fix the typo
 

 Bump version to 1.55.1
 

 address audit2 performance findings (safe, result-preserving subset)

Precompute integer alphabet-power tables in the C++ k-let counters and
sequence generators instead of calling pow() at every sequence position
(P1): klet_counter / get_lastlet / eulerian_walk / markov_generator /
create_sequences in shuffle_sequences.cpp, and klet_counter_NA in
get_bkg.cpp. Replace the 11 pow(x, 2.0) calls in the per-column
compare_motifs metrics with plain multiplication (P8). Hoist the
loop-invariant tscore out of the inner j loop in the motif_pvalue
multi-split DP (P6). Add a 64-bit overflow guard in expand_scores_cpp so
the exhaustive path stops cleanly rather than overflowing a 32-bit int,
independent of the R-side cap (P4). Drop the per-column NumericVector
temporaries in the scan PWM quantisation (P2; the audit's parallelise
suggestion is unsafe because it touches the R API).

All numerically identical; the targeted test suites pass unchanged.
Informal benchmarks show roughly 10-20% on the affected paths.

Bump version to 1.31.29.
 

 igblastr 1.3.4

install_IMGT_germline_db() now emits a warning if the computed
"internal data" that it includes in the germline db has disagreements
with the "internal data" shipped with IgBLAST.

Add show_intdata_disagreements() to show disagreements (if any) between
the computed "internal data" included in a germline db and the "internal
data" shipped with IgBLAST.
 

 tried different ways for optimisation.
 

 optimised IVT tab
 

 version bump
 

 fix tsv reading for large files
 

 allow setting headers with gemma_call
 

 require R 4.1.0
 

 remove p vals from plot
 

 diff exp plotting
 

 fix author description for bioconductor
 

 bump version to 1.3.2 and fix plotVenn default fills for partial overlaps
 

 return a message when dry.run = TRUE and quarto sysdep is not installed
 

 Bump version to 0.99.1
 

 Improve the auxdata produced by install_IMGT_germline_db()

Improve the computed auxiliary data produced by install_IMGT_germline_db()
by completing it with the auxiliary data shipped with IgBLAST.
The completion process consists in eliminating missing values in the
computed auxiliary data where possible. This is done by replacing each
missing value with the corresponding value from the auxiliary data shipped
with IgBLAST, if the latter is available.
 

 ci: retrigger build
 

 ci: retrigger build
 

 ci: retrigger build
 

 ci: retrigger build
 

 fix: remove cyclocomp_linter exclusion from lintr defaults
 

 ci: retrigger build
 

 ci: retrigger build
 

 ci: trigger build
 

 ci: trigger build
 

 ci: trigger build
 

 ci: trigger build
 

 ci: trigger build
 

 ci: trigger build
 

 fix: add legacy verbs to VALID_VERBS for backward compatibility
 

 fix: only lint latest NEWS.md section, keep VALID_VERBS as infinitives
 

 ci: trigger build
 

 fix: extend VALID_VERBS to cover historical NEWS.md entries
 

 fix: resolve remaining gDRstyle linting violations
 

 ci: trigger build
 

 refactor: revert cyclocomp refactoring, defer to separate PR
 

 chore: bump version and update NEWS.md
 

 fix: export lintNewsEntries, fix self-lint violations, allow <<-/:::

- Add lintNewsEntries to NAMESPACE (was missing, causing all packages to fail)
- Allow <<- and ::: operators (needed for closures and tests)
- Fix trailing whitespace, paste_linter, seq_linter violations in gDRstyle
 

 fix: add cyclocomp to Imports to ensure cyclocomp_linter works
 

 feat: forbid Jira ticket references in NEWS.md entries
 

 chore: revert version bump, add NEWS entry to 1.11.3
 

 fix: avoid f-string interpolation of diff content in auto-changelog
 

 refactor: unify linter config by bumping lintr requirement to >= 3.2.0
 

 feat: add testthat linters and document all active linting rules in style_guide
 

 chore: remove CONTRIBUTING.md in favor of style_guide.Rmd vignette
 

 chore: bump version to 1.11.3 and update NEWS.md
 

 feat: extend linter config and add auto-changelog workflow
 

 ci: trigger build
 

 ci: retrigger build
 

 ci: retrigger build
 

 ci: retrigger build
 

 ci: retrigger build
 

 ci: trigger build
 

 ci: retrigger build
 

 ci: retrigger build
 

 fix: use infinitive verbs in NEWS.md entries
 

 chore: update date to 2026-05-27
 

 fix: resolve remaining gDRstyle linting violations
 

 fix: complete nrow/ncol to NROW/NCOL replacement
 

 fix: restore logic changes incorrectly introduced by lint fixes
 

 docs: update NEWS.md entry wording
 

 fix: resolve gDRstyle linting violations

Address lint violations from updated gDRstyle rules:
- Fix trailing whitespace and blank lines
- Replace nrow/ncol with NROW/NCOL
- Fix paste_linter (paste0+collapse, toString, strrep, file.path)
- Fix seq_linter (seq_along, seq_len)
- Refactor cyclocomp_linter violations (extract helper functions)
- Fix test linters (yoda, expect_true_false)
- Remove undesirable operators (|> pipes)
 

 bump version to 1.31.28; NEWS for the audit follow-up
 

 fix two pre-existing crashes uncovered while writing the audit tests

- shuffle_sequences: k larger than the shortest input sequence used to
  read past the end of the sequence buffer inside the C++ backend and
  crash R. Added an R-side check that errors with a clear message
  before the dispatch. Order of validation inside enrich_motifs() also
  shifted so the "widest motif" check fires before the shuffle, keeping
  the existing error message for that path.
- compare_motifs (pval_extractor): the per-comparison row search bumped
  n1/n2 each iteration looking for a matching db.scores row, but when
  it ran off the table it set row = -1 without setting ok = true, so
  the outer while loop kept incrementing past the table forever. Bail
  with ok = true on the same branch.
 

 audit follow-up: correctness fixes across C++ and R readers

Fixes the items from the audit:

- compare_motifs.cpp: pairwise similarity in compare_motifs_some_cpp was
  passing bkg[index1[i]] twice instead of bkg[index1[i]], bkg[index2[i]],
  which mis-scored every comparison whose two motifs had different
  background frequencies.
- compare_motifs.cpp: pval_extractor used to call R::pnorm / R::plogis /
  R::pweibull from inside an RcppThread::parallelFor, all of which touch
  R's internal state and are not thread-safe. Split into a parallel row
  search and a serial p-value calculation; correctness no longer depends
  on the operating system's pthread scheduling being kind on macOS.
- shuffle_sequences.cpp: renamed the local firslet/firstlet typo so the
  variable name matches the helper.
- read_homer.R: replaced ifelse(is.na(...), numeric(0), ...) (which
  silently returned NA_real_ instead of an empty vector) with explicit
  if/else so missing nsites/bkgsites parse to numeric(0) as documented.
- convert_motifs.R: motifStack pcm conversion used to pick nsites via
  unique(colSums(mat))[1], silently masking unequal column sums. Now
  checks within tolerance and errors with a clear message when columns
  disagree.
- universalmotif-class.cpp: the PCM branch of check_motif_and_type only
  inspected the nsites slot; added an equal-column-sum check on the
  motif matrix itself, with tolerance matched to the existing PPM
  column-sum tolerance so PPM-derived PCMs still validate.
- read_jaspar.R: guard ncol(motif) == 0 (and is.list(motif), the parse
  shape produced by header-only matrices) before max(colSums(motif)),
  which otherwise produced an -Inf nsites slot that only blew up later
  in convert_type.
- read_jaspar.R / read_cisbp.R / read_meme.R / read_transfac.R: error
  with "no motifs found in ''" when the regex that locates headers
  returns an empty vector, instead of silently parsing to an empty list.

The audit also flagged C3, C4, C5, and C6. Each was investigated and is
either unreachable from R (C3 is gated by R/motif_pvalue.R, C4 by the
R wrapper in R/shuffle_sequences.R) or correct-but-obscure (C5's
unsigned arithmetic is held safe by its guard, C6's offset arithmetic
collapses to offset because forj == 1 in one branch and fori == 1 in
the other). None of them fires for any caller in the current package,
so they were dropped from the action list.
 </pre>
    </div>
  
    

      Package: universalmotif

      Commit: f7d7617fe025f67d63556e8edc7529e79eb09d0e

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-28 14:59:44 +0100

      Commit message:


	  
		
 convert_motifs: actually build TFBSTools-*MatrixList outputs

The list method documented PFMatrixList, PWMatrixList and ICMatrixList
as valid target classes but had no code path for them, so each motif
hit the universalmotif method's `unknown 'class'` stop. Now intercepted
in the list method: convert each motif to the singular matrix type and
wrap with the matching TFBSTools list constructor via do.call (the
constructors are variadic). Adds a test covering all three list classes
plus a PWMatrix-list input round-trip.
 
    
  
    

      Package: simPIC

      Commit: 9c476fcc17e088ab54f045893b52ea9391fc77d4

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-28 20:14:21 +1000

      Commit message:


	  
		
 Skip splatPop estimate tests without VariantAnnotation
 
    
  
    

      Package: simPIC

      Commit: 4e4754800a2c5a45ffa3bde7b85d48d2c743195e

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-28 15:11:46 +1000

      Commit message:


	  
		
 Guard splatPop estimate example optional dependencies
 
    
  
    

      Package: simPIC

      Commit: 84163fec557ed0128bb2c3e92a707b845ee259b3

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-28 12:59:00 +1000

      Commit message:


	  
		
 Guard Microglia example optional dependencies
 
    
  
    

      Package: simPIC

      Commit: 466edf35aa51347d0761ee9106b8cf72f4be62e4

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-28 11:17:34 +1000

      Commit message:


	  
		
 Skip Microglia vignette chunks when optional deps are unavailable
 
    
  
    

      Package: simPIC

      Commit: 1b04b52910ba81967210c6753c22cbc1ac655437

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 22:55:30 +1000

      Commit message:


	  
		
 Reduce test data size and install CI vignette dependencies
 
    
  
    

      Package: simPIC

      Commit: 80a39f395bb6ff862e7635e25b005a25c88a2251

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 22:22:18 +1000

      Commit message:


	  
		
 Install CI dependencies without pak lockfile
 
    
  
    

      Package: HiCDOC

      Commit: ee91ddbbcb8f86c7192de9c7358d25c67560868a

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-28 14:31:26 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: HiCDOC

      Commit: d2fbefa9f90768cb8781120ca08d4cef401b33d5

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-28 14:22:28 +0200

      Commit message:


	  
		
 recompile doc
 
    
  
    

      Package: HiCDOC

      Commit: 18bed5ea3c603cb68831278602e9fc55bf748170

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-28 13:14:30 +0200

      Commit message:


	  
		
 uses HiCParser to import HiCData
 
    
  
    

      Package: HiCDOC

      Commit: ea0789dd79794d7227952b1d6c5093c32fe948e5

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-27 16:26:58 +0200

      Commit message:


	  
		
 redocument
 
    
  
    

      Package: HiCDOC

      Commit: f99a3d9e23d506d5d0d7184a89d62ab7a31bfea3

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-27 16:26:43 +0200

      Commit message:


	  
		
 add script to generate example data (ignored in build)
 
    
  
    

      Package: HiCDOC

      Commit: dfb049b806a4d13ab368012d0bf551c3f693e0af

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-27 16:26:01 +0200

      Commit message:


	  
		
 uses default parameters in tests and examples to retrieved data and fix typos (bad copy paste)
 
    
  
    

      Package: HiCDOC

      Commit: 087cbb06b974a6d07949054a4db9b211c40384e0

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-26 15:38:54 +0200

      Commit message:


	  
		
 changing default parameter for smallChromosomesThresholds to 0
 
    
  
    

      Package: gDRcore

      Commit: 4e3e80b92f1f345e7db066a77a1e26a2f8332c34

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-05-28 14:17:11 +0200

      Commit message:


	  
		
 Merge pull request #196 from gdrplatform/GDR-1014

fix: resolve gDRstyle linting violations 
    
  
    

      Package: gDRcore

      Commit: a73a08c482d9e3e9e81884ba45e0275f5677189f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 12:01:17 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: ca7dd1ff874e23fef58d96c2dad6fda894f8e13e

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:55:23 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: d34af1ea6e0f7a1dd14dcf163e02b38196ba874f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:42:18 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: f0de2c8924df8b40ea519341b6f77492a9c2141b

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:34:19 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: d93e7b090bc1f4fc63e9aa17bb01ff6327d1ed77

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 09:27:52 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: 88b76cd9fc561dba1dba883e56e2aa6dabb58f56

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 08:33:34 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: 78ad015ae6a27174233952fd157f0a793cdc1b06

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 07:34:09 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: 65233d6ab8853b838ef592227220954b998e56d6

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 22:05:40 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRcore

      Commit: c0e3db82b52df52e4120b7f352afc106bc74e3c0

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:23:27 +0200

      Commit message:


	  
		
 docs: regenerate documentation
 
    
  
    

      Package: gDRcore

      Commit: de06d6e501374d80c51113f248bc52708341dcfd

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:14:01 +0200

      Commit message:


	  
		
 fix: use fixed substring match in validate_data_models_availability test
 
    
  
    

      Package: gDRcore

      Commit: 51fefb60df5716b32d560e8a978b3b6c5c0a929c

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:06:07 +0200

      Commit message:


	  
		
 fix: collapse multi-line error message and resolve merge conflict
 
    
  
    

      Package: gDRcore

      Commit: 987578755452cf19b0e06e1467b5d4e0ad861d00

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:00:08 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries
 
    
  
    

      Package: gDRcore

      Commit: daa3708230cfa6e5e57641a099999923d2166536

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:38:17 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries
 
    
  
    

      Package: gDRcore

      Commit: 5c83a5c1d43fb3bc801fb6ff7f3b45b2ba2a4cd5

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:30:38 +0200

      Commit message:


	  
		
 chore: update date to 2026-05-27
 
    
  
    

      Package: gDRcore

      Commit: 10149c680e0d3598b3043338e858895723424531

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:18:28 +0200

      Commit message:


	  
		
 fix: add missing terminal newlines
 
    
  
    

      Package: gDRcore

      Commit: 0006e23e53c01f033e577755c848e72df919c789

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 15:48:26 +0200

      Commit message:


	  
		
 fix: resolve remaining gDRstyle linting violations
 
    
  
    

      Package: gDRcore

      Commit: 77bc7bce8f3f54cd4288062c37e4a348d0da696d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:27:39 +0200

      Commit message:


	  
		
 chore: trigger CI
 
    
  
    

      Package: gDRcore

      Commit: aa93fbba4e32061c4832e8cfb2b088e9bb25aeb4

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:08:02 +0200

      Commit message:


	  
		
 fix: complete nrow/ncol to NROW/NCOL replacement
 
    
  
    

      Package: gDRcore

      Commit: 72a16e14899803d6c6cfbfffaaa34dd9e8756048

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:05:43 +0200

      Commit message:


	  
		
 docs: update NEWS.md entry wording
 
    
  
    

      Package: gDRcore

      Commit: bc62905b144a8df8d23242473e7a978d6e064a79

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:17:19 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 
    
  
    

      Package: gDRcore

      Commit: 4ca19ef4c68dffbafc9fa3863a0b04acdb5ff5e7

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 10:07:49 +0200

      Commit message:


	  
		
 fix: resolve gDRstyle linting violations

Address lint violations from updated gDRstyle rules:
- Fix trailing whitespace and blank lines
- Replace nrow/ncol with NROW/NCOL
- Fix paste_linter (paste0+collapse, toString, strrep, file.path)
- Fix seq_linter (seq_along, seq_len)
- Refactor cyclocomp_linter violations (extract helper functions)
- Fix test linters (yoda, expect_true_false)
- Remove undesirable operators (|> pipes)
 
    
  
    

      Package: gDRcore

      Commit: b1ab7f09a88dcc53cae805b11dfa30b3764a3e76

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-14 17:24:08 +0200

      Commit message:


	  
		
 fix: replace nrow/ncol with NROW/NCOL to satisfy gDRstyle linting rules
 
    
  
    

      Package: gDR

      Commit: aa689b6ad34be68cc8ec8b64d9748535559e4def

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-05-28 08:29:43 +0200

      Commit message:


	  
		
 Merge pull request #59 from gdrplatform/GDR-1014

fix: resolve gDRstyle linting violations 
    
  
    

      Package: gDR

      Commit: 1b0be1952756128f657442505f58a62cbc5fd6a9

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 07:34:25 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDR

      Commit: d224c300a082b396a1773736738a296c07bda90e

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 22:05:53 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDR

      Commit: 94c47ba3c0d6dcef9351b2d5010cfe449a63ba8d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 19:40:54 +0200

      Commit message:


	  
		
 docs: regenerate documentation
 
    
  
    

      Package: gDR

      Commit: 44e006fc3014746ea570186fbcb7b77e706d14ac

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:00:35 +0200

      Commit message:


	  
		
 fix: fix malformed version header in NEWS.md
 
    
  
    

      Package: gDR

      Commit: 5dc46e0acd026ba02287e9832e09d8811925845d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:27:46 +0200

      Commit message:


	  
		
 chore: trigger CI
 
    
  
    

      Package: gDR

      Commit: a037055172b9425e574d68f016b8040894b4b126

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-26 10:42:59 +0200

      Commit message:


	  
		
 fix: correct typos in documentation
 
    
  
    

      Package: gDR

      Commit: 4b1f3e0293f0f4364c9a7e6b3bef0b9d39aa6325

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:06:10 +0200

      Commit message:


	  
		
 docs: update NEWS.md entry wording
 
    
  
    

      Package: gDR

      Commit: 1d9eac2716e75ecc51a59e80a1d2455b912bec3e

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:18:06 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 
    
  
    

      Package: gDR

      Commit: 52081f4b70dd78d799294b65f6c35477f29f5a13

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 10:07:50 +0200

      Commit message:


	  
		
 fix: resolve gDRstyle linting violations

Address lint violations from updated gDRstyle rules:
- Fix trailing whitespace and blank lines
- Replace nrow/ncol with NROW/NCOL
- Fix paste_linter (paste0+collapse, toString, strrep, file.path)
- Fix seq_linter (seq_along, seq_len)
- Refactor cyclocomp_linter violations (extract helper functions)
- Fix test linters (yoda, expect_true_false)
- Remove undesirable operators (|> pipes)
 
    
  
    

      Package: gDRimport

      Commit: 6b292201b76678b4e7b0355e66bbfcdf64028256

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-05-28 08:27:49 +0200

      Commit message:


	  
		
 Merge pull request #121 from gdrplatform/GDR-1014

fix: resolve gDRstyle linting violations 
    
  
    

      Package: gDRimport

      Commit: b78f11d4d8d64562c97c9e15e9d14648de06e04a

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 07:33:44 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRimport

      Commit: 70429f5adab4fa548653710335fdca0190cde121

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 22:05:23 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRimport

      Commit: 2ee7cfd66279ff7c4ab319b46f23712f749cec1d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:23:28 +0200

      Commit message:


	  
		
 docs: regenerate documentation
 
    
  
    

      Package: gDRimport

      Commit: 2e8067ae2b17cd950043c0dd11dc6ae2f54ba923

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:00:10 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries
 
    
  
    

      Package: gDRimport

      Commit: b0f037c0812f785ef7cffe77834469530d3b9b38

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:38:19 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries
 
    
  
    

      Package: gDRimport

      Commit: 774b658b6a149aeaa1901b9839cdb5d332f04632

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:30:40 +0200

      Commit message:


	  
		
 chore: update date to 2026-05-27
 
    
  
    

      Package: gDRimport

      Commit: 1966941316c38b18b6c6728d9fe182b31122fc87

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:18:30 +0200

      Commit message:


	  
		
 fix: add missing terminal newlines
 
    
  
    

      Package: gDRimport

      Commit: 71aa2f598ac283316af8668a936d67a3d880f105

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 15:48:28 +0200

      Commit message:


	  
		
 fix: resolve remaining gDRstyle linting violations
 
    
  
    

      Package: gDRimport

      Commit: 9c19db3a41ead5aaa15cd6714d5f962f1dd757bd

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:27:42 +0200

      Commit message:


	  
		
 chore: trigger CI
 
    
  
    

      Package: gDRimport

      Commit: 3cf8f6f7b1c525c81952baa8b69fbe60773db78d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:08:02 +0200

      Commit message:


	  
		
 fix: complete nrow/ncol to NROW/NCOL replacement
 
    
  
    

      Package: gDRimport

      Commit: b6f8aeb8ce968090c227dd514be397ecb718bc9f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-26 10:43:00 +0200

      Commit message:


	  
		
 fix: simplify matrix initialization
 
    
  
    

      Package: gDRimport

      Commit: b3c6d745cc19049860ad1383a85a9becbaed9356

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-26 10:27:43 +0200

      Commit message:


	  
		
 fix: restore qs2::qs_read calls in test-load_files.R

Reverts accidental reversion from qs2 back to qs package calls.
 
    
  
    

      Package: gDRimport

      Commit: 95087dfee143117072ddbe855706150af5f5147f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:14:47 +0200

      Commit message:


	  
		
 fix: restore paste0 for multi-arg concatenation with collapse
 
    
  
    

      Package: gDRimport

      Commit: 9928c5315089fa0fbd98d63bad6cf9741febc99f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:05:45 +0200

      Commit message:


	  
		
 docs: update NEWS.md entry wording
 
    
  
    

      Package: gDRimport

      Commit: 76e71e7d0a3d976efb26d2e8c0dbe411d020666f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 07:54:06 +0200

      Commit message:


	  
		
 refactor: revert cyclocomp refactoring, defer to separate PR
 
    
  
    

      Package: gDRimport

      Commit: 2fc1d68f3d5489eb30606ba1a0060d5cbcf9cf32

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:17:21 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 
    
  
    

      Package: gDRimport

      Commit: b1f4d05cc89328b588cd009433c7560d46b03b12

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 10:07:49 +0200

      Commit message:


	  
		
 fix: resolve gDRstyle linting violations

Address lint violations from updated gDRstyle rules:
- Fix trailing whitespace and blank lines
- Replace nrow/ncol with NROW/NCOL
- Fix paste_linter (paste0+collapse, toString, strrep, file.path)
- Fix seq_linter (seq_along, seq_len)
- Refactor cyclocomp_linter violations (extract helper functions)
- Fix test linters (yoda, expect_true_false)
- Remove undesirable operators (|> pipes)
 
    
  
    

      Package: gDRimport

      Commit: 328ce132e7018d72532fead8a0241f75f9a9edc1

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-14 17:40:58 +0200

      Commit message:


	  
		
 fix: replace nrow/ncol with NROW/NCOL to satisfy gDRstyle linting rules
 
    
  
    

      Package: gDRtestData

      Commit: 24bc077c204c89080e73211a09f1ef603ea99bea

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-05-28 08:26:17 +0200

      Commit message:


	  
		
 Merge pull request #76 from gdrplatform/GDR-1014

fix: resolve gDRstyle linting violations 
    
  
    

      Package: gDRtestData

      Commit: 6f6a034e99f8e5db70928050e627b821f2ad3f5a

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 07:33:43 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRtestData

      Commit: b5b023b64e53d34b83823770dfcbb9c069284ebd

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 22:05:21 +0200

      Commit message:


	  
		
 ci: retrigger build
 
    
  
    

      Package: gDRtestData

      Commit: 2c6bb832bf54d0982e85c552ddef73d7d2790826

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:23:32 +0200

      Commit message:


	  
		
 docs: regenerate documentation
 
    
  
    

      Package: gDRtestData

      Commit: 310b0f93594edbcddc59cfbb7a71bf54102dcb36

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:00:33 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries and fix malformed header
 
    
  
    

      Package: gDRtestData

      Commit: 462a012951ca085e6e737697d500b52a9e618473

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:27:44 +0200

      Commit message:


	  
		
 chore: trigger CI
 
    
  
    

      Package: gDRtestData

      Commit: 46e2936e765648cd0928d2d637b7f621ceefa5d2

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:15:00 +0200

      Commit message:


	  
		
 fix: restore paste0 for multi-arg concatenation with collapse
 
    
  
    

      Package: gDRtestData

      Commit: 00e6754595850a8c99ef6eaabe3e49ab3c61229d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:06:08 +0200

      Commit message:


	  
		
 docs: update NEWS.md entry wording
 
    
  
    

      Package: gDRtestData

      Commit: 337a8a645dc64153e8874eef6a9f2433d358bcad

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:18:04 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 
    
  
    

      Package: gDRtestData

      Commit: d827d18076bcc9e19d1cfed16e0ef6f28b33b77d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 10:07:50 +0200

      Commit message:


	  
		
 fix: resolve gDRstyle linting violations

Address lint violations from updated gDRstyle rules:
- Fix trailing whitespace and blank lines
- Replace nrow/ncol with NROW/NCOL
- Fix paste_linter (paste0+collapse, toString, strrep, file.path)
- Fix seq_linter (seq_along, seq_len)
- Refactor cyclocomp_linter violations (extract helper functions)
- Fix test linters (yoda, expect_true_false)
- Remove undesirable operators (|> pipes)
 
    
  
    

      Package: gDRtestData

      Commit: e3fad77ff30a9215ccbbc0acb96fa499a3a91d6b

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-14 17:41:29 +0200

      Commit message:


	  
		
 fix: replace nrow/ncol with NROW/NCOL to satisfy gDRstyle linting rules
 
    
  
    

      Package: enrichplot

      Commit: 8adce9ad89d02c81d44298917b439e4acdca66dd

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-04-29 12:11:21 +0800

      Commit message:


	  
		
 update bioc version
 
    
  
    

      Package: Rsubread

      Commit: 2bf5428ac73feed2244d0e065c5b557d2a1ebdb7

      Author:  Yang Liao (Monash University) <yliao@m3v109.massive.org.au> 

      Date: 2026-05-28 09:57:56 +1000

      Commit message:


	  
		
 added some hints about memory alloction failure.
 
    
  
    

      Package: Rsubread

      Commit: f6bdbe14e492e2b80913633f182546a3b21307f7

      Author:  Yang Liao <yang.liao@monash.edu> 

      Date: 2026-05-28 09:24:07 +1000

      Commit message:


	  
		
 removed two bugs in file-based realign buffer
 
    
  
    

      Package: Rsubread

      Commit: c219f59ec5226ec2fffaeb50071664bccad7454f

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-28 08:57:36 +1000

      Commit message:


	  
		
 improved speed for index loading
 
    
  
    

      Package: AnVILPublish

      Commit: 4cae77a6baf74f26c96d8e66ba0a6189b2a25405

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:28:45 -0400

      Commit message:


	  
		
 version bump 1.23.3
 
    
  
    

      Package: AnVILPublish

      Commit: 89d6cfd5e030b0d4894011dc13188b8ddc0e5780

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:28:26 -0400

      Commit message:


	  
		
 update NEWS.md

assisted-by: Gemini 3.5 Flash
 
    
  
    

      Package: AnVILPublish

      Commit: 551f95edd5c9c52d4c1bb33ff75aa09e9e360c27

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:24:39 -0400

      Commit message:


	  
		
 add AnVILBase to Suggests
 
    
  
    

      Package: AnVILPublish

      Commit: 7d8f26ad0e51f06ff5a5bcb7b19804c4b28b9850

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:16:49 -0400

      Commit message:


	  
		
 version bump 1.23.2
 
    
  
    

      Package: AnVILPublish

      Commit: 726626c1ac2384b5ec3763851dc0483e3cbc5f4a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:16:46 -0400

      Commit message:


	  
		
 modularize as_workspace
 
    
  
    

      Package: AnVILPublish

      Commit: 834ba861047dff3acef235be0987eca2161fca6c

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:16:26 -0400

      Commit message:


	  
		
 fix indentation for BiocCheck
 
    
  
    

      Package: AnVILPublish

      Commit: b3bfd09c6d777c8b7c453d09c728a398dcbb1f79

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 16:39:26 -0400

      Commit message:


	  
		
 use assignment operator <- instead of equals =
 
    
  
    

      Package: ggcyto

      Commit: 2484d0d88328e9ff72d36f422dd4eaef9755b571

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:51:51 -0700

      Commit message:


	  
		
 bump version to 1.41.1
 
    
  
    

      Package: ggcyto

      Commit: 23a6ad5432207cc89348bd0cfde514f4577ba767

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:51:39 -0700

      Commit message:


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

      Package: ggcyto

      Commit: 7ef1a8c4d40f6b73fd8d8ac9fcfc1971a04122d4

      Author:  Hervé Pagès <hpages@users.noreply.github.com> 

      Date: 2026-05-27 13:33:35 -0700

      Commit message:


	  
		
 Use new BiocGenerics::transform() with new signature (#115) 
    
  
    

      Package: ncdfFlow

      Commit: 7e2647d5551571303c4c8fa5618f185113eb59f2

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:51:12 -0700

      Commit message:


	  
		
 bump version to 2.59.1
 
    
  
    

      Package: ncdfFlow

      Commit: 9f90a42e048651de08c36a6975076e83a806a52a

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:51:01 -0700

      Commit message:


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

      Package: ncdfFlow

      Commit: 6493dc4f3f2cad222061fb0611ec9b5399b107ed

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:35:28 -0700

      Commit message:


	  
		
 Merge pull request #59 from hpages/devel

Use new BiocGenerics::transform() with new signature 
    
  
    

      Package: ncdfFlow

      Commit: 9087d54b47c550e0c40affa9178ebd8cbd525afe

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

      Date: 2026-05-27 10:26:39 -0700

      Commit message:


	  
		
 Use new BiocGenerics::transform() with new signature
 
    
  
    

      Package: ncdfFlow

      Commit: f91af9cafbb8e3d7c6f1347c9590189ad490aca4

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2025-01-13 10:46:45 -0800

      Commit message:


	  
		
 Merge pull request #58 from RGLab/hotfix/deprecate-zlibbioc

Hotfix/deprecate zlibbioc 
    
  
    

      Package: flowWorkspace

      Commit: 510b28a41fccfd6f637ae940bd056aaf51eba26e

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:50:29 -0700

      Commit message:


	  
		
 bump version to 4.25.1
 
    
  
    

      Package: flowWorkspace

      Commit: b0d5c2440db9a11a1bdf28c02732ed60da06dd02

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:50:10 -0700

      Commit message:


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

      Package: flowWorkspace

      Commit: b966ea1a4b404c27fed3a39eb3d5fabc0e8951b6

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:50:05 -0700

      Commit message:


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

      Package: flowWorkspace

      Commit: 37b44557ae78474e4eb79b02c941d998f4302285

      Author:  Hervé Pagès <hpages@users.noreply.github.com> 

      Date: 2026-05-27 13:32:57 -0700

      Commit message:


	  
		
 Use new BiocGenerics::transform() with new signature (#408) 
    
  
    

      Package: flowWorkspace

      Commit: 103dbbe1028da62a48c5f76f2b3a7ce7a2d3e1e3

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-02-19 13:08:42 -0800

      Commit message:


	  
		
 Add cytoset_factors and GatingSet_factors classes to preserve factor levels in pData by delegating to flowSet's phenoData slot
 
    
  
    

      Package: flowCore

      Commit: 4935c7bf318697b3128ee50dae81018a6b246ab8

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:43:03 -0700

      Commit message:


	  
		
 pump
 
    
  
    

      Package: flowCore

      Commit: 371be28eaf0c47c65a93213e54babb46021bb649

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:39:04 -0700

      Commit message:


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

      Package: flowCore

      Commit: 1070ccc950e309da4782813efbd9e4b7088783f0

      Author:  Hervé Pagès <hpages@users.noreply.github.com> 

      Date: 2026-05-27 13:31:38 -0700

      Commit message:


	  
		
 Use new BiocGenerics::transform() with new signature (#281) 
    
  
    

      Package: AnVILPublish

      Commit: 17a65b390ce334bada43a13a712d80ec84a5b7ec

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 16:11:13 -0400

      Commit message:


	  
		
 version bump 1.23.1
 
    
  
    

      Package: AnVILPublish

      Commit: 56e485c8fedf896bfe1ccd8a3e3eba136ad36af9

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 15:34:43 -0400

      Commit message:


	  
		
 add fnd role with NHGRI grant number
 
    
  
    

      Package: AnVILPublish

      Commit: a7688dc50ef7398957571ac48705b64abf56464b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 15:06:33 -0400

      Commit message:


	  
		
 remove qualified mentions of AnVILPublish functions
 
    
  
    

      Package: AnVILPublish

      Commit: 9f93f00702d27a18c618fefd5c646aa4d1ce1e79

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 15:05:57 -0400

      Commit message:


	  
		
 update system2 call in vignette to show output
 
    
  
    

      Package: AnVILPublish

      Commit: 49af015be1ab1c8027b54320b2b8d0205be6b8d1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 15:05:46 -0400

      Commit message:


	  
		
 update ref links in vignette
 
    
  
    

      Package: AnVILPublish

      Commit: 843a6bcfd8bacd01013c9fae96519920322ecd14

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:55:35 -0400

      Commit message:


	  
		
 produce error when not using quarto

- remove mentions of notedown
 
    
  
    

      Package: AnVILPublish

      Commit: 5c0c443af3d2ae09cf76c0ad83395778a6adbaaa

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:45:45 -0400

      Commit message:


	  
		
 update quarto arg doc for as_notebook and as_workspace
 
    
  
    

      Package: AnVILPublish

      Commit: 15e6a3b79f26095172d956b487d5e5f7673be46a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:42:00 -0400

      Commit message:


	  
		
 handle lowercase .rmd files in as_notebook
 
    
  
    

      Package: AnVILPublish

      Commit: cf2fa7469b92935397bd3ec3a5675cd2b6a494e6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:36:25 -0400

      Commit message:


	  
		
 minor formatting to .rmd_to_quarto
 
    
  
    

      Package: AnVILPublish

      Commit: 551aa662320c97d6b1ed64d01b39eabbf78dc2a7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:09:21 -0400

      Commit message:


	  
		
 add quarto-cli to SystemRequirements
 
    
  
    

      Package: AnVILPublish

      Commit: da0994a42a09e6bdd4b3232eb11ae41921b724ef

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:04:34 -0400

      Commit message:


	  
		
 use roxygen2 v8
 
    
  
    

      Package: AnVILPublish

      Commit: acc73c6d780a4cf81a36637da5a4500b3b5ef0e6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:04:24 -0400

      Commit message:


	  
		
 add example Rmd for vignette
 
    
  
    

      Package: AnVILPublish

      Commit: 8f23b76e79c61c88f254f18436102e91ccc89b88

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:53:05 -0400

      Commit message:


	  
		
 add named chunk checkQuarto
 
    
  
    

      Package: AnVILPublish

      Commit: 7bd2977db778a5bbf366b3d138466cd622026eb1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:52:51 -0400

      Commit message:


	  
		
 update examples to use dry.run
 
    
  
    

      Package: AnVILPublish

      Commit: ef9c9a35ea9f35e909eb99c01b87b646e7b8ec01

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:51:58 -0400

      Commit message:


	  
		
 remove duplicate & unevaluated chunk
 
    
  
    

      Package: AnVILPublish

      Commit: aa864264e732ed8ecb483b740ad1c2435fc4501d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:51:25 -0400

      Commit message:


	  
		
 remove old email
 
    
  
    

      Package: AnVILPublish

      Commit: d38c017f9d1392d5903939406aea6abd13d81173

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:50:07 -0400

      Commit message:


	  
		
 add GCPtools to section title
 
    
  
    

      Package: AnVILPublish

      Commit: 247ee664469f0082f609c56ffdd1433a92b44bdd

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:42:48 -0400

      Commit message:


	  
		
 update install and load sections
 
    
  
    

      Package: AnVILPublish

      Commit: 24a84f9f3b573bf309d272d46410131b4b52a1b6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 12:31:48 -0400

      Commit message:


	  
		
 add conditional chunk on availability of gcloud
 
    
  
    

      Package: AnVILPublish

      Commit: 240236101c5a3c3caf124e9fb9a15d8793c9e998

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 12:26:47 -0400

      Commit message:


	  
		
 remove old email from vignette
 
    
  
    

      Package: AnVILPublish

      Commit: 9674b60e136ec75f7e7e1fafe33912d43302cd28

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 12:26:32 -0400

      Commit message:


	  
		
 simplify documentation and remove unnecessary roxygen tags
 
    
  
    

      Package: AnVILPublish

      Commit: d8765103ed429d6699180fb52ef68bc7b8f9ba57

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 12:18:32 -0400

      Commit message:


	  
		
 add dry.run arguments to add_access, as_notebook, and as_workspace
 
    
  
    

      Package: AnVILPublish

      Commit: 0365bdbf8a0c8f5806b052dba067819b9f411780

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 17:52:45 -0400

      Commit message:


	  
		
 add examples for add_access, as_notebook, and as_workspace
 
    
  
    

      Package: AnVILPublish

      Commit: 4f867a684be46dd68a6549e234552c26c6f5c322

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 17:38:02 -0400

      Commit message:


	  
		
 set install package chunk to eval=FALSE
 
    
  
    

      Package: AnVILPublish

      Commit: 9a7121115e3d95368506965861539a7821c08f71

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 17:37:11 -0400

      Commit message:


	  
		
 add testthat.R to run unit tests via R CMD check
 
    
  
    

      Package: AnVILPublish

      Commit: 87917d744be518ae12f05d0ce0a1ed4c10c404f5

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 17:36:40 -0400

      Commit message:


	  
		
 add URL and BugReports fields in DESCRIPTION
 
    
  
    

      Package: scRNAseqApp

      Commit: da7dd5afa4544aac90f0486ec205b290f3d654f1

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2026-05-27 13:56:08 -0400

      Commit message:


	  
		
 replace size with linewidth.
 
    
  
    

      Package: friends.test

      Commit: 95d11a75a181784dd9a51d29448940f515df64b1

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-27 11:40:51 -0400

      Commit message:


	  
		
 Add MulticoreParam parallel tests (skip on Windows)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 
    
  
    

      Package: friends.test

      Commit: b38c68bdbaf8e0709bf6fbcce21b29c9b091cfa8

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-27 11:18:30 -0400

      Commit message:


	  
		
 Fix SnowParam workers: propagate .libPaths() and use local(envir=globalenv())

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 
    
  
    

      Package: friends.test

      Commit: 979b9579b82fab4d0e58d642b419018cb75e6ffb

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-27 10:58:06 -0400

      Commit message:


	  
		
 Fix SnowParam worker serialization: wrap lambdas in local(envir=globalenv())
 
    
  
    

      Package: friends.test

      Commit: b39cd46f5e4ba108019684bb48a8a96ba13e0936

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-27 03:19:23 -0400

      Commit message:


	  
		
 Fix SnowParam workers; fix broken doc links; add pkgload to Suggests

- BPOPTIONS(packages='friends.test') in bplapply/bpmapply wrappers
- skip_if(is_dev_package) in parallel tests (workers need installed pkg)
- Remove broken \link{} to deleted fullmesh.enum from docs
- pkgload added to Suggests

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 
    
  
    

      Package: friends.test

      Commit: 77fcf0c151ee823445b5ebe6644b516db9211f8b

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-26 19:06:16 -0400

      Commit message:


	  
		
 Sync with devel: O(ncol) step fitter, BiocParallel, test cleanup

- step.fit.ln.likelihoods: new compact return format (best_ll_by_k1, best_l1_by_k1, uniform_ll)
- step.fit.ln.likelihoods.fullmesh: new function, restores full ll-profile format
- step.fit.ln.likelihoods.fullmesh.enum: removed from public API
- Tests replaced 100-random loop with 7 targeted cases (637 -> 83 tests)
- BiocParallel parallel backend (BPPARAM)
- NEWS.md and .Rbuildignore updated

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 
    
  
    

      Package: friends.test

      Commit: d3663ecd264391c6a582d7c10d57c0a957463c53

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-26 02:50:31 -0400

      Commit message:


	  
		
 Fix package name in testthat.R: best.friends -> friends.test

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 
    
  
    

      Package: friends.test

      Commit: 3e03da3a72ced62c3375d8272c38dc8b3e900495

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-26 02:45:40 -0400

      Commit message:


	  
		
 0.99.19
 
    
  
    

      Package: Fancy

      Commit: 7f84e30fa93ba2f94fbb0d1d3680028e74dc3e2b

      Author:  wala-github <graceca.norsk@gmail.com> 

      Date: 2026-05-27 19:06:35 +0200

      Commit message:


	  
		
 Update of version number for submission to bioconductor
 
    
  
    

      Package: CoSIA

      Commit: 090a204b0e3f808a0752d33af163146ef618ffa1

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-27 11:21:22 -0500

      Commit message:


	  
		
 Version bump in devel
 
    
  
    

      Package: CoSIA

      Commit: 8d3d88f343ec59fa5d4ee93fb89e7749114411b8

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-27 11:03:24 -0500

      Commit message:


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

      Package: CoSIA

      Commit: ac19826fc8ac105adfd2d46c85a26e9cd963cf9c

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-08 13:22:04 -0500

      Commit message:


	  
		
 Make test project paths relative
 
    
  
    

      Package: CoSIA

      Commit: abd4615418a1c9fbc5fcbbb4518ad6c5328b0f84

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-06 12:18:14 -0500

      Commit message:


	  
		
 Ensure container directory exists before SIF check

mkdir -p now runs unconditionally in ensure_sif so the bin/container
directory is created even when the SIF is already present.

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

      Package: CoSIA

      Commit: ea2ad1b2cbe0ca8196d2a66d85c66fc43ad2d2bb

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-06 12:04:11 -0500

      Commit message:


	  
		
 Add runners for test and validations
 
    
  
    

      Package: CoSIA

      Commit: 9cba678b81e0c87d8f3b133443b7cf1d0aaae5b4

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-05 12:19:37 -0500

      Commit message:


	  
		
 Bump to 1.11.2 and revise validation scripts for 1.11.1 vs 1.11.2 comparison

1.11.1 is the Bioconductor production version with the CV_Tissue bug.
1.11.2 is the fixed release.

Validation strategy:
- CV_Tissue: confirm 1.11.1 crashes (bug), 1.11.2 succeeds (fix), with
  structural checks and cross-species consistency check on the fixed output
- CV_Species and DS_* metrics: unchanged code paths, so values must match
  exactly between versions

All scripts now cover all six metric types with a shared set of inputs.

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

      Package: CoSIA

      Commit: d6da95311bc470c0f2ed021502b9dd88a1f7560c

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-04-23 14:58:59 -0500

      Commit message:


	  
		
 Instruct Claude to read CLAUDE_CHANGELOG.md at session start

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

      Package: CoSIA

      Commit: 0c2f99452abe817b6386834adc711eb2acec0b71

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-04-23 13:18:36 -0500

      Commit message:


	  
		
 Add GitHub Actions workflow for running the test suite

Runs devtools::test() on push/PR to devel and main using the official
bioconductor/bioconductor_docker:RELEASE_3_22 container. Caches R
packages keyed to DESCRIPTION and ExperimentHub data (EH7858-EH7863)
with a static key to avoid redundant downloads across runs.

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

      Package: CoSIA

      Commit: d8001e5bc203c047e9593c11180eaa85c98ed24b

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-04-23 13:08:47 -0500

      Commit message:


	  
		
 Add CV_Tissue validation scripts and update .Rbuildignore

Three scripts in validation/ compare Bioconductor release against the dev
version to verify correctness of the CV_Tissue merge rewrite:
- 01_run_bioc.R: captures reference output from installed Bioconductor CoSIA
- 02_run_dev.R:  captures output from the modified dev version
- 03_compare.R:  compares results with structural checks, exact value
  comparison for single-species, and manual spot-check instructions

.Rbuildignore updated to exclude validation/, CLAUDE.md, CLAUDE_CHANGELOG.md.

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

      Package: CoSIA

      Commit: b0fbf7a2304f275b7143c6c88a3deaf6f68f9f37

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-04-22 15:56:48 -0500

      Commit message:


	  
		
 Fix CV_Tissue merge loop producing duplicate columns and missing Anatomical_entity_name

The original loop fed the accumulated result back into each merge iteration,
creating a Cartesian product with cascading .x/.y column duplicates and a
broken Anatomical_entity_name column (also contained a typo in the fallback
rename). Rewritten to join each species independently against the original
id_dataframe and combine on all ID columns + Anatomical_entity_name.

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

      Package: CoSIA

      Commit: 7a07a9e1ed4091f27a11298a33a29f0776c74238

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-04-22 14:24:56 -0500

      Commit message:


	  
		
 Add test suite, fix viewCoSIAn and CV_Tissue bugs, remove deprecation markers

- Add tests/testthat/ suite with 59 tests covering CoSIAn constructor,
  viewCoSIAn, getConversion, getGEx, and getGExMetrics (all 6 metric types)
- Fix viewCoSIAn: replace ifelse() with if/else so data frame slots are
  returned intact rather than coerced to a scalar
- Fix CV_Tissue in getGExMetrics: guard Anatomical_entity_name.x filter
  behind a column existence check so single-species calls no longer crash
- Remove PackageStatus: Deprecated from DESCRIPTION and .Deprecated() call
  from R/zzz.R; package remains active in Bioconductor 3.22
- Add Config/testthat/edition: 3 to DESCRIPTION
- Add CLAUDE.md and CLAUDE_CHANGELOG.md

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

      Package: tximeta

      Commit: d9a028e53c6f687abd621957e353ad6fb0f58b1c

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

      Date: 2026-05-27 11:10:53 -0400

      Commit message:


	  
		
 Merge branch 'devel' of github.com:thelovelab/tximeta into devel
 
    
  
    

      Package: tximeta

      Commit: 894467ad2a9c43cd2a207898390318ca91a2327a

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

      Date: 2026-05-27 11:10:51 -0400

      Commit message:


	  
		
 cleaning up getTxDb code
 
    
  
    

      Package: tximeta

      Commit: 35872c0cc73434485b8358f43bd5fe3f5c201e18

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

      Date: 2026-05-26 08:54:59 -0400

      Commit message:


	  
		
 adding new diagrams
 
    
  
    

      Package: tximeta

      Commit: e58c5650ab7027b2692457c56f773f228ae0260c

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

      Date: 2026-05-22 10:52:03 -0400

      Commit message:


	  
		
 adding new argument gencode_gtf_prefix, for flexibility with the GTF file that is downloaded
 
    
  
    

      Package: simPIC

      Commit: 6a69e49b24f4b71dd72dc18913a1614c944ca918

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 22:13:10 +1000

      Commit message:


	  
		
 Use development pak for CI dependency resolution
 
    
  
    

      Package: universalmotif

      Commit: 36a8a72a904a38b622810ed06245cc9123613df6

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-27 13:03:52 +0100

      Commit message:


	  
		
 ChIPseqWorkflow: attach GenomeInfoDb so keepSeqlevels() resolves

The vignette attached GenomicRanges (which re-exports seqlevels()) but
not GenomeInfoDb, where keepSeqlevels() actually lives, so the Bioconductor
build machine failed the vignette with "could not find function
keepSeqlevels". Attach GenomeInfoDb in the setup chunk and declare it in
Suggests. Bumps the version to 1.31.26.
 
    
  
    

      Package: simPIC

      Commit: acd9550073b411940f5cc1c65e4ab2bb92b6ece9

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 21:55:47 +1000

      Commit message:


	  
		
 Fix CI dependencies and deprecation warnings
 
    
  
    

      Package: simPIC

      Commit: 1ede624444aa9bd3bd7ca798d375234132efaba7

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 20:42:29 +1000

      Commit message:


	  
		
 Resolve devel version after upstream merge
 
    
  
    

      Package: simPIC

      Commit: eab64bbe9b21e537ec13c81ea8a32cbfbdef8b03

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 20:34:37 +1000

      Commit message:


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

      Package: simPIC

      Commit: d60e655843e7d7c13ce1ecac0ce7955d0efbc6cf

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 20:27:26 +1000

      Commit message:


	  
		
 Add population simulation workflow
 
    
  
    

      Package: simPIC

      Commit: 93c1dc6882edf066546f52617bd16163cf4acbed

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 16:33:58 +1000

      Commit message:


	  
		
 Exclude GitHub files from R build
 
    
  
    

      Package: simPIC

      Commit: 0897f400ce732b823d27d674c10a8b54791b01cf

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-23 09:58:33 +1000

      Commit message:


	  
		
 Fix CI: Remove oldrel-1 testing and refresh dependencies
 
    
  
    

      Package: simPIC

      Commit: f6b43cfcfcb4e03f5a2663541adf909a41e3da6b

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-23 02:35:33 +1000

      Commit message:


	  
		
 R-CMD-check badge
 
    
  
    

      Package: simPIC

      Commit: 007b0d0c1a7d54740913840299b34b668abcd340

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-23 02:33:38 +1000

      Commit message:


	  
		
 R-CMD-check badge
 
    
  
    

      Package: simPIC

      Commit: c71d97e828c7719d5eddfc2e62b2cf4e4ce22d94

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-22 16:57:17 +1000

      Commit message:


	  
		
 make sure .yml interprets R script add single quotes
 
    
  
    

      Package: simPIC

      Commit: bf01536f75a2e5de4030808dba9b67266b7c68fc

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-22 16:54:22 +1000

      Commit message:


	  
		
 make sure .yml interprets R script add quotes
 
    
  
    

      Package: simPIC

      Commit: 4324f9e3c0b809f81536298f955304040425f142

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-22 16:47:41 +1000

      Commit message:


	  
		
 make sure .yml interprets R script
 
    
  
    

      Package: simPIC

      Commit: fb2837808985fe47b32c9bab9be47adbf7c167c5

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-22 16:37:18 +1000

      Commit message:


	  
		
 Add BiocCheck workflow for devel-- fixed indent
 
    
  
    

      Package: simPIC

      Commit: 0b32bd82810a06bf67c030ea285c31bd139c3052

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-22 16:27:58 +1000

      Commit message:


	  
		
 Add BiocCheck workflow for devel
 
    
  
    

      Package: universalmotif

      Commit: c09ae09e266d94b2ea4e7c7f44ce5e5cc743cc9e

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-27 11:38:14 +0100

      Commit message:


	  
		
 README: refresh overview to cover the current feature set

Brings the landing page up to date with the package as it stands: notes
CWM support, de novo discovery, co-occurrence testing, and the faster
DNA/RNA comparison and scanning functions; adds the ChIP-seq workflow and
motif database curation vignettes to the list; introduces a CWM section
with a plotted contribution logo; and reworks the comparison example
around compare_motifs2(), merge_motifs2() and view_motifs2(), regenerating
the example figures. Also bumps the version to 1.31.25.
 
    
  
    

      Package: Rarr

      Commit: bbc893ebd576e0cfe031b82903d489e41bff3941

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-27 08:52:56 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: 4dd1708bf9fb810f51a0b70324b27acf172b3089

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-27 08:52:34 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: Rarr

      Commit: 1d8a577443e3b5c457e3ec0f18e0c7646c2d3a19

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-27 08:52:22 +0200

      Commit message:


	  
		
 Fix compatibility with older ZarrArray
 
    
  
    

      Package: epiregulon

      Commit: 4d04502f71982894976ccaac7384e01505292c0c

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2026-05-26 06:32:24 +0000

      Commit message:


	  
		
 update github workflow to Bioc3.24
 
    
  
    

      Package: epiregulon

      Commit: b9f6be6a9bc56ff16646c38112fed805ded3c242

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2026-05-26 06:31:14 +0000

      Commit message:


	  
		
 update github workflow
 
    
  
    

      Package: epiregulon

      Commit: a8fa50e9d32144ec8e1c6ba53768ca4947787935

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2026-05-26 05:58:32 +0000

      Commit message:


	  
		
 version 2.3.2. replace scran::findMarkers with internal findMarkersSimple
 
    
  
    

      Package: Rsubread

      Commit: f2c356364060e3089e1beb442a3fe7f42432ea17

      Author:  Yang Liao <yang.liao@onjcri.org.au> 

      Date: 2026-05-27 15:11:52 +1000

      Commit message:


	  
		
 used normal sort for very few items for sorting
 
    
  
    

      Package: Rsubread

      Commit: c044a6e7348db22b75e11938585f7930b78ace46

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-27 15:07:19 +1000

      Commit message:


	  
		
 disabled sample-level junction list
 
    
  
    

      Package: BiocGenerics

      Commit: fab8ae09376803fd8bb7d2d7a7c2638d94046ca8

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

      Date: 2026-05-26 21:50:21 -0700

      Commit message:


	  
		
 BiocGenerics 0.59.6: Add S4 generic rotate()
 
    
  
    

      Package: Rsubread

      Commit: 6277cc92e632aa3cf6301f1a089bb6b1e027fe2d

      Author:  Yang Liao <yang.liao@onjcri.org.au> 

      Date: 2026-05-27 13:55:02 +1000

      Commit message:


	  
		
 added some comments.
 
    
  
    

      Package: Rsubread

      Commit: 92bbda8745d398a8881806cd5c24de2761dfa353

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-27 13:22:31 +1000

      Commit message:


	  
		
 Added unassigned read output in cellCounts
 
    
  
    

      Package: IRanges

      Commit: 10ce23b0f4e889c60b495c18cc69b637540919ad

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

      Date: 2026-05-26 19:39:38 -0700

      Commit message:


	  
		
 IRanges 2.47.2: Use new transform() signature in method definitions
 
    
  
    

      Package: S4Vectors

      Commit: 6b6e8b0396cf84d00b05199a0580ea25284ed4b8

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

      Date: 2026-05-26 19:24:47 -0700

      Commit message:


	  
		
 S4Vectors 0.51.3: Use new transform() signature in method definitions
 
    
  
    

      Package: Rsubread

      Commit: a9e162b08cfa02b5b481c78533d1232ce2fc9f8f

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-27 11:19:19 +1000

      Commit message:


	  
		
 added vbuf to many file pointers
 
    
  
    

      Package: glmGamPoi

      Commit: 95cffb79b02ce1239112d3c8b4adabfb448940bf

      Author:  const-ae <artjom31415@googlemail.com> 

      Date: 2026-05-26 22:40:39 +0100

      Commit message:


	  
		
 Update NEWS
 
    
  
    

      Package: glmGamPoi

      Commit: 7a4ace6be5e446ecaf46ee1b95b3f4a11b81fdf1

      Author:  const-ae <artjom31415@googlemail.com> 

      Date: 2026-05-26 22:39:34 +0100

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: glmGamPoi

      Commit: a9eeed642020303b350bcf072e0b2150f593de24

      Author:  const-ae <artjom31415@googlemail.com> 

      Date: 2026-05-26 22:39:28 +0100

      Commit message:


	  
		
 Change license to MIT
 
    
  
    

      Package: glmGamPoi

      Commit: 8d9a005741307f13115073687fd9dbbc239ee2f0

      Author:  const-ae <artjom31415@googlemail.com> 

      Date: 2026-05-26 22:36:11 +0100

      Commit message:


	  
		
 Add check for degenerate model_matrix in predict.glmGamPoi for se.fit=TRUE
 
    
  
    

      Package: AnVILAz

      Commit: 89e3a4bc79c91664afd02f0fb8fcc59878191a0e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 16:27:05 -0400

      Commit message:


	  
		
 version bump 1.7.2
 
    
  
    

      Package: AnVILAz

      Commit: b276ea3e2d963089ead2b7ef4b8239880378e514

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 16:26:56 -0400

      Commit message:


	  
		
 fix showClass typo
 
    
  
    

      Package: universalmotif

      Commit: 411e104c944df24322c4348da8c89654c0f24d85

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 21:09:39 +0100

      Commit message:


	  
		
 clean up news
 
    
  
    

      Package: universalmotif

      Commit: a45fb4c4175988d9c243e8dcf50c862138fa1050

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 21:02:24 +0100

      Commit message:


	  
		
 NEWS: frame 1.32.0 entries relative to the last release

The release notes should describe net changes since the last
release (1.30.x), not changes between intra-development states.
Two entries were written against mid-cycle states and don't make
sense to a user upgrading from the last release:

- Dropped the standalone "merge_similar2(return.clusters) now
  returns a universalmotif_df instead of a data.frame" entry:
  merge_similar2() is itself new this cycle, so there is no prior
  released behavior to migrate from. The return.clusters output is
  now described as part of the merge_motifs2()/merge_similar2()
  feature entry.

- Dropped the rev_comp_mat()/view_motifs2() reverse-complement
  bug-fix entry: view_motifs2() is new this cycle, so that bug
  never shipped in a release.

Also narrowed the negative-letter-stack rendering fix to
view_motifs() (the released function that actually carried the
bug; view_motifs2() is new).
 
    
  
    

      Package: universalmotif

      Commit: 6f8bb7b039e77342455adb6a30c504919aabed68

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 20:58:54 +0100

      Commit message:


	  
		
 NEWS: document CWM matrix I/O and the two view_motifs rendering fixes

Add the two outstanding bug-fix entries from the CWM / v2 work:
the negative-letter-stack cumulative-offset fix in
flip_neg_letters() (3+ negative letters used to overlap in
view_motifs / view_motifs2), and the rev_comp_mat() row-name fix
(view_motifs2 drew the column-reverse instead of the reverse
complement of RC'd motifs). Also note read_matrix() / write_matrix()
CWM round-trip via type = "CWM" in the CWM feature entry.
 
    
  
    

      Package: universalmotif

      Commit: 54599e74275ce439a33581d4cf6c33a5f20dbce2

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 20:53:16 +0100

      Commit message:


	  
		
 vignettes: cross-reference v2 functions throughout the prose

Mention the v2 siblings (compare_motifs2, merge_motifs2,
merge_similar2, scan_sequences2, enrich_motifs2, view_motifs2,
motif_tree2) alongside their v1 counterparts where the docs
introduce or describe each function, so readers discover the
leaner alternatives in context. Also tidies assorted phrasing
and trims yamtk-subcommand-specific references to the bare
project link.
 
    
  
    

      Package: universalmotif

      Commit: ba46d951acbee0e380bd047442a2618d3c10dea9

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 20:24:26 +0100

      Commit message:


	  
		
 merge_similar2(return.clusters): return universalmotif_df; CWM doc pass

merge_similar2(return.clusters = TRUE) now returns a
universalmotif_df (the to_df() view of the input motifs, motif
objects in the `motif` column and names in `name`) augmented with
`motif.i` and `cluster` columns, via a new clusters_to_df()
helper applied across the empty-input, single-motif, and
multi-motif paths. Previously it returned a bare three-column
data.frame whose `motif` column held name strings. Callers that
relied on that should switch to `name`; `motif.i` / `cluster` are
unchanged. test_merge_similar2.R updated to assert the new class
and columns; MotifDatabaseCuration.Rmd switched from
clusters$motif to clusters$name and prints the assignment columns
explicitly.

CWM documentation pass: convert_type(), create_motif(),
read_matrix(), write_matrix(), read_meme(), and write_meme() man
pages now document the CWM type / CWM argument, including the
TF-MoDISco |cwm|/sum convention, the one-way nature of the
conversion (no *->CWM), and round-trip examples. convert_type
gains a dedicated CWM @details section and Shrikumar et al.
(2017, 2018) references. A test_cwm.R case covers the
write_matrix / read_matrix CWM round-trip.

Also folds in roxygen prose tidy-ups across several v1/v2
function headers (compare_motifs, dedup_hits, motif_finder,
sample_sites, and cross-references to the v2 siblings) and the
corresponding regenerated .Rd files; NEWS updated.
 
    
  
    

      Package: universalmotif

      Commit: f7306500104e457f45cc9939f2b709d7dc572a40

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 17:03:07 +0100

      Commit message:


	  
		
 view_motifs: fix overlap in negative-letter stacks of 3+

flip_neg_letters() positions each negative letter by shifting it
down from the baseline by the cumulative height of every letter
above it in the stack. The shift table is computed at the bottom
of the function:

  letMins <- c(0, letMins)
  for (i in seq_along(lets)) d$y[j_i] <- d$y[j_i] + letMins[i]

`letMins` here is the per-letter min-y (i.e. each letter's height
expressed as a negative number after the flip). With this version,
letter i was shifted by *only* letter (i-1)'s height instead of
the sum of heights for letters 1..i-1, so any 3-or-more letter
negative stack had letters 2..N piling on top of each other. With
a CWM display the bug was glaring (3 equal-magnitude negative
contributions per core column rendering as 2 visible rows);
PWM logos with 3+ significant negative letters had the same
defect but more rarely.

The fix is the one-line cumsum the previous developer left
commented out directly above:

  letMins <- c(0, cumsum(letMins))

For 1- and 2-letter negative stacks the two formulas are
arithmetically identical, so PWM logos that used to render
correctly continue to do so. Full test suite still passes with
no new failures.
 
    
  
    

      Package: universalmotif

      Commit: 0c0ef0f55549e6f85582f9b031834fcc4c8f621e

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 16:56:13 +0100

      Commit message:


	  
		
 view_motifs CWM: derive maxheight from positive+negative col sums

The CWM branch in prep_single_motif_plot_data() previously used
max(abs(mat)) for the per-letter height scale, which captures only
the largest single cell and ignores how much vertical space the
stacked negative letters actually need. The result: y.spacer was
too small relative to the rendered logo height and the negative
letter rows visually blended into each other.

Use the same shape as the PWM branch: maxheight = max(colSums of
positive part) + abs(min(colSums of negative part)). This is the
actual rendered range of the logo, so y.spacer is scaled in
proportion and the top-and-bottom rows of the negative stack
separate cleanly. A pre-existing limitation in
make_position_polygon_data() (outer letters get half the y.spacer,
middle letters get the full y.spacer) still squeezes the middle
letter of a 3-letter negative stack — that affects PWM equally and
is out of scope here.
 
    
  
    

      Package: universalmotif

      Commit: acc259f433e5ed9becf055256d0867b57ea3313d

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 15:25:31 +0100

      Commit message:


	  
		
 add CWM (Contribution Weight Matrix) motif support

Adds CWM as a first-class fifth motif type alongside PCM / PPM /
PWM / ICM, with TF-MoDISco / DeepLIFT-style attribution scores
in mind: signed per-position per-letter contribution values, no
column-sum constraint, no probabilistic interpretation.

C++ layer (src/universalmotif-class.cpp,
src/utils-exported.cpp): accept "CWM" as a 5th type string in
both TYPES2_e and TYPES_e enums; matrix-constraint check
(check_motif_and_type) falls through (no positivity, no
column-sum check) just as it does for PWM; auto-detection of
type from a matrix is unchanged (CWM is explicit-only);
position_icscoreC and get_consensusC / get_consensusAAC each get
a CWM branch that column-normalises absolute values into a
PPM-shaped column before the existing IC / consensus logic runs.

R conversion (R/convert_type.R, R/utils-motif.R): new
MATRIX_cwm_to_ppm() helper computing
ppm[i,j] = |cwm[i,j]| / sum_i |cwm[i,j]| (TF-MoDISco convention,
with a uniform fallback for all-zero columns). convert_type()
gains "CWM" as an accepted source; convert_from_cwm() routes
CWM -> PPM directly and CWM -> PWM / ICM / PCM via PPM (so
CWM -> PWM produces a real log-odds matrix, not a relabel).
The reverse direction (PPM/PWM/ICM/PCM -> CWM) errors with a
clear message.

I/O (R/read_meme.R, R/write_meme.R): both gain a CWM = FALSE
argument. With CWM = TRUE, read_meme() tags the parsed matrices
as type = "CWM" and skips the PPM normalisation check;
write_meme() emits CWM values verbatim into the
letter-probability matrix block (matching what TF-MoDISco-lite
writes). With CWM = FALSE (default), CWM motifs are first
converted to PPM via |cwm|/sum before serialisation, keeping
the output strictly MEME-spec-compliant for downstream FIMO /
AME / CentriMo consumers. No "# CWM" comment marker is added,
matching TF-MoDISco-lite's output.

Display (R/view_motifs.R, R/view_motifs2.R): both accept
use.type = "CWM"; the renderer captures the original CWM
matrices before convert_type_internal() coerces them to PPM,
then splices them back at display time so signed contributions
show with their actual heights. Y-axis labelled "contribution".
prep_single_motif_plot_data() learns a CWM branch that scales
letter heights by the per-motif max(|cwm|). PWM-specific blocks
(zero-baseline geom_hline, signed-axis breaks/ylim) widen to
also cover CWM.

Trimming (R/trim_motifs.R, R/trim_cwm.R NEW): trim_motifs()
automatically works on CWM input via the new C++ IC branch
(no R-side change needed; type tag is preserved). The new
trim_cwm() function is a dedicated CWM-aware trimmer that drops
edge columns by absolute column sum. Two modes:
fraction-of-peak (trim.threshold = 0.3 default, matching
TF-MoDISco-lite's --trim_threshold) or absolute-value cutoff
(abs.threshold non-NULL takes precedence). Walks inward from
the chosen edges only, mirroring trim_motifs()'s edge semantics.

Hardcoded type whitelists in create_motif(), get_consensus(),
get_consensusAA(), view_motifs(), view_motifs2(), and
convert_type() all extended to include "CWM".

Every v1 and v2 analysis function that routes its input through
convert_type_internal() now accepts CWM motifs automatically:
compare_motifs(), compare_motifs2(), scan_sequences(),
scan_sequences2(), enrich_motifs(), enrich_motifs2(),
merge_motifs(), merge_motifs2(), merge_similar(),
merge_similar2(), motif_pvalue(), motif_tree(), motif_tree2(),
motif_rc(). Out of scope (continue to require probabilistic
types): motif_finder(), add_multifreq(), create_sequences(),
shuffle_sequences(), get_bkg(), match_bkg(),
sequence_complexity().

Tests (tests/testthat/test_cwm.R, tests/testthat/test_trim_cwm.R):
32 new assertions covering create_motif type="CWM",
convert_type CWM<->PPM contract (including the error on
PPM->CWM), read_meme/write_meme round-trip with CWM=TRUE,
display via use.type="CWM" in v1 and v2, motif_rc/trim_motifs
type preservation, trim_cwm default vs abs.threshold,
trim.from variants, and a no-op-on-uniformly-strong-CWM
invariant. Full test suite still passes with no regressions.

DESCRIPTION version 1.31.22 -> 1.31.23.
 
    
  
    

      Package: CNViz

      Commit: b8122896563c9021f62345fdcc8cfe4586d2be23

      Author:  rebeccagreenblatt <rebecca.greenblatt@gmail.com> 

      Date: 2026-05-26 14:55:16 -0400

      Commit message:


	  
		
 Make karyoploteR and CopyNumberPlots optional dependencies

Move these packages from Imports to Suggests and gate the karyotype
download handler behind requireNamespace() checks. The karyotype
button is hidden when the packages are unavailable. This prevents
build failures caused by upstream dependency breakage (bamsignals ->
karyoploteR -> CopyNumberPlots cascade).
 
    
  
    

      Package: BiocGenerics

      Commit: 54579afe1b17dca0c59f085cad64cbfb0a2492ce

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

      Date: 2026-05-26 12:33:16 -0700

      Commit message:


	  
		
 BiocGenerics 0.59.5: Add S4 generics sequence() and transform()
 
    
  
    

      Package: daVis

      Commit: 755b92ea0f395ab9c33598fe5f91815223415ccd

      Author:  Katarzyna Gorczak <katarzyna.gorczak@openanalytics.eu> 

      Date: 2026-05-26 21:33:43 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: Rarr

      Commit: e8e93d3ac9477611fddc592a7c7fae2f3c4e98f5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 16:53:29 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: Rarr

      Commit: 517e2a62ee44a6c3a8cc1487306d6a224415228b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 16:33:41 +0200

      Commit message:


	  
		
 Replace missing fill value default by NULL
 
    
  
    

      Package: Rarr

      Commit: 2ffcb60aa1a3ae48bae04bb2834cadad4a23272b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 11:55:43 +0200

      Commit message:


	  
		
 Avoid duplicated .normalize_array_path() in write_zarr_array()
 
    
  
    

      Package: Rarr

      Commit: 18e98e095685f967907e8a5db1cae37d66988a1d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 11:55:06 +0200

      Commit message:


	  
		
 Add 'order' arg input checking
 
    
  
    

      Package: Rarr

      Commit: 84c76aaa4064f3984eceb8e96c00fbd349132906

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 11:54:32 +0200

      Commit message:


	  
		
 Add dimension_names input checking
 
    
  
    

      Package: Rarr

      Commit: 68b0c3208917422fcb5e38064569e113ee090271

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 11:47:30 +0200

      Commit message:


	  
		
 Move costly steps and dir creation after input checking
 
    
  
    

      Package: Rarr

      Commit: 7ab5c882a04a0f0d7f50d0da2283292878e3b7e8

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 08:55:48 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: 96974f0dc9270b2fbbb2c30c0e88165a52db3591

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 08:55:29 +0200

      Commit message:


	  
		
 Mention zstd level 0 in NEWS
 
    
  
    

      Package: Rarr

      Commit: 79aa8d2e6cc4746c08484f67b0e09ef530554e4d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 08:51:40 +0200

      Commit message:


	  
		
 Make 0 a valid and default zstd compression lvl
 
    
  
    

      Package: Rarr

      Commit: 2a253b736c5729dc91a974f6aca63e63acd09609

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 09:02:23 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: Rarr

      Commit: a6518261c3b0e30512911a281aae9afc22a3a707

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 09:02:12 +0200

      Commit message:


	  
		
 Make it clearer that both v2 and v3 are supported
 
    
  
    

      Package: Rarr

      Commit: 0e71ca5c7a1471541745e64f48243cf789ab6891

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 15:24:29 +0200

      Commit message:


	  
		
 Create .store_list()
 
    
  
    

      Package: Rarr

      Commit: 9c5c4d7e2dcd44820ed91ca6a882bd0ac52522f4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 14:45:32 +0200

      Commit message:


	  
		
 Move more functions to store_utils
 
    
  
    

      Package: Rarr

      Commit: 65b0c44c49286d039d249a8ab113dd450de3fba7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 14:29:21 +0200

      Commit message:


	  
		
 Rename .file_or_blob_exists to .store_check_exist
 
    
  
    

      Package: Rarr

      Commit: b223547255fc90bc8f84659b7d2ee002d3f55af3

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 14:18:47 +0200

      Commit message:


	  
		
 Mark 4.2 as min required R version
 
    
  
    

      Package: DelayedArray

      Commit: 877dbfb555937986fc101e3b37fe50330f396d5f

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

      Date: 2026-05-26 09:57:22 -0700

      Commit message:


	  
		
 DelayedArray 0.39.3: Use scale() S4 generic from BiocGenerics

The package no longer defines its own scale() S4 generic but uses the
new scale() S4 generic from BiocGenerics instead.
 
    
  
    

      Package: DelayedArray

      Commit: 0d1f170e392e8e78515c44a9d6317fc76050ebfc

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

      Date: 2026-05-26 09:55:22 -0700

      Commit message:


	  
		
 get rid of .onUnload hook
 
    
  
    

      Package: BiocGenerics

      Commit: b2215575e5dd51a9c104b743b1c7a98e1fb5ae57

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

      Date: 2026-05-26 09:36:26 -0700

      Commit message:


	  
		
 BiocGenerics 0.59.4: Add scale() generic

Define scale() S4 generic with base::scale() as default method.
 
    
  
    

      Package: gVenn

      Commit: 693ee66172cf84ef24261dc30f412d28683848b1

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-05-26 12:15:57 -0400

      Commit message:


	  
		
 bump version to 1.3.1 and document plotVenn fix in NEWS
 
    
  
    

      Package: gVenn

      Commit: ed0b9a76c750df9e48dac4466376a8507076f062

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-05-26 12:11:39 -0400

      Commit message:


	  
		
 fix plotVenn
 
    
  
    

      Package: gVenn

      Commit: b6ef0b148ed771ce0ee5b328d2f55ec956745a21

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-05-26 11:51:14 -0400

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel'
 
    
  
    

      Package: gVenn

      Commit: 7e0f2257321d65dcceeffb18a148619fdf569100

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-05-26 11:51:09 -0400

      Commit message:


	  
		
 ignore .Rhistory
 
    
  
    

      Package: gVenn

      Commit: 1d1bc3324ce43818402e17940c4bfc5da56c9c02

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2025-12-26 23:06:08 +0100

      Commit message:


	  
		
 update README
 
    
  
    

      Package: gVenn

      Commit: 8417eb2fe1e7d52ce4e6a6f0bb90476c786523ca

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2025-12-26 01:45:52 +0100

      Commit message:


	  
		
 update
 
    
  
    

      Package: gVenn

      Commit: 701d47cd26f5720a6759fdde7240276bb2ed224e

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2025-12-12 23:44:47 -0500

      Commit message:


	  
		
 add general link for zenodo doi
 
    
  
    

      Package: gVenn

      Commit: 8aa311f2544645e4327e672f54f7ab09fa2ca254

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2025-12-12 23:39:41 -0500

      Commit message:


	  
		
 add badge Zenodo in readme
 
    
  
    

      Package: gVenn

      Commit: 3ce0907d483d70e02f636ffe31d438d1d13ca1af

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2025-12-09 21:47:39 -0500

      Commit message:


	  
		
 mention hexSticker R package for the logogo
 
    
  
    

      Package: Hiiragi2013

      Commit: 34daed6ce0d791c4d06bcf7134b72e76ecc00137

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 16:32:06 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Hiiragi2013

      Commit: b26fefc0c44ec4e6bdd6d2ab09f8532ba6ec9773

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 16:31:50 +0200

      Commit message:


	  
		
 Use texttt instead of code
 
    
  
    

      Package: universalmotif

      Commit: ed200b1de094c02e36517c619b0693a6ed7c8e6d

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 14:10:13 +0100

      Commit message:


	  
		
 vignettes: switch drop-in view_motifs/motif_tree calls to v2

Where a v1 call can be replaced with its v2 counterpart by renaming
the function alone (no other arg changes), prefer v2. Scope kept
narrow on purpose:

ChIPseqWorkflow.Rmd: three view_motifs() calls -> view_motifs2().
All args (sort.by, show.positions, show.positions.once, names.pos)
are present in v2.

MotifDatabaseCuration.Rmd: three view_motifs() and one motif_tree()
call swapped, plus four prose mentions updated to match. The AP-1
cluster view now also flags FOS::JUN, FOS::JUNB, FOSL1::JUNB, and
FOS::JUND with [RC], which is biologically correct information that
v1's ALLR backend was missing.

IntroductionToSequenceMotifs.Rmd: two single-motif view_motifs()
calls -> view_motifs2(). Single-motif rendering goes through the
same code path in both versions, so the visual output is identical.

Skipped (not drop-in):
- MotifManipulation.Rmd: prose explicitly introduces the v1
  functions (view_motifs, merge_motifs, merge_similar) by name.
- MotifComparisonAndPvalues.Rmd: vignette deliberately demonstrates
  v1 mechanics (the EUCL/WEUCL/etc. method comparison, the manual
  compare_motifs() + ggtree workflow).
- SequenceSearches.Rmd: scan_sequences -> scan_sequences2 would
  always require renaming threshold to pvalue; use.freq = 2 and
  threshold.type = "logodds" have no v2 equivalents.
 
    
  
    

      Package: universalmotif

      Commit: b6693152fe006ebe653611b0482e099bb3493a96

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 14:09:52 +0100

      Commit message:


	  
		
 fix rev_comp_mat() row-name handling for name-indexed consumers

rev_comp_mat() reverses columns and then permutes rows via
m[c(4,3,2,1), ], which physically rearranges the data AND carries
the input row names over in the new T,G,C,A order. That worked for
merge_motifs2()'s per-position accumulator (which adds the columns
positionally into an out_mat with alphabetical A,C,G,T row names,
ignoring the source row names) but produced visually wrong logos in
view_motifs2(): the logo renderer reads each column by row name,
so a position whose physical row-1 data was "the original T row"
got drawn as a "T" letter instead of an "A" (its proper RC).

The MotifDatabaseCuration vignette's AP-1 cluster view exposed the
bug: motifs flagged [RC] rendered as the reverse of TGACTCA
(ACTCAGT) instead of its proper RC (TGAGTCA). Restoring the
alphabetical row names after the permutation fixes it. Physical
data placement is unchanged, so merge_motifs2() behaviour and
tests are unaffected.
 
    
  
    

      Package: universalmotif

      Commit: ccf8158857717d66eeb74c71677f13f09abd370b

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 14:09:33 +0100

      Commit message:


	  
		
 add suggest_motif_tree2() hint to motif_tree()

Completes the v1->v2 suggestion family for the package's user-facing
analysis and visualisation functions. motif_tree() now emits the same
one-time-per-session "Tip: this call uses only arguments supported by
motif_tree2(), a leaner counterpart..." message that compare_motifs(),
enrich_motifs(), merge_motifs(), merge_similar(), and scan_sequences()
already emit. The hint fires only when the v1 caller is using the
default for every argument that motif_tree2() doesn't expose (method,
use.type, min.mean.ic, min.position.ic, relative_entropy, score.strat,
db.scores) so users who have actively customised a v1-only knob are
left alone. Per-session opt-out via
options(universalmotif.suggest.motif_tree2 = FALSE).

view_motifs() deliberately has no suggester.

Bumps DESCRIPTION 1.31.21 -> 1.31.22.
 
    
  
    

      Package: universalmotif

      Commit: dc0e37157efb36d603d37dd628924b2f26ae04ff

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 12:51:37 +0100

      Commit message:


	  
		
 add view_motifs2() and motif_tree2()

Two v2-backend siblings of the package's most user-facing
visualisation functions, following the established v2 pattern
(compare_motifs2, scan_sequences2, enrich_motifs2,
merge_motifs2, merge_similar2): leaner Pearson-correlation
alignment via compare_motifs2_align_cpp, fewer arguments, and a
small, focused public surface.

view_motifs2: picks the highest-IC motif as the anchor (same as
merge_motifs2 / view_motifs), aligns every other motif against
it in one compare_motifs2_align_cpp call, applies reverse
complement where the best alignment lands on the - strand,
pads each oriented motif into a shared column frame, and runs
the result through the same logo renderer as view_motifs.
Drops the v1-only arguments (method, score.strat, min.mean.ic,
min.position.ic, normalise.scores). DNA / RNA only.

motif_tree2: builds the distance matrix from
compare_motifs2(matrix.out = "score") and converts it to a
symmetric distance via (1 - score) / 2, then feeds it into the
same hclust / ape::as.phylo / ggtree::ggtree pipeline that
motif_tree uses. The is(motifs, "dist") short-circuit path is
preserved, so users can pre-compute their own distance matrix
and pass it in directly. Drops the v1-only arguments
(method, use.type, score.strat, relative_entropy,
min.mean.ic, min.position.ic).

Both default to nthreads = 1 to match every other user-facing
function in the package.

The v1 functions view_motifs() and motif_tree() are untouched
beyond a one-sentence cross-reference pointing readers to their
v2 counterparts. Adds tests covering the single/multi-motif
paths, RC detection on non-palindromic motifs, sort.by /
names.pos branches, alphabet rejection, dist short-circuit, and
distance-range invariants. DESCRIPTION version 1.31.20 to
1.31.21; new files added to the Collate field.
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: cbb249664f58635e3e7d0e2571395f9352271150

      Author:  Goncalo Graca <45899755+gggraca@users.noreply.github.com> 

      Date: 2026-05-26 13:19:40 +0100

      Commit message:


	  
		
 Bump version to 1.1.1 and update release date

Updated version and date in DESCRIPTION file. 
    
  
    

      Package: MetaboAnnotatoR

      Commit: 353c261d520fcc87538fa7e271faa66cd51c1bd6

      Author:  Gomes Da Graca <ggomesda@ic.ac.uk> 

      Date: 2026-05-26 13:10:11 +0100

      Commit message:


	  
		
 version name change
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: f6a8fb9e804dc563e959ddff8fc79a8af62953f4

      Author:  Gomes Da Graca <ggomesda@ic.ac.uk> 

      Date: 2026-05-26 12:56:00 +0100

      Commit message:


	  
		
 updates
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: be9ff720865d88fd54b6a5bd59f945a25cf6974f

      Author:  Gomes Da Graca <ggomesda@ic.ac.uk> 

      Date: 2026-05-26 12:52:47 +0100

      Commit message:


	  
		
 version updated after adding ISF annotation
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: 9b9340cb886d58a06e11bfbf12a4e5d69f02fe3e

      Author:  Gomes Da Graca <ggomesda@ic.ac.uk> 

      Date: 2026-05-26 12:50:44 +0100

      Commit message:


	  
		
 annotateISF function added to list
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: 39e0ba5da3036b754a783f2864024fc285d7e368

      Author:  Gomes Da Graca <ggomesda@ic.ac.uk> 

      Date: 2026-05-26 12:48:09 +0100

      Commit message:


	  
		
 addtions to allow ISF annotated results to be saved
 
    
  
    

      Package: MetaboAnnotatoR

      Commit: 58f284c1082f67fd7594b05046c0a9d9d3f8bcbe

      Author:  Gomes Da Graca <ggomesda@ic.ac.uk> 

      Date: 2026-05-26 12:47:09 +0100

      Commit message:


	  
		
 ISF annotation function added
 
    
  
    

      Package: ExperimentHubData

      Commit: da56e777980ccb3155c1946d317acaf810f356a0

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

      Date: 2026-05-22 15:09:18 -0700

      Commit message:


	  
		
 ExperimentHubData 1.39.1: Drop dependency on utils

Package utils doesn't seem to be used anywhere in ExperimentHubData, so
can go away. This will also make the following 'R CMD check' warnings go
away:

* checking whether package ‘ExperimentHubData’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘utils::data’ by ‘BiocGenerics::data’ when loading ‘ExperimentHubData’
  Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ExperimentHubData’
 
    
  
    

      Package: iSEEtree

      Commit: e4fd1ef538117635f8010f37eb2244ed112605aa

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-05-20 15:57:33 +0300

      Commit message:


	  
		
 Merge pull request #51 from federicomarini/patch-1

Update iSEEtree.Rmd 
    
  
    

      Package: iSEEtree

      Commit: 9639f87c9a1c90e1448105f2e0b58eb0da0153fa

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-05-20 15:57:07 +0300

      Commit message:


	  
		
 Merge pull request #52 from federicomarini/patch-2

Update panels.Rmd 
    
  
    

      Package: iSEEtree

      Commit: db0092ae6588b7ad62087a45bfde0544414429c5

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

      Date: 2026-05-20 11:18:16 +0200

      Commit message:


	  
		
 Update panels.Rmd

to have the name rendered correctly on Bioc - at the moment, both vignettes are "called" `iSEEtree` there 
    
  
    

      Package: iSEEtree

      Commit: 23b2ce0573f52eae2caeca09c24416413ac624eb

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

      Date: 2026-05-20 11:17:24 +0200

      Commit message:


	  
		
 Update iSEEtree.Rmd

to have the name rendered correctly on Bioc 
    
  
    

      Package: BgeeCall

      Commit: cac40f400647e84759a644e03d5648b266fb1b51

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-05-26 13:34:22 +0200

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: BgeeCall

      Commit: 4c60914d0c1d3ed6209b8f032cf615fc3e73084d

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-05-26 13:32:58 +0200

      Commit message:


	  
		
 fix the intergenic release used in the vignette
 
    
  
    

      Package: universalmotif

      Commit: 57cead6feb7eda4ad168b7de1b68d9608824a704

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 10:22:51 +0100

      Commit message:


	  
		
 add MotifDatabaseCuration vignette

End-to-end recipe for consolidating motif sets from several public
sources into one deduplicated, trimmed, metadata-decorated MEME
file. Pulls Homo sapiens motifs from three MotifDb sub-collections
(JASPAR2022, HOCOMOCOv11-core-A, cisbp_1.02), stamps the originating
source onto each motif's family slot, inspects pairwise q-value
distribution via compare_motifs2() in matrix mode, picks a q
threshold by visually examining the largest cluster, deduplicates
with merge_similar2() at q = 1e-6, renames merged clusters to
compact "name1+name2[+N more]" lineage labels, visualises the
cross-source clade structure with motif_tree(), trims low-IC
flanks with trim_motifs() (selecting the demo motif by maximum
trim delta so the before/after is visible), decorates the survivors
with db.sources, n.contributors, and curation.date metadata via
to_df()/update_motifs(), and round-trips the curated library
through write_meme() and read_meme(). Adds a cross-reference from
the MotifManipulation vignette and a NEWS entry. Bumps DESCRIPTION
version 1.31.19 to 1.31.20.
 
    
  
    

      Package: pipeComp

      Commit: b629c236b16207e9b6037dc8cb82310bfe00c6e1

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-05-26 10:08:05 +0200

      Commit message:


	  
		
 updated ggplot2 deprecated fns
 
    
  
    

      Package: pipeComp

      Commit: 5f657f80c5e4040104787d4210d1f9f063ef1721

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-05-26 10:00:29 +0200

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: pipeComp

      Commit: a384611064cf86e65c0bb6a5f314662edd9c1406

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-05-26 10:00:07 +0200

      Commit message:


	  
		
 avoiding deprec warnings
 
    
  
    

      Package: pipeComp

      Commit: b0dda546e550f8580d0b22070eaa5cb508489e8e

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-05-26 09:42:55 +0200

      Commit message:


	  
		
 fix type.convert as.is
 
    
  
    

      Package: GenomicScores

      Commit: 162043feaa092bfd5f4d162b60184551a5539b92

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

      Date: 2026-05-26 09:39:59 +0200

      Commit message:


	  
		
 Remove importing utils::data() b/c (1) is not used and (2) it has been promoted to BiocGenerics; see issue #22
 
    
  
    

      Package: cellNexus

      Commit: d7f0137d1c71be379107844554c6370f3a1b6ffe

      Author:  Mengyuan Shen <129487421+myushen@users.noreply.github.com> 

      Date: 2026-05-26 17:15:53 +1000

      Commit message:


	  
		
 Merge pull request #113 from myushen/metadata_new_release

Metadata new release 
    
  
    

      Package: cellNexus

      Commit: 54f266ec1373f996934f4ff8759de386c17d38cc

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-05-26 16:49:36 +1000

      Commit message:


	  
		
 vignette and readme rendering
 
    
  
    

      Package: cellNexus

      Commit: bd2ef66221949137eda4e73353f393170b44950d

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-05-26 15:45:29 +1000

      Commit message:


	  
		
 metadata version up
 
    
  
    

      Package: rhdf5

      Commit: 1dd62c41d01b482616e27461f12db3f662cc0256

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 09:18:55 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: rhdf5

      Commit: 990596f7e56030d4555c93efd8c6d7f2b7022e91

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 09:18:32 +0200

      Commit message:


	  
		
 Use startsWith() instead of grep()
 
    
  
    

      Package: rhdf5

      Commit: a93770304856829db5d3e13dc197cf898314603a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-26 09:16:56 +0200

      Commit message:


	  
		
 Document S3 support in H5Fopen()
 
    
  
    

      Package: rhdf5

      Commit: 8260b333bdf6b2837775079375cb2cfc7a176198

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 22:07:01 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: rhdf5

      Commit: 383feb93bee4aa354b3ac1e53db1c1b5866d001b

      Author:  Michael Sumner <mdsumner@gmail.com> 

      Date: 2026-05-20 04:35:25 +0000

      Commit message:


	  
		
 enable remote H5open
 
    
  
    

      Package: rhdf5

      Commit: 621edf0a03408f1ade107eabd1b30302d8392834

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-24 17:07:32 +0200

      Commit message:


	  
		
 Fix configure files line endings
 
    
  
    

      Package: rhdf5

      Commit: 3eb5165a387e8d23878a4951ec4fa3739ec1ee57

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-24 15:52:55 +0200

      Commit message:


	  
		
 Set R CMD check level back to WARN
 
    
  
    

      Package: rhdf5

      Commit: 3e5f53f746376d2ff47e7e96d3fe351ca3faa154

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-24 15:52:37 +0200

      Commit message:


	  
		
 Use PRIu64 for next_dim in snprintf()
 
    
  
    

      Package: rhdf5

      Commit: 8b811a7f25b4105a1108bd0d8f79435fec618e87

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-24 17:06:34 +0200

      Commit message:


	  
		
 Reduce duplication in h5checktype
 
    
  
    

      Package: rhdf5

      Commit: c4ca3dbcedd2a301b9b03db2e707ba139d9063f8

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-24 14:58:08 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: rhdf5

      Commit: 8b937db1ddcef841d14ffad5a98737dce57a5b4e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-24 12:02:54 +0200

      Commit message:


	  
		
 Add de.NBI ROR
 
    
  
    

      Package: rhdf5

      Commit: 3da5f556b8011b0943e3a510d7d1313772ad1f01

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-22 15:15:02 +0200

      Commit message:


	  
		
 Use more traditional R CMD check workflow 
    
  
    

      Package: scDblFinder

      Commit: 8f8c295ffef5bed9ae8449a8d129ef549ccbac71

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-05-26 09:16:37 +0200

      Commit message:


	  
		
 version
 
    
  
    

      Package: scDblFinder

      Commit: 54f778e8a6cb37565e17cf11de13999dd56c8424

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-05-26 09:15:20 +0200

      Commit message:


	  
		
 porting xgboost using-all-threads fix
 
    
  
    

      Package: BamScale

      Commit: 026ff90e052d4769cd73251ec81124cc2fb3bfd1

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-05-26 15:52:36 +1000

      Commit message:


	  
		
 Increment version number to 0.99.10
 
    
  
    

      Package: BamScale

      Commit: e13d0d35ed7280921f42ca79d7be4061fddb1708

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-05-26 15:50:03 +1000

      Commit message:


	  
		
 Fix auto thread allocation in test
 
    
  
    

      Package: BamScale

      Commit: 3bed5ef97cd7ae0c7a4f9c8b8db13fa0e21da323

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-05-26 15:49:25 +1000

      Commit message:


	  
		
 Fix README
 
    
  
    

      Package: Rsubread

      Commit: 75ee69b53e151f73e31150ad06ef5d42cda2670a

      Author:  Yang Liao (Monash University) <yliao@m3v106.massive.org.au> 

      Date: 2026-05-26 14:34:27 +1000

      Commit message:


	  
		
 Updatd version number
 
    
  
    

      Package: Rsubread

      Commit: 6a500052a143b234ba966934340e70228c6dc7d7

      Author:  Yang Liao (Monash University) <yliao@m3v106.massive.org.au> 

      Date: 2026-05-26 14:31:33 +1000

      Commit message:


	  
		
 since cellCounts now works well, the env check is removed.
 
    
  
    

      Package: Rsubread

      Commit: 16771dfe8566fdeee9ccfaaa79ea2844200f002a

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-26 10:03:30 +1000

      Commit message:


	  
		
 moved memory check to outside for speed
 
    
  
    

      Package: Rsubread

      Commit: 7798b9ee12b13e7af207aef444d4852ea5c237e5

      Author:  Yang Liao (Monash University) <yliao@m3v106.massive.org.au> 

      Date: 2026-05-26 09:49:32 +1000

      Commit message:


	  
		
 removed debug output
 
    
  
    

      Package: dnaEPICO

      Commit: 4d418dabfe1d9e6efe62dfbec7d1f49fbbe9975c

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

      Date: 2026-05-26 09:47:02 +1000

      Commit message:


	  
		
 Bioconductor 0.99.21 Vignettes
 
    
  
    

      Package: Rsubread

      Commit: 3e5b91bc2b7c9ac34ec0da3dc3edef75c54bab2e

      Author:  Yang Liao <yang.liao@monash.edu> 

      Date: 2026-05-26 09:31:16 +1000

      Commit message:


	  
		
 Fixed many bugs in memory-realign buffer
 
    
  
    

      Package: minfi

      Commit: fa38de784663c77840904f4878a7a97b1629f268

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

      Date: 2026-05-25 16:10:36 -0700

      Commit message:


	  
		
 minfi 1.59.1: Import data() from BiocGenerics instead of utils
 
    
  
    

      Package: SynExtend

      Commit: ff73121bf0b617589be75b89ae0d1f1da0acd7f2

      Author:  npcooley <npcooley@gmail.com> 

      Date: 2026-05-25 23:59:48 +0100

      Commit message:


	  
		
 version bumps and news
 
    
  
    

      Package: SynExtend

      Commit: 296b1ec1551503475da61f5490f050fe27d4e17f

      Author:  npcooley <npcooley@gmail.com> 

      Date: 2026-05-25 23:54:53 +0100

      Commit message:


	  
		
 ambitious rewrite
 
    
  
    

      Package: SynExtend

      Commit: beaba15154b649185966502f94753f7aefbe0198

      Author:  npcooley <npcooley@gmail.com> 

      Date: 2026-05-25 15:38:33 +0100

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/npcooley/SynExtend into devel

update version number
 
    
  
    

      Package: SynExtend

      Commit: 04824a28cba79c0daaf371117357e97abdd6d4a2

      Author:  npcooley <npcooley@gmail.com> 

      Date: 2026-05-25 13:23:54 +0100

      Commit message:


	  
		
 1.25 devel update
 
    
  
    

      Package: SynExtend

      Commit: 07021850ff8701e7a6743b8ffe8a62a79eeee2b5

      Author:  Nicholas Cooley <39340402+npcooley@users.noreply.github.com> 

      Date: 2026-04-23 11:18:05 +0100

      Commit message:


	  
		
 Merge pull request #82 from ahl27/master

Documentation fixes 
    
  
    

      Package: SynExtend

      Commit: b3be43e5c054f0d881790be696518d7de4b64abc

      Author:  ahl27 <30053966+ahl27@users.noreply.github.com> 

      Date: 2026-04-15 15:43:17 -0400

      Commit message:


	  
		
 update supertree.rd references
 
    
  
    

      Package: SynExtend

      Commit: 78b562e04531824683bcf88f914b5a18662ba599

      Author:  ahl27 <30053966+ahl27@users.noreply.github.com> 

      Date: 2026-04-14 17:24:53 -0400

      Commit message:


	  
		
 update documentation
 
    
  
    

      Package: SynExtend

      Commit: 44644af986d4a1ef3f6a99fee822b764f29ac660

      Author:  Aidan Lakshman <30053966+ahl27@users.noreply.github.com> 

      Date: 2026-04-14 17:06:56 -0400

      Commit message:


	  
		
 Merge branch 'npcooley:devel' into master
 
    
  
    

      Package: SynExtend

      Commit: a380653d6ace5ac7246a6da6ebc2dab2f226e1a9

      Author:  npcooley <npcooley@gmail.com> 

      Date: 2026-03-09 13:09:51 +0000

      Commit message:


	  
		
 add function, fix indexing bug
 
    
  
    

      Package: SynExtend

      Commit: 5b4c818008aac2c0555eb657bf4b44ce7756bd7b

      Author:  npcooley <npcooley@gmail.com> 

      Date: 2026-03-04 10:10:25 +0000

      Commit message:


	  
		
 large rewrite of NucleotideOverlap
 
    
  
    

      Package: SynExtend

      Commit: e7912685b340962bfa228b06ee501c1c006234e5

      Author:  ahl27 <30053966+ahl27@users.noreply.github.com> 

      Date: 2026-01-21 16:32:29 -0500

      Commit message:


	  
		
 Fix issue with Standardize_Subset where something inexplicable was happening.

Not sure what I was even intending to do. Previous state of this system was doing
something crazy when passed input of `Subset` that was an integer vector.

I've simplified this codepath to make it more understandable and left some
documentation. Should be working correctly now.
 
    
  
    

      Package: Rsubread

      Commit: 872c0e464ad0fa00f1600356d5323af42fcc53e0

      Author:  Yang Liao (Monash University) <yliao@m3v106.massive.org.au> 

      Date: 2026-05-26 08:49:22 +1000

      Commit message:


	  
		
 further improved memory temp
 
    
  
    

      Package: bumphunter

      Commit: 51b589f2c3be64859df7b50431005b8cec3b72d7

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

      Date: 2026-05-25 14:13:00 -0700

      Commit message:


	  
		
 bumphunter 1.55.1: No need to import data() from utils

Package internal code doesn't use utils::data() so there's no need
to import it.
 
    
  
    

      Package: Rsubread

      Commit: 0bf51d49ec5b7619683189af8043e92ae82d7907

      Author:  Yang Liao <yang.liao@monash.edu> 

      Date: 2026-05-26 07:04:25 +1000

      Commit message:


	  
		
 fixed many bugs in the new memory realign space.
 
    
  
    

      Package: GSVA

      Commit: 3644b54d300072a7fc6710f30811355b762290e7

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

      Date: 2026-05-25 22:50:16 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: GSVA

      Commit: a7730d014f8acf2e2b786fb61e416370058241c6

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

      Date: 2026-05-25 22:48:15 +0200

      Commit message:


	  
		
 Merge pull request #267 from rcastelo/266-split-gsva-ranks-calculations

Split GSVA ranks calculations, enabling distribution of computations 
    
  
    

      Package: GSVA

      Commit: 85eac2a6a5d999fe0e3c2cc956ead5263a93a4e5

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

      Date: 2026-05-25 21:07:10 +0200

      Commit message:


	  
		
 Fixed in the documentation
 
    
  
    

      Package: GSVA

      Commit: 8178bcbba97d5f5cd0d2c27ae2b5137fa7eb5fc7

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

      Date: 2026-05-25 21:06:19 +0200

      Commit message:


	  
		
 Missing comma in help page

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

      Package: GSVA

      Commit: 72e056b9031090e0fa478089fa50ce0335d04b0e

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

      Date: 2026-05-25 21:01:52 +0200

      Commit message:


	  
		
 Fix parameter whdim in call to .check_ondisk()

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

      Package: GSVA

      Commit: 64d5f0527c9c494e893502a6fc35f91d3b35be84

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

      Date: 2026-05-25 21:00:16 +0200

      Commit message:


	  
		
 Fix whdim argument in call to .check_ondisk()

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

      Package: GSVA

      Commit: f3fccf56ae5198a85be7b7a2b3c336374b4be9df

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

      Date: 2026-05-25 20:11:02 +0200

      Commit message:


	  
		
 Fixed saveHDF5GSVAranks() and loadHDF5GSVAranks()
 
    
  
    

      Package: GSVA

      Commit: af5941ab45426cb44ae0fb28fde8d63f463d05fc

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

      Date: 2026-05-25 17:07:11 +0200

      Commit message:


	  
		
 Added first and last parameters to enable restricting calculations to a range of rows in gsvaRowNorm(), or columns in gsvaColRanks() and gsvaColScores(). Added corresponding unit tests
 
    
  
    

      Package: GSVA

      Commit: bf082248a311b722f517ccf1469219ad19bb1d21

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

      Date: 2026-05-25 10:50:33 +0200

      Commit message:


	  
		
 Added dropExistingAssays parameter to gsvaRowNorm() and gsvaColRanks(). Added corresponding unit tests
 
    
  
    

      Package: GSVA

      Commit: 4ee72889ffa303f92a95667f73eabf499131d9b4

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

      Date: 2026-05-24 21:55:26 +0200

      Commit message:


	  
		
 Added deprecation of gsvaRanks() and gsvaScores()
 
    
  
    

      Package: GSVA

      Commit: 1776d568282f368e35c6952854f558696f35d6f4

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

      Date: 2026-05-24 21:00:13 +0200

      Commit message:


	  
		
 Fixed gsvaEnrichment(), updated show() method, updated scRNA-seq vignette
 
    
  
    

      Package: GSVA

      Commit: 36df55d6845b5d9f7bb187f63edc726f64368446

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

      Date: 2026-05-23 03:08:43 +0200

      Commit message:


	  
		
 Fixes on code, documentation and unit tests
 
    
  
    

      Package: GSVA

      Commit: ca5e7ebdce5b3a90cca5d41a1e4b2bb29b45928e

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

      Date: 2026-05-22 17:49:14 +0200

      Commit message:


	  
		
 Added gsvaColRanks() and gsvaColScores() functions
 
    
  
    

      Package: GSVA

      Commit: da448ad9e5ab2add6c80bf1b6d66b46f593dbbbf

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

      Date: 2026-05-22 05:45:39 +0200

      Commit message:


	  
		
 Added gsvaRowNorm() function
 
    
  
    

      Package: Rsubread

      Commit: 450cf989409f8fbaf8db0a49a45ce5dcfd95b8a4

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-26 05:58:22 +1000

      Commit message:


	  
		
 load index once only
 
    
  
    

      Package: Rsubread

      Commit: 0851a34ac33402fb11558a7017ae3bb118f426d4

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-26 05:53:29 +1000

      Commit message:


	  
		
 added memory-only realign temp mode
 
    
  
    

      Package: universalmotif

      Commit: 9233d18ee71f4c69ce02a71a65292b5c345f0655

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-25 16:40:31 +0100

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: universalmotif

      Commit: ace6eea331e31b4422bcc79922e799ad0159cf48

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-25 16:36:51 +0100

      Commit message:


	  
		
 vignette: tighten ChIPseqWorkflow figure placement

Load the LaTeX float package and set figure placement to H so figures
land where they are defined rather than floating onto the next page,
which was leaving big white-space gaps below several code chunks.
Trim the 12-motif view_motifs at fig.height=7 to 6, and the merged-set
view_motifs at fig.height=7 to 4, so both fit on the same page as their
preceding code. Drop the duplicate view_motifs at the end of the summary
section since the merged motifs were already shown twice earlier, which
closes the last remaining gap. Page count drops from 18 to 16.
 
    
  
    

      Package: universalmotif

      Commit: 113a9b6086aeb10387a223e61f8ddb9d955f5080

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-25 15:48:08 +0100

      Commit message:


	  
		
 update description
 
    
  
    

      Package: Rarr

      Commit: e58bdc67cc3f2a580188185839ec1194162a3161

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 12:10:02 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: Rarr

      Commit: 999a2da277a949ced8a930ebe3feed6da8ff3a55

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 11:36:45 +0200

      Commit message:


	  
		
 Use rlang::inject() instead of .create_replace_call()
 
    
  
    

      Package: Rarr

      Commit: 3f2ec41342bef27ad3ca16ca208562511f85e96e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 10:42:03 +0200

      Commit message:


	  
		
 Extract lossy conversion steps during write in .prepare_write_data()
 
    
  
    

      Package: Rarr

      Commit: 117dbbc80335c7442bbc7967d98b50a8f9e1f8bd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 10:34:45 +0200

      Commit message:


	  
		
 Use global variables for supported codecs
 
    
  
    

      Package: Rarr

      Commit: 2c0c081037450c0bc989d20ab66335c637e527bd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 09:29:06 +0200

      Commit message:


	  
		
 Extract .normalize_v3_metadata() in its own helper
 
    
  
    

      Package: Rarr

      Commit: b9221bd8ba313f4731737a95031bd693a52c7089

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-25 09:20:14 +0200

      Commit message:


	  
		
 Refactor json S3/local reading
 
    
  
    

      Package: universalmotif

      Commit: 1470689469ab4a55b7871be6bfe055c77a0289b3

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-25 12:09:01 +0100

      Commit message:


	  
		
 clean up news
 
    
  
    

      Package: universalmotif

      Commit: 79b2495e9767a7c2f97bc18641e325cd7baec323

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-25 11:59:28 +0100

      Commit message:


	  
		
 add ChIP-seq workflow vignette + view_motifs sort.by + match_bkg genome path

New end-to-end ChIPseqWorkflow.Rmd vignette walks through a complete
motif analysis on real ChIP-seq peaks, using a newly bundled BED
(VAL1-GFP peaks in Arabidopsis from Yuan et al. 2021, NAR 49:98-113)
that lives in inst/extdata. The workflow: import peaks via
rtracklayer, extract sequences from BSgenome.Athaliana.TAIR.TAIR9,
build a composition-matched genomic background with match_bkg(),
discover motifs with motif_finder(bkg.sequences=...), deduplicate
with merge_similar2(), label clusters by their biological identity
(RY, G_box, ...), compare to JASPAR2022 plants via MotifDb,
validate enrichment with enrich_motifs2(), test central positional
bias with motif_peaks(), and examine RY-self and RY-other spatial
clustering with motif_coocc() plus per-pair distance histograms.
The biological story: six distinct real TF families (B3-domain
ABI3, bZIP ABF3, BPC1, DOF CDF5, RVE8, SPL7) come out of one
peak set.

match_bkg() gains a `genome` argument (BSgenome object) plus
companion `exclude` (GRanges to skip), `n.candidates`, and
`chromosomes` knobs. When supplied, the function samples random
non-overlapping genomic windows internally, replacing the
sample-and-getSeq boilerplate that was otherwise duplicated in
every ChIP-seq workflow. Mutually exclusive with `universe`.

view_motifs() gains a `sort.by` argument with options
"none" (default; input order preserved while alignment still
uses the highest-IC anchor), "ic" (descending information
content), and "similarity" (hierarchical clustering on Pearson
correlation between aligned columns, so visually similar motifs
are adjacent).

DESCRIPTION: adds rtracklayer and BSgenome.Athaliana.TAIR.TAIR9 to
Suggests; version 1.31.13 -> 1.31.16. New BibTeX entry yuan2021val.
Added 11 new tests (7 for match_bkg, 4 for the genome path) and
all 643 tests pass.
 
    
  
    

      Package: universalmotif

      Commit: 4f0d4397237f956886ad07680dcdfe12a3c76b43

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-23 12:50:16 +0100

      Commit message:


	  
		
 vignette: tighten motif_coocc max.distance paragraph wording
 
    
  
    

      Package: universalmotif

      Commit: 58b46f55bc7df492a7a60c0edd08b69ac123983c

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-23 12:49:11 +0100

      Commit message:


	  
		
 drop plot_motif_coocc and the motif_clusters stub

- plot_motif_coocc() removed; users with the data.frame can build any
  ggplot2 heatmap they want without a thin wrapper.
- R/motif_clusters.R removed -- unfinished v1 stub (empty function
  body, never exported, never tested). Dropped from Collate.
- NEWS, vignette, tests, NAMESPACE, man/ all cleaned up.
 
    
  
    

      Package: universalmotif

      Commit: 16469bca8280014868712de58ae11a79c8166624

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-23 12:42:50 +0100

      Commit message:


	  
		
 plot_motif_coocc: drop all axis lines + ticks for a cleaner heatmap
 
    
  
    

      Package: universalmotif

      Commit: 880a478ea62e986cd83bc56c2c471c5678960370

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-23 12:40:38 +0100

      Commit message:


	  
		
 motif_coocc(): make spatial mode descriptive, not part of the Fisher test

The previous implementation filtered the `both` cell by spatial
distance but kept `a_only` and `b_only` based on the unfiltered
presence sets, leaving the 2x2 internally inconsistent
(a_only + b_only + both could exceed n.sequences, neither clamped to
zero). The resulting Fisher p-value lost its meaning.

The conceptual issue is bigger than the math: a proper spatial test
(SpaMo-style) is conditional on co-presence and tests the distance
distribution against a null -- not a 2x2 Fisher.

New semantics: the Fisher test always answers the SET question (do
these motifs co-occur in the same sequences?). When `max.distance`
is supplied, two descriptive columns are added:
  - both.clustered: subset of `both` with a within-distance pair.
  - median.distance: median nearest-pair distance.

Read together: pvalue/qvalue say "do they co-occur?", median.distance
hints "when they co-occur, do they cluster?". Heterodimer-like
arrangements show up as small q AND small median.distance.
 
    
  
    

      Package: universalmotif

      Commit: dcc767f11af61cc387d9790d0cf9bbcd68139b2a

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-23 11:54:16 +0100

      Commit message:


	  
		
 add motif_coocc() and plot_motif_coocc(): motif pair co-occurrence

motif_coocc() finds significantly co-occurring motif pairs in a set of
sequences via one-sided Fisher's exact test on per-sequence 2x2
presence/absence, BH-corrected across all tested pairs. Mirrors HOMER's
pairwise-Fisher convention; optional `max.distance` adds a SpaMo-lite
spatial constraint.

Two input paths:
  - Internal scan via scan_sequences2() -- DNA/RNA only.
  - Precomputed hits + n.sequences -- any alphabet (AA, custom).

Companion plot_motif_coocc() returns a clustered ggplot tile heatmap
of -log10(qvalue) or odds_ratio.

DNA/RNA only on the scan path; any alphabet on the hits path. Pure R;
no C++. 36 unit tests pass. Version bump 1.31.12 -> 1.31.13.
 
    
  
    

      Package: universalmotif

      Commit: 15eca64225de371d77168fde544e36f1604b77f3

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-23 11:31:47 +0100

      Commit message:


	  
		
 vignette: tone down implant_motifs() blurb
 
    
  
    

      Package: universalmotif

      Commit: b3fcf01a0a2aefdb2989381b4a86d4d7d23e5280

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-23 11:29:46 +0100

      Commit message:


	  
		
 implant_motifs(): return.indices = TRUE now returns list(sequences, indices)

Previously returning only the data.frame forced callers to either run
the function twice with the same seed (to also keep the modified
sequences) or accept losing one of the two outputs. Returning both
in a single call eliminates the awkward double-call idiom and matches
how the ground truth is actually used downstream (you almost always
need both the planted sequences and the answer key together).
 
    
  
    

      Package: universalmotif

      Commit: ee5a0b4f57b7ba66af4cc8b56bb552344534a6ea

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-23 11:26:48 +0100

      Commit message:


	  
		
 drop rng.seed from match_bkg() and implant_motifs()

Both are pure-R and used set.seed(rng.seed) inside the function body,
which silently mutated the caller's global .Random.seed -- a real
side-effect bug.

Caller now controls reproducibility via set.seed() before the call,
which is the standard R idiom. Tests and vignette examples updated to
match. rng.seed remains on functions that pass the seed into C++ RNG
state (create_sequences, motif_pvalue, motif_finder, shuffle_sequences,
enrich_motifs, enrich_motifs2, shuffle_string) where it doesn't touch
R's global state.
 
    
  
    

      Package: universalmotif

      Commit: e90d0c9cf2aaf50e8c025737760405b30302df66

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-23 11:13:21 +0100

      Commit message:


	  
		
 add implant_motifs(): plant motif instances into sequences

Inspired by yamtk seed. Generates ground-truth positive sequences for
benchmarking scan_sequences / motif_finder / enrich_motifs2 / motif_peaks.

Three insertion modes (n.per.seq / rate / positions), centre.bias for
ChIP-seq-style clustering, min.spacing for non-overlapping placement,
strand control, deterministic via rng.seed. Returns either the
implanted XStringSet or a ground-truth data.frame (sequence.i,
motif.i, start, width, strand, planted).

DNA/RNA only. Pure R; no C++. 52 unit tests pass.

Version bump 1.31.11 -> 1.31.12.
 
    
  
    

      Package: universalmotif

      Commit: 679b920d6a07502cfc4bd58bab76801c1eb1d41c

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-23 10:54:57 +0100

      Commit message:


	  
		
 mark candidate sites for RcppThread::isInterrupted() in long C++ hot paths
 
    
  
    

      Package: universalmotif

      Commit: 66586fdc97ba782d7475d25563ab660dabf40dc8

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 14:45:38 +0100

      Commit message:


	  
		
 bump to 1.31.11 and document match_bkg()/plot_match_bkg() in NEWS
 
    
  
    

      Package: universalmotif

      Commit: 4c61eccd62a6a4fadade536ec9804c0570dd5071

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 14:43:39 +0100

      Commit message:


	  
		
 match_bkg: fix sample() length-1 gotcha + ring-cap fallback

Two related bugs caused match_bkg() to return wildly-mismatched
backgrounds when the target distribution was narrow and the home
bin's available pool dropped to a single index:

  1. R's `sample(x, n)` treats a length-1 numeric `x` as `1:x` and
     returns sample.int(x, n). So `sample(c(201), 1)` returns a
     random integer in [1, 201], not the value 201. The find_candidates
     loop was hitting this when a cell had only one universe
     sequence available after dedup -- which then produced an
     arbitrary universe index unrelated to the target's bin.

  2. The original unbounded ring-expansion (up to max(n.gc.bins,
     n.len.bins) rings) was too aggressive: once nearby cells got
     drained via unique=TRUE, ring expansion would walk far out to
     bins compositionally unlike the target before finally hitting
     the global random fallback.

Fixes:
  - All sample() calls switched to `pool[sample.int(length(pool), n)]`
    which is immune to the length-1 gotcha.
  - Ring expansion is now capped at MAX_LOCAL_RING = 2. Beyond that,
    the function falls back to with-replacement sampling from the
    accumulated *local* pool (rings 0-2). This preserves the
    composition match at the cost of occasional duplicates, instead
    of degrading into a global random sample.

On the canonical demo fixture (target GC ~0.68/length ~400, universe
GC ~Beta(2,2)/length ~U(200,800)):
  - Before: matched bkg GC = 0.52 +/- 0.22, length = 474 +/- 154
  - After:  matched bkg GC = 0.67 +/- 0.05, length = 389 +/-  61

Includes the linter's incidental polish to match_bkg.R / man /
vignette (drop the chromVAR reference, tighten markdown emphasis).
 
    
  
    

      Package: universalmotif

      Commit: f3364a5590c37c9cdb97f8563ade07b1197ea55f

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 14:09:47 +0100

      Commit message:


	  
		
 docs: add match_bkg() / plot_match_bkg() section to the sequence searches vignette
 
    
  
    

      Package: universalmotif

      Commit: 00ad929e7317b0997d8bef8129ade441adb832c4

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 14:09:41 +0100

      Commit message:


	  
		
 add match_bkg() and plot_match_bkg(): composition-matched backgrounds

`match_bkg()` samples background sequences from a universe XStringSet
that match the input set on GC fraction and sequence length, the
HOMER-style binned approach:

  1. Bin the universe by (GC equal-width, length quantile-based).
  2. For each target, find its (GC, length) cell and sample
     n.per.target universe sequences from it.
  3. If the home cell is empty / undersized, expand outward in
     Manhattan-distance rings (with a warning). Fall back to global
     with-replacement sampling only if the universe is truly too
     small to cover the target set.

Returns either the matched XStringSet (default) or a data.frame of
per-pair match indices (return.indices = TRUE) for traceability.

Complements (does NOT replace) shuffle_sequences(): the shuffle path
randomises each input in place; match_bkg() instead samples real
sequences from a larger genomic universe. Use the latter when the
input has composition bias relative to the genome that you want to
control for in enrich_motifs2() / motif_finder().

plot_match_bkg() is a companion ggplot helper that overlays GC and
length density curves for target vs matched-background, useful for
visually verifying the match landed. Same theme conventions as
plot_motif_peaks() (no interior gridlines, L-frame axes).

20 unit tests including: shape/class, GC-match quality, length-match
quality, determinism, unique-without-replacement, indices output,
n.per.target = N, AA rejection, alphabet mismatch, small-universe
fallback, empty-bin ring expansion, plot ggplot class. Integration
test through enrich_motifs2 round-trips cleanly.

No new package dependencies. No C++ code.
 
    
  
    

      Package: universalmotif

      Commit: b66bcbe55f7f6cef75a40e24ed786dd8fb308aa9

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 13:39:50 +0100

      Commit message:


	  
		
 bump to 1.31.10 and document motif_peaks() rewrite in NEWS
 
    
  
    

      Package: universalmotif

      Commit: 413e16485eeac61b415a267d71c55e859a5a7489

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 13:38:33 +0100

      Commit message:


	  
		
 motif_peaks: add v1 GRanges test + polish plot_motif_peaks() output

- Add a unit test covering scan_sequences() (v1) GRanges round-trip:
  motif_peaks() auto-resolves seq.length from seqlengths(hits) for v1
  GRanges the same way it already did for v2 GRanges.

- plot_motif_peaks() polish:
    * black bars (was grey25)
    * no interior grid lines
    * L-frame axes only (kill panel border, draw bottom + left axis
      lines explicitly)
    * bottom x-axis line, ticks, and tick labels on every facet (via
      axes = "all_x" / axis.labels = "all_x")
    * strip-title outline removed
    * per-motif p-value / enrichment annotation moved into the strip
      label via a labeller -- avoids the overlap that happened when
      the tallest bar landed at the top-left corner of a panel
 
    
  
    

      Package: universalmotif

      Commit: 014efe0d8491884f2e7514fafe091b3fedaf6652

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 13:22:58 +0100

      Commit message:


	  
		
 docs: add motif_peaks() / plot_motif_peaks() section to the sequence searches vignette
 
    
  
    

      Package: universalmotif

      Commit: 0db48b3dfad6f1ea9faec74ea697719883dd5ca7

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 13:22:51 +0100

      Commit message:


	  
		
 rewrite motif_peaks(): CentriMo-style positional enrichment

Wholesale replacement of the old kernel-density-with-permutation-null
implementation, which never matched the function's intended CentriMo
semantics. The new version takes its input directly from
scan_sequences() / scan_sequences2() (either data.frame or GRanges)
and answers the actual question: "are this motif's hits non-uniformly
distributed along the sequences?"

Algorithm (Bailey & Machanick 2012):
  1. Normalise hits (best score per (motif, sequence) pair).
  2. For each motif and each candidate window width, compute the
     one-sided binomial p-value for hit-count-in-window under the
     null "hits uniform over [1, seq.length]".
  3. Pick the best (smallest-p) window per motif; Bonferroni-correct
     over windows tested; BH-correct across motifs.

Two modes:
  - mode = "central" (default): only centre-of-sequence windows.
  - mode = "local": window centre is also varied across the sequence.

Companion plot_motif_peaks() returns a ggplot faceted by motif with a
hit-centre histogram and the best window shaded. It consumes the new
`centers` list-column on motif_peaks()'s return, so users don't have
to thread their scan results back in.

The C++ helpers used by the old stub (peakfinder_cpp, linbin_cpp in
src/motif_peaks.cpp) are gone -- they were unique to that stub and
unreferenced elsewhere.

This is a hard incompatible rewrite under the same name: the v1
signature (hits, seq.length, seq.count, bandwidth, max.p, peak.width,
nrand, plot, BP) has no v2 counterpart. NEWS notes the break.
 
    
  
    

      Package: universalmotif

      Commit: dcf5b8e90ac19bb87a8576defff130d8683e7fd0

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 12:47:37 +0100

      Commit message:


	  
		
 bump to 1.31.9 and document merge_motifs2()/merge_similar2() in NEWS
 
    
  
    

      Package: universalmotif

      Commit: 1e3094880ee982fa87d3ccf87d6c6e96997b4bad

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 12:44:02 +0100

      Commit message:


	  
		
 docs: polish merge_motifs/similar wording + cross-link v1 docs to v2
 
    
  
    

      Package: universalmotif

      Commit: 81f9538b361f78b898a3f0afca2deaf11cb16a0e

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 12:33:44 +0100

      Commit message:


	  
		
 docs: add merge_motifs2/merge_similar2 vignette section + polish merge_motifs2 docstring
 
    
  
    

      Package: universalmotif

      Commit: ada9de3375beec9c0b30a5fc939077f762ba7ca8

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 12:33:15 +0100

      Commit message:


	  
		
 add merge_motifs2() and merge_similar2(): significance-based motif merging

Companion v2 functions to merge_motifs() and merge_similar(), built on
compare_motifs2(). Both DNA/RNA only.

merge_motifs2(motifs):
  - Anchor-based progressive alignment via compare_motifs2()'s C++
    alignment finder. Picks the highest-IC input motif as the anchor;
    every other motif's best alignment offset / strand / overlap is
    computed against the anchor in a single C++ call.
  - Motifs whose best alignment is on the - strand are reverse-
    complemented before averaging, so the merged motif is always in
    the anchor's orientation. This removes the input-order dependence
    of merge_motifs()'s iterative pairwise scheme.
  - Column-union averaging in R: each output column at frame position p
    is the (optionally @nsites-weighted) mean of the per-motif PPM
    columns covering p. No automatic IC-trim -- users who want that
    can pipe through trim_motifs().

merge_similar2(motifs, qvalue):
  - Calls compare_motifs2(matrix.out = "qvalue") to get an N x N
    pairwise q-value matrix.
  - Symmetrises Q via pmin(Q, t(Q)) (pair linked if either direction
    is significant; per-query BH adjustment in compare_motifs2 makes
    Q asymmetric).
  - Connected-components clustering via a small union-find: motifs i
    and j are in the same cluster iff Qsym[i,j] <= qvalue. Each
    multi-motif cluster is collapsed via merge_motifs2(); singletons
    pass through unchanged.
  - Returns a list of universalmotif S4 objects shorter than the
    input, or a data.frame of cluster assignments when
    return.clusters = TRUE.

This is the STAMP / TOMTOM-clustering semantics ("group all motifs
that are pairwise significantly similar"), which is more interpretable
than v1's score-threshold hierarchical clustering and removes the
linkage-method / cutoff-unit ambiguity.

merge_motifs() and merge_similar() now emit one-line tips pointing at
the v2 functions when the user's argument set maps cleanly. Silence
with options(universalmotif.suggest.merge_motifs2 = FALSE) /
universalmotif.suggest.merge_similar2 = FALSE.
 
    
  
    

      Package: universalmotif

      Commit: a9b0a8017182457ffba9a8408f2ce66890247901

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 11:31:09 +0100

      Commit message:


	  
		
 bump to 1.31.8 and document motif_finder() in NEWS
 
    
  
    

      Package: universalmotif

      Commit: 04e8bbb58038641de99193b4975292a0fb101adf

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 11:25:51 +0100

      Commit message:


	  
		
 docs: tighten motif_finder() vignette section
 
    
  
    

      Package: universalmotif

      Commit: bec0aee4d38169676027b73a66e10d8fb5e90372

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 11:23:50 +0100

      Commit message:


	  
		
 docs: note STREME basis of motif_finder() and add Bailey 2021 reference
 
    
  
    

      Package: universalmotif

      Commit: 4bcaea08014e2fd47abc6060600c145dad7e988c

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 11:11:58 +0100

      Commit message:


	  
		
 motif_finder: tighten allocations, background, and interruptibility

Four follow-up improvements to the initial motif_finder() landing:

  1. Background from positives. The C++ side was being passed uniform
     (0.25, 0.25, 0.25, 0.25), which diverged from yamtk me's default
     (compute from the actual sequence composition). Now the R wrapper
     computes the bkg from the combined positives + bkg.sequences via
     Biostrings::letterFrequency (with yamtk's 0.001 floor + renorm) and
     forwards it both to the C++ scanner and to each discovered motif's
     @bkg slot.

  2. Allocation churn. Three hot loops were rebuilding scratch buffers
     on every call:
       - fill_cdf()'s tmp_pdf is now a member of the Motif struct,
         grown but never shrunk across CDF builds.
       - enumerate_seeds()'s per-sequence `seen` unordered_set is now
         hoisted out of the inner loop and clear()'d, so the bucket
         capacity is reused across sequences.
       - discover_for_width()'s `covered` bitmask is pre-allocated once
         per width and zeroed in-place between seed attempts (only
         re-shaped if a previous attempt moved it into local_results).

  3. Drop the manual consensus workaround. Now that the upstream
     create_motif() matrix-dispatch bug is fixed (737d8e4),
     create_motif() correctly populates @consensus and motif colnames,
     so the per-column get_consensus() loop in the R wrapper is
     redundant. Twelve lines deleted.

  4. Safety. RcppThread::checkUserInterrupt() now fires at the top of
     each per-width iteration -- the RcppThread variant throws a C++
     exception (vs longjmp), so STL destructors run cleanly and per-
     width buffers are released on Ctrl-C. Also added defensive input
     guards at the motif_finder_cpp entry (empty seqs, bad pvalues,
     non-positive bkg, etc.) so direct C++ callers can't wander into
     runaway allocations or divide-by-zero.

All 21 motif_finder tests still pass. No behavior change on valid
inputs beyond the bkg-from-positives shift (which makes the discovered
PWM log-odds correct for non-uniform sequence sets).
 
    
  
    

      Package: universalmotif

      Commit: 28973d28f18122f0397a2122f14ae2de6782162a

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 10:09:15 +0100

      Commit message:


	  
		
 docs: add motif_finder() section to the sequence searches vignette
 
    
  
    

      Package: universalmotif

      Commit: 6eae7434fe9a0871f18eebb79a2501da9fa8d3d9

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 10:08:58 +0100

      Commit message:


	  
		
 rewrite motif_finder(): yamtk me-aligned de novo discovery

Replaces the 109-line, unexported, never-tested stub with a real
implementation modelled after the yamtk me command-line tool
(https://github.com/bjmt/yamtk). The new function is exported and
returns a universalmotif_df, slotting into the v2 stack alongside
scan_sequences2() / compare_motifs2() / enrich_motifs2().

Pipeline (faithful port of yamtk/src/yamme.c):
  - For each motif width in [min.width, max.width], iterate up to
    nmotifs:
    - enumerate over-represented k-mer seeds (Fisher's exact log-p
      on per-sequence canonical-strand presence)
    - build initial PPM by aligning Hamming-1 neighbours of the
      best seed
    - convert PPM -> integer PWM, build score CDF, choose threshold
      by hit p-value
    - refine PPM twice (re-scan, rebuild, re-threshold)
    - evaluate on positives + negatives; accept if Fisher's per-seq
      presence p-value below stop.pvalue
    - mask covered positions and try the next seed
  - merge per-thread results in (width, discovery_seq) order
  - re-evaluate every motif on pristine positives so cross-width
    dedup compares apples-to-apples
  - drop motifs whose coverage overlap with a lower-p-value motif
    exceeds dedup.overlap (default 0.5)
  - BH q-values across survivors; filter by qvalue cutoff
  - IC-trim low-information flanks

Width-level parallelism via RcppThread::parallelFor. Background is
auto-generated by k=2 euler-shuffle of positives if not supplied.
DNA/RNA only (matches yamtk me).

src/motif_finder.cpp is a fresh ~700-line file; the old C++ helper
(calc_seq_probs_cpp, which only served the stub) is gone.
 
    
  
    

      Package: universalmotif

      Commit: 737d8e4a050369e3d37f3dd91441dafe586fdfed

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-22 11:02:48 +0100

      Commit message:


	  
		
 fix: preserve explicit alphabet arg in create_motif() matrix dispatch

When create_motif() was called with both a matrix carrying rownames and
an explicit alphabet="DNA"/"RNA"/"AA" argument, the matrix-dispatch
else-if chain in create_motif() fell through to a clause that overwrote
the user-supplied alphabet with collapse_cpp(rownames(matrix)) ("ACGT"
for DNA). That collapsed string is not a key in the C++ ALPHS_e
alphabet lookup, so universalmotif_consensus()'s switch fell into the
default case, leaving @consensus empty and colnames(@motif) NULL.

Net effect: create_motif(mat, alphabet="DNA", type="PPM") produced a
motif with empty @consensus, even though create_motif(mat, type="PPM")
(no alphabet arg) populated it correctly. Downstream this broke
to_list() round-trips via update_motifs() (slot comparison error) and
left the consensus column in to_df() output empty.

Add the missing `&& missing(alphabet)` guard to the offending clause so
an explicit DNA/RNA/AA alphabet arg passes through unchanged.
 
    
  
    

      Package: universalmotif

      Commit: 619a7b0001be2ef447a9bead0e044e8a689f8a78

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-21 16:52:22 +0100

      Commit message:


	  
		
 bump to 1.31.7 and document enrich_motifs2() in NEWS
 
    
  
    

      Package: universalmotif

      Commit: cc994220b4c006e2cca53b7a97f987a3765e88a9

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-21 16:51:41 +0100

      Commit message:


	  
		
 docs: add enrich_motifs2() section to the sequence searches vignette
 
    
  
    

      Package: universalmotif

      Commit: 252224c2f9a86495e1c21df44ffc59ac15f5ebf2

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-21 16:41:22 +0100

      Commit message:


	  
		
 add enrich_motifs2(): minimalist yamtk-aligned motif enrichment

Companion to scan_sequences2() and compare_motifs2(): a 10-formal
DNA/RNA enrichment function whose default surface mirrors
yamtk enr (https://github.com/bjmt/yamtk). Internally calls
scan_sequences2() on target and (auto-shuffled or user-supplied)
background sets, aggregates per-motif counts, runs
fisher.test(alternative = "greater"), applies BH q-value
adjustment, and returns a plain data.frame whose 13 columns mirror
yamtk's TSV one-for-one (motif, motif.i, consensus,
target.seq.n / .seq.hits / .site.hits, bkg.seq.n / .seq.hits /
.site.hits, enrichment, log2.enrichment, pvalue, qvalue).

Two test modes via the test argument:
  - "seqs"  (default): Fisher on per-sequence hit presence
  - "sites": Fisher on per-position rate
matching v1's mode = "seq.hits" / "total.hits". The "ranksum"
yamtk mode is intentionally out of scope for v2.

enrich_motifs() also gains a one-line suggestion hint that fires
when a call's argument set maps cleanly onto enrich_motifs2().
Silence with options(universalmotif.suggest.enrich_motifs2 = FALSE).
 
    
  
    

      Package: universalmotif

      Commit: df7c90c24808e8d5375aeb5fa1101c7473ca03ff

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-21 13:48:26 +0100

      Commit message:


	  
		
 docs: point compare_motifs() at compare_motifs2() in the title note

R/compare_motifs.R: add a one-line note in the function description
pointing DNA/RNA + PCC users at compare_motifs2(), matching the
parallel pointer already present in scan_sequences().

man/compare_motifs.Rd regenerated.
DESCRIPTION: 1.31.5 -> 1.31.6.
 
    
  
    

      Package: universalmotif

      Commit: f4981b5f8660d8c1569399f659650de3cd74139a

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-21 13:46:20 +0100

      Commit message:


	  
		
 bump to 1.31.5 and document compare_motifs2() in NEWS

DESCRIPTION: 1.31.4 -> 1.31.5 (patch bump, development cycle).

NEWS: under "CHANGES IN VERSION 1.32.0", add a NEW FEATURES entry for
compare_motifs2() (yamtk-aligned motif-vs-motif comparison with both
empirical and parametric null modes) and a MINOR CHANGES entry for
the new compare_motifs() -> compare_motifs2() suggestion hint.
 
    
  
    

      Package: universalmotif

      Commit: b4c1b389854c11d218bb4c5242ccd76accf82a81

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-21 13:44:52 +0100

      Commit message:


	  
		
 docs: add compare_motifs2() section to the comparison vignette

Adds "A faster alternative: compare_motifs2()" to the "Motif
comparisons" section of MotifComparisonAndPvalues.Rmd, mirroring the
scan_sequences2() write-up in the sequence-scanning vignette. The new
section includes:

- A short overview of compare_motifs2()'s feature surface and the two
  null-PMF modes (empirical / parametric).
- A non-evaluated code chunk showing matrix mode (`matrix.out` =
  "score" / "pvalue" / "qvalue") and long-format mode (`compare.to`).
- A baked-in speed comparison table for yamtk cmp, compare_motifs(),
  and compare_motifs2() in both score-only and pvalue modes, at
  nthreads = 1 and 4, on 50x50 and 200x200 HOCOMOCO fixtures.

Numbers are not recomputed at vignette build time; the benchmark
script that generated them lives at
benchmarks/compare_motifs2_vignette.log in the package repository.

Also: minor whitespace clean-up in SequenceSearches.Rmd (blank lines
before two code chunks for consistent rendering).
 
    
  
    

      Package: universalmotif

      Commit: 34196e9dd448da0fe53e9f0e7492bb844fcd077d

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-21 13:21:18 +0100

      Commit message:


	  
		
 add compare_motifs2(): minimalist yamtk-aligned motif comparison

compare_motifs2() is the motif-comparison counterpart to
scan_sequences2(): a deliberately stripped-down version of
compare_motifs() whose defaults and algorithm mirror the command-line
tool `yamtk cmp` (Tremblay 2026, https://github.com/bjmt/yamtk). It
uses Pearson correlation per column as the only similarity metric and
computes p-values from a TOMTOM-style empirical null PMF built from
the target database, with Bonferroni + Benjamini-Hochberg adjustment.

Signature (eight formals):

  compare_motifs2(motifs, compare.to = NULL,
                  qvalue = 0.1, min.overlap = 5L, RC = TRUE,
                  null = c("empirical", "parametric"),
                  bkg = NULL,
                  matrix.out = c("score", "pvalue", "qvalue"),
                  nthreads = 1)

Two null-PMF modes, both ported verbatim from yamcmp.c:

  - "empirical" (default): per-query column, histogram PCC against
    every target-database column, convolve to overlap length L. Best
    for large databases.
  - "parametric": enumerate 56 simplex-grid columns weighted by a
    Dirichlet-Multinomial PMF (alpha = 4 * bkg). Best for small
    databases or when histogram sparsity would distort the empirical
    estimate.

Two output shapes:

  - compare.to = NULL: square numeric matrix (motif x motif) holding
    the value selected by matrix.out (mean PCC, p-value, or q-value).
  - compare.to provided: long-format data.frame of pairs filtered by
    qvalue, with the same column shape yamtk emits to TSV (subject,
    target, offset, strand, overlap, score, consensus strings,
    pvalue, qvalue).

The reported `score` is mean PCC over the overlap (always in [-1, 1])
rather than the raw sum yamtk reports. The underlying sum is still
what the p-value lookup indexes into.

Output conventions diverge slightly from compare_motifs() to match
yamtk and universalmotif convention: column names are subject/target
(universalmotif), the score is unit-normalised (this package), and
the per-motif p-value asymmetry of the empirical null is preserved
(non-symmetric pvalue/qvalue matrix; the score matrix remains
symmetric).

Performance: 100% hit-set overlap with yamtk in both modes on a
50-motif HOCOMOCO fixture; all score/offset/overlap/strand exactly
identical; p/q-value relative error < 4e-6. Threading scales 3.1-3.3x
at 4 threads. matrix.out = "score" skips the p-value path entirely,
giving a 6-10x speedup when significance isn't needed.

Implementation:

  - src/compare_motifs2.cpp: ~450 lines. Per-pair best alignment
    scanner + yamtk-style p-value path + IUPAC consensus helper.
    Three Rcpp exports, RcppThread-parallelised over queries with
    pre-extract/parallelise/wrap idiom.
  - R/compare_motifs2.R: ~220 lines. Arg validation, motif
    normalisation, mode dispatch, BH adjustment, output reshape.
  - utils-internal.R: suggest_compare_motifs2() hint emitted from
    compare_motifs() when arguments map cleanly onto compare_motifs2().
    Silence with `options(universalmotif.suggest.compare_motifs2 = FALSE)`.

Tests: 16 test blocks / 47 assertions covering matrix symmetry,
diagonal = 1, score range, matrix.out variants, self-comparison
sanity, both null modes, custom bkg behaviour, qvalue filtering,
empty results, AA rejection, character-name compare.to.
 
    
  
    

      Package: ensembldb

      Commit: 159ed8be7de21619c5912cd81d784174cb016dc8

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

      Date: 2026-05-25 11:21:41 +0200

      Commit message:


	  
		
 Add the actual change
 
    
  
    

      Package: ensembldb

      Commit: 31a36769ea0fea4be6d883f254027c42ee00a05e

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

      Date: 2026-05-25 11:21:05 +0200

      Commit message:


	  
		
 Update script
 
    
  
    

      Package: ensembldb

      Commit: 4db05d68b1973b899176bc38e27ad20194aee517

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

      Date: 2026-05-25 11:18:34 +0200

      Commit message:


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

      Package: ensembldb

      Commit: 28960976ad87c4922fd62089cf120ada09eca504

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

      Date: 2025-08-18 14:49:24 +0200

      Commit message:


	  
		
 feat: add genome<- method for EnsDb

- Add a `genome<-,EnsDb` method to allow manually changing/setting the Genome
  version (related to issue #159).
 
    
  
    

      Package: assorthead

      Commit: c6fe5cb105ccb62d773245a548663bc0486907bd

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

      Date: 2026-05-25 15:47:02 +1000

      Commit message:


	  
		
 Updated the version of the gesel library.
 
    
  
    

      Package: scMitoMut

      Commit: b32b9b661e609709d5664c4f593ea52d87ceca19

      Author:  Wenjie Sun <sunwjie@gmail.com> 

      Date: 2026-05-25 01:28:27 -0400

      Commit message:


	  
		
 Declare NSE globals for check
 
    
  
    

      Package: scMitoMut

      Commit: a501c454afb4a4f53962251b91c2c36b24d99c44

      Author:  Wenjie Sun <sunwjie@gmail.com> 

      Date: 2026-05-25 01:23:52 -0400

      Commit message:


	  
		
 fix the segmentfault error
 
    
  
    

      Package: TCGAutils

      Commit: 8b02352fe80408c8b965e2f107e4b093112f2341

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-24 22:23:57 -0400

      Commit message:


	  
		
 version bump 1.33.2
 
    
  
    

      Package: TCGAutils

      Commit: 6b8d8a84f9d48852e6256147818f2ea524f68869

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-24 19:32:13 -0400

      Commit message:


	  
		
 update importFrom lines for roxygen2
 
    
  
    

      Package: TCGAutils

      Commit: cfce0315e12d7426a287015d0321aa847d844f8d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-24 22:23:57 -0400

      Commit message:


	  
		
 un-defunct mirToRanges
 
    
  
    

      Package: TCGAutils

      Commit: e4a82cc4b6e608d6cccf9a669bed7e897e8eb73a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-24 19:18:52 -0400

      Commit message:


	  
		
 remove slides argument in filenameToBarcode
 
    
  
    

      Package: Rarr

      Commit: 7ac65fe51ba8b0b7524c50369551231638ede67d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-24 14:38:50 +0200

      Commit message:


	  
		
 Bump version
 
    
  
  


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