Bioconductor 3.22 Released

Menu

Source Code & Build Reports:

Source code is stored in Git. Software packages are built and checked nightly.

Development Version

Bioconductor packages under development:

Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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

GIT Logs

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

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

Package: mobileRNA
Commit: b58cca24d0f89b5500b8778d1b92175892816fd6
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-11-03 11:51:23 -0600
Commit message:

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

# Conflicts:
#	DESCRIPTION
Package: mobileRNA
Commit: d30185c3993ed131507a1b3f5cd7246f833d158b
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-11-03 11:45:01 -0600
Commit message:

 VERSION CONTROL
Package: mobileRNA
Commit: 0d692d29a2803fa31322a797161c77f96c92f205
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-11-03 11:36:01 -0600
Commit message:

 Seqinfo to namespace

Namespace dependency missing from DESCRIPTION Imports/Depends entries: ‘Seqinfo’
Package: smoppix
Commit: fe4ac0dcb7829d0fe77454f7509b211f49c984b9
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-11-03 18:32:49 +0100
Commit message:

 version chqnge

Merge branch 'devel' of git.bioconductor.org:packages/smoppix
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
Package: smoppix
Commit: 5733e3d48a37a5b664a0588e3532f7c7756560de
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-11-03 18:30:46 +0100
Commit message:

 R version bump
Package: smoppix
Commit: aa6894c2938bc1847d05eb6c820700f92a53490b
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-11-03 18:20:09 +0100
Commit message:

 Document plotCells
Package: smoppix
Commit: d724a7f76635d897b072cdd16150154b1b1005ef
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-11-03 17:25:51 +0100
Commit message:

 Remove weird feature number restriction
Package: smoppix
Commit: c09cb4412cb43e4121236e20e86fa33c69443e60
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-27 16:50:57 +0100
Commit message:

 More space for the scale bar
Package: LACHESIS
Commit: 0cbd1e498faa282f4ec2522ea06ff9a363bed98e
Author: VerenaK90 <ve.koerber@web.de>
Date: 2025-11-03 15:21:55 +0000
Commit message:

 version bump
Package: eisaR
Commit: 7a06cdb610f7b6cd6065d1fc0e20c1abbefde352
Author: mbstadler <stadler.michael@gmail.com>
Date: 2025-11-03 15:29:00 +0100
Commit message:

 skip missing-library tests also on r-universe

Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Package: MetaProViz
Commit: 5d2405206e5945f166149fee824d1798fccdd2b3
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-11-03 13:15:41 +0100
Commit message:

 nothing
Package: MsBackendSql
Commit: c6833d3d76cbec02dd3decba0abd43e8736da54b
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-11-03 12:57:03 +0100
Commit message:

 Merge pull request #33 from rformassspectrometry/jomain

Ensure peaks are ordered correctly with longForm() and duckdb
Package: MsBackendSql
Commit: 2a72440121346993bf607cf9cd8d22bbcb7b9f4c
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-11-03 11:47:38 +0100
Commit message:

 update version
Package: MsBackendSql
Commit: 0d4a5ed1a19697b809f670eb594ee628d788140c
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-11-03 11:42:40 +0100
Commit message:

 ci: use devel versions of R
Package: MsBackendSql
Commit: d63ecc6eced96b231840dea241d4441197f196d1
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-11-03 11:39:40 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into jomain
Package: MsBackendSql
Commit: 085ff671b208fde89c229026b4ffbe8d15399da3
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-11-03 11:37:47 +0100
Commit message:

 refactor: use ORDER BY with JOIN query for duckdb

- For `longForm()` and duckdb backend: include an ORDER BY statement to the
  JOIN query (issue #31).
Package: MsBackendSql
Commit: 69e8aa564680319b88d820958261179713798923
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-30 17:16:23 +0100
Commit message:

 refactor: prepare full duckdb support (issue #31)

- For storage of peaks data in long-form add a peak_id_ database table column
  depending on the database used (e.g. duckdb).
Package: spatialFDA
Commit: bd8c241aacd70eec883ad5cbea6d3cd804744c87
Author: mjemons <martin.emons@gmail.com>
Date: 2025-11-03 11:07:08 +0100
Commit message:

 removed scam option added news to all changes so far
Package: spatialFDA
Commit: a174d57bcb749c1c1c6fa111594d44793ae06ffd
Author: mjemons <martin.emons@gmail.com>
Date: 2025-11-03 09:28:55 +0100
Commit message:

 merge version Bump
Package: spatialFDA
Commit: 570ed9e8a3d1785bc6230848fcbcf895682f7e0f
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-31 11:31:06 +0100
Commit message:

 Merge branch 'devel' of github.com:mjemons/spatialFDA into devel
merge formula fix and prefit arg passing
Package: spatialFDA
Commit: e6916ca33e526adec47fc5767fd1c5da8a2b3acf
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-31 11:30:10 +0100
Commit message:

 pass arguments to prefit
Package: spatialFDA
Commit: 2a7217d5929e504f92d8fc41b0ceb4bd9e18e094
Author: Martin Emons <55688661+mjemons@users.noreply.github.com>
Date: 2025-10-28 16:14:14 +0100
Commit message:

 Merge pull request #21 from mjemons/FixEnvCall

fix environemnt problems
Package: spatialFDA
Commit: f1f50098ac06dd3c50dc4f20804917f9d8bb677c
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-28 15:39:05 +0100
Commit message:

 fix environemnt problems
Package: spatialFDA
Commit: fb7e3bdff11d49a583166ce3b44239ff307b1369
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-26 13:44:04 +0100
Commit message:

 option to sqrt transform weights
Package: spatialFDA
Commit: d6a512ea7b313360080efa48705f64eea5999362
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-23 12:58:02 +0200
Commit message:

 changed cutoff calculation
Package: spatialFDA
Commit: 5789b3c953b4fdc346505c50ecd94c4f51ad2a7a
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-22 18:44:34 +0200
Commit message:

 implemented AR1.rho parameter
Package: spatialFDA
Commit: 59fa04d9d031d17a0cc1b4cdcb806a34d46d74a3
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-22 11:20:27 +0200
Commit message:

 implemented shape constraint with scam
Package: spatialFDA
Commit: 4fb29b64c13d12f4d2cce54fb0a81df683bbb79f
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-20 17:51:56 +0200
Commit message:

 remove message statement
Package: spatialFDA
Commit: 6c6aec9b08b523dbfb2d6aa27b5f7655389414c9
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-20 17:48:02 +0200
Commit message:

 fix ID
Package: spatialFDA
Commit: ad271eee4dc13b25dbea666c7fee7565ef20a945
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-20 17:42:57 +0200
Commit message:

 fix call of ID variable
Package: spatialFDA
Commit: 6f0ae0493bb2eb648ecb512e3f67402807fa1ff1
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-20 17:30:40 +0200
Commit message:

 fix Errors in UpperDeltaProb
Package: spatialFDA
Commit: 1d97e6b0ed5f8a8bcd2c9a0b8a93619340520a60
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-20 16:40:41 +0200
Commit message:

 for G functions, add a filtering of the constant 1 part
Package: spatialFDA
Commit: e107c9d2dae62346733c77149814a1dff4cbc5d3
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-16 10:36:27 +0200
Commit message:

 pass H explicitly to the gam
Package: spatialFDA
Commit: 004a9665455b37ee76bf5808155ebdc04c629001
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-16 08:06:41 +0200
Commit message:

 correct dimenions for H with prefit
Package: spatialFDA
Commit: 6ebc362cac881c98bd19207507045e53562dd8d9
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-15 20:52:24 +0200
Commit message:

 add option to define a ridge penalty
Package: spatialFDA
Commit: 95b67b4bda060fcac067988697129e5a37bed89f
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-13 11:30:08 +0200
Commit message:

 bug fix for GAM
Package: alabaster.base
Commit: 1d97e98f8966c6f7124c7c0114113c0cd584054f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-11-02 23:55:31 -0800
Commit message:

 Set default bit64conversion= argument for updated rhdf5.
Package: SVP
Commit: e8643518b2e10dc19c90710c95218fd6f68d9320
Author: xiangpin <xshuangbin@163.com>
Date: 2025-11-03 15:03:04 +0800
Commit message:

 bump version and update news
Package: SVP
Commit: 1d4c0b14d805ea653f49c0bc12f6c68bcaa72f33
Author: xiangpin <xshuangbin@163.com>
Date: 2025-06-15 17:13:00 +0800
Commit message:

 bump version
Package: SVP
Commit: 951bd752e1d1a7c50bcb26a2ab321d2a531f1778
Author: xiangpin <xshuangbin@163.com>
Date: 2025-06-15 17:11:04 +0800
Commit message:

 update the visualization of plot_lisa_feature
Package: SVP
Commit: a49b5bf82b1729eb506dbde9b4f8dedc3401ae50
Author: xiangpin <xshuangbin@163.com>
Date: 2025-06-15 16:28:54 +0800
Commit message:

 Merge branch 'main' into RELEASE_3_21
Package: SVP
Commit: 795043f6c238032353361c82d613e56245adb696
Author: xushuangbin <xshuangbin@163.com>
Date: 2025-06-13 19:02:22 +0800
Commit message:

 update knn.k.use arg
Package: SVP
Commit: 5bbb304924c679fef74e0e64e896f1fe0f7abfee
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-05-08 12:30:33 -0400
Commit message:

 Version bump to trigger rebuilding/propagation of Windows and Mac binaries
Package: SVP
Commit: ecd5f0785ccd0239a037b3a3ac90a335ca34a3e8
Author: xushuangbin <xshuangbin@163.com>
Date: 2025-04-17 17:06:19 +0800
Commit message:

 bioc3.21 release
Package: sesameData
Commit: 6ec5de603daa0c31a1eb02765b7f8bb7c3094219
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2025-11-02 20:50:11 -0500
Commit message:

 bump to 1.29.1, updated data using zenodo upload
Package: tidySpatialExperiment
Commit: 9871264f23563e1a5d8850e4845cc8c6cd3b3ad7
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-11-03 11:43:39 +1100
Commit message:

 Version up
Package: tidySpatialExperiment
Commit: ab73876ae0767bae980c1e2832b4037816fa9ca3
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-11-03 11:43:16 +1100
Commit message:

 Merge BioConductor repository version bumps
Package: tidySpatialExperiment
Commit: fa6d5f3d0645b427c4aa7084db1ef2f577e4e9a8
Author: william-hutchison <william.8191@fastmail.com>
Date: 2025-11-03 11:37:00 +1100
Commit message:

 Merge pull request #47 from william-hutchison/remove-conflicting-functions

Remove conflicting functions
Package: tidySpatialExperiment
Commit: 069aeb8771c088f7197ac183d05195600db8cc38
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-11-03 11:22:02 +1100
Commit message:

 Version up
Package: tidySpatialExperiment
Commit: 77c2b87bc7d544f92c1398e40fb92c1dfc6cad5f
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-11-03 11:21:47 +1100
Commit message:

 Udpate 'bind_cols()' and 'bind_rows()' tests
Package: tidySpatialExperiment
Commit: 1736874d0451cf19b93d42edbab18cfb7d8f6c25
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-11-03 11:15:29 +1100
Commit message:

 Udpate 'bind_cols()' and 'bind_rows()' examples
Package: tidySpatialExperiment
Commit: b5569de1409f691bb4388fb76a909049a05c81c5
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-31 17:11:18 +1100
Commit message:

 Version up
Package: tidySpatialExperiment
Commit: 72509422a37c352fbc2ab33f46a21e9fd0828d6c
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-31 17:11:00 +1100
Commit message:

 Move ttservice to Depends field
Package: tidySpatialExperiment
Commit: 540688a56bba7d7782e5d36eb29cddeda1ce4eb1
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-31 16:33:39 +1100
Commit message:

 Version up
Package: tidySpatialExperiment
Commit: 66dfb4e59d883ad567ace4397db2eade0b389ac5
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-31 16:33:24 +1100
Commit message:

 Add missing function import
Package: tidySpatialExperiment
Commit: 6dfa2a18da90b818b6b46fc2de03a78983e41148
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-31 16:21:26 +1100
Commit message:

 Remove redefinition of 'bind_cols()' and 'bind_rows()'
Package: tidySpatialExperiment
Commit: 7261a13bd29b467269aa84fcc8e8a842c96739c8
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-31 16:09:13 +1100
Commit message:

 Add missing function import
Package: tidySpatialExperiment
Commit: 83be70103f67dff8f12ce5c5d2fdc9d8181615d3
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-31 16:04:47 +1100
Commit message:

 Remove unused import
Package: tidySpatialExperiment
Commit: e0d8f0a68049b82aa752c2235efc3949e39cb381
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-31 16:00:03 +1100
Commit message:

 Remove redefinition of 'aggregate_cells()'
Package: tidySpatialExperiment
Commit: e8f82a3f56a33c3843ccb6b37acda1c1f6928b36
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-31 15:57:16 +1100
Commit message:

 Consolidate unnesting functions
Package: SplicingGraphs
Commit: 8abbef909f4c249fc62e4aa05c89b3a1fcaefb2d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-02 09:50:45 -0800
Commit message:

 drop use of precomputed SplicingGraphs object 'sg_with_reads' in vignette
Package: SplicingGraphs
Commit: 0f477f251da074de5f54a7072a6f2cb54307089c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-02 01:00:36 -0700
Commit message:

 SplicingGraphs 1.51.1: Repair vignette

The latest TxDb.Hsapiens.UCSC.hg19.knownGene (v 3.22.1, based on UCSC
track GENCODE V48lift37) is no longer suitable for the SplicingGraphs
vignette so we've switched to TxDb.Hsapiens.UCSC.hg19.refGene.
Package: clusterProfiler
Commit: c6e07d0e9c363a5102ca04de419b7d72bf739495
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-01 22:45:20 +0800
Commit message:

 bump version
Package: clusterProfiler
Commit: 8669269d14d4f948d5975e56e6fb2d44367b885c
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-01 22:43:26 +0800
Commit message:

 bump version
Package: clusterProfiler
Commit: f0243622a9d885dca2a44bd69383f2a3a76fe4ba
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-30 16:10:09 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: clusterProfiler
Commit: 3e5d5a4b2ae2a486cbf72b7c2f540e0fbf4f0315
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-30 16:08:35 +0800
Commit message:

 update enrich-pc
Package: clusterProfiler
Commit: 394892e4ff69fb14fc0d451adfca028fb72a69c3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-23 21:05:53 +0800
Commit message:

 update
Package: clusterProfiler
Commit: 39395ce1f997da2f29a5a4b2d92d4d9e72923d53
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 09:51:00 +0800
Commit message:

 update bioc version
Package: SwarnSeq
Commit: 8f1ca0a58c8de9676dcdb81f4bcdc419f271bbc3
Author: Samarendra Das <samarendra.das@icar.org.in>
Date: 2025-11-01 17:15:27 +0530
Commit message:

 SingleCellExperiment was used in modification.
Package: splatter
Commit: 646e458e9556ff2feaa712e60e8fa3d88a8ddd93
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-11-01 12:08:53 +0100
Commit message:

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

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: splatter
Commit: 2e75db7706855754b14aeb33586007fe5adc0769
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-11-01 12:05:04 +0100
Commit message:

 Bioconductor 3.22 release
Package: splatter
Commit: 319c55c6d00007a78c8dd61ac8c815f9d4e68b4e
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-11-01 12:03:18 +0100
Commit message:

 Merge remote-tracking branch 'upstream/RELEASE_3_22' into devel

* upstream/RELEASE_3_22:
  bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: splatter
Commit: 65286c7789f10c4ebc7f34b0e5a8fdc6616472a2
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2025-08-12 07:00:48 +0200
Commit message:

 Bump actions/checkout from 4 to 5 (#182)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Package: splatter
Commit: 5c03bcf28383ee4fbe9f4eee8e778984ef89bf86
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-07-10 17:47:12 +0200
Commit message:

 Add write permissions to pkgdown workflow
Package: splatter
Commit: 4e21ebc92774f23139d3ee8e85115141287817f5
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-07-09 21:24:38 +0200
Commit message:

 Update check GHA (#181)

* Update check GHA

* Fix missing biocversion_str in check GHA

* Fix typo in check GHA
Package: zellkonverter
Commit: 38b921d8aa6cf264b9d8140f981cf1dd0f8e0b83
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-11-01 12:21:07 +0100
Commit message:

 Fix version in NEWS
Package: zellkonverter
Commit: 57b9d7a337d0cad27d4c9b9320425e8e37c73994
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-11-01 12:20:22 +0100
Commit message:

 Bioconductor 3.23 devel
Package: zellkonverter
Commit: e34e43c8e309fec966d3a46f13207944f6aed68e
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-11-01 12:19:23 +0100
Commit message:

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

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: zellkonverter
Commit: 4a98e5cb1ce541d6182bd1700466b8c8cceca3dd
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-11-01 12:14:25 +0100
Commit message:

 Bioconductor 3.22 release
Package: zellkonverter
Commit: c357324e8ee9e81b72c88dacb41d90067ea1f785
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-11-01 12:13:20 +0100
Commit message:

 Merge remote-tracking branch 'upstream/RELEASE_3_22' into devel

* upstream/RELEASE_3_22:
  bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: Rsubread
Commit: 8fedb934b06a7a72aa56a51d4ca0a6ef5f086036
Author: Yang Liao (Monash University) <yliao@m3-login2.massive.org.au>
Date: 2025-11-01 17:11:35 +1100
Commit message:

 altered cellCounts for testing features
Package: smoothclust
Commit: 1246c80e932cd1a18dccfa1359c8490b461fa539
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-11-01 10:00:55 +0800
Commit message:

 update GHA
Package: OrganismDbi
Commit: a63751b6cc056aff02cfdedc1ef981d3317729a0
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-31 15:33:12 -0700
Commit message:

 OrganismDbi 1.53.2: Post-release cleanup

Argument 'miRBaseBuild' (to functions makeOrganismDbFromUCSC() and
makeOrganismDbFromBiomart()) is now gone after being defunct in
BioC 3.22.

Also arguments 'url' and 'port' are now defunct after being
deprecated in BioC 3.22.
Package: leapR
Commit: 5e355f7e8d673a5f1cf5bb93909be726bba775d4
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-31 13:11:57 -0700
Commit message:

 updated documentation
Package: leapR
Commit: 4cdd6344f88838c68806c35f56bb8083c61b7eec
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-31 12:44:33 -0700
Commit message:

 made last bits of changes
Package: leapR
Commit: bd8d9ffeff39c4694c1bab7c8fa90245875a45bc
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-30 15:42:33 -0700
Commit message:

 updated to account for additional bioC issues

- figured out the seq_len vs seq_along issue
- shortened lines
- added input checking
- fixed typos
- added man page
Package: scrapper
Commit: 1a313d952522e945e6ef66e342a36d378e3a54a6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-31 00:26:44 -0700
Commit message:

 Updated bindings for the latest version of scran_graph_cluster.

Also minor bug fix for creating unweighted graphs.
Package: scrapper
Commit: d6a9e9e51335abfc3794dd9e7413cc33120e912c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-29 15:39:30 -0700
Commit message:

 Updated the ignore file, moved Rigraphlib to LinkingTo.
Package: scrapper
Commit: 875fd4c9f972eb7807ec54523585560afce7bcf8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-29 15:18:17 -0700
Commit message:

 Stripped out the analyze() function from the vignette.

Now that it's been moved to scrapple::analyze.se().
Package: assorthead
Commit: 16d94c97a39c30c5e6768f44b765c9e40083062f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-30 21:01:35 -0700
Commit message:

 Updated vendored copies of raiigraph, scran_graph_cluster.
Package: Rigraphlib
Commit: 445817dc273b67afbf41d48a0b9a150bc075dec8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-30 20:59:58 -0700
Commit message:

 Updated vendored version of igraph to 1.0.0.

Also commit the source code directly instead of storing a tarball, to get
around the BioC Git server's file size limits.
Package: ShortRead
Commit: c488f2966454c7bd2cadccb96415f3ef97ac3134
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-31 09:50:57 -0700
Commit message:

 ShortRead 1.69.1: Import pattern() from pwalign instead of Biostrings
Package: GXwasR
Commit: a56e631c0f0f781be8645062656bd0e792f2fc65
Author: Banabithi Bose <banabithi.bose@gmail.com>
Date: 2025-10-31 10:03:32 -0500
Commit message:

 Version bumped.
Package: GXwasR
Commit: 20442b403ef8da8d09d1dd180604692f7511e36a
Author: D Mayer <32186106+the-mayer@users.noreply.github.com>
Date: 2025-10-31 06:19:33 -0600
Commit message:

 Merge pull request #60 from boseb/misc-bioc

Vignette and Style
Package: GXwasR
Commit: d4fd65bd42b3c6b4b2fcac25a0b02d901524382d
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-30 08:45:20 -0400
Commit message:

 changes for BiocCheck
- F to FALSE in preimputationQC
- apply biocthis::bioc_style()
Package: bsseq
Commit: 46b4295329703d0bf694c707c816772bfbf4c037
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-31 11:03:21 -0400
Commit message:

 Making read.modkit and read.modbam2bed defunct
Package: bsseq
Commit: 13d941106f789484620bf16c62feff3d9f877c6c
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-31 09:58:40 -0400
Commit message:

 merging from release
Package: bsseq
Commit: a0f3ce3f5728d805476f0aad9e44a4748323a028
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-10 11:25:36 -0400
Commit message:

 getting rid of Travis since we have been using Github Actions for a while
Package: MetaProViz
Commit: 06811fcdb5a4cc52185613d4bdf5a2e380ed8f37
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 15:22:56 +0100
Commit message:

 code formatting: break long argument lists
Package: MetaProViz
Commit: 47cc5a9af900ada0782bc9d7e2a58f50facf9e88
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 11:55:36 +0100
Commit message:

 Bump version: 3.99.17 → 3.99.18
Package: MetaProViz
Commit: da03ed010c71f69526dfac528350166045b15623
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 11:55:33 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: db946fdfec3526daa164a215d2e4fec045f71529
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 11:54:50 +0100
Commit message:

 moved examples of ID translation functions into `\dontrun` due to 15 min BioC timeout for R CMD check
Package: dmGsea
Commit: 248aa7cd204a3a7eb4cb6aa0e3138ecc660b9aa3
Author: xuz1 <xuz@niehs.nih.gov>
Date: 2025-10-31 09:40:12 -0400
Commit message:

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
Package: DESpace
Commit: 3dbd101c6483dc2e536fc8eced1da63fbdc94e69
Author: peicai <peiying.cai@gmail.com>
Date: 2025-10-31 13:13:38 +0100
Commit message:

 updated citation
Package: rhdf5
Commit: 8cd8dc6e82333e4baaa093d59d2f20f6f5586118
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-31 09:46:45 +0100
Commit message:

 Bump version
Package: rhdf5
Commit: 97e6d85586c8d5a105b6786df227bc3ef0a2ec64
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-31 09:46:29 +0100
Commit message:

 Mention fix in NEWS
Package: rhdf5
Commit: ca84366af7955b3ae300c53b6b4444b7377cd8f8
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 20:15:03 +0200
Commit message:

 Fix orientation on native unsigned int
Package: rhdf5
Commit: 514f9f1f63d60ce9cc5d6787b07c443b175cf72c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 18:33:23 +0200
Commit message:

 Add regression test for #157
Package: rhdf5
Commit: 74937b0c7afb6f6dd1b63dda214cc8091a4082f0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-31 09:14:16 +0100
Commit message:

 Bump version
Package: rhdf5
Commit: f81b9097ca9da16e43addfd3fdc7299b42153bca
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-31 09:12:57 +0100
Commit message:

 Run devtools::document()
Package: rhdf5
Commit: 31b7c2e9288835c3cddb386b7bdc4d25bc164070
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 15:08:11 +0200
Commit message:

 Use double quotes
Package: rhdf5
Commit: 7b422fbaf166df85fadb11180ac304d8a4606a5b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 14:33:59 +0200
Commit message:

 Use dedicated ...length() base function where appropriate
Package: rhdf5
Commit: 0ed9fb9673dd5b7c238241637b9b471022dd4c69
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 14:33:33 +0200
Commit message:

 Use dedicated nzchar() base function where appropriate
Package: rhdf5
Commit: 5ea680b34dbd6cba2bec7fe75e4789e6271c127e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 14:33:02 +0200
Commit message:

 Do not pass functions as characters
Package: rhdf5
Commit: a32b4a3096ef8d58e0cbaca5bee629e19c5ac53d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 14:06:10 +0200
Commit message:

 Make bit64conversion default explicit
Package: rhdf5
Commit: 7d7eb9e6ef6e9b706ed477db7f829715986fc67d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 14:05:54 +0200
Commit message:

 Remove unnecessary ifelse()
Package: rhdf5
Commit: 6040f892c6c9f43dcb85e64949ee5196050bf667
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 14:05:40 +0200
Commit message:

 document return
Package: rhdf5
Commit: 966e5c10ace603fc729d2878f2a0117529ff7e08
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 14:04:45 +0200
Commit message:

 Reduce nesting and remove unnecessary parentheses
Package: rhdf5
Commit: 460149fd55b36ca3637a166d8653d80397337069
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 12:46:36 +0200
Commit message:

 Fix some long lines
Package: rhdf5
Commit: 48148dfa9d4f0a0db2184cab120206c23857c9c3
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 12:31:19 +0200
Commit message:

 Fix package name in vignette
Package: rhdf5
Commit: 3133c72125d4ec5bed648cf507998a60ed288fbf
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 11:44:22 +0200
Commit message:

 Remove unused variables
Package: rhdf5
Commit: ee3e7eb49dcefcda154fa124399655a6e73092fc
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 11:35:47 +0200
Commit message:

 Use seq_along() where possible
Package: rhdf5
Commit: 4be344a10a2954d4482e18fd91ce0a3870a14ebc
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 11:32:17 +0200
Commit message:

 Simplify newnames definition
Package: rhdf5
Commit: 89ea65ea690a2bfc39461f3614c5ed94f9d79076
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 11:25:29 +0200
Commit message:

 Remove sapply() where possible
Package: rhdf5
Commit: 1454dddd24abc35212a589d7abaf42dfb7b362ab
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 11:13:06 +0200
Commit message:

 Use shortcircuit boolean operator where appropriate
Package: rhdf5
Commit: 04d998f8b476e45200c1d200af4f60b00556021c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 11:08:06 +0200
Commit message:

 Use anyNA() where appropriate
Package: rhdf5
Commit: 8a011597e6910e8f8c40f36a38c585e6712071d1
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 10:55:08 +0200
Commit message:

 Setup lintr
Package: rhdf5
Commit: 425e4616b4ef9d85b50d9e65a2651cb11ac81a36
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-15 15:25:39 +0200
Commit message:

 Fix R CMD check NOTE about method consistency
Package: rhdf5
Commit: 65a1611cd377311ee5ef150e58df101946d5fc8c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-15 15:00:48 +0200
Commit message:

 Add curl as a devel dependency

Since it is required for testthat::skip_if_offline()
Package: rhdf5
Commit: c80c3aebee0a32d0128953b4e529f201bd88edc7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-30 19:32:59 +0100
Commit message:

 Bump version
Package: rhdf5
Commit: b8eda3c92e355a8fcc0af994988c9e7bf8ce7a3e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-24 18:15:03 +0200
Commit message:

 Mark deNBI as funder
Package: rhdf5
Commit: afba574a116b85d0b5558b8c79b5fe31db12a2bd
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-24 18:12:44 +0200
Commit message:

 Update logo location in README
Package: rhdf5
Commit: 23c0bf600d50dafcee763f4b6ff11c416afeb45d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-24 18:12:05 +0200
Commit message:

 Update logo & favicon
Package: rhdf5
Commit: 8aa529c74586f07b7670fff5ab1117db540d3776
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-24 18:09:55 +0200
Commit message:

 Add pkgdown link to DESCRIPTION
Package: rhdf5
Commit: 9b6dc3554666736f50f4d91fa0e74246d4a43495
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-24 18:09:24 +0200
Commit message:

 Fix settings
Package: rhdf5
Commit: c585976b4cd518da14b61c71a9bd61e315744324
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-24 18:08:08 +0200
Commit message:

 Add pkgdown.yaml GHA workflow
Package: rhdf5
Commit: 8c3c468cb57475a02f9145b91cf3467a8dd9c417
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-24 18:07:45 +0200
Commit message:

 Fix _pkgdown.yml
Package: rhdf5
Commit: 17e09a5d824cfdcf45d41df79b6c639ee4ada64a
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-24 16:03:04 +0200
Commit message:

 Bump version
Package: rhdf5
Commit: b77315e2755bf0d1e2f99ecd85ff98880720ea10
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-24 16:00:25 +0200
Commit message:

 Run ignored test
Package: rhdf5
Commit: 93e1df44d5f5bc805147e1ad3e1044b0b628c0c4
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-30 19:05:05 +0100
Commit message:

 Fix ref to git blame ignore after force push
Package: rhdf5
Commit: 99c048f38908d7851a8017d42db76e0226e50a53
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 10:47:21 +0200
Commit message:

 Remove travis config file
Package: rhdf5
Commit: bf471b18935a0031eedd30868eb746a3b7a2d2c0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 10:46:48 +0200
Commit message:

 Gitignore venvs
Package: rhdf5
Commit: ffa8132a43223c1f41e22ce86e42709ab7aa8539
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-15 10:51:22 +0200
Commit message:

 Use simpler r-hub workflow for big endian platforms
Package: rhdf5
Commit: 72fc7c925e704b168873546cf1df1791f7ac9d85
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-15 10:50:51 +0200
Commit message:

 Ignore reformatting commits in git blame
Package: rhdf5
Commit: 77041f3d63e3dcb185e5a7a72fe70d0f4e239b7c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-14 20:17:43 +0200
Commit message:

 Reformat code via air & styler (#173)
Package: UCell
Commit: 1e041f76a552ea7821f8e1e4bc46c9e60505b007
Author: Massimo Andreatta <massimo.andreatta@unil.ch>
Date: 2025-10-31 09:53:43 +0100
Commit message:

 Update README.md
Package: UCell
Commit: 14f793cfac4b90cc2f877befa98a7f60b5d730ee
Author: Massimo Andreatta <massimo.andreatta@unil.ch>
Date: 2025-10-31 09:32:23 +0100
Commit message:

 Merge branch 'devel'
Package: UCell
Commit: 4f824e3ec02839c250093d4e8bee9b3caafd1425
Author: Massimo Andreatta <massimo.andreatta@unil.ch>
Date: 2025-10-06 13:28:31 +0200
Commit message:

 Update README.md
Package: Rarr
Commit: f1e408688a973613c15a6845501d30a19df76782
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-31 08:54:37 +0100
Commit message:

 Bump patch version
Package: Rarr
Commit: c0ae2d5d47a459486e4cceddd03bdae92a66438e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-31 08:54:30 +0100
Commit message:

 Mention new vignette in NEWS
Package: Rarr
Commit: a94170c2391bef6041c41fe5dfd404385c876cc5
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-28 16:03:49 +0100
Commit message:

 Move table of supported feature to a dedicated vignette

So that it's more easily findable on the Bioconductor landing page
Package: Rarr
Commit: fa55d187b360f855cc9a2360bbe601f576981d6d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-22 17:33:02 +0200
Commit message:

 Delint NEWS
Package: FLAMES
Commit: 78876583058a5fadca22c5172216afed07b7250e
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2025-10-31 17:11:54 +1100
Commit message:

 Merge branch 'RELEASE_3_22' into devel
Package: FLAMES
Commit: 41bbd55e1d26366696ff33d3a8055cdb6223aaf0
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2025-10-31 16:50:56 +1100
Commit message:

 version bump
Package: FLAMES
Commit: a97a0058712a32856f6fd5dc1f8f9d6c8537eae2
Author: Ching Yin, WAN <126227662+chingyinwan@users.noreply.github.com>
Date: 2025-10-31 13:45:21 +1100
Commit message:

 Fix the expect_cell_number check
Package: FLAMES
Commit: 57a56ff86aa8c74c41736df9fc72f223c545f111
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2025-10-31 16:47:51 +1100
Commit message:

 update citation and authors
Package: MetaProViz
Commit: 8f122b35da767ae92e14cd52d472d6f29908fabb
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 02:17:17 +0100
Commit message:

 Bump version: 3.99.16 → 3.99.17
Package: MetaProViz
Commit: a77dd16505394cb81eb7b6e7250038157650b8fa
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 02:17:10 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 0d8601314178acaf1936e3b3430e0dd884fa2742
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 02:00:55 +0100
Commit message:

 Bump version: 3.99.15 → 3.99.16
Package: MetaProViz
Commit: 8d73415c33319f6002b46915f6203f8c642cb956
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 02:00:07 +0100
Commit message:

 cleaned up stray docstring lines, redundant file headers, consolidated messy formatting of "section title" comments in code
Package: MetaProViz
Commit: a502e7c700db4bc2136c0ad640840d89af0b01d4
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 01:06:45 +0100
Commit message:

 Bump version: 3.99.14 → 3.99.15
Package: MetaProViz
Commit: ee09bbf4dcbb93c4cb95a22d98f23d5199ea6c31
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 01:06:24 +0100
Commit message:

 `.Rbuildignore`: maybe this helps with the warning about `inst/scripts` empty directory on Bioc build servers
Package: MetaProViz
Commit: d690bbc9b1bda93f0982cf0f17e597ccedae3f9a
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 00:50:38 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 046bb300d0274a9f7baf6369c9d74074abaaef21
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 00:11:12 +0100
Commit message:

 docstring examples code formatting & 80 char line length
Package: MetaProViz
Commit: 8819461fb58b1a04728c03981588e84db788bacd
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 23:01:36 +0100
Commit message:

 docstrings: title lengths, line lengths, indentation
Package: MetaProViz
Commit: b489f48e907d95f33d45308ce144fc04da0995fd
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 18:23:15 +0100
Commit message:

 Merge branch 'main' of github.com:saezlab/MetaProViz
Package: MetaProViz
Commit: 7a58e57a7693c4cd85335558215a1ff6798021a5
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 18:14:12 +0100
Commit message:

 `vignettes/prior-knowledge`: missing comma (syntax)
Package: MetaProViz
Commit: 21accc849f2bdfc53a36ec05f751599db0b9eb7e
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-30 17:46:18 +0100
Commit message:

 Merge pull request #120 from saezlab/devel

Devel
Package: MetaProViz
Commit: a59fa56ebb3f3b84d6acb1193542afcfeb5b3838
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-30 17:20:18 +0100
Commit message:

 Merge pull request #119 from saezlab/devel

Merge Devel into main
Package: SparseArray
Commit: 148eea94c07e455a7717479ebade706f7f3fb45f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-30 21:21:39 -0700
Commit message:

 SparseArray 1.11.1: Small teak to unit tests
Package: Biostrings
Commit: 778d5f9589e114e13aa23c71c861ce1aa594a8f5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-30 18:41:20 -0700
Commit message:

 Biostrings 2.79.1: Post-release cleanup

Remove all the functions that went to the pwalign package in BioC 3.19,
that is: writePairwiseAlignments(), nucleotideSubstitutionMatrix(),
errorSubstitutionMatrices(), qualitySubstitutionMatrices(),
insertion(), deletion(), unaligned(), aligned(), indel(), nindel(),
PairwiseAlignments(), pattern(), alignedPattern(), alignedSubject(),
PairwiseAlignmentsSingleSubject, nedit(), mismatchTable(),
mismatchSummary(), compareStrings(), pid(), pairwiseAlignment(),
stringDist().

Note that these functions got formally deprecated in Biostrings in
BioC 3.21 and defunct in BioC 3.22.

Additionally, the XStringPartialMatches class and following functions
are now gone after being defunct in BioC 3.22 or non-functional for
years: matchprobes(), subpatterns(), pmatchPattern(), lcsubstr().
Package: txdbmaker
Commit: 5069001b1b008174f6896ce604dd64cf1e4e479f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-30 17:12:43 -0700
Commit message:

 txdbmaker 1.7.1

Utility function supportedMiRBaseBuildValues(), argument 'miRBaseBuild',
and argument 'port' are now gone after being defunct in BioC 3.22.
Note that 'miRBaseBuild' and 'port' were arguments of several functions
in the txdbmaker package.
Package: HPO.db
Commit: 5d27546bae6a1d2f2221f08400b533ca6c37d8eb
Author: huerqiang <13766876214@163.com>
Date: 2024-07-29 21:58:53 +0800
Commit message:

 update data
Package: HPO.db
Commit: e916f92e3017e3a280894d678259b914bfa418d2
Author: huerqiang <13766876214@163.com>
Date: 2024-07-25 20:34:28 +0800
Commit message:

 update metadata.R
Package: OrganismDbi
Commit: ba2e70db159bd71ebe4f62ccc115d3455f9d4603
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-30 10:58:09 -0700
Commit message:

 OrganismDbi 1.53.1: microRNAs() was removed from GenomicFeatures 1.63.1
Package: MetaProViz
Commit: 1cfb3b14d2ea2d061177eff8ded82be9cdb225a8
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 18:05:03 +0100
Commit message:

 Bump version: 3.99.13 → 3.99.14
Package: MetaProViz
Commit: 455926da7b219e47fc76f7b904c92f63ecd51b36
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 18:04:54 +0100
Commit message:

 quick-start vignette: indent also html by 4 spaces
Package: MetaProViz
Commit: 92d4a873b02104ff608925839443b38740fe2d3e
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 18:01:43 +0100
Commit message:

 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
Package: MetaProViz
Commit: 365f10343ce7c7437020ea58dc89a555d3abcdda
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 18:01:36 +0100
Commit message:

 Bump version: 3.99.12 → 3.99.13
Package: MetaProViz
Commit: fd0153cf3ddb94255170feb24546c8c31116b517
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 18:01:28 +0100
Commit message:

 removed space(!) from file names; `vignettes/pkgdown` to `Rbuildignore`
Package: MetaProViz
Commit: 2787646eb0ead967946484e4513ca57a2db4e988
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 18:00:19 +0100
Commit message:

 `vignettes/pkgdown` to `Rbuildignore`
Package: MetaProViz
Commit: 45de17ea1bf38cd02334a989638a212216173715
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-30 17:45:03 +0100
Commit message:

 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
Package: MetaProViz
Commit: 959197be83ccbe7ac1306963629dfc1223fc8304
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-30 17:44:49 +0100
Commit message:

 added comma
Package: MetaProViz
Commit: 29d9371264be7b478da02ffe14150e5169f9014e
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 17:44:34 +0100
Commit message:

 Bump version: 3.99.11 → 3.99.12
Package: MetaProViz
Commit: c85b35fdc2bd908859acd62bea7181516db9cf11
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 17:43:16 +0100
Commit message:

 4 spaces indentation of vignette code
Package: MetaProViz
Commit: ef203ef6d14cef8097a29cc2d244d811bc8e3f00
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-30 17:38:50 +0100
Commit message:

 4 spaces indentation of R code
Package: MetaProViz
Commit: 1d4345816db5a0f1e68c0f6976640d856f5df18a
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-30 16:29:15 +0100
Commit message:

 included svg file for vignettes
Package: MetaProViz
Commit: a1a8487e1ff331cb184bae62e8f60b84a731c030
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-30 16:29:03 +0100
Commit message:

 comapre_pk() issue fixed by using echo=FALSE
Package: MetaProViz
Commit: 9f366874261ae3f9f8a388879d5126bcc472b350
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-30 16:22:13 +0100
Commit message:

 Added second image for sample-metadata vignette
Package: MetaProViz
Commit: 68ee2662303ad93b1f58d4dff42e6be37699280a
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-30 16:03:51 +0100
Commit message:

 Create sample-metadata.Rmd_compare-pk chunk.svg
Package: MetaProViz
Commit: 5fc6a48c8eaaa7e4b4f9ac99287a06b59427d8d6
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-30 16:03:47 +0100
Commit message:

 Added eval=FALSE to sample-metadata.Rmd
Package: MetaProViz
Commit: a2d0eb1c59e68eb30e01f26d8d3d3aebc768cf82
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-30 10:11:01 +0100
Commit message:

 Added some more details for the se object
Package: MetaProViz
Commit: 81391cac2a34311cc97a078099eda9bc7e1093f0
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-29 18:53:01 +0100
Commit message:

 Bump version: 3.99.10 → 3.99.11
Package: MetaProViz
Commit: 78d2a72f48c9e9d88d08e0c111b285c63188fa5f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-29 18:52:54 +0100
Commit message:

 a bunch of minor formatting
Package: MetaProViz
Commit: 740d2842688db2d2100fc88e5e304eddbd1ab228
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-29 18:00:46 +0100
Commit message:

 removed all `Suppress(Warnings|Messages)`
Package: MetaProViz
Commit: 4121bdd2dc29debe38510680d8b9ad72d0457f22
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-29 15:34:48 +0100
Commit message:

 `dma`: removed unused code
Package: MetaProViz
Commit: 472bf889dffd218607497428726ff20b8776d11d
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-29 15:16:43 +0100
Commit message:

 `DiffMetAn`: refactored messages to make them less ugly, and also to address NOTE `Avoid the use of "paste" in condition signals`
Package: MetaProViz
Commit: fbd9f964b302bc4ccef8fefe9e9ec0a6850dd232
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-29 14:34:14 +0100
Commit message:

 replaced newly introduced `1:...` with `seq_len(...)`
Package: MetaProViz
Commit: 8976ac946dadbcc989773db4afe0767d18d3bae1
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-29 14:13:14 +0100
Commit message:

 removed `<<-` leftover from some debugging works
Package: MetaProViz
Commit: 66c6674843301dcf1eda88a1c6e523b4685ffd72
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-29 13:51:08 +0100
Commit message:

 `NEWS`: filled past history based on GitHub Releases page
Package: MetaProViz
Commit: 4599afeb0b9f93ea26329f044c664d6311b19529
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 11:08:01 +0100
Commit message:

 updated documentation
Package: MetaProViz
Commit: 76b2380e09a7e8c0090a33afb9ded92f760e8db5
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 11:07:50 +0100
Commit message:

 added S4Vectors as dependency in description
Package: MetaProViz
Commit: 792c9f5fe257248e85bfb5f736583c1c84b04efb
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 11:07:35 +0100
Commit message:

 updated documentation of helper process_se
Package: MetaProViz
Commit: 25ab6e2b6fb5bc9c750b9bff41cd43c37a2620d0
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 11:07:12 +0100
Commit message:

 added importFrom updates in processing, replicate_sum, pool_estimation
Package: MetaProViz
Commit: 093e8b1d23f388f64da31d063a863eb31b791d41
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:54:33 +0100
Commit message:

 Update viz_superplot.Rd
Package: MetaProViz
Commit: de3da01e6e7411f21e9aeafe736f67178180e680
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:54:28 +0100
Commit message:

 enabled se object as input default for viz_superplot()
Package: MetaProViz
Commit: 7f5c5941eefc6d3d0d1ca1c02be3082f92d5fb4c
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:45:35 +0100
Commit message:

 updated documentation
Package: MetaProViz
Commit: e8b558287de381228be5fc7508e1827fb60b102e
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:45:10 +0100
Commit message:

 enabled se object input as default for viz_pca
Package: MetaProViz
Commit: 2e552461faaf532e8a2a11ab0f178bada7868641
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:38:59 +0100
Commit message:

 updated documentation
Package: MetaProViz
Commit: 7b4c2044a26ad22d3e7e8ad56c497a89eeff0767
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:38:49 +0100
Commit message:

 typo in parameter description of dma
Package: MetaProViz
Commit: dd48a4aa6d714c414dc585edf302550327b44b3c
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:38:37 +0100
Commit message:

 enabled se object input as default for viz_heatmap
Package: MetaProViz
Commit: 4b4ac08283d584232c4355e0777d50d5b9bd4b1d
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:26:14 +0100
Commit message:

 updated documentation
Package: MetaProViz
Commit: 5aef425a5774b01fddbc2dbe8f3626af44ff598f
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:26:05 +0100
Commit message:

 changed typo in parameter description
Package: MetaProViz
Commit: 86006fdf01a23be1915e6d53ceb8c8637c65c401
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:25:50 +0100
Commit message:

 added se object input as default
Package: MetaProViz
Commit: 7fedbfed17798e8bcfedfc22163b1609322e36b8
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:13:29 +0100
Commit message:

 updates documentation
Package: MetaProViz
Commit: 18f3b65d5962a458bc4d1ba812c935855033cae2
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:13:01 +0100
Commit message:

 enables se object input as default for metadata analysis
Package: MetaProViz
Commit: e5b4a8a00893f7e33dd6e92cfebf2a181fc0a34b
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:07:55 +0100
Commit message:

 aded tissue_norm_se to ToyData description
Package: MetaProViz
Commit: 454b459c79981fed016466396e3f8ef5ca120679
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 10:07:38 +0100
Commit message:

 Create tissue_norm_se.rda
Package: MetaProViz
Commit: b56ce2b43b798e32c1879fe3f44d2fcd394e3b64
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 09:27:09 +0100
Commit message:

 Update dma.Rd
Package: MetaProViz
Commit: 586532d9487990fb64dc7391ec1e3e030b43df29
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 09:27:02 +0100
Commit message:

 Aded se object input to dma()
Package: MetaProViz
Commit: a98a4fa151d73ec291eaebbf96f356265bd52714
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 08:59:12 +0100
Commit message:

 updated documentation for replicate_sum()
Package: MetaProViz
Commit: ee46b3faec76b48a4837da37f35c92f4fb1da13f
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 08:56:40 +0100
Commit message:

 Finished the export of the SE in pool_estimation
Package: MetaProViz
Commit: 6abbeb3d06b73175b6826b449c38d18171b9032f
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 08:56:12 +0100
Commit message:

 Extended Se helper to set DFs to NULL if they are empty.
Package: MetaProViz
Commit: f5fc33b72c727644eac94485820fa7c3f5b3a3fd
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-29 08:20:20 +0100
Commit message:

 Added rownames to se output of replicate_sum() and shortened example
Package: MetaProViz
Commit: f3bca9757246ea3a9ba9560eb9a242aa3bf8ad7d
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 17:03:08 +0100
Commit message:

 updated documentation
Package: MetaProViz
Commit: dc2fef77ccadb18510306edc4028f428d7532d65
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 17:02:34 +0100
Commit message:

 Added se object to pool_estimation()
Package: MetaProViz
Commit: 6ece920ca3ff923d984f331804ae9f766f844856
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 17:02:13 +0100
Commit message:

 updated example data for intracell_raw_se
Package: MetaProViz
Commit: de2cb903d1d66c0554b10b247833f7a9c422bbf0
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 16:19:36 +0100
Commit message:

 Allowed se onject input/output for replicate_sum()
Package: MetaProViz
Commit: 2dde802b05630829ca142da06b986b919dcaafbd
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 16:00:43 +0100
Commit message:

 Updated documentation
Package: MetaProViz
Commit: c110f3949388aa7f1f9756d156d5f41dc30d3a07
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 15:59:45 +0100
Commit message:

 Used the helper function in processing
Package: MetaProViz
Commit: 6ce85c629b73dac6d07c467d92be5a364fbc5260
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 15:59:35 +0100
Commit message:

 Created helper function to unpack se experiments for our functions
Package: MetaProViz
Commit: df73c9976b451982eb77c8f2b57402122d231e66
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 15:59:05 +0100
Commit message:

 Update intracell_raw_se.rda
Package: MetaProViz
Commit: bb174d6224bc649b91069f6e29b3cbfa6eb87570
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 15:26:37 +0100
Commit message:

 updated processing parameters documentation
Package: MetaProViz
Commit: d3dab295d2e2d2a8294136f5ec4bcdc87cf2d365
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 15:26:06 +0100
Commit message:

 Updated parameter default
Package: MetaProViz
Commit: a25863c60e7e7a6835fd4a983ff257739c9f0c38
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 15:09:54 +0100
Commit message:

 updated man
Package: MetaProViz
Commit: 6e5e009cf60c8cedbd3996183d0ccee92ee6c6d7
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 14:59:40 +0100
Commit message:

 load using data()
Package: MetaProViz
Commit: c8d04c01173fdde21377b24e57caecf92cfb04a7
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 14:51:50 +0100
Commit message:

 added an se file toydata for @example
Package: MetaProViz
Commit: 39560ad843cd61f3b0946c20f467f0f7433a807a
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 14:51:34 +0100
Commit message:

 Added example, and code to allow summarizedExperiment input
Package: MetaProViz
Commit: 1950bea2295245d89717897e274cc058ddf10d36
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-28 14:51:13 +0100
Commit message:

 Added SummarizedExperiment as dependency
Package: MetaProViz
Commit: 48def15677fb08c0737a64e02e5eb0cbf75b4188
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-28 04:49:25 +0100
Commit message:

 Bump version: 3.99.9 → 3.99.10
Package: MetaProViz
Commit: 341612d5445c1def1813c7eae73b75de181d023c
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-28 04:49:21 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 81fb78a0d1bd87fc120e4f8b8ba5e7a70ae0abba
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-28 04:49:11 +0100
Commit message:

 some more formatting issues fixed
Package: MetaProViz
Commit: 645924151d4ec744896ca9f8d211a5486b356834
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-28 03:40:16 +0100
Commit message:

 `mpv_shapiro`: return `NA` where `shapiro.test` fails due to no variance in one of the variables
Package: MetaProViz
Commit: cc91700cf723a87f6f6abed4d8a285daacf56aea
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-28 02:49:13 +0100
Commit message:

 Bump version: 3.99.8 → 3.99.9
Package: MetaProViz
Commit: 97c7dae3fdebb61a2b3c160f29a3f15887360e0c
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-28 02:47:45 +0100
Commit message:

 chunk names for `quick-start` vignette + removed duplicate eval/echo chunks
Package: MetaProViz
Commit: 0dbbaea3d6236f41a37b952f9cac1eec945e7b5f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-28 02:31:53 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 4a70dab0af4ada74f05f6dae77313bee2b4d7189
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-28 02:31:26 +0100
Commit message:

 formatting changes to address BiocCheck notes and for readability
Package: MetaProViz
Commit: 64587fcde421a2d67f71a01a0a3c3166698d9b87
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-27 16:44:31 +0100
Commit message:

 normalized indentation (4 spaces)
Package: MetaProViz
Commit: 5a9f86a73b8c7cdc7263412da5f6f47da6ee02e2
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-27 16:22:48 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 3bf465c66fe0dec5600a7fb6d335b9cab269f6ae
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-27 16:22:38 +0100
Commit message:

 `R code`: address `1:...` → `seq_len(...)`, `suppressMessages/Warnings`, `paste` in condition messages and other `BiocCheck` notes
Package: MetaProViz
Commit: a9ce991849a8de8d608a01baf477ae3786951714
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-27 16:21:14 +0100
Commit message:

 `vignettes`: chunk names
Package: MetaProViz
Commit: 4a97fd9db590f51d1c40e668e2b1434739484d7c
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-27 16:20:31 +0100
Commit message:

 `DESCRIPTION`: added `Clustering` and `Pathways` to `BiocViews`
Package: MetaProViz
Commit: a9cde62a824d76d11683c6e39d8c2d4fcc2beb4f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 22:19:18 +0100
Commit message:

 `DESCRIPTION`: added `fnd` role to Christina
Package: MetaProViz
Commit: 39ef5436a492cae7c73658d79086dc541fe99f90
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 22:07:18 +0100
Commit message:

 removed some `MetaProViz:::` and removed stray line with `equivalent_features`
Package: MetaProViz
Commit: e9852e07b287ebe5c17e882b6a9fc91d2fda6962
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 21:55:51 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: b71f4f13120a84979b7d7df7901767f3820d6291
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 21:55:32 +0100
Commit message:

 addressed remaining undeclared NSE variables and missing imports
Package: MetaProViz
Commit: fa8ba31f979f8e5146c699918347190ab55837e6
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 21:23:23 +0100
Commit message:

 `viz_superplot`: updated internal func name `aov` → `mpv_aov`
Package: MetaProViz
Commit: 7c6f038aaddd5f71141fdddb6c8eb30c3a2825fb
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 21:21:02 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 257dfc3d54063cee77caf36e1d800a32ebfbbcb5
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 21:18:20 +0100
Commit message:

 addressed remaining undeclared NSE variables and missing imports
Package: MetaProViz
Commit: e61d45635db3973bc1d53135ef3e54a56e3ce079
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 20:42:46 +0100
Commit message:

 `viz_superplot`: do not override `sd`, it is from `stats`
Package: MetaProViz
Commit: ff58f5d51c1f83110c2202620a9698b5506a75e9
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 19:38:06 +0100
Commit message:

 Bump version: 3.99.7 → 3.99.8
Package: MetaProViz
Commit: d0270aa5f3fc553152e8667e31d9a2d526905a15
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 19:37:50 +0100
Commit message:

 addressed partial argument match cases
Package: MetaProViz
Commit: d11da8423e56da7bd57f6ddb8233a6f998aee8cc
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 19:35:07 +0100
Commit message:

 addressed function and variable name chaos in `DMA.R`
Package: MetaProViz
Commit: 401ec38b8390cefead0a3d4e8a711ecfcaa5d2db
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 19:27:42 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 73f53506c8ba5b7993562b2331a3f7dcc0c83c6f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 19:27:31 +0100
Commit message:

 added NSE vs R CMD check variable declarations + missing imports to address "no visible binding/func def" notes
Package: MetaProViz
Commit: 487a8c4fa810cf26338fab91c4814d151dc38713
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 18:26:20 +0100
Commit message:

 `vignettes`: removed duplicate chunks with displayed code + scrollable plots
Package: MetaProViz
Commit: 4d2e01b55e787945c8da6e1ea1eb00e1e29f620e
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 17:58:40 +0100
Commit message:

 static figure used in `readme`
Package: MetaProViz
Commit: 7bba24cac74ece73b600e589b6ab59750ed42723
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 17:57:37 +0100
Commit message:

 removed old `README.Rmd`
Package: MetaProViz
Commit: df4f5e576fc14ce5765110c94b0c0eaa47a8431b
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 17:57:27 +0100
Commit message:

 `readme`: use a simple `md` file, do not generate from `Rmd`
Package: MetaProViz
Commit: 7d0c78ddb6d45a91c1c0eaf5d3d7adb4117266aa
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 17:56:41 +0100
Commit message:

 `rbuildignore`: readme file backups
Package: MetaProViz
Commit: 03411ad72ed001a64dc904d1f2b01a72ddbee68e
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 17:56:22 +0100
Commit message:

 fixed figure generating for the readme
Package: MetaProViz
Commit: 7313a25e3734c59fa9917d76258ca780208c07ad
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 17:39:11 +0100
Commit message:

 removed unused imports `SummarizedExepriment` and `cosmosR`
Package: MetaProViz
Commit: 81968f4cb37911f136457e7dc53faf51efe93085
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 17:31:58 +0100
Commit message:

 `viz_upset`: emmit message when rendering fails instead of crashing
Package: MetaProViz
Commit: 4399bc919511b24da03ca0f9ca48562c80d031cc
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-26 17:30:55 +0100
Commit message:

 bypass `ggsave` with `ComplexUpset` plots
Package: MetaProViz
Commit: 48a24a6e61bdc2578e0f91ed9e7fbd52a9738f65
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 22:29:55 +0200
Commit message:

 `viz_upset`: removed `axis.text.y` from set sizes plot
Package: MetaProViz
Commit: 2f5d6416305dfb656aa665c2aa18e53df8d48475
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 22:03:42 +0200
Commit message:

 `viz_upset`: removed `axis.text.x` from intersection size plot
Package: MetaProViz
Commit: 23ee79814e411ad6b76834c9ad83b87e9a420cc2
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 20:30:09 +0200
Commit message:

 `vignettes`: removed leading colon in front of some `viz_*` function calls
Package: MetaProViz
Commit: e1c27796d16baf94680cc14a84907c06dbcacce2
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 19:52:41 +0200
Commit message:

 Merge branch 'devel'
Package: MetaProViz
Commit: fa296c50edfffbb45c74db75e14fbc8046056c23
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 19:52:31 +0200
Commit message:

 `vignettes`: fixed calls to internal functions `plot_grob_*` (not sure why we have those in vignettes)
Package: MetaProViz
Commit: 0b9ba11451c876c7dc7e3a3d120e535d492dfe30
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 19:23:55 +0200
Commit message:

 Merge branch 'devel'
Package: MetaProViz
Commit: 9185ba6f15a010f47a16b7128d32499b72b524ba
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 19:23:48 +0200
Commit message:

 Bump version: 3.99.6 → 3.99.7
Package: MetaProViz
Commit: 3ad9fdac24ab3e1f5285c52d48f89054cd8c088f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 19:12:35 +0200
Commit message:

 `vignettes`: set output to `BiocStyle::html_document`
Package: MetaProViz
Commit: cbada7f6aab4f25a7efc00fa5db4403d65f45785
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 19:01:58 +0200
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 45e31d0c9f9f226a279b59214a1600df21efcf86
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 19:01:40 +0200
Commit message:

 `mca_core`: `data` call in docstring example
Package: MetaProViz
Commit: 61c82570e3c3e92fd1aab5ca9593058bb3bebc34
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 18:49:46 +0200
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 9d014354d4d76b8a6af9891871f2d9791d65f857
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 18:49:35 +0200
Commit message:

 `data` call in doc example of `checkmatch_pk_to_data`
Package: MetaProViz
Commit: 596900ba974d33975e79f4921b0ae5c280fb1f27
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 18:24:43 +0200
Commit message:

 Bump version: 3.99.5 → 3.99.6
Package: MetaProViz
Commit: 7cef3a4a84a44bc5c9a50c148aa21b9d7777ff26
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 18:24:26 +0200
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 7f24bea9c436253cfed1734b9bcd5764c9404704
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 18:24:04 +0200
Commit message:

 `data()` calls in docstring examples and R code since we have to disable `LazyData`
Package: MetaProViz
Commit: f3132c4cfbcc3cc2d4ef77e6b79f57f58281d559
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-25 18:08:53 +0200
Commit message:

 `test-check_param`: `data()` call since `LazyData` is disabled
Package: MetaProViz
Commit: c7fecc8e2d5c9541e7741ae25abb156f0e700525
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-24 22:07:21 +0200
Commit message:

 added `data()` calls to vignettes since we had to disable `LazyData`
Package: MetaProViz
Commit: 397732e4d3636ee88b5c5a0a624049622d2dea83
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-24 21:45:49 +0200
Commit message:

 Bump version: 3.99.4 → 3.99.5
Package: MetaProViz
Commit: 8ff1f1bf9a2363c1d0483eeb1d7704bb43346858
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-24 21:45:23 +0200
Commit message:

 moved figure code from `README.Rmd` to `inst/scripts/readme-figure.R`
Package: MetaProViz
Commit: 0e6249532c77b31a5a6f5478a29c5f37a942b77b
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-24 21:06:38 +0200
Commit message:

 removed `MetaProViz::` from vignette code
Package: MetaProViz
Commit: 9a1343a235879a4aba36cd683ec774394d757765
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-24 21:02:55 +0200
Commit message:

 fixed `.bumpversion.cfg` and `omnipathr-log` in `.Rbuildignore`
Package: MetaProViz
Commit: d11fa5da6e0832ea281feb02bb3bcdebab97ba1b
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-24 21:00:09 +0200
Commit message:

 created `NEWS.md`
Package: MetaProViz
Commit: 58436c4f3d5041e172bc74bf55568eaf74fd3413
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-24 20:58:04 +0200
Commit message:

 `DESCRIPTION`: set `LazyData` to `false`; added `Software` to `BiocViews`
Package: MetaProViz
Commit: 021af0c728cfe594b230fc499938a4d72a89020d
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-24 20:56:58 +0200
Commit message:

 removed `eval=FALSE` chunk from `README.Rmd`
Package: MetaProViz
Commit: da67a0e4aacf63082e1f4b17574f25bee92a8cce
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-24 20:46:19 +0200
Commit message:

 moved `_pkgdown.yml` under `pkgdown/`
Package: MetaProViz
Commit: 2f3d7d6dde539bb26cb79df7372c74b0a89a8bfc
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-24 19:46:21 +0200
Commit message:

 `github ci`: install `EnhancedVolcano` in build & check workflow: it is not yet BioC 3.22, will see if it gets removed
Package: MetaProViz
Commit: 6bf081a116154387739ee2de2609672758d3585b
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-24 13:03:59 +0100
Commit message:

 reverting last commit
Package: MetaProViz
Commit: ce82bac24f538faac99b81994d2774f8ab70cfb3
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-24 12:48:19 +0100
Commit message:

 test explicit installation of EnhancedVolcano
Package: MetaProViz
Commit: dfedddc3a18059a1125fb3e47673b4791ae5dec4
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-24 11:31:24 +0100
Commit message:

 formatting
Package: MetaProViz
Commit: 5403e5e4981b3366025d6f0057bd977337b4900a
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-23 17:44:08 +0100
Commit message:

 code refactoring of count_id function
Package: MetaProViz
Commit: 8b6b3bb03a33e69fd57750ff789b136b1082bdc5
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-09 23:04:08 +0200
Commit message:

 `pkgdown`: copied over bibliography to `vignettes/pkgdown`
Package: MetaProViz
Commit: 75125aabfe630c75fd3eee1c0514461ace735534
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-09 22:09:25 +0200
Commit message:

 `pkgdown`: attempt to fix articles menu item definitions
Package: MetaProViz
Commit: 242f0ce81b5b0091ff6bed7ffd028cbe7fadcf50
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-09 21:38:08 +0200
Commit message:

 `pkgdown`: fixed yaml formatting issue
Package: BiocVersion
Commit: 252d7c8f03a39a9b83f6de7e9dbf9a5ee6584365
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-30 11:29:14 -0400
Commit message:

 version bump 3.23.1
Package: BiocVersion
Commit: d18b787362277e2aee51497e93641fcbdb6a0b7f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-30 11:29:12 -0400
Commit message:

 bump R version requirement
Package: ggtree
Commit: af2f26ce0d73af29ee6bd627b032af4c87c5760e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-30 22:26:19 +0800
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: ggtree
Commit: 848117f4035fb4ba3d70d3c903fd03c3c624e6de
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-30 22:18:04 +0800
Commit message:

 Merge pull request #677 from xiangpin/geom_strip_update

Geom strip update
Package: ggtree
Commit: 08392bcac5ed9c34215fec4cfeeb39e1f26faba1
Author: xiangpin <xshuangbin@163.com>
Date: 2025-10-29 20:58:18 +0800
Commit message:

 update for striplabel object
Package: ggtree
Commit: 6e8cdebebd7ff0c43a69336897168f018b15e695
Author: xiangpin <xshuangbin@163.com>
Date: 2025-10-29 20:51:27 +0800
Commit message:

 typo
Package: ggtree
Commit: 3c718256c39a0481a683b88636bb2b339c300d68
Author: xiangpin <xshuangbin@163.com>
Date: 2025-10-29 11:51:10 +0800
Commit message:

 update geom_strip
Package: ggtree
Commit: 7389dfac6c4c63237d9357561e0fe5076cf70cdb
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-30 22:22:26 +0800
Commit message:

 bug fixed
Package: DMRcaller
Commit: 9bc02194dd099645f2de36a85166e9708f2a7993
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-30 09:44:07 -0400
Commit message:

 Update NEWS

 - please format news correctly
Package: plaid
Commit: 4214e5c2e9701abf46e7409217c7ae8c1593e427
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-10-30 11:08:49 +0100
Commit message:

 add test coverage
Package: gDRstyle
Commit: 25af3a58eb47fdef2de53673957aeaccf4825177
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2025-10-30 10:33:37 +0100
Commit message:

 Merge pull request #94 from gdrplatform/GDR-3164

Gdr 3164
Package: gDRstyle
Commit: 7c5e90196c4a6d56dc313c77bf1361c7aece6de0
Author: Arek Gladki <gladki.arkadiusz@gmail.com>
Date: 2025-10-30 07:15:15 +0100
Commit message:

 chore: bump v+c
Package: gDRutils
Commit: 4a412dcdde9445bfc22df02ad8bae48ec7ffbb09
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2025-10-30 10:33:15 +0100
Commit message:

 Merge pull request #175 from gdrplatform/GDR-3164

Gdr 3164
Package: gDRutils
Commit: 78a0036a2af5dff3425091c9ec4a0212b30b2a20
Author: Arek Gladki <gladki.arkadiusz@gmail.com>
Date: 2025-10-30 07:17:14 +0100
Commit message:

 chore: bump v+c
Package: gDRimport
Commit: 16632cf8742f5d0dae1d8300ab730d679b41a9ec
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2025-10-30 10:32:55 +0100
Commit message:

 Merge pull request #109 from gdrplatform/GDR-3164

Gdr 3164
Package: gDRimport
Commit: 8b2f59e960b10bc8c024e6888a69970081e87ee0
Author: Arek Gladki <gladki.arkadiusz@gmail.com>
Date: 2025-10-30 07:21:49 +0100
Commit message:

 chore: bump v+c
Package: gDRtestData
Commit: dde35d0a211555c178577accb2b0777ad9164f26
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2025-10-30 10:32:19 +0100
Commit message:

 Merge pull request #73 from gdrplatform/GDR-3164

Gdr 3164
Package: gDRtestData
Commit: 51c3696af4f673e0592370e4eb00305277e2e946
Author: Arek Gladki <gladki.arkadiusz@gmail.com>
Date: 2025-10-30 07:24:27 +0100
Commit message:

 chore: bump v+c
Package: gDRcore
Commit: 6b41ab3c89949301491e93c4850bd9da5247e123
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2025-10-30 10:31:59 +0100
Commit message:

 Merge pull request #186 from gdrplatform/GDR-3164

Gdr 3164
Package: gDRcore
Commit: 608a3195b220cfdf3d1adb3d87278b4713e4dc0a
Author: Arek Gladki <gladki.arkadiusz@gmail.com>
Date: 2025-10-30 07:19:54 +0100
Commit message:

 chore: bump v+c
Package: gDR
Commit: 9871bb8b277020860c967a6cfbed5075acaaafd3
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2025-10-30 10:31:39 +0100
Commit message:

 Merge pull request #57 from gdrplatform/GDR-3164

Gdr 3164
Package: gDR
Commit: a62acd6e7fa3e2a76e0f2575c2f9e2df1174bf1c
Author: Arek Gladki <gladki.arkadiusz@gmail.com>
Date: 2025-10-30 08:18:11 +0100
Commit message:

 build: trigger build
Package: gDR
Commit: dd8b0d85ca408668fb55ef84267f5345ad48c83f
Author: Arek Gladki <gladki.arkadiusz@gmail.com>
Date: 2025-10-30 07:26:21 +0100
Commit message:

 chore: bump v+c
Package: GenomicFeatures
Commit: d92f2d08fddfda772940a4ec1e4d50449f05910e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 23:00:29 -0700
Commit message:

 GenomicFeatures 1.63.1: Remove all defunct functions

After they got formally deprecated in GenomicFeatures in BioC 3.21 and
defunct in BioC 3.22, all the functions that went to txdbmaker in BioC 3.19
are now gone for good.
Package: igblastr
Commit: 2880899d1422b9b7c26bf7ec10ba7e9c21b9e37c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 20:02:06 -0700
Commit message:

 update TODO
Package: CBN2Path
Commit: d38f8865b00b14d27cc272ce2f3821e01506e14a
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-29 21:14:05 -0500
Commit message:

 fix maintainers
Package: CBN2Path
Commit: 6c77e1c71d41cf8bacf986af3c7ed6003d00b591
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-29 20:16:43 -0500
Commit message:

 bump
Package: CBN2Path
Commit: dcca0871fb2ea5f8de27dcdc1e75b5c07ae4746a
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-29 20:16:25 -0500
Commit message:

 fix output in vignette
Package: CBN2Path
Commit: 008ec1140a3f44ae2442698b2b1e625431f37e0c
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-29 20:02:41 -0500
Commit message:

 bump
Package: CBN2Path
Commit: 363638bde89ddd251be8ef15a792f23ba5abf69c
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-29 20:02:36 -0500
Commit message:

 fix title
Package: ontoProc
Commit: a09f239272f1f0b6432299902a6b7d3cb610569d
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 19:20:08 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: ontoProc
Commit: f2c1b3f170ce3e23ed97712695fb8309b0888c6d
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 19:20:08 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: ontoProc
Commit: 8aa7338665702565e010f1d02be2fa37c7ac2d39
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-08 11:44:19 -0400
Commit message:

 introducing calls to .Defunct, fix vignette
Package: ontoProc
Commit: 869e2926838d1fc6a1cbda399c406577a31bd2b1
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-09-01 14:39:18 +0000
Commit message:

 Replace .Deprecated with .Defunct for specified functions

Co-authored-by: vjcitn <4624066+vjcitn@users.noreply.github.com>
Package: ontoProc
Commit: 991f8631f7024a7a8c59296926a579a388aa8c3f
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-09-01 14:29:52 +0000
Commit message:

 Initial plan
Package: BiocCheck
Commit: 09886edfc32ebe81d0ccf979be47d29d7a014df5
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 19:20:08 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: BiocCheck
Commit: 79a36192a2e7be561fed684325f5a7474297f601
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 19:20:08 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: BiocCheck
Commit: 9a9c0c117c7f4689bab50ccf4f9c498be4f3b265
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-14 12:27:27 -0400
Commit message:

 version bump 1.45.20
Package: BiocCheck
Commit: 2ae2a644bcf8306d1272558160fa5415bb7e73fd
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-14 12:27:25 -0400
Commit message:

 add chunk labels
Package: BiocCheck
Commit: 6c045d7ec60703e81c1d706663ece0d748ff8ff4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-14 12:19:29 -0400
Commit message:

 version bump 1.45.19
Package: BiocCheck
Commit: e08267bf500a457632e52946c1a58c452d951250
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-14 12:19:26 -0400
Commit message:

 update checkFormatting recommendation
Package: BiocCheck
Commit: 9f7d48187c16e795c3370ced9dcf9c5186db9e3b
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-26 17:26:27 -0400
Commit message:

 version bump 1.45.18
Package: BiocCheck
Commit: f29991f0e5493988c17c142a6b929ac72ebb9f5d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-26 17:25:32 -0400
Commit message:

 use .RdTags from tools internally
Package: BiocCheck
Commit: 51f668194d788ef88dbcdde6326133196bc617b2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-26 17:04:59 -0400
Commit message:

 minor formatting
Package: BiocCheck
Commit: bf08c5162814a5ab85f025bc69619c292063f42f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-26 15:24:03 -0400
Commit message:

 simplify checkUsageOfDont
Package: BiocCheck
Commit: 0c2774a92cb0503016d574654b9e1b8dcc258a0c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-26 14:36:26 -0400
Commit message:

 simplify operation in checkExportsAreDocumented
Package: BiocCheck
Commit: 76717748d312728f469172f217a9431fae6fe480
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-26 11:40:41 -0400
Commit message:

 version bump 1.45.17
Package: BiocCheck
Commit: e5c74a53806f1e8c3736c683b91ee81902f31f92
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-26 11:40:34 -0400
Commit message:

 update docs re --no-check-namespace
Package: BiocCheck
Commit: 899a2f59e17a71c9bc78aa81385caeba6c9310cc
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-25 15:35:00 -0400
Commit message:

 version bump 1.45.16
Package: BiocCheck
Commit: e3fca390e1251206dd58c560243b80d382adf94c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-25 15:34:32 -0400
Commit message:

 add note about using BiocCheckGitClone
Package: BiocCheck
Commit: c60b365351c4ac7bbf4f11211df9fafc8f49828d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-25 15:19:58 -0400
Commit message:

 add checkNAMESPACE to BiocCheckGitClone
Package: BiocCheck
Commit: d30e2e5ef546d8c0a5718647970c9f008d8a24a4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-25 14:36:28 -0400
Commit message:

 version bump 1.45.15
Package: BiocCheck
Commit: 88a7b96e8d28dbbfa2da884cfcfdec3139e26a4f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-25 14:36:22 -0400
Commit message:

 add GPL (>= 3) test for checkLicenseForRestrictiveUse
Package: BiocCheck
Commit: 6d7d744120cbc2ebcf6bb1dbfb62410265b34f78
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-25 14:20:21 -0400
Commit message:

 update NEWS
Package: BiocCheck
Commit: 26999008abedbf15d9bbdf27b077202727c1800e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-25 14:04:41 -0400
Commit message:

 version bump 1.45.14
Package: BiocCheck
Commit: 972b24f7f8b70a13b5ebfd6c50a5524d7e743bec
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-25 13:53:41 -0400
Commit message:

 add checkNAMESPACE for catch all exportPattern
Package: BiocCheck
Commit: 304cf4ea27500a7c708329fe134d999af8aab845
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-25 13:53:15 -0400
Commit message:

 version bump 1.45.13
Package: BiocCheck
Commit: dc640717763e962fe2cc6aa395ba35a284aa62fb
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-25 19:51:10 +0200
Commit message:

 Sort BiocCheck() options alphabetically in documentation (#229)
Package: AnVIL
Commit: b498d04e6660e4ce7ea1d504dda5b312c58035f8
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 19:20:07 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: AnVIL
Commit: d87ee9cc4182ea9e9d3179939e1037bcfd5e78e5
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 19:20:07 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: AnVIL
Commit: 1e39a3fe05596973e2552f2408ec7cfe988f5407
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-22 10:20:32 -0400
Commit message:

 version bump 1.21.10
Package: AnVIL
Commit: e783cd8e22507678d98f82ee95c571f8aab6762e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-22 10:20:30 -0400
Commit message:

 update Dockstore API
Package: AnVIL
Commit: 62ae1fecc26c92011b1e47c7eea87a3750194256
Author: nektos/act <nektos/act@users.noreply.github.com>
Date: 2025-09-22 14:07:06 +0000
Commit message:

 Update API
Package: AnVIL
Commit: 5a3c6094936de699856f9801010ce21a3289fd24
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-11 11:36:03 -0400
Commit message:

 action uses workflow_dispatch branch
Package: SpiecEasi
Commit: 18c9537d1f632c34aa4e9e571d8e67503c0c9d75
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-29 15:53:57 -0400
Commit message:

 Bump version: 1.99.2 → 1.99.3
Package: SpiecEasi
Commit: c0c492954e78508cd98a36d206a11ac42e975c63
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-29 15:10:30 -0400
Commit message:

 remove unecessary Rbuildignore entries 2
Package: SpiecEasi
Commit: 39a1340d789cf4f314c27aaf01a4ef7ce8c2ef22
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-29 15:10:03 -0400
Commit message:

 remove unecessary Rbuildignore entries
Package: SpiecEasi
Commit: 933aac0d51bbc9afe6468d3961acd2308bef3f5f
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-29 13:48:57 -0400
Commit message:

 fixes and update NEWS
Package: SpiecEasi
Commit: 14d53ac238972b2e14d34acda7cc9a26a8090ab1
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-29 13:42:28 -0400
Commit message:

 address reviewer comments
Package: GXwasR
Commit: 52839c3e53179d813dc1a3f009c2666062ade386
Author: Banabithi Bose <banabithi.bose@gmail.com>
Date: 2025-10-29 14:07:14 -0500
Commit message:

 Version bumped.
Package: GXwasR
Commit: 6b8e873c5b5423e96b213893e4257a401e2dc1c4
Author: D Mayer <32186106+the-mayer@users.noreply.github.com>
Date: 2025-10-29 13:02:22 -0600
Commit message:

 Merge pull request #59 from boseb/55-bug-qcsample-fails-given-settings-from-the-tutorial

QCsample() Fix

fixes #55
Package: GXwasR
Commit: c5c1bd6a7ec242afb051be9f3d3ff625b02a0f1c
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-28 17:19:52 -0400
Commit message:

 Merge commit 'a3a4d3d648646f7f95a9fc0509ac419ff90e820d'
Package: GXwasR
Commit: 56c18a698e9fbb609420cd2433b503b058571348
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-28 17:03:05 -0400
Commit message:

 cleanup pathing
Package: GXwasR
Commit: eadf866f9a02e3d0898090b28459c6606dde4dc9
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-28 17:00:52 -0400
Commit message:

 add test for `het <- NULL`
Package: GXwasR
Commit: daf8d9ecef705bbd4c56bd3ee2e053c0c63d04d3
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-28 16:30:53 -0400
Commit message:

 Fix [BUG] QCSample() fails, given settings from the tutorial
Fixes #55

Co-authored-by: Jacklyn Ashmus <jacklyn-ashmus@users.noreply.github.com>
Package: GXwasR
Commit: a3a4d3d648646f7f95a9fc0509ac419ff90e820d
Author: D Mayer <32186106+the-mayer@users.noreply.github.com>
Date: 2025-10-28 11:48:01 -0600
Commit message:

 Merge pull request #58 from boseb/misc-fixes

Fix LaTeX Unicode errors in .Rd documentation
Package: GXwasR
Commit: 90ec31b9244e210cd90f626c0579ffd66a31e679
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-27 17:10:25 -0400
Commit message:

 apply bioc styling
Package: GXwasR
Commit: f48b470f4b7d2046f6e4175b88842d16ae188748
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-27 17:06:35 -0400
Commit message:

 bioc convention, use FALSE instead of F
Package: GXwasR
Commit: 9f418165160fd9366d393a05bb09b6c894eded89
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-27 17:04:31 -0400
Commit message:

 remaining rd fixes for pdf manual
Package: GXwasR
Commit: 90a07c5ca159408a6c70f3a7ebc7277151d10f93
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-27 15:28:36 -0400
Commit message:

 fix equations in PvalComb documentation
Package: GXwasR
Commit: e1a123b28acfbbb9c8ca7b4e5e507aad5b78290d
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-27 15:10:52 -0400
Commit message:

 GXwas() documentation fixes:
- address LaTeX in equations
Package: GXwasR
Commit: 3121d14094da480077ba7bcf90ed1089eb9cba56
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-27 14:29:40 -0400
Commit message:

 fix: You can't use `macro parameter character #' in math mode.
Package: GXwasR
Commit: 258ee070d61af8284cc40b2b357c852c6fef4f00
Author: David Mayer <david.mayer@cuanschutz.edu>
Date: 2025-10-27 14:09:12 -0400
Commit message:

 fix CITATION warning
- replace curly apostrophe with straight (UTF8 compliant)
Package: iscream
Commit: b1bda1ce7d0ecfd506170a0d8e3c510a72fbb323
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-29 14:17:07 -0400
Commit message:

 chore(DESCRIPTION): bump version
Package: iscream
Commit: e860cdce34b791c581649e4bf8d6d39e8572eddd
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-29 14:07:40 -0400
Commit message:

 fix(configure): don't check for pkg-config so hts check is correctly run

checking of pkg-config existence makes the whole condition false when
its available and falls into error when using rhtslib with non-empty
$RHTSLIB_CFLAGS
Package: Rhtslib
Commit: 0dcad2a3b6e818dcc5d763d896c8e8fd88f50d8b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:52:40 -0700
Commit message:

 update NEWS
Package: Seqinfo
Commit: 17fc74a1922470a86ae999ad33314f34ad7c9abb
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:52:20 -0700
Commit message:

 update NEWS
Package: GenomeInfoDb
Commit: f31cf8b472e426f00a9425752e3c3258fe30c40c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:52:07 -0700
Commit message:

 update NEWS
Package: S4Arrays
Commit: 6660826fc80007a1f3cbc2e75a5f3c3eee606c3c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:51:51 -0700
Commit message:

 update NEWS
Package: IRanges
Commit: 167f22b933c30e37902a32b8f632434a3936ec43
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:51:39 -0700
Commit message:

 update NEWS
Package: GenomicRanges
Commit: 1dfb82d3ddf83e1d751be4b42576f0e491611c27
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:50:52 -0700
Commit message:

 update NEWS
Package: Biostrings
Commit: fb3d33011c84a442efde15436b93aca4b7e7c8db
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:50:40 -0700
Commit message:

 update NEWS
Package: GenomicAlignments
Commit: 085e9df7b3aa4f13c5cd31bca06e767fad680b6b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:50:25 -0700
Commit message:

 update NEWS
Package: h5mread
Commit: 376f55fb8d8e1548e6e48bb89784a820fad662c3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:49:58 -0700
Commit message:

 update NEWS
Package: txdbmaker
Commit: 9bfc03435c75132d1da54a2a3e6a94a09d824b12
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:49:40 -0700
Commit message:

 update NEWS
Package: SummarizedExperiment
Commit: 7a9787ce769f9e22d5791e6b01a776846eca0ce9
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:49:30 -0700
Commit message:

 update NEWS
Package: DelayedArray
Commit: a1ebb83a81013d3eb14c18d2a516393013c1bfe9
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:49:13 -0700
Commit message:

 update NEWS
Package: S4Vectors
Commit: cead68c81c2e52b2afb148d2e065af70b81108f3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:48:28 -0700
Commit message:

 update NEWS
Package: BiocGenerics
Commit: 5fcc999682961471c83a0c17e38b8a7f4d42d570
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:48:01 -0700
Commit message:

 update NEWS
Package: GenomicFeatures
Commit: 39d50f6f7b2707e78e0e6170c8859891ad1bab9d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:47:40 -0700
Commit message:

 update NEWS
Package: BSgenome
Commit: ed2fb5832bf91f7ecea2f79c4daaf39c898eb47f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:47:19 -0700
Commit message:

 update NEWS
Package: BSgenomeForge
Commit: c7d1729bac87cf0ec7497d769d57d39f1a742dbe
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:46:49 -0700
Commit message:

 update NEWS
Package: pwalign
Commit: a8e536a6decdb3c2aa9ee00301ff3296c57a375d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:46:16 -0700
Commit message:

 update NEWS
Package: UCSC.utils
Commit: 959bf10dd713587e7a7efe3c17607aff5d61c9fa
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:45:25 -0700
Commit message:

 update NEWS
Package: updateObject
Commit: 13c59eaca5476a0a8024ec5ccc1afb13464941c8
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:44:40 -0700
Commit message:

 update NEWS
Package: SparseArray
Commit: 3a9f3f1aff0d8a0241734d55413cafcbc2d3e26e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:43:33 -0700
Commit message:

 update TODO
Package: SparseArray
Commit: 5e824cd4f90867edc03570e7604d2aebe87de449
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:42:16 -0700
Commit message:

 update NEWS
Package: UCSC.utils
Commit: 1e902a148fdaa3660e44c224e21360b440ea13a1
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 11:29:33 -0700
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: UCSC.utils
Commit: baefc5a0ef9239f2b9fd7d6025d4c6a3d05fcf19
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-24 15:54:26 -0700
Commit message:

 fix .github/workflows/check-bioc.yml
Package: HDF5Array
Commit: 538f96939338e70654b45fdffc85ef92cf9b804a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-29 09:21:26 -0700
Commit message:

 update NEWS
Package: cigarillo
Commit: f89db3d462a069e3c5b6ec5acf7f6af906fdd8ac
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:18 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: cigarillo
Commit: 8775adf6c85995de7c778f0a0b4311c9c6a82068
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:18 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: omicsGMF
Commit: 66f9d2d59adb899f0d19401e95004180a82c909b
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:15 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: omicsGMF
Commit: 665af6c2908f01ba98cb77ae4f29d05c5549efb1
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:15 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: DspikeIn
Commit: 18fc5b8c005665f1dae65a5239edb145359671f7
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:12 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: DspikeIn
Commit: 8a427ff4e61cba46ede54bf23612f02693d70288
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:12 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: iscream
Commit: 3cad033f30f98a81a5bf60247fee5eb7f8dd0b81
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:09 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: iscream
Commit: faf115f5efe1359641bfdbbc1e032d9ad79228c8
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:09 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: anndataR
Commit: 3ebeca051b0bc6aeb7f1222b19738d9d064a6e46
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:06 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: anndataR
Commit: 243ac84e8174265d34ae700e7646694869d6f329
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:06 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: MSstatsResponse
Commit: 048d39d3f3f8e7018466be45f2ca2b346639a4f1
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:03 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: MSstatsResponse
Commit: 7b935dfc9f0bc16795be9cad499b3974436d05d4
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:03 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: CBN2Path
Commit: 77fb151a0dd2730eef96d2517de0e07d67d5a4f9
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:00 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: CBN2Path
Commit: bb06034b7727dc33a2fda98085b7f68e478b40d5
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:39:00 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: iModMix
Commit: 096c0d65f7e160c5821fa557ff87fcf610122c5f
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:57 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: iModMix
Commit: f1207f891a2798910f9e7d616aba91f40b47d316
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:57 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: SmartPhos
Commit: 9abaf07e422a6c6cf3f199e441bec2c3eafbf036
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:54 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: SmartPhos
Commit: a7a52e6ff9b582cdb1419d7624619298ee4aa704
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:54 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: scLANE
Commit: 52d4406dd83c182aa158ab9b7c9920a024531111
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:52 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: scLANE
Commit: 571c6175e84498e787667763dd34625d35a37b68
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:52 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: scGraphVerse
Commit: 1e63abe30a19b0d984aaaf2129894e0f4770d936
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:49 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: scGraphVerse
Commit: 425f2dcf1ee1e8ec05e9afc96dbdfd0c519b9e9d
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:49 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: DOtools
Commit: 527ea7322491875762b3cf3621584f87104349d5
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:46 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: DOtools
Commit: 95a24044ca168f7f324a5ae0882812160813096c
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:46 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: CalibraCurve
Commit: 251148ae6891aa6d8977c7d902ecfb7db7dae000
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:43 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: CalibraCurve
Commit: f737cac957f09395e5872d57a6032c9c549b0f52
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:43 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: STADyUM
Commit: 6b6c41db542bfb574345b6c499458ead263f4eb9
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:40 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: STADyUM
Commit: 55e95773399d62ce6ea47beddd080368c3ca9f9e
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:40 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: anansi
Commit: d5ff74aabc9d954eec0730fa6f942403d7ad4242
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:37 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: anansi
Commit: 78b4ccb4b71291b391d94ebd523ee16cd9dbacc1
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:37 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: notameViz
Commit: 1590e89266b70b7eb98ebb26cdad7c5b5f9e8fdd
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:35 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: notameViz
Commit: bb6e677fee643b2114cbcebf0581d942a932a556
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:35 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: notameStats
Commit: 87a06cd0f7170209de9cd004d7cad01d42a7359b
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:32 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: notameStats
Commit: 58a6cb53bead31b945cca2983b1b53399caabccf
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:32 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: peakCombiner
Commit: 266aae698d78fbca95b369077f5cc6db5cd42e63
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:29 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: peakCombiner
Commit: 152407dee554c7babd78afcdc2f685378092f6ec
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:29 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: Ibex
Commit: 1dadb5258f5d631bf007a7c1b2f156e8f5ff84be
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:26 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: Ibex
Commit: 92396daeb0b512d50a3fa8988fd6e014395ffe52
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:26 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: notame
Commit: 778b0636561783a132f790753810a17c2cb008e9
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:23 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: notame
Commit: e9edc04283a224db7e114aaeaed586132b87ef58
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:23 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: PMScanR
Commit: 1e526c3374058e086345d93aa11a30cec4cec55c
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:20 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: PMScanR
Commit: b9f2642283af5e494dd7f23835f689ea38f06761
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:20 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: looking4clusters
Commit: 7fb974efee0e982b2301e498226ed157dec0a4aa
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:18 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: looking4clusters
Commit: 8c0f82c01cf045a2644c1c979c680a5a70d93925
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:18 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: SETA
Commit: 4f2c9973aeccb1e351bc9daec70c99a51065d2da
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:15 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: SETA
Commit: 2e2876990ad5196d07b99343dbc42787db7c5369
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:15 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: blase
Commit: 7118ee13972e72f33eb547a746d00d3f25735f81
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:12 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: blase
Commit: 874f31bf9c5660d06c6f2bc8b6010b5570b48eff
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:12 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: anglemania
Commit: fee34a32f6105f58a3bdff61befb2459267ca0fa
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:09 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: anglemania
Commit: 3acc9da7a506248365a35e024ee0d5000a9fa99b
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:09 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: markeR
Commit: 7a7e63fedc11a459ea6f9198e25f3cbaae21802a
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:06 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: markeR
Commit: defebad0849686a12cd2dd9f824079a47be8ee18
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:06 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: SuperCellCyto
Commit: 0098ab2ffec2b2f4c9ce98de0627502b7a8b7ca6
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:04 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: SuperCellCyto
Commit: 1e49305513d047a8fb882cf75b5adbe6425b42fc
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:04 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: gVenn
Commit: 617952c67f5d1d96e06e03ca4cc1d27e989e8bbe
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:01 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: gVenn
Commit: 27b5dfc28e14d0bcbcc6c081dfc33029d84ff7da
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:38:01 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: goatea
Commit: 15d475f90c3d80e874c660326b12ebea142aeedf
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:58 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: goatea
Commit: c7a7b1e90b828923b76f6a293ef8c246a4e0201c
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:58 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: shinybiocloader
Commit: 4ca9aed458c3407726187a0555e495cf19f0835b
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:55 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: shinybiocloader
Commit: 80a07b211334dcd029e38724668a41731f734830
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:55 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: SPICEY
Commit: a5c4c208c5e56220461328299923ced8defb3381
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:52 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: SPICEY
Commit: 625bc2e20512e78622836c361ea3591fe07d26c5
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:52 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: FinfoMDS
Commit: a94fee5d6185e5147064af77f3d6d40774486e39
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:49 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: FinfoMDS
Commit: 91ad4bd6252ea72dca2bf93ca9e4397f3f5b1a30
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:49 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: MetaDICT
Commit: b0ced9bdf182b6374b4af8d4f261c1e12fce81a1
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:46 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: MetaDICT
Commit: 2dfcaa84b2cff83379ac972f243941271bc7118f
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:46 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: CSOA
Commit: c51650a02b16a32f1eb270fc169f2504de1a398e
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:44 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: CSOA
Commit: 9b11f08d175947d071f37fe22cd22e08abbc0635
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:44 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: stPipe
Commit: 3b726e38de1377379371ba595b8eacc2d22f2800
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:41 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: stPipe
Commit: f234c12bf8f12086e7ea0d3845adb7e6ccbbed94
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:41 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: Chromatograms
Commit: c10498e70aaaa10633af7a49cd453dd211842fc7
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:38 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: Chromatograms
Commit: 74743d67be8537f46c1587e53723dea02351a7d4
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:38 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: Bioc.gff
Commit: a3d386397ac2b727f81c03e123456c70c46823c4
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:35 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: Bioc.gff
Commit: 5bbebdec690a8a559d2b1c4296983c9f3009ecb5
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:35 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: mutscan
Commit: 30e36695fd64f8e4ad82882e24069ef618735fbc
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:32 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: mutscan
Commit: 79672e3c3ae4e210bd096e72f31cb1ec34bc840e
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:32 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: cellmig
Commit: 6f4bad2f5e301c8a4ed30cc78b871cdc06d46cf0
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:29 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: cellmig
Commit: e77030e81bfdb7facf72bbe44f04e105ec0fbca2
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:29 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: HiCaptuRe
Commit: 342bae39c8fb1fd63caa83f59b3bc7112a57f4ee
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:26 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: HiCaptuRe
Commit: 0a37211d3e8cb4650667141d7182e1596d8a5fd7
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:26 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: spARI
Commit: 537c9145ed520d426a86a049972feda60f6604d8
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:24 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: spARI
Commit: 4a3384b3518c077186ceb4890fea35230bbc2850
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:24 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: DeeDeeExperiment
Commit: 482df351e95d67d023bed0d2b1503ef892b892bf
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:21 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: DeeDeeExperiment
Commit: 8d413acdb917aed7055db585d8ec7a5b0d0be92f
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:21 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: AWAggregator
Commit: 5b7083c22ac4075e13b96d5f3d26150b2e38a1a5
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:37:18 -0400
Commit message:

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