:33 -0400

      Commit message:


	  
		
 version bump - change maintainer
 

    

  
    

      Package: GExPipe

      Commit: 00bad9d1440fb1314dc169fe66da912e978093dd

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-10-06 00:18:23 +0500

      Commit message:


	  
		
 Sync with GitHub main: GExPipe 0.99.108
 

    

  
    

      Package: MSstatsBioNet

      Commit: bbc153ceec8d26b3495e61c48cee4c736460dd9f

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-05 14:57:31 -0400

      Commit message:


	  
		
 chore: roxygen 8.1.0 update (#114) 

    

  
    

      Package: maPredictDSC

      Commit: 2a34fd8224d02fa29d657ea19d080c6956e2255f

      Author:  Adi Tarca <atarca@med.wayne.edu> 

      Date: 2026-10-05 14:53:03 -0400

      Commit message:


	  
		
 Update maPredictDSC package and dependencies
 

    

  
    

      Package: GExPipe

      Commit: ee27ea86fc41fc821be9722068b5d8f0180d04ee

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

      Date: 2026-10-05 23:50:46 +0500

      Commit message:


	  
		
 Sync with GitHub main: GExPipe 0.99.107

Per-platform QC/batch outputs, consensus figures, AUC CIs, signature validation, BiocCheck fixes. Brings devel up to date with https://github.com/safarafique/GExPipe (0.99.52-0.99.107; see NEWS.md).
 

    

  
    

      Package: grayleafspotr

      Commit: 60c50b06c52a587eb8f889b1a5878a614a6e79c6

      Author:  rotsl <wot25kir.nbi@gmail.com> 

      Date: 2026-10-05 19:56:13 +0100

      Commit message:


	  
		
 Merge 0.99.12 Basilisk test correction into devel
 

    

  
    

      Package: grayleafspotr

      Commit: 8d2cc8fd8cbb2296665e0d4208a2ca586c69c49e

      Author:  rotsl <wot25kir.nbi@gmail.com> 

      Date: 2026-10-05 19:55:56 +0100

      Commit message:


	  
		
 Skip pipeline test when Basilisk cache is unavailable (0.99.12)
 

    

  
    

      Package: MSstatsBioNet

      Commit: 68cca5d72b247776b89eeeb08879826f8bc5e83a

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-10-05 14:50:37 -0400

      Commit message:


	  
		
 refactor: Added validate_network() and the edge and node contract (#113) 

    

  
    

      Package: motifbreakR

      Commit: 70cdbfd6479bc5b4285aef63a9bfe5c3c298e483

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-05 10:15:12 -0500

      Commit message:


	  
		
 Bump version to 2.27.3

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: 49a35b8ae6a980c8befe5d0f057989d760a4ea7b

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 23:56:37 -0500

      Commit message:


	  
		
 Run the biomaRt snps.from.rsid example only under donttest

The example queries the Ensembl archive, so a slow or unavailable
server failed R CMD check; other network-dependent examples are
already in \donttest{}.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: c9ad5f110f370f5c0e323369f55a33be85f32296

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 23:56:37 -0500

      Commit message:


	  
		
 Add a testthat suite

Covers variant import (BED/VCF, indels, multi-allelic and symbolic
alleles), prepareVariants() context construction, motifbreakR() scoring
against a brute-force reference and the bundled example results,
filterp, duplicate providerIds, bkg options, no-hit runs, multicore and
SnowParam back-ends, calculatePvalue(), exportMBbed()/exportMBtable()
and plotMB(). Each bug fixed on this branch was reintroduced to confirm
a test fails. Inputs are built from BED files and the bundled data, so
no SNPlocs or network access is needed (plotMB is skipped on CRAN).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: 4a1f39e78c686d02417054d02c5adac8858f3b1a

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 23:02:46 -0500

      Commit message:


	  
		
 Cite motifbreakR v2 and note the Factorbook 2.0 update

Add the motifbreakR v2 paper (Bioinformatics Advances 2024,
doi:10.1093/bioadv/vbae162) to CITATION, the README and the vignette's
indel section. Note in ?factorbook that the bundled 2012 motif set
predates Factorbook 2.0 (Pratt et al. 2022), which is not included.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: 224a4cac5bc4f1bce5f8ee16ba0d0123df1810dd

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 22:38:51 -0500

      Commit message:


	  
		
 Refresh README, DESCRIPTION and CITATION

README: install from Bioconductor, drop the obsolete ghostscript/MotIV/
dbSNP 2012 instructions, add the citation. DESCRIPTION: title case,
mention indel support, drop stale genome counts. CITATION: use
bibentry() with volume, issue and pages.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: e84c374da3ee06ae8f98702878bd3ab1a77d6e49

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 22:38:51 -0500

      Commit message:


	  
		
 Update vignette for current behavior and fix errors

Describe indel import with snps.from.file(), the new result columns and
seqMatch, bkg options, method = "notrans", effect cutoffs and
pseudocounts with bkg; correct the relative entropy equation and
equation references, the Windows/BiocParallel advice, motif and SNP
counts, broken footnotes and links, and typos.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: c80d843b5f349dc9e4eff6c2c861e4446724043f

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 22:38:51 -0500

      Commit message:


	  
		
 Review function and dataset documentation for accuracy

- motifbreakR: document all bkg options (including "pwm") and where the
  background is used, threshold semantics for filterp, method =
  "notrans", the pseudocount formula, log2 scoring, the strong/weak/neut
  cutoffs on alleleDiff, and BPPARAM splitting by motif; fix Equation
  4.2 (b_j) and which methods use Equation 2.
- snps.from.rsid/snps.from.file: correct the returned columns (SNP_id
  keeps "rs"; no alleles_as_ambig), document indel, multi-allelic and
  symbolic-allele handling; variants.from.file is now an alias.
- Datasets: fix motif counts, update dead HOCOMOCO/HOMER/Factorbook/
  ENCODE/PubMed links, note newer HOCOMOCO releases in MotifDb, and
  describe how example.results was generated.
- Add package anchors to cross-package links, drop the internal
  calculateAllPositions help page, remove trailing periods from titles,
  write example output to tempfile(), and fix typos.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: b2d16b0b5bd96e6314e63f64d3cd4dcb86755fb8

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 22:20:34 -0500

      Commit message:


	  
		
 Use the lowest p-value for exportMBbed(color = "best_sig")

best_sig was documented as the lower of pValueRef and pValueAlt but
picked the p-value of the allele with the weaker score. Also point the
missing-p-value error at calculatePvalue(), the function that exists.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: 1c8226a847a7723b37ea3167e5f955dff8d39146

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 22:20:12 -0500

      Commit message:


	  
		
 Fix unequal context widths when the longest allele has even length

prepareVariants() centred each allele in a context sized from the
longest allele in the input. When that length was even, alternate
contexts for even-length ALT alleles came out two bases longer than the
rest, and scoring failed with "'x' strings are not equal-width" (e.g. a
2 bp deletion or MNV alongside SNVs). Round the shared allele length up
to odd and give the reference context the same width; results for
inputs whose longest allele is odd are unchanged.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: b4989a4d0e38eebe685f4a6ea63874d12e98457d

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 22:07:44 -0500

      Commit message:


	  
		
 Remove stale undocumented data/example.pvalue.rda

The file held an old-format copy of the rs1006140 p-value example
under a different object name, was undocumented (R CMD check
WARNING) and unused; the vignette loads inst/extdata/example.pvalue.rda.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: db45f761e5a278c5586e2f620bb3f58117d1f2d4

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 22:07:32 -0500

      Commit message:


	  
		
 Fix SnowParam by letting BiocParallel manage workers

clusterEvalQ() on a BiocParallel SnowParam backend breaks the worker
protocol, so motifbreakR() and calculatePvalue() failed with any
SnowParam (the recommended back-end on Windows). Drop the manual
bpstart()/clusterEvalQ()/bpstop() handling and instead import the
MotifList class from MotifDb so workers load MotifDb with the
motifbreakR namespace. A cluster started by the caller is now left
running. Also remove the unreachable try-error branches and the
now-unused parallel import.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: 5d33ad9cfa45162dd218d9b73a92a931413bc005

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 21:43:38 -0500

      Commit message:


	  
		
 Regenerate NAMESPACE with roxygen2 8.1.0

roxygen2 8.1.0 groups importFrom() directives per package; the set of
imports and exports is unchanged.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: 82c814ac4f88f43d056c1b06a88c383549ab78d4

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 17:39:17 -0500

      Commit message:


	  
		
 Update dataset Rd usage and vignette library call

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: ceecf8aa373580b51f83289b5e83f0c6e83c20c7

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 17:39:17 -0500

      Commit message:


	  
		
 Rewrite scoring engine with vectorized window scoring

- Score all variants per PWM in one vectorized pass with masked
  windows, and parallelize across PWMs instead of across SNPs.
- Replace motifPos/altPos with explicit coordinate columns
  (calculateAllPositions) plus pwmConsensus and strongerIn, and
  rewrite plotMB/DNAmotifAlignment.2snp on top of them.
- bkg now accepts "genome", "aggregate" or "pwm"; the resolved
  background is stored on the results and used by calculatePvalue(),
  which drops its `background` argument. log scoring uses log2.
- Rename Refpvalue/Altpvalue/pvalueEffect to
  pValueRef/pValueAlt/pValueEffect.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: c5913e353566975557bd885d8ef75d341a7b08fb

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 17:39:17 -0500

      Commit message:


	  
		
 Always import indels in snps.from.file and filter invalid nucleotides

Drop the `indels` argument: VCF and BED input now always keep indels.
Factor the non-standard nucleotide filtering into a shared
cleanVariants() helper applied to both REF and ALT, and format
rsid-derived variants with formatVcfOut().

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: motifbreakR

      Commit: de393245b34d9abddff066e186d8d88544493df8

      Author:  Simon-Coetzee <coetzee@uthscsa.edu> 

      Date: 2026-10-04 17:39:17 -0500

      Commit message:


	  
		
 Ignore macOS metadata and .positai files

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 

    

  
    

      Package: seqsetvis

      Commit: 7b4db88343743d31f09a1d6ed65bf99e1b3f21eb

      Author:  Boyd <joseph.boyd@med.uvm.edu> 

      Date: 2026-10-05 10:58:59 -0400

      Commit message:


	  
		
 v bump 1.33.3 skip windows test calling bigwig fetch
 

    

  
    

      Package: seqsetvis

      Commit: b2370fee4e4bad32314104d0606228a5f48b1c41

      Author:  Joe Boyd <boydjr7@gmail.com> 

      Date: 2026-10-02 12:45:47 -0400

      Commit message:


	  
		
 v bump 1.33.2. bugfix for as.data.table behavior change on GRanges
 

    

  
    

      Package: rhdf5

      Commit: 06c6431e64a9ec85cdb4460effeb96cd70a4a76c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-05 15:38:42 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: c17b83cb96ab2d007270ab5d25f7cbea4c3fe3eb

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-05 15:38:15 +0200

      Commit message:


	  
		
 Mention callGeneric deprecation in NEWS
 

    

  
    

      Package: rhdf5

      Commit: 9bd2fbda0b9a0bd85e0273a5637752cdd4fa5717

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-05 15:37:12 +0200

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: rhdf5

      Commit: 5515b546e40e1cc3d3d62ba1c1bb59d0b6273d14

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-05 15:36:24 +0200

      Commit message:


	  
		
 Mark callGeneric arg as deprecated
 

    

  
    

      Package: rhdf5

      Commit: b36da4d31de08c5da093d897fd62a97ab1f87ddc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-24 16:03:41 +0200

      Commit message:


	  
		
 Fix outdated test in failing tests

Fixed by 98c8a7581553b43f8aa62575958b0a595394bb84
 

    

  
    

      Package: rhdf5

      Commit: f621746e2d91182d550f649c63f3bfba1b2456a8

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-09-24 16:00:16 +0200

      Commit message:


	  
		
 Remove duplicated definition
 

    

  
    

      Package: mitology

      Commit: 4c6814ba32302c57078d4e768b38c1accc691942

      Author:  Stefania Pirrotta <s.pirrotta.sp@gmail.com> 

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

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: mitology

      Commit: a5ae479abcd70cf37873e8d85176604c4ba09950

      Author:  Stefania Pirrotta <s.pirrotta.sp@gmail.com> 

      Date: 2026-10-05 15:59:26 +0200

      Commit message:


	  
		
 Update vignette for publication
 

    

  
    

      Package: mitology

      Commit: 8e5c312ca47babf79398a8c4597cff925aee919c

      Author:  Stefania Pirrotta <s.pirrotta.sp@gmail.com> 

      Date: 2026-10-05 15:59:00 +0200

      Commit message:


	  
		
 update gitignore
 

    

  
    

      Package: MetaboDynamics

      Commit: c248f563c93f7704b0ebb0b36682bfae20ac66d1

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-10-05 15:28:30 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: MetaboDynamics

      Commit: b8313a84a5e89c8f41eebf13643ed0b592002c89

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-10-05 15:15:48 +0200

      Commit message:


	  
		
 bug fix in plot_estimates
 

    

  
    

      Package: BiocBookDemo

      Commit: 4d03607849b3e9c982fecfc7e7cf70084edebb2b

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-05 13:32:44 +0200

      Commit message:


	  
		
 BiocBookDemo 1.11.5: from_bookdown() converts a bookdown book in place (#2)

* doc: from_bookdown() converts a bookdown book in place

BiocBook 1.11.4 converts the book in its own repository, on its current
branch, one commit per step, rather than into a new repository.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* bump to 1.11.5

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

--------- 

    

  
    

      Package: BiocBookDemo

      Commit: 8fd3dd0c8395193b4bf5d7ba3069dd0823a2de50

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-04 12:37:21 +0200

      Commit message:


	  
		
 BiocBookDemo 1.11.4: template 1.1.0, llms.txt and from_bookdown() sections (#1)

* feat: apply template 1.1.0 (llms.txt, BuildKit secret, action versions)

- Dockerfile, `biocbook` workflow and vignettes/Makefile from template
  1.1.0: GITHUB_PAT as a BuildKit secret, python environment provisioned
  only when a page runs python, current major versions of every action,
  quarto pinned to 1.11.5, `llms` quarto profile switched on when quarto
  supports it, no more tinytex install
- `llms.txt`: `inst/_quarto-llms.yml` and the post-render hook adding BiocBook
  context to it (`BiocBook::enrich_llms_txt()`), and a short section about it
  in Chapter 3
- remove `site-url`, which pointed at the GitHub repository rather than the
  book (quarto uses it to build absolute links in llms.txt, and a versioned
  book has no single site URL)
- Chapter 4: environments are re-used as long as `requirements.yml` is
  unchanged (BiocBook >= 1.11.2), `python_envs()`; the book's conda
  environment is named after it

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* bump to 1.11.3

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* ci: manual book builds on any branch, index of llms.txt versions (template 1.1.0)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* doc: migrating a bookdown book with from_bookdown()

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* bump to 1.11.4

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* doc: the book's Docker image keeps the micromamba it downloads

It does not install one on the PATH: setup_python() downloads a pinned
micromamba into BiocBook's cache while the image is built.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: retry the quarto download on transient errors (template 1.1.0)

GitHub answered HTTP 503 to the quarto download in OHCA's first devel build
on template 1.1.0, which failed before anything was installed. curl now
retries transient errors 5 times, 10 s apart (js2264/BiocBook.template
f08bf49).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: portable vignettes/Makefile (template 1.1.0)

R CMD check warned about GNU make extensions in vignettes/Makefile (`:=` and
`$(shell ...)`, which switched the `llms` profile on with quarto >= 1.11),
and rworkflows fails on warnings. The quarto version is now tested in the
recipe's shell, in portable make syntax; with quarto < 1.11, QUARTO_PROFILE
is no longer set at all.

Rendered through `make` with quarto 1.11.5 (llms profile: llms.txt and the
pages' Markdown copies) and 1.10.18 (minimal llms.txt), and R CMD check's own
test for GNU extensions no longer flags the file.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

--------- 

    

  
    

      Package: BiocBook

      Commit: 15e8d15ab3cb31005512d1058337a4c82029d725

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-05 11:53:33 +0200

      Commit message:


	  
		
 BiocBook 1.11.4: from_bookdown() converts a bookdown book in place, one commit per step (#11)

* feat: from_bookdown() converts a bookdown book in place, one commit per step

from_bookdown() used to create a new repository, whose history had nothing
in common with the bookdown one: the conversion could not be reviewed,
squashed or rebased onto the book's main branch. It now converts the book
in its own folder and, in a git repository, on its current branch, one
commit per step: the template, the pages moved to inst/ as they are (git
follows them), the book settings, the removal of the bookdown build, the
landing page, cross-references, callouts, figure options, the shared setup
and DESCRIPTION. Steps with nothing to change are skipped.

- arguments: `package` (default: the book_filename of the book, else the
  folder) replaces `new_package`, `commit` replaces `push`, and `user`
  defaults to the owner of the origin remote on GitHub
- the book keeps its README (which gets the badges), .gitignore and
  .Rbuildignore (which get the template's entries); it must be the root of
  its repository, with no uncommitted changes
- licence: a Creative Commons licence the pages link to, the book's LICENSE
  file, or the template's MIT licence written for the book's authors
- rewrites only collapse the blank lines they create, and pages keep their
  final newline, or its absence
- MIGRATION.md is written but not committed, and also lists the top-level
  files that are not part of a BiocBook

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* bump to 1.11.4

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: from_bookdown() writes pages byte for byte, whatever the locale

In a C locale, the badges added to README.md lost their emojis (written as
<9f><93>): the template's README was read without an encoding, and
enc2utf8() then escaped its bytes. Files are now read as UTF-8 and written
byte for byte.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: from_bookdown() converts books in linked git worktrees

gert::git_find() gives the git folder of a linked worktree
(.git/worktrees) rather than its root, so from_bookdown() took the
worktree for a subfolder of a repository and refused to convert it.
The root now comes from gert::git_info().

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: from_bookdown() no longer claims untranslated output options have no quarto equivalent

MIGRATION.md said so of every output option it does not translate, highlight
included, which quarto calls highlight-style. For highlight, it now says that
the book uses the code highlighting of the BiocBook theme, and which
highlight-style keeps the book's own; other options are to be set in
_format.yml, if quarto has them.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* feat: from_bookdown() numbers its commits, [BiocBook 1/10] to [BiocBook 10/10]

Each commit of the conversion now says, in its subject, that it is a step
towards a BiocBook, and where it stands in the series ("[BiocBook 3/10] Move
the book settings to the BiocBook config"). Steps with nothing to do make no
commit, so the commits are numbered once all are made: each is made again
with the same files, only HEAD and the index move.

The messages are short, and say what a BiocBook expects rather than what
bookdown or quarto do. The repository needs a first commit to convert on
top of.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

--------- </pre>
    </div>
  
    

      Package: BiocBook

      Commit: 3229586bb2914f5c543a10f196a7939c002e4a4b

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-04 12:44:29 +0200

      Commit message:


	  
		
 fix: template's vignettes/Makefile is portable again (#10)

Rebuilt from js2264/BiocBook.template 8e43d87. Template 1.1.0 switched the
`llms` profile on with GNU make extensions (`:=` and `$(shell ...)`), which
R CMD check reports as a warning in every book (BiocBookDemo's rworkflows
failed on it). The quarto version is now tested in the recipe's shell.

R CMD check of a new book: `Status: 1 WARNING` with the previous Makefile,
`Status: OK` with this one.


Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

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

------- 

    

  
    

      Package: BiocBook

      Commit: 9f32ed42d1c0f740ceb44c015385bb4f9d7fc208

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-04 12:05:05 +0200

      Commit message:


	  
		
 BiocBook 1.11.3: template 1.1.0, python environments keyed on requirements.yml, llms.txt, from_bookdown() (#9)

* feat: key conda environments on the contents of requirements.yml

`setup_python()` re-used `/envs/` whenever that folder existed,
whatever `requirements.yml` now said. Editing the file therefore never
rebuilt the environment on a machine that already had one (authors' laptops,
and the Bioconductor builders, which rebuild every day on the same machines),
and two books declaring the same `name:` shared whichever environment was
built first.

Environments are now named `-<12 first characters of the sha256 of
requirements.yml>`: the same file gives the same environment, any edit gives
a new one, and two books only share an environment when they declare exactly
the same thing. Docker builds are unaffected: they still return early on
`RETICULATE_PYTHON`.

Add `python_envs()` to list cached environments (name, path, size, last
modified) and `python_envs(remove = ...)` to delete them, by full name, by
bare `name:` (every generation of a book's environment) or "all".

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* feat: add_python_chapter() declares BiocBook and reticulate

A python page calls `BiocBook::setup_python()` and runs its chunks through
`reticulate` while the book builds, so the book package must declare both or
the build machines will not install them. `add_python_chapter()` now adds
them to the book's `Suggests` when missing (books created from templates
older than 1.1.0 do not list them).

The page also gets `engine: knitr` in its front matter, so that it stays on
knitr (and therefore on reticulate) even if its R chunk is later deleted.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* feat: enrich_llms_txt() adds BiocBook context to a book's llms.txt

quarto >= 1.11 renders `llms.txt` (an index for AI assistants, see
llmstxt.org) and a Markdown copy of every page for book projects.
`enrich_llms_txt()`, meant to run as a post-render hook, adds what only
BiocBook knows, as a list right after the summary blockquote:

- the book package, its version and Bioconductor release, and its source
- how to install it (Bioconductor or GitHub)
- its Docker image
- its python environment (from inst/requirements.yml), if a page runs python
- where the other versions of the book live

The block sits between ``/``
markers, so running it again replaces rather than duplicates it. A summary
is taken from DESCRIPTION when the book declares none.

With an older quarto, which writes no llms.txt for books, it writes a
minimal one: title, summary, context and the chapters listed in `_book.yml`
(parts as nested lists), linking to the HTML pages.

It also tidies two quirks of quarto 1.11's output: chapter numbers left as
raw pandoc spans in llms.txt links, and R code blocks labelled `downlit`
(from `code-link: true`) in the `.llms.md` pages.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* feat: template 1.1.0

The template archive had not changed since 2023 (template 1.0.6), so books
created today did not get the python support BiocBookDemo was fixed by hand
for, and their `biocbook` workflow failed on `actions/upload-artifact@v3`.
Rebuilt from js2264/BiocBook.template (template 1.1.0):

- `python.reticulate: true`; requirements.yml lists conda-forge, bioconda
  and nodefaults (no Anaconda `defaults`), pins python 3.12 and names the
  environment after the book (`init()` fills the placeholder)
- Dockerfile: GITHUB_PAT as a BuildKit secret (#6), python environment
  provisioned only when a page runs python, optional QUARTO_VERSION pin,
  `remotes` installed, no more tinytex
- biocbook.yml: current major versions of every action, GITHUB_PAT secret,
  QUARTO_VERSION build argument (1.11.5)
- llms.txt: an `llms` quarto profile, which vignettes/Makefile switches on
  only with quarto >= 1.11 (quarto <= 1.8 rejects the option and would fail
  the build), and a post-render hook calling `enrich_llms_txt()`
- no PDF output; Q&A callout CSS uses `.callout-titled` (quarto >= 1.3)
- the archive now includes `.gitignore` files

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* ci: end-to-end render test

`test-e2e.R` creates a book from the template, adds a python chapter passing
values between R and python, renders it with quarto and checks the output,
including llms.txt and its links. It builds a conda environment, so it is
skipped unless BIOCBOOK_E2E is set, and runs in the new `e2e` workflow
(bioconductor:devel container), with the image's quarto and with quarto
1.11.5. It fails if the template's `python.reticulate` is switched off.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* ci: allow manual runs of rworkflows

So that R CMD check and BiocCheck can be run on a work branch before it is
merged into devel.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* doc: add NEWS.md

Bioconductor's release announcements quote package NEWS.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* bump to 1.11.2

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: tidy the titles of chapters with an id in llms.txt

quarto wraps them in one more pandoc span, e.g.
`[[4 Executing python code]{#sec-python .quarto-section-identifier}](...)`.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: chapters() drops header attributes from chapter titles

`# Introduction {#sec-intro}` gave the title "Introduction {#sec-intro}";
only `{-}` was removed.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: template Q&A callouts styled through wrapper divs

quarto (>= 1.3) drops extra classes from callouts, so the template's
`.callout-question`/`.callout-answer` rules never applied. They now target
a callout wrapped in a div with that class (js2264/BiocBook.template e39a038).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* feat: from_bookdown() migrates a bookdown book to a BiocBook

`from_bookdown(path, new_package)` creates a book from the template, as
`init()` does, and converts a bookdown project into it:

- pages: `index.Rmd` becomes the landing page (BiocBook's header chunk and
  Docker, RStudio and session info sections, with the preamble as welcome
  text), every chapter `inst/pages/.qmd`, listed in `_book.yml` in
  order, with `(PART)` headers as parts and `(APPENDIX)` as appendices
- syntax, outside code (inline code included): `\@ref()` to sections,
  figures, tables and equations (a type word before the reference is
  dropped, since quarto adds its own; others render their number only, as in
  bookdown), `(\#eq:x)` labels, referenced chunk labels and header ids,
  `fig.margin`/`fig.fullwidth`, and the msmbstyle question/solution blocks.
  The rules are kept as data, one list per style
- assets: bibliographies and CSS to `inst/assets/`, asset folders (`img/`)
  next to the chapters; `margin_references`, `toc_depth`, `css` and
  `link-citations` translated
- DESCRIPTION: Title, Description, Authors@R (with a placeholder email) and
  the packages the pages use (renv::dependencies, as `check_deps()`)
- shared session: the `library()`/`options()` calls of `index.Rmd` (and the
  `before_chapter_script`) are repeated at the top of each chapter
- MIGRATION.md lists how often each rule was applied, and what still needs a
  human: downloads while the book builds, cached chunks, `write_bib()`
  calls, unresolved references (including leftovers found by
  `quarto::detect_bookdown_crossrefs()`), GitHub-only dependencies and output
  options with no quarto equivalent

Tests convert a fixture covering every rule (no network) and snapshot the
converted pages and `_book.yml`/`_format.yml`. `.setup_git()` takes the
commit message; `desc` is now imported and BiocManager suggested.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* feat: template biocbook workflow runs manually on any branch, indexes llms.txt versions

Manual runs (workflow_dispatch) build the book from any branch against
Bioconductor devel without deploying it; deploys now also write an index of
the llms.txt of every deployed version to docs/llms.txt on gh-pages
(js2264/BiocBook.template), which enrich_llms_txt() links to.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: read and write pages as UTF-8 in from_bookdown() and enrich_llms_txt()

Outside a UTF-8 locale, lines holding non-ASCII characters (e.g. an en dash)
could not be matched by the perl regular expressions, and their references
were left unconverted with an 'invalid UTF-8' warning. Pages are now read
as UTF-8 and written back byte for byte.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* doc: NEWS for 1.11.3

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* bump to 1.11.3

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* doc: the book's Docker image downloads micromamba, it does not install it

The template's Dockerfile never put micromamba on the PATH: setup_python()
downloads the pinned binary into BiocBook's cache while the image is built,
and the image keeps it (R_USER_CACHE_DIR).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: MIGRATION.md names the bookdown project by its git remote, not its local path

from_bookdown() wrote the absolute local path of the bookdown project into
MIGRATION.md, which is committed to the new book's repository. It now names
it by the URL of its git repository (without credentials, ssh remotes as
https URLs), with the subfolder if the book is not at the root, or by its
folder name when it is not in a git repository.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: template retries the quarto download, and warns about matplotlib >= 3.11

Rebuilt from js2264/BiocBook.template a438ce3:

- the Dockerfile retries the quarto download on transient errors (5 times,
  10 s apart): GitHub answered HTTP 503 to it in OHCA's first devel build on
  template 1.1.0, which failed before anything was installed
- requirements.yml warns that matplotlib >= 3.11 fails to import on the
  Bioconductor images, and how to pin it

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* ci: retry the quarto download in the e2e workflow

Same transient errors as in the template's Dockerfile (HTTP 503 from GitHub):
retry 5 times, 10 s apart.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* doc: matplotlib >= 3.11 cannot be imported on the Bioconductor images

New section of ?BiocBook-python: conda-forge's matplotlib >= 3.11 links
libraqm, which needs a more recent harfbuzz than Ubuntu 24.04's. The R session
has already loaded the system's harfbuzz when a page renders, so `import
matplotlib` fails (undefined symbol: hb_ft_font_get_ft_face), and importing
python packages first does not help (js2264/OHCA, runs 38 and 39). Pin it
below 3.11 in requirements.yml. NEWS for this and the template's quarto
download retries.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

--------- </pre>
    </div>
  
    

      Package: GSVA

      Commit: 62670afe11aee1c2d1478c4f6b4ff52c35d8af83

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

      Date: 2026-10-05 12:45:35 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: GSVA

      Commit: 47ac6e20fe971b6bfd24f521dbac82f22812eb62

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

      Date: 2026-10-05 12:45:17 +0200

      Commit message:


	  
		
 Fix progress reporting in the C code of the GSVA method
 

    

  
    

      Package: onlineFDR

      Commit: 266c1e989bccf5b5b91674a3ea3b0aa580c2ddca

      Author:  dsrobertson <38322298+dsrobertson@users.noreply.github.com> 

      Date: 2026-10-05 11:36:18 +0100

      Commit message:


	  
		
 Merge Bioconductor devel; bump version to 2.21.1

Bring Bioconductor devel up to date with GitHub master
(ADDIS_exhaustive, ADDIS and LOND fixes). Bump version above
Bioconductor's 2.21.0, update NEWS, and fix the dead diagram link in
the onlineFDR vignette.
 

    

  
    

      Package: onlineFDR

      Commit: 1d89c48f1a5c046dc150c06b1688bdf8ad72607d

      Author:  dsrobertson <38322298+dsrobertson@users.noreply.github.com> 

      Date: 2026-02-02 18:21:49 +0000

      Commit message:


	  
		
 Merge pull request #64 from nikotinz/master

ADDIS_exhaustive() update 

    

  
    

      Package: onlineFDR

      Commit: dbb1df44000afe819fb50e877a360b221ca73b5a

      Author:  dsrobertson <38322298+dsrobertson@users.noreply.github.com> 

      Date: 2026-02-02 17:59:41 +0000

      Commit message:


	  
		
 Update documentation for ADDIS-exhaustive
 

    

  
    

      Package: onlineFDR

      Commit: 1d35507d3f80045ac2b772bf9b3176d9f294949f

      Author:  Nikita Mozgunov <41270344+nikotinz@users.noreply.github.com> 

      Date: 2025-12-18 16:32:12 +0000

      Commit message:


	  
		
 rm old files
 

    

  
    

      Package: onlineFDR

      Commit: 17574c348a0544e23a9689bd12cc4fa70c5f086a

      Author:  Nikita Mozgunov <41270344+nikotinz@users.noreply.github.com> 

      Date: 2025-12-18 16:27:56 +0000

      Commit message:


	  
		
 Prep for Bioconductor submission
 

    

  
    

      Package: onlineFDR

      Commit: edae66369143fe7adf904d5539b4cdf52e68482c

      Author:  Nikita Mozgunov <41270344+nikotinz@users.noreply.github.com> 

      Date: 2025-08-11 19:42:35 +0100

      Commit message:


	  
		
 print diff
 

    

  
    

      Package: onlineFDR

      Commit: 7bd7696ebd0bc1689f0442b11e77a6852fae3e74

      Author:  Nikita Mozgunov <41270344+nikotinz@users.noreply.github.com> 

      Date: 2025-07-19 22:28:10 +0100

      Commit message:


	  
		
 MacOS fix #2
 

    

  
    

      Package: onlineFDR

      Commit: 67be2652556da6d242692b1807ef93b583542da4

      Author:  Nikita Mozgunov <41270344+nikotinz@users.noreply.github.com> 

      Date: 2025-07-19 19:54:04 +0100

      Commit message:


	  
		
 fixing macOS precision issue
 

    

  
    

      Package: onlineFDR

      Commit: b89bab0fe4d21cecc03f9d1f25de48871b78f351

      Author:  Nikita Mozgunov <41270344+nikotinz@users.noreply.github.com> 

      Date: 2025-07-19 15:13:12 +0100

      Commit message:


	  
		
 upd R-CMD-check
 

    

  
    

      Package: onlineFDR

      Commit: 829eb873b5dab3ca5ec49d54a8cdc7d9f44422d2

      Author:  Nikita Mozgunov <41270344+nikotinz@users.noreply.github.com> 

      Date: 2025-07-19 14:28:19 +0100

      Commit message:


	  
		
 test commit
 

    

  
    

      Package: onlineFDR

      Commit: 8f5806570ab001ee8d397e74e1a29eca86836c40

      Author:  Nikita Mozgunov <41270344+nikotinz@users.noreply.github.com> 

      Date: 2025-07-19 14:16:27 +0100

      Commit message:


	  
		
 Update R-CMD-check.yaml 

    

  
    

      Package: onlineFDR

      Commit: 9c4c8b322b9e7c6ff7712b6bd8ec334ba74eff66

      Author:  dsrobertson <38322298+dsrobertson@users.noreply.github.com> 

      Date: 2025-07-18 17:16:19 +0100

      Commit message:


	  
		
 Merge pull request #63 from nikotinz/master

Update 2.7.1 

    

  
    

      Package: onlineFDR

      Commit: 93029e9f34f90086469922d21422c5e11d103a67

      Author:  Nikita Mozgunov <41270344+nikotinz@users.noreply.github.com> 

      Date: 2025-07-18 08:27:07 +0100

      Commit message:


	  
		
 upd 2.7.1
 

    

  
    

      Package: scMultiome

      Commit: f0adfb38f41478ef4b392a4d8fc93ac9c988db2d

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-10-05 09:47:01 +0000

      Commit message:


	  
		
 v1.13.2
 

    

  
    

      Package: scMultiome

      Commit: c6dd9cc93488d2f36ce4b852d3fd7dd42458ba69

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-10-05 09:45:50 +0000

      Commit message:


	  
		
 documentation update
 

    

  
    

      Package: scMultiome

      Commit: 4f4e1d983b6930aea42f3e2de8c5561c0f9251df

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-25 21:44:58 +0200

      Commit message:


	  
		
 Merge pull request #1 from xiaosaiyao/test_issue

Test issue 

    

  
    

      Package: scMultiome

      Commit: 9e7b3aeb2c45a68e09dd5efb27b95366940a7688

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-24 15:07:51 +0000

      Commit message:


	  
		
 change of the TEADi_resistance description
 

    

  
    

      Package: scMultiome

      Commit: 257ddb418873b8cd070c1f20fed57ecf8e23a709

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-22 15:55:48 +0200

      Commit message:


	  
		
 Install 'remotes' package in R-CMD-check workflow

Added installation of the 'remotes' package before dependency checks. 

    

  
    

      Package: scMultiome

      Commit: c0038122ba3092aba9816fdd7a50323bbfe283e6

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-22 10:36:11 +0000

      Commit message:


	  
		
 v1.13.1
 

    

  
    

      Package: scMultiome

      Commit: 0590f395eaf55518cba73ba4b03a215c1c7f81e0

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-22 10:35:54 +0000

      Commit message:


	  
		
 documentation completion
 

    

  
    

      Package: scMultiome

      Commit: fb876d8e9505da085ecf7970817c8e3ff8c65444

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-22 09:36:46 +0000

      Commit message:


	  
		
 v1.13.1
 

    

  
    

      Package: scMultiome

      Commit: 335026842e08f955a8f37c130b5895bc4ab5e031

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-22 09:36:25 +0000

      Commit message:


	  
		
 update of metadata after adding raw counts
 

    

  
    

      Package: scMultiome

      Commit: aa19a3572a3259657328bb1d16220248d6d49448

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-22 09:25:38 +0000

      Commit message:


	  
		
 do not use names to avoid extra metadata column in the reconstructed GRanges object
 

    

  
    

      Package: scMultiome

      Commit: 1dcba85e91938ef8079f3635d38cc09aa9979f0b

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-22 09:08:28 +0000

      Commit message:


	  
		
 Revert "do not use names to avoid extra metadata column in the reconstructed GRanges object"

This reverts commit f1db6cabfb2631dc2bec49697ff7c50238e84bcd.
 

    

  
    

      Package: scMultiome

      Commit: df929fbd82fba3b237fce36ede964913938a8ebf

      Author:  Tomasz Włodarczyk <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2026-09-22 09:08:06 +0000

      Commit message:


	  
		
 Revert "v1.13.1"

This reverts commit 340dce2e4e62dbc092f3e94ce2812993d20ac222.
 

    

  
    

      Package: HiCool

      Commit: 377aab9a79302524f749422ad1c7023a16327379

      Author:  Jacques <jacquesserizay@gmail.com> 

      Date: 2026-10-05 11:04:41 +0200

      Commit message:


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

# Conflicts:
#	DESCRIPTION
 

    

  
    

      Package: HiCool

      Commit: 3f1a076c374c5b01bb359fa0baf3277762ea7686

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-04 17:48:12 +0200

      Commit message:


	  
		
 Fix the Bioconductor build: run hicstuff and chromosight outside the R session, hicstuff 3.2.5 (#10)

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

* bump x.y.z version to odd y following creation of RELEASE_3_23 branch

* Add Config/Bioconductor/UnsupportedPlatforms

- Replaces .BBSoptions UnsupportedPlatforms in R Universe build system
- Excludes specific binaries from distribution via Bioconductor

* Bump version

* fix: configure creates the conda environment with basilisk.utils

configure called basilisk::configureBasiliskEnv(), which only creates
BasiliskEnvironment objects: R/basilisk.R defines the basilisk.utils
arguments HiCool_args, so with BIOCCONDA_USE_SYSTEM_INSTALL=1 no environment
was created at installation, and createEnvironment() then failed to find it.
configure now calls basilisk.utils::configureEnvironments('R/basilisk.R'),
as documented in basilisk.utils.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7K6whxFpW6S41wxyfSFKr

* fix: run hicstuff and chromosight in a separate process; hicstuff 3.2.5

On the Bioconductor builders, the vignette failed with
  AttributeError: module 'hicstuff' has no attribute 'pipeline'
`import hicstuff` worked in the R session but `import hicstuff.pipeline`
did not, and reticulate hides why: `$` on a module tries to import the
submodule and, if that fails for any reason, raises this AttributeError.
hicstuff.pipeline imports matplotlib, pysam, cooler/h5py, pairtools...,
whose shared libraries are loaded in the R process, next to those R has
already loaded. Whether they clash depends on the machine: the same code
builds on GitHub's bioconductor_docker:devel, and the duplicated OpenMP
runtime worked around with KMP_DUPLICATE_LIB_OK was the same problem.

HiCool now runs the `hicstuff pipeline` and `chromosight detect` command
lines of its conda environment with system2(): bin/ of the environment
first on PATH, without the user's site-packages, PYTHONPATH or PYTHONHOME,
and with MPLBACKEND=Agg (the builders set DISPLAY for Xvfb). Python is no
longer loaded in the R session, so reticulate, basilisk and
KMP_DUPLICATE_LIB_OK are no longer needed (BiocCheck warned about
Sys.setenv()). When a tool fails, the error shows the end of its output.

Conda environment (version 0.3.0, so that cached environments are rebuilt):
- hicstuff 3.2.5, cooler 0.10.4
- pandas pinned to 2.3.3: chromosight 1.6.3 cannot detect patterns with
  pandas 3, which conda now installs by default (getLoops() failed with
  `TypeError: len() of unsized object` on bioconductor_docker:devel)
It solves on linux-64, linux-aarch64, osx-64 and osx-arm64.

Also:
- getHicStats() reads the logs of hicstuff >= 3.2.5, which write
  `(613/53553 pairs)` instead of `(613 / 53553 pairs) `: nDups and nUnique
  were NA. Results on logs of hicstuff 3.2.4 are unchanged, and stringr is
  no longer needed.
- threads are passed as an integer: `threads = 12` made hicstuff run
  `sort --parallel=12.0` (see #8)
- getLoops() passes its `norm` argument to chromosight, instead of 'auto'
- the report gives the python version of the conda environment and lists
  its packages from conda-meta/, without loading python in R

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7K6whxFpW6S41wxyfSFKr

* bump to 1.13.2

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01H7K6whxFpW6S41wxyfSFKr

--------- 

    

  
    

      Package: HiCool

      Commit: 8d225d218b36a37466f90c87359b3d41108e4ae8

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-04-02 21:50:17 +0200

      Commit message:


	  
		
 bumpt to 1.11.4
 

    

  
    

      Package: HiCool

      Commit: 13ed338d7ae5c1d1ea210c466072c0ee6288a4ac

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-04-02 21:50:07 +0200

      Commit message:


	  
		
 fix: add Config/Bioconductor/UnsupportedPlatforms: windows
 

    

  
    

      Package: GSVA

      Commit: 703bd4ad5d13f7a042c9d775511390f61036c3d5

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

      Date: 2026-10-05 11:01:30 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: GSVA

      Commit: 559769ecb1c4f42aaaa3c0777442ee8faa3c4e41

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

      Date: 2026-10-05 10:59:51 +0200

      Commit message:


	  
		
 Wrap bplapply() into a private .gsva_bplapply() function that replaces the uninformative error that BiocParallel gives when a forked worker process ends without returning its result, by an error that tells what actually happened. This may not be necessary once this is addressed in Bioconductor/BiocParallel#249
 

    

  
    

      Package: GSVA

      Commit: ffae34dbae7ae2765479d34b937354eb0afed8da

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

      Date: 2026-10-05 10:25:57 +0200

      Commit message:


	  
		
 Fix in the bptry() calls within .processMatrixCols()
 

    

  
    

      Package: MetaboDynamics

      Commit: 2250b31674efbd99d426e538c95da9d94b7a18c6

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-10-05 10:35:23 +0200

      Commit message:


	  
		
 bug fix in plot_estimates
 

    

  
    

      Package: GSVA

      Commit: 3669e6a0c0eb51656937a20b53f63f5a4382a8ac

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

      Date: 2026-10-05 09:51:19 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: GSVA

      Commit: 1b9e1f80933bb6c10ada7082996ba462cd057cd5

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

      Date: 2026-10-04 20:21:27 +0200

      Commit message:


	  
		
 Add for consistency anyNA() getter methods for zscoreParam and plageParam. Fix zscoreParam unit test
 

    

  
    

      Package: GSVA

      Commit: 368795216520af87ca528285ff1bf12ada18aa2c

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

      Date: 2026-10-04 18:47:57 +0200

      Commit message:


	  
		
 Fix to avoid updating the users BPPARAM argument, since it is a reference class
 

    

  
    

      Package: GSVA

      Commit: 01dba559960c5f7ef119b617f99f6e36b62b924d

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

      Date: 2026-10-03 20:25:13 +0200

      Commit message:


	  
		
 Fix to avoid updating the users BPPARAM argument, since it is a reference class
 

    

  
    

      Package: MetaboDynamics

      Commit: c6dd1072dc2d57ca9dfd382be86c13d94fdbc474

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-10-05 09:51:22 +0200

      Commit message:


	  
		
 bug fix in plot_ORAe
 

    

  
    

      Package: h5vc

      Commit: c99b5b9ee6691af62b894fbdc4018b66594c9bd3

      Author:  PaulPyl <paul.theodor.pyl@gmail.com> 

      Date: 2026-10-01 10:17:07 +0200

      Commit message:


	  
		
 Replace deprecated aes_string() with aes(); don't write into installed files

- plotting.R: switch all aes_string() calls (deprecated since ggplot2
  3.0.0) to aes() with the .data pronoun; require ggplot2 (>= 3.0.0).
- h5vc.tour vignette: work on a temporary copy of h5vcData's
  example.tally.hfs5 instead of calling setSampleData() on the installed
  file, which fails when the library is read-only (e.g. a Nix store).
- getSampleData example: copy with copy.mode = FALSE so the temporary
  copy is writable even when the source file is read-only.

Assisted-by: Claude Opus 5.5 (Anthropic)
 

    

  
    

      Package: h5vc

      Commit: 5c8052a421557c656d4f383b439e4757aabf2e55

      Author:  PaulPyl <paul.theodor.pyl@gmail.com> 

      Date: 2026-10-01 09:51:39 +0200

      Commit message:


	  
		
 Tighten imports, fix R CMD check NOTEs and four latent bugs

Imports:
- import(Biostrings) -> importFrom(Biostrings, getSeq); drop import(grid)
  and import(gridExtra), neither of which the package code uses. This
  removes the "replacing previous import 'Biostrings::pattern' by
  'grid::pattern'" install warning.
- Drop grid and gridExtra from Depends; declare R (>= 3.0.2) for the
  versioned LinkingTo.
- Import binom.test/fisher.test (stats), hist (graphics) and
  globalVariables (utils); declare subset() column names in R/globals.R.

Bugs surfaced by the undefined-globals NOTE:
- resizeCohort() used undefined `newSamples` instead of its
  `newNumberOfSamples` argument, so it always errored.
- tallyRangesBatch() used `bamFiles` instead of `bamfiles` when creating
  a new tally file, and referenced an undefined `verbose`; add a
  documented `verbose = FALSE` argument.
- plotMutationSpectrum(plotCounts = FALSE) looped over undefined `tmp`
  instead of `ms`.

Also remove the unused pileup_func_old() debug function (and )
from tallyBAM.cpp, and fix lost braces in prepareTallyFile.Rd.

Assisted-by: Claude Opus 5.5 (Anthropic)
 </pre>
    </div>
  
    

      Package: h5vc

      Commit: 5b07e444a5e7fc3f2979d0d0d799bf151933b445

      Author:  PaulPyl <paul.theodor.pyl@gmail.com> 

      Date: 2026-10-01 08:50:20 +0200

      Commit message:


	  
		
 Vignette: use shipped exon snapshot instead of live BioMart query

Ensembl 116 (June 2026) is the last release with BioMart; www.ensembl.org
now redirects BioMart to jun2026.archive.ensembl.org, which is slow and
intermittently returns unusable responses, breaking the h5vc.tour vignette
on the build machines ("incompatible version of BioMart" / "dataset not
valid").

Ship the exons the chunk used to fetch (chr16:29-30Mb, GRCh38, Ensembl 116)
as inst/extdata/exons.chr16.29-30Mb.GRCh38.ensembl116.txt, keep the biomaRt
code as an eval=FALSE example, and drop biomaRt from Suggests.

Assisted-by: Claude Opus 5.5 (Anthropic)
 

    

  
    

      Package: MetaboDynamics

      Commit: 02da5d947c5efb0a253fb9aa6ae093a1f91ced7a

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-10-05 08:33:21 +0200

      Commit message:


	  
		
 bug fix in vignette
 

    

  
    

      Package: seqpac

      Commit: cc9824622562adc476ef2657271a5f9599696c3a

      Author:  Alessandro Gozzo <alego91@liu.se> 

      Date: 2026-10-05 08:13:17 +0200

      Commit message:


	  
		
 Prepare seqpac 1.13.1 for Bioconductor devel
 

    

  
    

      Package: seqpac

      Commit: 626ec0c3276750d2f556168820dac0e6ad87eae0

      Author:  Alessandro Gozzo <alego91@liu.se> 

      Date: 2026-10-05 08:11:22 +0200

      Commit message:


	  
		
 Merge branch 'devel' into bioc-devel
 

    

  
    

      Package: seqpac

      Commit: b9cd900ccc9661f55412022c2e11e6e22be15d2d

      Author:  Alessandro Gozzo <alego91@liu.se> 

      Date: 2026-10-05 07:26:47 +0200

      Commit message:


	  
		
 Update gitignore for BiocCheck and RStudio files
 

    

  
    

      Package: seqpac

      Commit: b9da07e18d5971f9665c71d24a94035511b74eda

      Author:  Alessandro Gozzo <alego91@liu.se> 

      Date: 2026-10-05 07:06:38 +0200

      Commit message:


	  
		
 R dependency update 

    

  
    

      Package: seqpac

      Commit: 375b360e9feb8707d522a82f3ed2e0b9b551bd65

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-10-04 16:21:01 +0200

      Commit message:


	  
		
 Changing a F to FALSE to solve BiocCheck warning
 

    

  
    

      Package: seqpac

      Commit: ecc69925f41251598f48d8d446ffed3893feebb3

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2026-10-02 07:42:24 +0200

      Commit message:


	  
		
 Merge pull request #57 from OestLab/SpringSummer26

Merging SpringSummer work to main for BioC push 

    

  
    

      Package: seqpac

      Commit: b511adc89a360ae31b0d28b3170a448662ff99ce

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-09-30 16:36:02 +0200

      Commit message:


	  
		
 fix get trim fetch
 

    

  
    

      Package: seqpac

      Commit: 07dda80211647ccdfaa9092d92e591832011971e

      Author:  AAsratian <anna.asratian@liu.se> 

      Date: 2026-09-28 19:40:41 +0200

      Commit message:


	  
		
 Included PAC_map description in vignette and added some changes to clarify and update text.
 

    

  
    

      Package: seqpac

      Commit: 5b8d3c5fe99aea9db670d59c964d96ffb4d3dd3d

      Author:  signeisacson <skog.signe@gmail.com> 

      Date: 2026-09-25 15:17:08 +0300

      Commit message:


	  
		
 bug fixing in the wrapper functions
 

    

  
    

      Package: seqpac

      Commit: 31bdd5d6368eb1aa79a1e03e5f0b0ddc5b2137d5

      Author:  signeisacson <skog.signe@gmail.com> 

      Date: 2026-09-25 13:06:26 +0300

      Commit message:


	  
		
 Manual changing of the fasta references to ensure they actually map to example fastq files :)
 

    

  
    

      Package: seqpac

      Commit: 949409ddc3abfba2e06ff0ab3f4b409cc7a725aa

      Author:  signeisacson <skog.signe@gmail.com> 

      Date: 2026-09-25 10:45:58 +0300

      Commit message:


	  
		
 Refinement of the PAC_map functions, merging the two into one, that will make assumptions about the input if not provided further info
 

    

  
    

      Package: seqpac

      Commit: 92efde7f3844ff86f89313e0e18a097ad7a52c97

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2026-09-24 10:45:13 +0200

      Commit message:


	  
		
 Merge pull request #56 from OestLab/Dev

Merging Dev into SpringSummer26 for easier pushing to BioC 

    

  
    

      Package: seqpac

      Commit: 9cc53ff52980326d4a1e0e90bae55dcb5a04aeb9

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2026-09-24 10:44:49 +0200

      Commit message:


	  
		
 Merge branch 'SpringSummer26' into Dev 

    

  
    

      Package: seqpac

      Commit: f37911679b820f5931bf7ecc09b8401d8b070037

      Author:  signeisacson <skog.signe@gmail.com> 

      Date: 2026-09-24 11:37:39 +0300

      Commit message:


	  
		
 Adding a "master" function for Seqpac, called Seqpac, that runs a simplified version of the full pipeline in one function. (also doing minor bug fixes and similar checks)
 

    

  
    

      Package: seqpac

      Commit: b17ddf3729a5f218e55ef2a599748c21f9c9079a

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-09-18 16:12:58 +0200

      Commit message:


	  
		
 Fix ggplot deprecated language
 

    

  
    

      Package: seqpac

      Commit: 4728df1233a0f363370dadcab230828185138056

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-09-18 15:32:24 +0200

      Commit message:


	  
		
 Implemented summary_target behaviour [[2]]
Fixed ggplot issues
Changed parallelization BiocParallel
Added % table feature to stackbar
Added Pheno title to pie
 

    

  
    

      Package: seqpac

      Commit: 247df2852d2877e8266ca21b184914770cb9a021

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2026-09-17 15:14:55 +0300

      Commit message:


	  
		
 fixing potential issue for issue no. 51

Added libraries for Seqpac, BiocParallel, and DESeq2 to the differential expression section to make it easier for user to run 

    

  
    

      Package: seqpac

      Commit: 7a4c5ee776821f4836f1deebcd31bb0a767df23a

      Author:  signeisacson <skog.signe@gmail.com> 

      Date: 2026-07-22 11:08:29 +0300

      Commit message:


	  
		
 Addition of a more comprehensive mapping function (and changing of documentation concerning that function)
 

    

  
    

      Package: seqpac

      Commit: 57cfd30efd64561c56d2fdfb79254de90f108609

      Author:  signeisacson <skog.signe@gmail.com> 

      Date: 2026-07-20 09:11:19 +0300

      Commit message:


	  
		
 updating documentation
 

    

  
    

      Package: seqpac

      Commit: 31a88294ea3ff08412a8812735c68dcaaa1c1e35

      Author:  signeisacson <skog.signe@gmail.com> 

      Date: 2026-07-17 14:39:44 +0300

      Commit message:


	  
		
 Removing digest to reduce no. of dependencies
 

    

  
    

      Package: seqpac

      Commit: c81f9dac979cba45d2e10049d792fbdeadc8cd34

      Author:  signeisacson <skog.signe@gmail.com> 

      Date: 2026-07-17 13:58:21 +0300

      Commit message:


	  
		
 Adding a new function to merge functinality between the reanno-workflow and PAC_mapper workflow (still will add addition back into PAC object and possibly also the cleavage site information?)
 

    

  
    

      Package: seqpac

      Commit: 0174ebf8e515896d020bb45ed5b3d04eb612fbdb

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2026-04-30 13:23:42 +0300

      Commit message:


	  
		
 Updated how to install

Updated installation from deprecated devtools install and made BiocManager follow bioc lingo 

    

  
    

      Package: seqpac

      Commit: 328bc5f19dc6dadd99cc8ba3c3da804fffc05148

      Author:  signeisacson <skog.signe@gmail.com> 

      Date: 2026-04-30 11:18:47 +0300

      Commit message:


	  
		
 Correcting code so no warning or notes appear in checks
 

    

  
    

      Package: seqpac

      Commit: 8d90b2367ace5ab522d56232ec3dddfbff41ad18

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2025-11-24 08:39:46 +0200

      Commit message:


	  
		
 Created new branch for dev instead of the old one

Fixed so pdf's can be printed from PAC_analyze  

    

  
    

      Package: seqpac

      Commit: 846b119b115e1685513bc145397ceba39aebad62

      Author:  signesiacson <skog.signe@gmail.com> 

      Date: 2025-11-21 15:54:50 +0200

      Commit message:


	  
		
 Fixed so pdf's can be printed from PAC_analyze and changed minor spelling mistakes
 

    

  
    

      Package: ctdR

      Commit: 57961d56c89dda51cec7c8dcc4c91ed89f454aa2

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

      Date: 2026-10-04 07:32:40 +0200

      Commit message:


	  
		
 Merge pull request #56 from drake69/ci/release-reminder-text

ci: bring the release reminder in line with how releases work now 

    

  
    

      Package: ctdR

      Commit: eed3574c9e596565ecdbe5cea8bdaa0c10b99817

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

      Date: 2026-10-04 07:32:36 +0200

      Commit message:


	  
		
 Merge pull request #55 from drake69/chore/sync-bioc-devel-0.99.11

Merge the Bioconductor devel history before pushing 0.99.11 

    

  
    

      Package: ctdR

      Commit: 4b3f720e1d6d9fe0d86f5e02d3071cd054f445c4

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

      Date: 2026-10-04 07:24:05 +0200

      Commit message:


	  
		
 ci: bring the release reminder in line with how releases work now

The monthly reminder still said that merging the version bump tags
and publishes the GitHub Release. That stopped being true when the
release workflow became manual, so following the checklist left the
version unreleased: 0.99.10 never got a GitHub Release. The checklist
now says to run the release workflow by hand.

The Bioconductor step referred to the review, which is over: the
package is accepted, and a new version reaches Bioconductor only when
main is pushed to its devel branch. The issue body also cited an
internal document that readers of this repository cannot open.
 

    

  
    

      Package: ctdR

      Commit: 9605e22c72a09d85d1831ed6a64dc571604c2883

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

      Date: 2026-10-04 07:23:42 +0200

      Commit message:


	  
		
 Merge the Bioconductor devel history before pushing 0.99.11

The Bioconductor devel branch carries merge commits that main does
not have, so main cannot be pushed there as a fast-forward. This
merge records that history and keeps the tree of main unchanged:
the content to publish is exactly what main already has.
 

    

  
    

      Package: ctdR

      Commit: 433912bce9bab910cb772a1158eeb5c25aef6ee0

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

      Date: 2026-10-04 07:23:24 +0200

      Commit message:


	  
		
 chore(deps): bump trufflesecurity/trufflehog from 3.97.1 to 3.97.9 (#52)

Bumps [trufflesecurity/trufflehog](https://github.com/trufflesecurity/trufflehog) from 3.97.1 to 3.97.9.
- [Release notes](https://github.com/trufflesecurity/trufflehog/releases)
- [Commits](https://github.com/trufflesecurity/trufflehog/compare/v3.97.1...v3.97.9)

---
updated-dependencies:
- dependency-name: trufflesecurity/trufflehog
  dependency-version: 3.97.9
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

    

  
    

      Package: ctdR

      Commit: 731ffe16437a10d905346faa2d000f468b6cb880

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

      Date: 2026-10-03 22:33:16 +0200

      Commit message:


	  
		
 Merge pull request #54 from drake69/docs/bioc-devel-install

docs: install instructions for the accepted Bioconductor package 

    

  
    

      Package: ctdR

      Commit: ea90d8f85096f88845235c07db51ec5d4dc21934

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

      Date: 2026-10-03 22:24:54 +0200

      Commit message:


	  
		
 docs: install instructions for the accepted Bioconductor package

ctdR has been accepted into Bioconductor, but the README and the
vignette still said it was under review and pointed to GitHub as the
only source. The vignette is also what the Bioconductor package page
shows, so the page itself contradicted the acceptance.

Both now give the Bioconductor devel installation as the current
method, matching the snippet on the package page (R 4.6,
BiocManager::install(version = "devel")), explain that after the next
Bioconductor release a plain BiocManager::install("ctdR") from the
standard repository is enough, and keep GitHub as the source of the
latest development version.

Version bumped to 0.99.11 so the Bioconductor builder picks up the
corrected vignette.
 

    

  
    

      Package: ctdR

      Commit: c2e1541e755a5a31158aa82d56864d64f834f66e

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

      Date: 2026-09-29 10:54:02 +0200

      Commit message:


	  
		
 Merge pull request #51 from drake69/chore/site-url-in-metadata

Name the documentation site in the package metadata 

    

  
    

      Package: ctdR

      Commit: 7792c1dffcd21c5e0171e615a3906bb8d717c930

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

      Date: 2026-09-29 09:55:47 +0200

      Commit message:


	  
		
 Name the documentation site in the package metadata

The URL field is what the Bioconductor package page shows to whoever has just
installed the package, and it named only the repository. Sending a user who wants
to read the documentation to a source tree is a small waste at the exact moment
attention is highest, so the documentation site comes first and the repository
stays second.

The site also moved, together with the personal site it was hosted under, so the
badge and the reading link in the README are updated with it. The link label had
the old host spelled out in the visible text as well, not only in the href.

The changelog entry that mentions the old address is left alone: it records what
was true at that release.
 

    

  
    

      Package: MetaboDynamics

      Commit: 557647f904767a012825d7e89c3e040529eec818

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-10-04 21:00:35 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: MetaboDynamics

      Commit: 403ee0d8a65ab2ececc795dfd358c5a1dfbde922

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-10-04 20:59:53 +0200

      Commit message:


	  
		
 nomenclature and visualization fixes
 

    

  
    

      Package: EMMA

      Commit: 21c6ef830030b2ba4991effc8690f58b7d351ebe

      Author:  Najla Abassi <abassi.nejla96@gmail.com> 

      Date: 2026-10-04 19:15:21 +0200

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: EMMA

      Commit: 7240f127464d88e15f1c1c72257a8daa2b4736ed

      Author:  Najla Abassi <abassi.nejla96@gmail.com> 

      Date: 2026-10-04 19:15:12 +0200

      Commit message:


	  
		
 update tests
 

    

  
    

      Package: EMMA

      Commit: 1a93818564e23b0b68c7ae33d877ed12782a998b

      Author:  Najla Abassi <abassi.nejla96@gmail.com> 

      Date: 2026-10-04 19:15:02 +0200

      Commit message:


	  
		
 update EMMA_run to return null when no FEA was generated
 

    

  
    

      Package: OHCA

      Commit: 91046331ed017154b9ab1af5f3d9a175cbc109aa

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-04 15:27:41 +0200

      Commit message:


	  
		
 bump to 1.9.1 

    

  
    

      Package: OHCA

      Commit: 66ec0b70a2f2acc9a62b1e83a2a8633d9475dd6b

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-04 12:44:50 +0200

      Commit message:


	  
		
 Portable vignettes/Makefile, and retry the Quarto download (#6)

* fix: retry the quarto download on transient errors

GitHub answered HTTP 503 to the quarto download in the first devel build after
merging #5 (run 42), which failed before anything was installed. curl now
retries transient errors 5 times, 10 s apart, as in BiocBook template 1.1.0
(js2264/BiocBook.template f08bf49).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: portable vignettes/Makefile (BiocBook template 1.1.0)

R CMD check warns about GNU make extensions in vignettes/Makefile, and the
template 1.1.0 Makefile used two (`:=` and `$(shell ...)`) to switch the
`llms` profile on with quarto >= 1.11. rworkflows does not show it yet, since
its check stops earlier on HiCool, but the Bioconductor builders would. The
quarto version is now tested in the recipe's shell (js2264/BiocBook.template
8e43d87).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

--------- 

    

  
    

      Package: SpliceWiz

      Commit: 2640d44f6b10ea386e283f9ceff2558074eedd37

      Author:  alexchwong <80015046+alexchwong@users.noreply.github.com> 

      Date: 2026-10-04 23:55:21 +1100

      Commit message:


	  
		
 Version bump to 1.15.1

fixes for bioc 3.24
 

    

  
    

      Package: SpliceWiz

      Commit: ea2a55e6c5d59b0f2366535b8199143696dd3fdc

      Author:  alexchwong <80015046+alexchwong@users.noreply.github.com> 

      Date: 2026-10-04 23:23:41 +1100

      Commit message:


	  
		
 disable mappability testing

Rsubread internal errors should not weigh on SpliceWiz; it is not the only way to run mappability
 

    

  
    

      Package: SpliceWiz

      Commit: f44f6013f086858ca6ac0ec6a27ec229138f832d

      Author:  alexchwong <80015046+alexchwong@users.noreply.github.com> 

      Date: 2026-10-04 22:29:33 +1100

      Commit message:


	  
		
 switch testing mappability to use gapped index

Suspect OOM error in Win11 test environment at building chrZ reference
 

    

  
    

      Package: SpliceWiz

      Commit: 6c43ffce70ce24529590bc9fd93151b03acdfc2c

      Author:  alexchwong <80015046+alexchwong@users.noreply.github.com> 

      Date: 2026-10-04 14:45:06 +1100

      Commit message:


	  
		
 updated make_plot_data docs
 

    

  
    

      Package: SpliceWiz

      Commit: 7f2bcf77908d39fc021926bdbc725d1afd51a3d2

      Author:  alexchwong <80015046+alexchwong@users.noreply.github.com> 

      Date: 2026-10-04 14:44:54 +1100

      Commit message:


	  
		
 fix getCoverage_df

IRanges::Views does not emit a value column
New implementation uses the right-most column as value column
 

    

  
    

      Package: SpliceWiz

      Commit: e2445eecc0e09683409af01a1b4e8481c484ef3b

      Author:  alexchwong <80015046+alexchwong@users.noreply.github.com> 

      Date: 2026-10-03 23:25:52 +1000

      Commit message:


	  
		
 add GHA
 

    

  
    

      Package: SpliceWiz

      Commit: c7403772c21e5d051b9e5547f1edefe94ed00beb

      Author:  alexchwong <80015046+alexchwong@users.noreply.github.com> 

      Date: 2026-10-03 23:16:35 +1000

      Commit message:


	  
		
 initial update for bioc devel 3.24

fixed seqinfo no longer having row names when coerced to df
roxygen update
 

    

  
    

      Package: grayleafspotr

      Commit: 0e5230c7a43a529c3808dc888ea3ce6f3ff9b193

      Author:  rotsl <wot25kir.nbi@gmail.com> 

      Date: 2026-10-04 12:48:07 +0100

      Commit message:


	  
		
 Merge 0.99.11 Bioconductor DOI update into devel
 

    

  
    

      Package: grayleafspotr

      Commit: c9e640321762b8f6cfc07f2c38d176cdab607b58

      Author:  rotsl <wot25kir.nbi@gmail.com> 

      Date: 2026-10-04 12:47:47 +0100

      Commit message:


	  
		
 Add Bioconductor DOI to package citation (0.99.11)
 

    

  
    

      Package: grayleafspotr

      Commit: ba22b48712151a8c2a1f59ebec3d047f09e6e271

      Author:  rotsl <wot25kir.nbi@gmail.com> 

      Date: 2026-10-04 12:39:59 +0100

      Commit message:


	  
		
 Merge 0.99.10 Bioconductor build corrections into devel
 

    

  
    

      Package: grayleafspotr

      Commit: 750e696fb28be4fdc872b7b7aa36843a41674ee0

      Author:  rotsl <wot25kir.nbi@gmail.com> 

      Date: 2026-10-04 12:39:21 +0100

      Commit message:


	  
		
 Fix Bioconductor vignette builds and heading numbering (0.99.10)
 

    

  
    

      Package: OHCA

      Commit: e53a46145b174816a6f7968f7e512b80843301a6

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-03 23:54:35 +0200

      Commit message:


	  
		
 BiocBook template 1.1.0, python (cooltools) chapter, and fixes for Bioconductor devel (#5)

* feat: execute python while the book builds (BiocBook template 1.1.0)

- `python.reticulate: true`, and a pinned `conda` environment in
  inst/requirements.yml (python 3.12, cooler, cooltools, bioframe, pandas),
  created at build time by `BiocBook::setup_python()`. It solves on linux-64,
  linux-aarch64 and osx-arm64 (about 6 s to solve, 1.5 GB installed)
- DESCRIPTION: BiocBook (>= 1.11.2) and reticulate in Suggests
- Dockerfile from template 1.1.0: python environment provisioned when a page
  runs python, GITHUB_PAT as a BuildKit secret (the image installs
  js2264/HiContactsData from GitHub), optional QUARTO_VERSION pin, remotes
- biocbook.yml from template 1.1.0: extract the pkg bundle and book from the
  image built by this run (`${{ env.IMG }}`) rather than from
  `ghcr.io/js2264/ohca:latest`, which is the devel image on RELEASE_* branches;
  current major versions of every action; quarto 1.11.5
- llms.txt: `llms` quarto profile and post-render hook (BiocBook::enrich_llms_txt)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* feat: new chapter, interoperability with python (cooltools)

`pages/interoperability-python.qmd`, in "Advanced Hi-C topics" after the
R interoperability chapter. It runs `cooltools` on the micro-C `.mcool` file
fetched in R, while the book builds:

- insulation scores and boundaries on the chr17 long arm (5 kb, 100 kb
  window), as in the topological features chapter
- A/B compartments: bins listed in python, their GC content computed in R
  from BSgenome.Hsapiens.UCSC.hg38, passed back to python to phase the
  eigenvectors
- a comparison with HiContacts: compartment eigenvectors correlate at
  r = 0.999 and insulation scores at r = 0.92, while boundary calls differ
  (21 vs 31 boundaries, 3 within 10 kb of each other)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* ci: manual book builds on any branch, index of llms.txt versions (template 1.1.0)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* ci: temporarily patch HiCExperiment to test the book on Bioconductor devel

To be reverted. HiCExperiment (<= 1.13.0) does not import BiocGenerics'
as.data.frame() generic; since S4Vectors 0.51.10 its as.data.frame() calls
on GRanges/GInteractions fail ('no method for coercing this S4 class to a
vector'), which stops the devel build in data-representation.qmd. Patch its
NAMESPACE in the image to see whether the rest of the book builds.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* ci: patch HiCExperiment from its source package (temporary, to be reverted)

The Bioconductor devel image installs binary packages, whose NAMESPACE is
not parsed again at installation: download HiCExperiment's source package
instead.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* ci: revert the temporary HiCExperiment patch

Reverts ae32735 and 09950ba, which patched HiCExperiment's NAMESPACE in the
image only to test the rest of the book on Bioconductor devel. The fix belongs
in HiCExperiment (import BiocGenerics' as.data.frame() generic).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: turn interactions into a tibble through as.data.frame() (workflow-centros)

tibble::as_tibble() fails on Bioconductor 3.24: S4Vectors
0.51.10 no longer sends S3 as.data.frame() calls on Vector objects to the S4
generic, and InteractionSet has no S3 method of its own. Convert with
as.data.frame() first, which needs HiCExperiment to export BiocGenerics'
generic (js2264/HiCExperiment, branch claude/new-session-craecj). Results
are unchanged on current Bioconductor.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* doc: describe how HiContacts and cooltools call boundaries correctly

getBorders() keeps local minima whose prominence against the next local
maximum reaches a fixed threshold (0.2 by default); cooltools.insulation()
uses the topographic prominence and an automatic threshold (Li's method). The
chapter had it the other way round. Also name the normalizations of the
insulation scores (median in cooltools, mean in HiContacts), and say that
setup_python() fetches micromamba when it finds none, not when conda is
missing.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: import matplotlib before attaching R packages (python chapter)

On Bioconductor devel, the python chapter failed at `import cooltools`:
conda-forge's matplotlib (3.11) links libraqm, which needs a harfbuzz more
recent than the system's (Ubuntu 24.04: 8.3.0, without
hb_ft_font_get_ft_face). R packages attached before had already loaded the
system's libharfbuzz.so.0, and the process cannot load a second one under the
same name:

    ImportError: .../libraqm.so.0: undefined symbol: hb_ft_font_get_ft_face

The chapter now activates its python environment and imports matplotlib
before attaching any other package: conda's harfbuzz is loaded first, and the
R packages loaded later use it, being backward compatible. It rendered locally
only because R there comes from conda, with a recent harfbuzz.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* Revert "fix: import matplotlib before attaching R packages (python chapter)"

This reverts commit 101d80e. A test build on Bioconductor devel showed that
the R session has already loaded the system's libharfbuzz.so.0 when the
chapter's first chunk runs, before any of its packages is attached: importing
matplotlib first cannot avoid the clash, and the chapter failed the same way.
The next commit removes the cause from the environment instead.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* fix: pin matplotlib 3.10 in the python chapter's environment

On Bioconductor devel, the python chapter failed at `import cooltools`:

    ImportError: .../libraqm.so.0: undefined symbol: hb_ft_font_get_ft_face

conda-forge's matplotlib 3.11 links libraqm, which needs a harfbuzz more
recent than Ubuntu 24.04's (8.3.0). On the Bioconductor images, the R session
has already loaded the system's libharfbuzz.so.0 when the chapter starts, and
the process cannot load a second library under that name. matplotlib-base
3.10 (3.10.9) does not depend on libraqm.

Checked here by loading the system's harfbuzz before importing matplotlib,
bioframe and cooltools: the import fails with the 3.11 environment and works
with this one, and the chapter renders with the same results. It rendered
here before only because R comes from conda in this container.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

---------

Co-authored-by: Claude <noreply@anthropic.com> </pre>
    </div>
  
    

      Package: OHCA

      Commit: 27b097b0f6b75b28096980d5ec8308c0a12e5d74

      Author:  Claude <noreply@anthropic.com> 

      Date: 2026-10-03 21:35:09 +0000

      Commit message:


	  
		
 Merge Bioconductor devel into devel: version 1.9.0

Brings in the version bumps of the 3.22 and 3.23 releases from
git.bioconductor.org (1.5.0 -> 1.9.0). GitHub's devel keeps its July 2025
commits, which Bioconductor does not have yet.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q
 

    

  
    

      Package: OHCA

      Commit: 7839208cac3bdcad51d7f55550032325fc296727

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2025-07-11 19:13:03 +0200

      Commit message:


	  
		
 fix: move some packages (including HiCool) to Suggests to avoid raising warnings in check
 

    

  
    

      Package: OHCA

      Commit: d1de5ee9c433006e308688fdbcf747c4575be416

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2025-07-11 18:42:59 +0200

      Commit message:


	  
		
 ci: rm manual install of rtracklayer
 

    

  
    

      Package: OHCA

      Commit: 46574b82e0318c0413d1e2b0e93d514cbd27e771

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2025-07-11 18:39:13 +0200

      Commit message:


	  
		
 ci: update actions
 

    

  
    

      Package: OHCA

      Commit: 3f8244bddc2f2be9276173a69341bf8d2966cf03

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2025-07-11 18:37:34 +0200

      Commit message:


	  
		
 doc: add citation to README
 

    

  
    

      Package: OHCA

      Commit: d915897928aa7b1f9231b1a265df9639fddbef79

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2025-07-11 18:37:22 +0200

      Commit message:


	  
		
 ci: fix docker IMG hash
 

    

  
    

      Package: plyinteractions

      Commit: e02edb20e2517952136be1676e5df5dba6c0e304

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-03 23:19:59 +0200

      Commit message:


	  
		
 bump to 1.11.1

Bump version from 1.11.0 to 1.11.1 in DESCRIPTION file. 

    

  
  


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