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Bioconductor packages under development:

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GIT Logs

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

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Package: smartid
Commit: 9f60653a1afad57734f9510c135b1b377d3b6897
Author: Gene233 <chen_jj97@163.com>
Date: 2026-03-13 12:00:10 +1100
Commit message:

 Version bump.
Package: smartid
Commit: b205e2cdbae2ed729d106932bc9e0266222f5e15
Author: Gene233 <chen_jj97@163.com>
Date: 2026-03-13 11:40:32 +1100
Commit message:

 Fix dplyr defunct.
Package: igblastr
Commit: aac6a26c3db42a9d8023e2ef72992cdc79318d4d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-03-12 17:54:48 -0700
Commit message:

 Complete compute_V_gene_delineations()'s man page
Package: flowCore
Commit: ed9419653343ad9a77a589eb8dc84fa6647ee7ac
Author: Mike Jiang <mike@ozette.com>
Date: 2026-03-12 17:50:24 -0700
Commit message:

 fix: Add LAPACK/BLAS linker flags to Unix Makevars

flowCore failed to install on BioC nebbiolo1 builder with 'undefined
symbol: dgelsd_' because cytolib bundles Armadillo with ARMA_USE_LAPACK
but the Unix Makevars did not link against LAPACK/BLAS. The Windows
Makevars already included these flags. Add $(LAPACK_LIBS) $(BLAS_LIBS)
to PKG_LIBS in src/Makevars to match Makevars.win and Makevars.ucrt.
Package: HiCool
Commit: 4627d6d0500d24f9c9e135d810721763d556f7ae
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-03-13 01:25:12 +0100
Commit message:

 bump to 1.11.1
Package: HiCool
Commit: 88e3767cc0e60048e2256a659e057ea49bc541c8
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-03-13 01:24:56 +0100
Commit message:

 fix: getLoops example
Package: GenomicCoordinates
Commit: fc36cdbe38bb204b6015e6195d7fa312cab25df7
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-03-13 01:17:08 +0100
Commit message:

 bump to 0.99.1
Package: GenomicCoordinates
Commit: 56489352ca8994f18499884e9d4d99d7ed633d7c
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-03-13 01:03:22 +0100
Commit message:

 fix: replaced setAs with as_*
Package: goSorensen
Commit: b2f0b05b16d1510018ba931ff94f6b373c491c4b
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2026-03-12 18:52:33 -0500
Commit message:

 add keyType
Package: goSorensen
Commit: 48a818103a80e926b15e2b7c0869e1c8f6bc0c05
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2026-03-12 18:34:55 -0500
Commit message:

 Entering keyType argument
Package: goSorensen
Commit: 74dacb0686ac02963d9b5f9aff9428d229ac5e59
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2025-04-16 19:38:07 -0500
Commit message:

 Merge branch 'devel'

merge branch devel into master to incorporate latest updates
Package: goSorensen
Commit: d8e0d3d5237ef727840694a2ed61f5b3a040d75d
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2025-03-18 18:02:55 -0500
Commit message:

 v.1.9.0
Package: goSorensen
Commit: e8ad700e7d609f4c53207addcb4176447fd767ef
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2025-03-18 16:43:40 -0500
Commit message:

 Merge branch 'master' of https://github.com/pablof1988/goSorensen
Package: goSorensen
Commit: 1589bb5d18ca6a7ab32900c12053923ebfcfac7a
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2025-03-18 16:36:19 -0500
Commit message:

 1.9.0
Package: goSorensen
Commit: afde6a2b19b832befe20d7354aef9d7409f89c9f
Author: JordiOcana <jocana@ub.edu>
Date: 2025-03-07 14:02:36 +0100
Commit message:

 Update test_gosorensen_funcs.R

Added comment on potential speed-up due to parallelization
Package: goSorensen
Commit: a560d0df6d6ada51fe0074973bd8f15bc526997d
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-12-14 15:14:09 -0500
Commit message:

 updating vignette 1.8.1
Package: goSorensen
Commit: 78341e8a5c400cadc7a9f5561dbd9bcceee32125
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-12-12 09:12:24 -0500
Commit message:

 updating allSorenThreshold v 1.8.1
Package: goSorensen
Commit: 5e041365900b5e9e27a4bfc875086f3b7e1691ed
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-12-11 18:11:16 -0500
Commit message:

 updating e-mails v1.8.1
Package: goSorensen
Commit: 042b154fd8a834c8ef99ef87e39fcdfc34511d8a
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-12-11 12:21:48 -0500
Commit message:

 updating README v1.8.1
Package: goSorensen
Commit: 5ef6c54fcef72428137e8e5524c88079f247ad1a
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-12-11 11:21:29 -0500
Commit message:

 updating documentation v1.8.1
Package: goSorensen
Commit: d549af8b446dbefb040b3e20e58785dacbb359c8
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-12-10 18:31:34 -0500
Commit message:

 Update vignette DissMatrix - 1.8.1.
Package: goSorensen
Commit: e4f294aa9255c96ac852df877cd06099a3d53924
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-12-10 17:12:12 -0500
Commit message:

 update vignette DissMatrix - 1.8.1
Package: goSorensen
Commit: a8ca2fc7f7e448a0be60f9e6cb5438550ae9b289
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-12-06 19:07:43 -0500
Commit message:

 updating outputs and vignette 1.8.1
Package: goSorensen
Commit: 5386946e388bcf3af1b2ee73d0e58005fc1c0122
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-12-02 12:38:40 -0500
Commit message:

 update v1.8.1
Package: goSorensen
Commit: 029e966835b7311c3c862e7e67b8cd763abc4554
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-11-30 15:31:08 -0500
Commit message:

 v-1.8.1.
Package: goSorensen
Commit: 9161df1dc3ec0821c13e6591acbd22fd134128e6
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-11-30 15:25:50 -0500
Commit message:

 v-1.9.1
Package: goSorensen
Commit: 1acbb0b7339a2325bd16b07cbf3d28faa77441c8
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-11-30 15:22:39 -0500
Commit message:

 v_1.8.1
Package: goSorensen
Commit: 99567c9d1c2090bf80e8699200ed9ea0e350f7d9
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-11-30 15:17:12 -0500
Commit message:

 v1.8.1
Package: goSorensen
Commit: b57e1b2470a93357010a4266c8bd44bc00449934
Author: pablof1988 <pablojfm1988@gmail.com>
Date: 2024-11-30 15:14:00 -0500
Commit message:

 v 1.8.1
Package: postNet
Commit: 68761bd3540e1b18f73c80c08e0490dc392a760b
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-12 21:54:15 +0000
Commit message:

 KS
Package: postNet
Commit: b1cdbd72b92548ec0b8e3f824efe5d004d72f2fc
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-12 21:31:46 +0000
Commit message:

 KS
Package: openCyto
Commit: 6c427362f5e43bf8779969249ce0b6c96e7eeb55
Author: Mike Jiang <mike@ozette.com>
Date: 2026-03-12 13:32:43 -0700
Commit message:

 bump version to 2.23.1
Package: openCyto
Commit: 5c8054a3ec2735fdf75d4ce69ca5223a052c4758
Author: Mike Jiang <mike@ozette.com>
Date: 2026-03-12 13:28:09 -0700
Commit message:

 Remove non-API ENVFLAGS/SET_ENVFLAGS usage from plugin framework (#273)

Replace namespace-unlocking approach (using internal R C-level macros
ENVFLAGS and SET_ENVFLAGS) with a dedicated environment for storing
dynamically registered plugin functions.

- Add .openCyto_plugin_functions environment in pluginFramework.R
- Add .resolve_plugin_function() helper that checks plugin env first,
  then falls back to package namespace for built-in functions
- Update .register()/.unregister() to use the new environment
- Update .gating_adaptor() and .preprocessing() to use the resolver
- Remove unlockNamespace.cpp and its cpp11 bindings

This eliminates the Bioconductor check warning about non-API entry
points while maintaining full backward compatibility for both built-in
gating methods and dynamically registered plugins.

Passes R CMD check with 0 errors, same pre-existing warnings/notes.
Package: iClusterPlus
Commit: 4afea9829de0fe0be49271df541ffebf4d329ec1
Author: qianxing.mo <qianxing.mo@moffitt.org>
Date: 2026-03-12 16:28:28 -0400
Commit message:

 add UM.rda
Package: iClusterPlus
Commit: 94791a8e627acfe3a61f3e43c24a0db612199716
Author: qianxing.mo <qianxing.mo@moffitt.org>
Date: 2026-03-12 13:28:28 -0400
Commit message:

 remove data/simuResult.rda man/simuResult.Rd
Package: iClusterPlus
Commit: 1c14e591d662ba4aa521c64f1938bdf2162afecf
Author: qianxing.mo <qianxing.mo@moffitt.org>
Date: 2026-03-12 13:25:30 -0400
Commit message:

 major update for iClusterPlus
Package: h5mread
Commit: df577fa189e1437464fa09e5a8d8d746f425d06b
Author: Jeroen Ooms <jeroenooms@gmail.com>
Date: 2026-03-12 21:09:38 +0100
Commit message:

 Add backport to unbreak build on R-4.5 (#3)

See https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Some-backports
Package: SparseArray
Commit: a7ca0a774124c6296e511f12c3bf55b253ad8309
Author: Jeroen Ooms <jeroenooms@gmail.com>
Date: 2026-03-12 21:05:03 +0100
Commit message:

 Add backport to unbreak build on R-4.5 (#24)

See https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Some-backports
Package: ChemmineOB
Commit: 4771ee7b7aee3e9e7d7f97e96c49d1ddc3ba9911
Author: khoran <khoran@cs.ucr.edu>
Date: 2026-03-12 11:03:04 -0700
Commit message:

 remove SET_S4_OBJECT calls
Package: DESeq2
Commit: 15f2ec90e8707705d43c1cd66d32b7e99fd6a741
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-03-12 13:58:58 -0400
Commit message:

 dont use threshold in looking at LFC sign, fixes #127
Package: igblastr
Commit: 3b78cad23658ecb30ef49e9f3106cd45ff58ddda
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-03-12 10:48:02 -0700
Commit message:

 fix unit tests
Package: ChemmineR
Commit: aea8b487ec71ca346155cc3d514f357f5905f48b
Author: khoran <khoran@cs.ucr.edu>
Date: 2026-03-12 10:30:58 -0700
Commit message:

 remove SET_S4_OBJECT calls
Package: iClusterPlus
Commit: 2c43d6a0268463be5c7e45b7bb450409db841a92
Author: qianxing.mo <qianxing.mo@moffitt.org>
Date: 2026-03-12 13:14:38 -0400
Commit message:

 Fix DESCRIPTION conflict
Package: iClusterPlus
Commit: dc5bc4e10d43da0694d9c700840ff0eda4604c7b
Author: qianxing.mo <qianxing.mo@moffitt.org>
Date: 2026-03-12 11:10:39 -0400
Commit message:

 update R/iClusterBayes.R
Package: iClusterPlus
Commit: 1ae7f302e6e43724db1073c69586dc0bfa2120f0
Author: qianxing.mo <qianxing.mo@moffitt.org>
Date: 2026-03-12 10:42:06 -0400
Commit message:

 update DESCRIPTION NAMESPACE
Package: casper
Commit: ac71ee6b306d8c06267006cb84ca400ee4f38908
Author: davidrusi <50999756+davidrusi@users.noreply.github.com>
Date: 2026-03-12 18:09:07 +0100
Commit message:

 reverted c changes from last commit
Package: fRagmentomics
Commit: 1d88720fbb6fbfee2b646b1eef06933e9914f796
Author: KillianMau <maudet.killian.loq@gmail.com>
Date: 2026-03-12 12:31:51 +0100
Commit message:

 Address Bioconductor review: use readVcf() for VCF import, return S4Vectors::DataFrame, replace magrittr with native pipe, replace incremental rbind with lapply/do.call, and fix vignette (startup messages, print, table vs count, dataset description)
Package: fRagmentomics
Commit: 5db8f3407568b48e0d00717fa079edb8e7c2f152
Author: KillianMau <maudet.killian.loq@gmail.com>
Date: 2026-02-25 23:26:37 +0100
Commit message:

 Modify figures of the README
Package: EpiDISH
Commit: 816f01d78464e4f9d5dace5bf4467d6ea7edc3b6
Author: GuoXiaolong <2472227329@qq.com>
Date: 2026-03-13 00:11:42 +0800
Commit message:

 Bump version to 2.27.2 and add genefilter
Package: Rhdf5lib
Commit: 0cbd187f3fef50093f0b5c0385b1d235212e4169
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 17:27:02 +0100
Commit message:

 Bump version
Package: Rhdf5lib
Commit: de7a88a469c00637cf20af90957518b50b2cca3a
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:02:31 +0100
Commit message:

 Test adding secur32 library when LinkingTo from windows
Package: Rhdf5lib
Commit: afb138a0c24f51cc9a5ccbf56259504247b89a00
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:19:20 +0100
Commit message:

 Delete auto-comment GHA workflow
Package: Rhdf5lib
Commit: b051054d68ad90a41e670404ac9d477597e503ef
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:07:26 +0100
Commit message:

 Trigger R-universe workflow manually only
Package: Rhdf5lib
Commit: 467b2aa67c18057c7a77a95e1018d74a9e551f95
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:04:00 +0100
Commit message:

 Add r-universe GHA workflow
Package: biomaRt
Commit: 303163f2bcec77c6ae47380018d03f62fe8c8280
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:34:54 +0100
Commit message:

 Bump version
Package: biomaRt
Commit: 59d0a2dd201937ee40db87cb5c55207ab8bda280
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:34:43 +0100
Commit message:

 Mention user agent in NEWS
Package: biomaRt
Commit: 852be768917bb27b5b5fdfda0c4e5c6c0ae1be60
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:33:34 +0100
Commit message:

 Add user agent to all requests send by biomaRt
Package: biomaRt
Commit: 0e5201f90397e59c66e8c1201822ccbe87708970
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 15:41:04 +0100
Commit message:

 Install tidyverse for lintr workflow

Required for lifecycle_linter()
Package: Hiiragi2013
Commit: 3d9836ce8efa3b5060c47dd87f2b1165f3c78c99
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:48:37 +0100
Commit message:

 Bump version
Package: Hiiragi2013
Commit: 1fe5a102d2445b8f680b98e903cd908a732fad10
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:28:49 +0100
Commit message:

 Use AuthorsR
Package: Hiiragi2013
Commit: 45d04a6aeb40729325003276e1354752887bcf88
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:27:58 +0100
Commit message:

 Mention Depends and NAMESPACE changes in DESCRIPTION
Package: Hiiragi2013
Commit: 3f7fc8dbdf5d1ad5f895784d1394116127c024ee
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:27:31 +0100
Commit message:

 Fix example
Package: Hiiragi2013
Commit: f271677dba5d099fd8737de2134d3dbcd9ce9b50
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 16:20:12 +0100
Commit message:

 Clean up NAMESPACE and move packages to Suggests
Package: Hiiragi2013
Commit: c49554acfe3c6aa9354c1827bcaf13dbb8064a5a
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 15:58:06 +0100
Commit message:

 Fix long lines in Rd
Package: Hiiragi2013
Commit: 1f9794409c24d30bc70d68c5046753353e475622
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 15:50:48 +0100
Commit message:

 Move packages from Depends to Imports
Package: Hiiragi2013
Commit: fd52a703101b8bd881ddb58595ebb678277636b1
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:48:31 +0100
Commit message:

 Add note about data("a") removal in NEWS
Package: Hiiragi2013
Commit: 672ae202502e95381e85cb2a4d95f01dd54cb062
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:53:57 +0100
Commit message:

 Remove references to a in docs
Package: Hiiragi2013
Commit: 7cf542ee63b893a264230a55b2e6b64db0cfd03c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 14:43:08 +0100
Commit message:

 Add more details about why "a" is not included and how to get it
Package: Hiiragi2013
Commit: 0cb68e79e3352f99ff868d07aa9609b961816910
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-03 16:13:58 +0100
Commit message:

 Make vignette section using "a" static
Package: Hiiragi2013
Commit: 9c7742d8867ad032388e4f9274f240ce36849c61
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-02 14:06:44 +0100
Commit message:

 Remove un-normalized data

- All examples in MSMB and all external uses rely on normalized data ("x")
- Files larger than 100 MB cause issues for integration in r-universe
Package: matter
Commit: ab718487bbb6c35bc71e5fde93eb941ae833129c
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2026-03-12 10:48:46 -0400
Commit message:

 v2.13.3 backport DATAPTR support for older R versions
Package: matter
Commit: 0324d6108a9ba3c7fa487dc9f536f873b1844ac4
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2026-03-12 10:41:34 -0400
Commit message:

 Merge pull request #45 from jeroen/devel

Add backport to unbreak build on R-4.5
Package: matter
Commit: fd45c028084312759ea399734f4f1c5cf4075e01
Author: Jeroen Ooms <jeroenooms@gmail.com>
Date: 2026-03-12 13:52:13 +0100
Commit message:

 Add backport to unbreak build on R-4.5
See https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Some-backports
Package: rhdf5
Commit: 193642d3fd5ee8e406fb5d7901066593ca9744db
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 13:54:06 +0100
Commit message:

 Bump version
Package: rhdf5
Commit: c8881d699b4ddb75ca353b019b92e4c583914ca6
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 13:53:15 +0100
Commit message:

 Document HDF5 version update
Package: rhdf5
Commit: 9bfca00c325bb307945ad819c0925a76b4672cde
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 13:52:15 +0100
Commit message:

 Remove use of Remotes
Package: rhdf5
Commit: b3253cd22cd60977d024e694d79e3d77e6cbe21a
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-17 12:17:21 +0100
Commit message:

 Remove H5Pget_version() entirely
Package: rhdf5
Commit: da9d3b3f6841ec2ba314dcab7ff16c4f9106bca2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-08 21:44:56 +1100
Commit message:

 Minor fixes for libver bounds to get tests to pass.
Package: rhdf5
Commit: fbf2a2900d94db6fac145e38a654d8af45f0d861
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-16 14:38:51 +0100
Commit message:

 Remove obsolete reference to version
Package: rhdf5
Commit: 539aa8a5153d09cd4de6a5cbf22a01897dd76e6b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-16 14:32:37 +0100
Commit message:

 Do not use private header to handle file locking

Co-authored-by: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Package: rhdf5
Commit: 57791513b4c3dbfb804897d914b3b139a91c220a
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-16 14:29:15 +0100
Commit message:

 Remove H5I_REFERENCE

Release notes say:

>     - Remove H5I_REFERENCE from the library
>
>      This ID class was never used by the library and has been removed.

https://github.com/HDFGroup/hdf5/blob/9b290ab389b9b560c32e751d0c92f2687a731b8e/release_docs/HISTORY-1_10_0-1_12_0.txt#L252C1-L254C72
Package: rhdf5
Commit: 225eb776bf711ed7b20ade5f3902410b8f76a00a
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-16 14:06:55 +0100
Commit message:

 Test with corresponding PR in Rhdf5lib
Package: rhdf5
Commit: bf8990ee49239d585eca403b48faca6a2137ebc7
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-15 20:23:57 +0100
Commit message:

 Update to HDF5 1.14
Package: rhdf5
Commit: 29bb2970ec8142084270b36dc07567387f69f14d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-15 19:29:20 +0100
Commit message:

 Update to HDF5 1.12

Move to API with token type
Package: cosmosR
Commit: 7f1e6ae16c766c7f494ab2b998ae99ebf22862df
Author: Aurelien Dugourd <dugourd@ebi.ac.uk>
Date: 2026-03-12 14:09:52 +0000
Commit message:

 fix: remove piano from Suggests (not used in any code)

piano is only mentioned in vignette prose but never imported or called.
Its unavailability on the macOS arm64 builder causes CHECK to fail.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Package: cosmosR
Commit: 51143b987b1493581e9dea7032efa6319aa00de2
Author: Aurelien Dugourd <dugourd@ebi.ac.uk>
Date: 2026-03-12 14:07:19 +0000
Commit message:

 fix: correct image path mismatches in MOFA_to_COSMOS vignette

Fix 4 broken image references in MOFA_to_COSMOS.md (hyphen/underscore
mismatches) and update resource_files in Rmd to point to the actual
M2Cf directory instead of non-existent MOFA_to_COSMOS_files.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Package: postNet
Commit: 062c8ad7e693c18f9d665156d0e6a6f327b15176
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-12 13:28:23 +0000
Commit message:

 KS
Package: msPurity
Commit: d893bfbf3df9b4b8250b3c466e9661c36a9fae70
Author: Thomas N Lawson <thomas.nigel.lawson@gmail.com>
Date: 2026-03-12 11:22:31 +0000
Commit message:

 v1.37.3 (patch2) - only tests updated - Add safer way to download library spectra for checking purposes (#112)
Package: Rhdf5lib
Commit: db0cadf32f8c13b88e214e78159f2facd4a10984
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 12:30:07 +0100
Commit message:

 Bump version
Package: Rhdf5lib
Commit: 6d52831a637884460b1c7ab041b0a80fc3824244
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 12:31:21 +0100
Commit message:

 Mention HDF5 version upgrade in NEWS
Package: Rhdf5lib
Commit: 899fb90246f53e0dda4155e3a9ae9064488e5f4d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 11:09:37 +0100
Commit message:

 Test marking libaec build as static
Package: Rhdf5lib
Commit: 2fffb2809e2d54e5c9e0a8bfad4561f6a5d0d54c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 16:39:40 +0100
Commit message:

 Update version number in tests
Package: Rhdf5lib
Commit: ddd024c90a2f8e8caa25311cab29d563b4bc1999
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-06 14:33:08 +0100
Commit message:

 Vendor HDF5 1.14.6
Package: Rhdf5lib
Commit: c12750cc0ae7aaa294849fd74625aedfb0d4f32e
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-06 14:32:49 +0100
Commit message:

 Update download script with HDF5 1.14.6
Package: Rhdf5lib
Commit: c6264f24e4daba08d325a2f5422eb28d08fabe4a
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 09:45:26 +0100
Commit message:

 Add CRAN machines GHA
Package: postNet
Commit: bf218124ce7b510dd937ce9f1035bd61082c75e7
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-12 12:13:29 +0000
Commit message:

 KS
Package: markeR
Commit: 3356098abea266fbe221ca9ae6c491580a29f030
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2026-03-12 12:02:29 +0000
Commit message:

 bump version to 1.1.2
Package: markeR
Commit: 11c0fce0af1bb8ad82d38051c5b96e0361099612
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2026-03-12 11:15:45 +0000
Commit message:

 clean up and fix build after python scripts added
Package: markeR
Commit: d4cc8f5a6aba0d29af7672203039ae5141cfd00c
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2026-03-12 10:48:56 +0000
Commit message:

 clean up python scripts
Package: markeR
Commit: 66ba8b5274ed9f7a1c9ecb9a16a212d22c886b5a
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2026-03-12 10:20:07 +0000
Commit message:

 move python scripts to main folder
Package: rhdf5
Commit: b8ed1d7c91b473b50f56d83335242b4ea5db982d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-11 13:26:58 +0100
Commit message:

 Use memcpy() instead of loop to copy string buffer
Package: rhdf5
Commit: 4f7a45443450a0eeb49a337602d2890f8d5f0c0f
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-11 11:07:28 +0100
Commit message:

 Remove unused variable initialization
Package: postNet
Commit: e630a050b5d6ea30a3d44e3a6c8492a8accd720e
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-12 10:43:36 +0000
Commit message:

 KS
Package: PRONE
Commit: 21d27fa7ca5321c6f33163d3490f70dbb2970078
Author: lisiarend <lisiarend@me.com>
Date: 2026-03-12 09:17:45 +0100
Commit message:

 merged with devel bioconductor
Package: PRONE
Commit: 2cc6368833e5cc8833c61b537812b524c504667f
Author: lisiarend <lisiarend@me.com>
Date: 2026-03-12 09:15:06 +0100
Commit message:

 version bump
Package: PRONE
Commit: b63074cb505fb111c9236470990053cd509f1ece
Author: lisiarend <lisiarend@me.com>
Date: 2026-03-12 09:07:35 +0100
Commit message:

 merge with release_3_22 bioconductor
Package: PRONE
Commit: 524efdafc1572b3d059cf02d8d8d6e06cf3ed7be
Author: lisiarend <lisiarend@me.com>
Date: 2026-03-12 09:01:56 +0100
Commit message:

 version bump
Package: PRONE
Commit: 8d0a51367dd020a7964023c9514fe64eaccc7668
Author: Arend Lis <55484713+lisiarend@users.noreply.github.com>
Date: 2026-03-12 08:58:51 +0100
Commit message:

 Merge pull request #12 from daisybio/main

Merge pull request #11 from daisybio/RELEASE_3_22
Package: PRONE
Commit: 4cb766caeb22e372288b7696af266032962e5854
Author: Arend Lis <55484713+lisiarend@users.noreply.github.com>
Date: 2026-03-12 08:57:40 +0100
Commit message:

 Merge pull request #11 from daisybio/RELEASE_3_22

Release 3 22
Package: PRONE
Commit: 8bb6306d14c7637ba60a8c9281d299b38e387cde
Author: lisiarend <lisiarend@me.com>
Date: 2026-03-12 08:56:36 +0100
Commit message:

 summarise_each of dplyr removed
Package: igblastr
Commit: 3b64e3811fa026563771b5dda97a0157977ad15a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-03-11 18:43:25 -0700
Commit message:

 igblastr 1.1.23

Rename the following functions:
  compute_imgt_intdata -> compute_V_gene_delineations
  read_V_ndm_data -> read_ndm_data
  write_V_ndm_data -> write_ndm_data
  check_V_ndm_data -> validate_ndm_rows
Package: ExpoRiskR
Commit: 7152b0def815211f34423eeaca9a842a6ee6877f
Author: ppchaudhary <luckypgi@gmail.com>
Date: 2026-03-11 20:51:21 -0400
Commit message:

 Fix NEWS parsing and bump version to 0.99.4
Package: ExpoRiskR
Commit: f0457e6dcd5fb7cc16e5b3c5493b8d4fc85c01f8
Author: ppchaudhary <luckypgi@gmail.com>
Date: 2026-03-11 20:36:10 -0400
Commit message:

 Bump version to 0.99.3 for Bioconductor rebuild
Package: ExpoRiskR
Commit: 122094794484d93775b9ecd7937b641862aae53d
Author: ppchaudhary <luckypgi@gmail.com>
Date: 2026-03-02 00:21:08 -0500
Commit message:

 Add tests and finalize vignette/README for Bioconductor review
Package: postNet
Commit: 5b391a2dfbf47b9a61dd597dce344d067621c524
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-12 00:33:01 +0000
Commit message:

 KS
Package: hpAnnot
Commit: 6129fc8bee017a4eaf17652941003e043e2a1c39
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-12 01:25:30 +0100
Commit message:

 bumping to version 1.1.2
Package: hpAnnot
Commit: 1c540c75749369895b04550d6e826e6ae5081f58
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-12 01:24:06 +0100
Commit message:

 adding v3 files
Package: hpAnnot
Commit: 572b5fc385651de7b3ab8c3f1548c14b40b96916
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-12 01:09:33 +0100
Commit message:

 changing DESCRIPTION and make-metadata.R files
Package: OSTA
Commit: 51af4cbd498adcc52b81b9675a82b8c2510e54ca
Author: Lukas Weber <8062417+lmweber@users.noreply.github.com>
Date: 2026-03-11 19:48:25 -0400
Commit message:

 version and date
Package: OSTA
Commit: 8558f61062c3df60b794722d05a24c0ba17b98a5
Author: Lukas Weber <8062417+lmweber@users.noreply.github.com>
Date: 2026-03-11 13:48:55 -0400
Commit message:

 update max cores for Harmony
Package: Rarr
Commit: d9f9b5a3df36e1842ab6c062d4d4e93b26e16d9a
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-11 23:55:46 +0100
Commit message:

 Bump version
Package: Rarr
Commit: 04bc1910fa1b2ed374ff983d4fe2f20db73211e0
Author: Jeroen Ooms <jeroenooms@gmail.com>
Date: 2026-03-11 22:03:19 +0100
Commit message:

 Fix build on R < 4.6
Package: postNet
Commit: 05c2ca4baf15c1d2adb541200ea574edcc0e6f5e
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-11 21:45:16 +0000
Commit message:

 KS
Package: tidyexposomics
Commit: 4ac49a596ebc6c60bbb0ccca6be44270851c18b3
Author: BioNomad <jlaird1@binghamton.edu>
Date: 2026-03-11 17:20:56 -0400
Commit message:

 association function fix
Package: VERSO
Commit: abde52586fd06b13ac821ee96b2bc1110afdc8c9
Author: DavideMaspero <d.maspero@campus.unimib.it>
Date: 2026-03-11 21:58:24 +0100
Commit message:

 Update DESCRIPTION
Package: LACE
Commit: 1ce1000e46bb9e84f42a0fbd118f24601e0e35bd
Author: DavideMaspero <d.maspero@campus.unimib.it>
Date: 2026-03-11 21:56:58 +0100
Commit message:

 Update DESCRIPTION
Package: lncRna
Commit: cc94632896c5dd1a518bbf2d224b3e45168dd227
Author: Dragon96pl <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-03-11 20:49:43 +0100
Commit message:

 Fix

Co-Authored-By: prodakt <bioinformatyka@gmail.com>
Package: lncRna
Commit: 594baa2b4a5ec4387595a4e2e12adbb0dd5bcb7a
Author: Dragon96pl <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-03-11 20:44:26 +0100
Commit message:

 Fix

Co-Authored-By: prodakt <bioinformatyka@gmail.com>
Package: lncRna
Commit: 6feee83245d4f102928a6696ea1deb97a5d2b64a
Author: Dragon96pl <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-03-11 20:41:59 +0100
Commit message:

 Fix error

Co-Authored-By: prodakt <bioinformatyka@gmail.com>
Package: lncRna
Commit: 5063a4e111e7147f58df088e010291293e722563
Author: Damian Czopek <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-03-11 15:47:45 +0100
Commit message:

 DESCRIPTION update
Package: lncRna
Commit: c23609b5a8244a78a199f17b9c84880c43c8679f
Author: Damian Czopek <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-03-11 15:41:57 +0100
Commit message:

 Update README.md
Package: lncRna
Commit: be3a5074195d0a5ef7e87b8a984a9dda1db90885
Author: Dragon96pl <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-03-11 15:39:18 +0100
Commit message:

 Update utils.R

Co-Authored-By: prodakt <bioinformatyka@gmail.com>
Package: lncRna
Commit: dc4ac32762bcecee3a8d27fe6a9ad2a370ca7955
Author: Dragon96pl <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-03-11 15:30:16 +0100
Commit message:

 Bioconductor 0.99.3 review changes

* Implemented comprehensive unit tests reaching >80% package coverage.

* Optimized confusion matrix calculations and performance evaluation pipeline.

* Added accessibility-friendly color palettes (Okabe-Ito) for all visualization functions.

* Merged recent feature updates and refactors into the main branch via Pull Request.

Co-Authored-By: prodakt <bioinformatyka@gmail.com>
Package: lncRna
Commit: 6ba0501f5371b10722cca0b97a2bf2328ad9b6d0
Author: Damian Czopek <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-03-11 12:27:19 +0100
Commit message:

 Merge pull request #1 from Bisaloo/bioc-review

Small fixes related to Bioconductor review
Package: lncRna
Commit: ae80435b44884ead0f3ffa0f6bac33b157c7035c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-05 16:02:16 +0100
Commit message:

 Simplify col_to_filter construction
Package: lncRna
Commit: 0c91baf82254fbf8761cf64efc7949ad6c5e608e
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-05 16:01:57 +0100
Commit message:

 Mark regex as fixed for better performance
Package: lncRna
Commit: 54d8772a4d2aeccc64995d70c47142a1f3a8d463
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-05 16:01:39 +0100
Commit message:

 Use dedicated lengths() function instead of vapply()
Package: lncRna
Commit: 9705080a152887560af3fa27fd1bf7e32401c502
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-05 16:01:17 +0100
Commit message:

 Rely on arguments defaults in match.arg()
Package: lncRna
Commit: a8325b36a0f6729d8bbee76b11996207d2079f85
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-05 14:19:10 +0100
Commit message:

 Add package man page
Package: lncRna
Commit: a1101b4ca9e7d79d93e5ca247181d7c7c4b6b836
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-18 17:36:09 +0100
Commit message:

 Fix NEWS.md section format
Package: lncRna
Commit: f1c4e426476c70702b411c9edb01769b55d3856f
Author: Damian Czopek <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-02-05 13:16:32 +0100
Commit message:

 Fix image links in README for venn diagrams

Updated image links in README to point to the correct directory.
Package: lncRna
Commit: 7b2d7d3eef739633f7f1ba76b353f9386e616137
Author: Damian Czopek <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-02-05 13:09:06 +0100
Commit message:

 Update logo image path in README.md
Package: matter
Commit: c2629bdf45d7752629bd9079cdc59be4e27e4ed6
Author: Kylie A. Bemis <k.bemis@northeastern.edu>
Date: 2026-03-11 16:02:31 -0400
Commit message:

 v2.13.2 remove DATAPTR() usage
Package: matter
Commit: d1ba794e628c2dfc621dd0a4b9e38c4a51e8d657
Author: Kylie A. Bemis <k.bemis@northeastern.edu>
Date: 2026-02-18 14:34:26 -0500
Commit message:

 v2.13.1 add args to chunk_mapply() and chunked_list()
Package: matter
Commit: f3d5051d2ab5b329c3cc66deeaafcb61a122c043
Author: Kylie A. Bemis <k.bemis@northeastern.edu>
Date: 2026-02-18 14:30:43 -0500
Commit message:

 add xlist to chunked_list and XS to chunk_mapply
Package: postNet
Commit: a0c28db217ae82592124abe0308e3aef4b857741
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-11 19:06:17 +0000
Commit message:

 KS
Package: postNet
Commit: 4babab615d4e0d3cfe89c807b631d082170b6bab
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-11 19:04:26 +0000
Commit message:

 KS
Package: ROC
Commit: 993d4a1a2dce084f51058308d62683aba74ac1ff
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2026-03-11 14:26:12 -0400
Commit message:

 Bump version to 1.87.2 and add URLs

Updated version number and added repository URLs.
Package: MSstatsBioNet
Commit: a5e9c4d41741e4457d878474ae2c64ebe653a947
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-03-11 14:23:19 -0400
Commit message:

 Bump version from 1.3.4 to 1.3.5
Package: MSstatsBioNet
Commit: 8123bd77d3053b807580a9d824d5f2a3dedf74e2
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-03-11 14:22:48 -0400
Commit message:

 feature(filter-subnetwork): Add feature to filter the subnetwork from INDRA by query context (#84)
Package: Voyager
Commit: 417ad22ff407d1f359c7d4f8d365d2e9100fe4dc
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2026-03-11 14:22:44 -0400
Commit message:

 Remember that biscale is suggested not imported
Package: MSstatsShiny
Commit: d3fab9518912ea81d36ef517a7fa60ac191b3f1b
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2026-03-11 14:12:01 -0400
Commit message:

 Update package version to 1.13.3

Bump version from 1.13.2 to 1.13.3
Package: MSstatsShiny
Commit: f955d16c64c72aa771d3f324aae1363b4d09343a
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2026-03-11 11:36:39 -0400
Commit message:

 feat(advanced-options): Set up advanced options panel for subnetwork search (#178)
Package: MSstatsShiny
Commit: e3b9fa2ffd71ad0e85322c2a1d0567b400016424
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2026-03-11 11:36:20 -0400
Commit message:

 docs(ptm): Fix documentation regarding MSstatsPTM groupComparisonPTM (#177)
Package: MSstatsShiny
Commit: 491b4db0831d57a17ede756042a723f41332d0e0
Author: Swaraj Patil <patil.swaraj@northeastern.edu>
Date: 2026-03-09 10:10:39 -0400
Commit message:

 feat(response-curves): download dose response curve plots (#174)
Package: MSstatsShiny
Commit: 520b3e4cfef6cefa303479cd48141ef88d2eb270
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2026-03-05 14:22:16 -0500
Commit message:

 feature(network-visualization): Add button to export HTML from Shiny (#176)
Package: goatea
Commit: b757c3aa130c61eb6342d00cb90b2bc2654ba1a2
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-11 19:00:04 +0100
Commit message:

 resolve merge conflict, bump version
Package: goatea
Commit: b0e2d0b8e70a2205ce6d19260119568bfe447222
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-11 18:57:32 +0100
Commit message:

 Merge branch 'main' of https://github.com/mauritsunkel/goatea
Package: goatea
Commit: 591c7f6412a1e7fa8b9bb8050e2a5c41cb2a44ee
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-11 18:57:10 +0100
Commit message:

 Updated DOSE::setReadable to clusterProfiler::setReadable as Bioc 3.23 DOSE does not export setReadable anymore
Package: goatea
Commit: abe80ca0ad767bc6c3f1e3a4c13519545b0d3fa9
Author: GitHub Actions <actions@github.com>
Date: 2026-03-09 14:58:57 +0000
Commit message:

 Update Bioconductor download stats
Package: goatea
Commit: 4091ad99a35f6d243bc0c9952ee68ce7f612ee3f
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 15:52:45 +0100
Commit message:

 Updated badge colors
Package: goatea
Commit: 333410e727501087f87d84c9e79d0c5ec513edbe
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 15:48:19 +0100
Commit message:

 Merge branch 'main' of https://github.com/mauritsunkel/goatea
Package: goatea
Commit: 9357b0f3833bc6694285d4fdfe40c3df8095c6ab
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 15:48:08 +0100
Commit message:

 Updated workflows
Package: goatea
Commit: 7d6caea43e91b72d87e52f3e6617284c30eb9ea1
Author: Mauws <47570265+mauritsunkel@users.noreply.github.com>
Date: 2026-03-09 15:45:37 +0100
Commit message:

 Fix badge link formatting in README.md
Package: goatea
Commit: 1b92899d7a912e0851c3333878a0d9edb576b6ed
Author: GitHub Actions <actions@github.com>
Date: 2026-03-09 13:26:27 +0000
Commit message:

 Update Bioconductor download stats
Package: goatea
Commit: ad5f42c478de14145dd11e5ad3c8cc49d3b38583
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 14:20:46 +0100
Commit message:

 Fixing downloads badge
Package: goatea
Commit: d8253c6d8a378d8b0a47746d3fc95606affd1b19
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 14:10:06 +0100
Commit message:

 Added data.table to DESCRIPTION, updated badge gh action workflow
Package: goatea
Commit: 3fb745767274baa5a12b32af17da054440de55f4
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 13:54:13 +0100
Commit message:

 Fixed example data, package imports, termtree example, updated vignettes
Package: goatea
Commit: 91cd6d4776186975ee4d712168b6bb9fd55054f4
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 13:18:20 +0100
Commit message:

 Updated and fixed vignettes for pkgdown docs, fixed GitHub Actions workflows
Package: goatea
Commit: 0cbce5012b9ad396301443c9c354d66ef0813d65
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 09:48:27 +0100
Commit message:

 Fixed bugs in plotting termtree and updated its docs, upgraded reading and validating genelists with automated .csv separator reading, minor fixes and code clarity updates
Package: goatea
Commit: 4a2509b6589403c8ed3e0c53a22775b9d8d4b3d8
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 09:46:55 +0100
Commit message:

 Added Docker files, accessible example data, pkgdown docs with new vignette and GitHub Action workflows
Package: goatea
Commit: f506568bfc8d999bdc7a2bd92a279f3cb8275081
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 09:39:29 +0100
Commit message:

 Updates for Bioc devel 3.23
Package: postNet
Commit: 5475a69533240f459981e3d04196212b7bab9ff6
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-11 17:37:26 +0000
Commit message:

 KS
Package: markeR
Commit: 6baef37eadcb8ecaea5e8caa83b8122db27da822
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2026-03-11 17:15:15 +0000
Commit message:

 Update README.md
Package: markeR
Commit: c9f63e5f40ab3ec079d08c662f99a73b28f8c703
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2026-03-11 17:09:43 +0000
Commit message:

 new version 1.1.1
Package: markeR
Commit: f33d137414bc6cf48485778200a6e03fb2a8cc1d
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2026-03-11 16:45:14 +0000
Commit message:

 new parameter p.adjust.method
Package: markeR
Commit: a9025cf42b33e7f1cd67b65084451b5eb3aa9fed
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2026-03-11 13:08:30 +0000
Commit message:

 add python
Package: markeR
Commit: 525b29dcfd3d79d46ebdb78202d1e9b48b1f50c8
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-10-31 09:53:17 +0000
Commit message:

 update version in readme file
Package: ROC
Commit: 8daa67f9adbead65274d280305f602cdfed746fb
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-03-11 13:13:57 -0400
Commit message:

 changing version
Package: igblastr
Commit: addeb4c67ed70a7e7e71a0d4310ea9ce0dd2369a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-03-11 09:14:50 -0700
Commit message:

 Display OGRDB citation information

Display OGRDB citation information when selecting OGRDB germline db
and in man pages for download_OGRDB_germline_sequences() and
download_OGRDB_germline_json().
Package: msPurity
Commit: 29955da4968d5ba2c0d761c098de96a1cd10cad5
Author: Thomas N Lawson <thomas.nigel.lawson@gmail.com>
Date: 2026-03-11 14:22:32 +0000
Commit message:

 1.37.3 (patch) - Update tests for createDatabase for CI/CD
Package: msPurity
Commit: 0a05477435b52d565a1391714c735567417c3ee2
Author: Thomas N Lawson <thomas.nigel.lawson@gmail.com>
Date: 2026-03-10 13:09:24 +0000
Commit message:

 v1.37.3 - update for tests only - library database path for library vs library spectral matching test updated (#110)

* Update library database path for lvl spectral matching test

* Bump version from 1.37.2 to 1.37.3

* Update readme

* Change package date in DESCRIPTION file

Updated the package date from 2025-02-19 to 2025-03-10.

* Update NEWS with clarification on database path change
Package: msPurity
Commit: 808690c8da9531466fc3d32d5b8509cfe60f1be9
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2026-02-26 14:40:55 +0000
Commit message:

 v1.37.2 - fix subsetting of grouped data frame (#109)

* Fix subsetting of grouped data frame

The `grpid` column in `pa@grped_df` is an integer factor.
The comparison `pa@grped_df$grpid==as.numeric(grp_idx)` fails when `grp_idx`
is 100000 because `as.numeric` returns type `double`.

`pa@grped_df$grpid == 100000` returns `FALSE` for all items even if 100000 is present.
`pa@grped_df$grpid == 100000L` returns `TRUE` for items that are 100000.

* v1.31.1 - updates following removal of library spectra from msPurityData package (too large for Bioconductor) (#108)

* Use zenodo reference to library spectra

* Update CI/CD

* troubleshoot vignette build issue

* Troubleshooting cache on github workflows

* Troubleshooting cache for github workflows

* more troubleshooting GH workflow cache

* Bump version and add entry to NEWS

* Fix email of contributor

---------

Co-authored-by: Thomas N Lawson <thomas.nigel.lawson@gmail.com>
Package: MSstatsBioNet
Commit: f02d61de14e9a884e1107e680fad5c7d5c083a17
Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Date: 2026-03-11 11:25:17 -0400
Commit message:

 docs: Weekly AI README upgrade — Contributing & Development Setup (#83)
Package: MSstatsBioNet
Commit: 734969f21a36e5887b1d2c04bb25a733da06c0dd
Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Date: 2026-03-11 11:15:02 -0400
Commit message:

 docs: Weekly AI doc upgrade for `previewNetworkInBrowser` (#82)
Package: MSstatsBioNet
Commit: 2d6546d7099ef72b38bad648f41c4ec615091a38
Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Date: 2026-03-11 11:12:45 -0400
Commit message:

 docs: Weekly AI doc upgrade for `renderCytoscapeNetwork` (#74)
Package: postNet
Commit: de681a53e65f223cab9cd1e7c8b0d28327aff0dd
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-11 13:01:01 +0000
Commit message:

 KS
Package: scRNAseqApp
Commit: dfe1dae5f21084380222a6e8beecd7460159e3e4
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-03-11 08:50:34 -0400
Commit message:

 Add 'download' button for webstats.
Package: hpAnnot
Commit: 9bcb785f74a13b6f8c49c3a8ea049671407a9c36
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-11 13:16:01 +0100
Commit message:

 changing version to v3 in upload_files_to_S3
Package: postNet
Commit: c94e854942cf2dc7ff30f74d0a31723b39ff5146
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-11 11:40:53 +0000
Commit message:

 KS
Package: Spectra
Commit: 4f4022e71073d9f7df85af8bf4722df0147843d1
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-03-11 11:54:07 +0100
Commit message:

 Merge pull request #380 from rformassspectrometry/jomain

refactor: improve matched peak reporting by compareSpectra
Package: Spectra
Commit: 1d2ab5a459ff3f1cef90c0f39b6097b484f49dbe
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-11 08:21:12 +0100
Commit message:

 refactor: improve matched peak reporting by compareSpectra

- `compareSpectra()` now relies on the similarity function to report the number
  of matched peaks on which the similarity score was calculated (instead of
  calculating it based on the results of `MAPFUN`). This has the advantage that
  correct matched peak counts are reported by e.g. the modified
  cosine (`gnps()`) similarity calculation. Issue #350.
Package: PhyloProfile
Commit: d8059e2479736f587ec6ec1a64f9bbe977b80484
Author: trvinh <trvinh@gmail.com>
Date: 2026-03-11 11:35:33 +0100
Commit message:

 append taxa from newTaxa.txt to currentNCBIinfo
Package: CalibraCurve
Commit: 5fe36d75ac0cb1e78bffe12740c96ad1e96ac5a2
Author: Karin Schork <schorkka@mpc-domain.local>
Date: 2026-03-11 10:20:54 +0100
Commit message:

 increase version number
Package: CalibraCurve
Commit: cd54c7bd8bfa71d6373ddeaf31a3dc8fde90e293
Author: KarinSchork <karin.schork@rub.de>
Date: 2026-03-09 13:04:53 +0100
Commit message:

 fix build warnings
Package: imageTCGAutils
Commit: e0335d8fbc1e60bb91c23156109f1a9e55d25b20
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-03-11 10:12:40 +0100
Commit message:

 version bump 0.99.18
Package: rhdf5
Commit: bed579a22401f496ddae82f51f8295c2b6874fbf
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 11:31:28 +0100
Commit message:

 Use scalar instead of vector of length 1
Package: rhdf5
Commit: 849f31a3b4b2709caa13306665aead6f42a6c963
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 10:45:09 +0100
Commit message:

 Use R_NamesSymbol to get names attribute
Package: wavFeatExt
Commit: 5d908c669fc116df77a7afd7c8dbce3a02432f99
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 14:34:09 +0700
Commit message:

 Rebuild after server issue
Package: CSOA
Commit: 0485b36f906759ed8e5ccd731101ed37d7ab210f
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-03-11 15:07:51 +0800
Commit message:

 Bumped version number
Package: CSOA
Commit: a5fdceea417473f367c09310b688cbbcc484dacc
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-03-11 15:07:19 +0800
Commit message:

 Removed extra file
Package: wavFeatExt
Commit: 438a89e5f72eba765d84cb842b6e69e9a6ae37bf
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 13:50:27 +0700
Commit message:

 Fix Error"
Package: CSOA
Commit: 4d07170fc2910a7f7a5713a19af1d3b1ebc23e76
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-03-11 14:39:30 +0800
Commit message:

 Bumped version
Package: CSOA
Commit: 6a4766e5de2cf1c99e5384b072c8e4af092bc70b
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-03-11 14:38:47 +0800
Commit message:

 Replaced .qs with .qs2
Package: igblastr
Commit: 196798dede2b93ece923eb01a659b4f5f7168ab4
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-03-10 23:27:48 -0700
Commit message:

 igblastr 1.1.22: Add download_OGRDB_germline_json()
Package: wavFeatExt
Commit: 9eb991492e8eb020170acfa8c581aa46ef19b76b
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 13:16:10 +0700
Commit message:

 Fix Error"
Package: wavFeatExt
Commit: 85963ce681bced4098191355cea7bd45fe8794dc
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 12:48:37 +0700
Commit message:

 Fix time out
Package: wavFeatExt
Commit: bc26d6f4ce056dedbbfff6042f329c56c4e3a13d
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 12:40:55 +0700
Commit message:

 Remove Rproj file from repository
Package: wavFeatExt
Commit: e814a4a9303dfdea00b3e525cb85fea6a2c22ed5
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 10:40:44 +0700
Commit message:

 Fix CBS error causing vignette build failure
Package: wavFeatExt
Commit: a12afa43306189fa17e1ec01d600015629542cae
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 10:31:11 +0700
Commit message:

 Fix BiocCheck issues
Package: wavFeatExt
Commit: 32847d681e7143bade8cb9cc4e21b409ed07a7f0
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 09:51:10 +0700
Commit message:

 Fix CBS error causing vignette build failure
Package: wavFeatExt
Commit: 36b364f5678553cf7e7baaf2993a666fe19d4311
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 09:50:09 +0700
Commit message:

 Fix CBS error causing vignette build failure
Package: wavFeatExt
Commit: 81fb6418f58e8b4709c04714af332d7338e6bb28
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 09:46:31 +0700
Commit message:

 Fix CBS error causing vignette build failure
Package: wavFeatExt
Commit: 532f9314da964691d13b8dfe9cca7973e9f8c4a2
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-11 09:36:39 +0700
Commit message:

 Fix BiocCheck issues
Package: wavFeatExt
Commit: 1fce02ba6d5a0d50edd0165d3881826b9e5fc838
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-10 15:49:11 +0700
Commit message:

 Fix BiocCheck errors and vignette
Package: wavFeatExt
Commit: 6a7ecf04da0452440698e863fd212a424c74be85
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-10 15:06:19 +0700
Commit message:

 Revision 3
Package: wavFeatExt
Commit: f6df713f78874849a0e720530f94e77de291b7c0
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-03-07 11:45:11 +0700
Commit message:

 Remove Rproj file from repository
Package: signatureSearch
Commit: 34f134f3e034487d019a91310459fbbeb65c4ab1
Author: brendangongol <brengong@gmail.com>
Date: 2026-03-10 19:27:27 -0700
Commit message:

 Merge branch 'devel' of https://github.com/girke-lab/signatureSearch into devel
Package: signatureSearch
Commit: e38fd16b988357ae5fc9509ae1d55bb11cea98e7
Author: brendangongol <brengong@gmail.com>
Date: 2026-03-10 19:26:22 -0700
Commit message:

 Addressing warning message
Package: OSTA
Commit: 6178784f982c9179989981aad0496e2130582722
Author: Lukas Weber <8062417+lmweber@users.noreply.github.com>
Date: 2026-03-10 18:32:50 -0400
Commit message:

 max cores for GHA
Package: OSTA
Commit: 09dbb4b2cada0e52e67ef42d8b9460b03ea418d9
Author: Lukas Weber <8062417+lmweber@users.noreply.github.com>
Date: 2026-03-10 16:40:04 -0400
Commit message:

 version and date
Package: OSTA
Commit: 6f7f9415d9e0d61dc3044439f86d238751d06404
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-10 20:56:40 +0100
Commit message:

 hide Python-related messages/warnings
Package: OSTA
Commit: 869cdf6a0f15f4972874ccfb0ca25b043c287937
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-10 20:50:27 +0100
Commit message:

 add BPPARAM flags; fix normalization
Package: SeqArray
Commit: c8e23317879b2e6a667a898a79bf90cc42c6edc3
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-03-10 19:22:21 -0500
Commit message:

 Reduce memory usage in seqParallel
Package: leapR
Commit: 96e17547a870155000e8170ecf065c1c61b89ce3
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-03-10 15:30:09 -0700
Commit message:

 removed docs from this branch, then updated
Package: leapR
Commit: cf251ca76940ff93207e55096d7853fccea99433
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-11 10:45:32 -0800
Commit message:

 add pkgdown
Package: leapR
Commit: a0cc189c1312b3a7e1f3ae4596b137e9a3768374
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-11 09:43:59 -0800
Commit message:

 test for gh pages
Package: leapR
Commit: 9886616e51d38541847032e0853ac1528c864c63
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-06 14:22:42 -0800
Commit message:

 Merge pull request #65 from pnnl/round2-bioc-updates

Round2 bioc updates
Package: leapR
Commit: 6c5908ddf5dd6390eaf0310ed8ed7d70ec3f35ad
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-06 13:58:41 -0800
Commit message:

 added depenency
Package: leapR
Commit: d898b9fb475215eaaa63a4e354cf97bbacae208b
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-06 13:27:39 -0800
Commit message:

 Updated with new vignette and z test
Package: leapR
Commit: 7e2f95c39dc9a4efd9024673dc09b272411edacb
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-05 15:32:28 -0800
Commit message:

 additional statistics added to leapR

These still require debug/testing here.
Package: leapR
Commit: 79c59df3449b9e700fdc518de50ce790ca29f21c
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-01-25 12:00:06 -0800
Commit message:

 Merge pull request #63 from pnnl/feat/forge-catalog

add catalog-info.yaml file for forge catalog
Package: leapR
Commit: 63eaeb24f0869349c31eb7605a79a69728318ac3
Author: pham259 <jennifer.pham@pnnl.gov>
Date: 2026-01-23 13:48:15 -0800
Commit message:

 add catalog-info.yaml file for forge catalog
Package: leapR
Commit: dfca7ddd48607a0ca925f9788884754a109d8e8a
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-02 11:47:56 -0800
Commit message:

 Merge pull request #60 from jjacobson95/data_visualization_update

looks great! will merge, and then close the other two PR s :)
Package: leapR
Commit: 6160c281415b7dcb32750b84499e7213091f6e24
Author: Jeremy <jeremy.jacobson3402@gmail.com>
Date: 2025-11-28 13:04:25 -0800
Commit message:

 Incremented the version. Added plotting throughout the vignette. Clarified a couple things in the vignette. Added a data inspection chunk
Package: leapR
Commit: 3e8f09f78d7cd98f6f108056723f5eb5d608ee0b
Author: Jeremy <jeremy.jacobson3402@gmail.com>
Date: 2025-11-28 13:04:01 -0800
Commit message:

 Incremented the version. Added plotting throughout the vignette. Clarified a couple things in the vignette. Added a data inspection chunk
Package: leapR
Commit: 32bdccb8cfb0b7df9e288f0f4fb83b941401ca19
Author: Jeremy Jacobson <85139244+jjacobson95@users.noreply.github.com>
Date: 2025-11-10 12:52:29 -0800
Commit message:

 small vignette modification
Package: leapR
Commit: 5722f73998de7d86f115f5e65ad38286a35f6d9c
Author: Jeremy <jeremy.jacobson3402@gmail.com>
Date: 2025-11-10 11:15:48 -0800
Commit message:

 Added barplot function. Addtions to code, test, vignette, and autogenerated roxygen2 files
Package: leapR
Commit: 9fd00ceb5ed633af5668c20a43195af88508a93f
Author: Jeremy <jeremy.jacobson3402@gmail.com>
Date: 2025-11-10 10:44:13 -0800
Commit message:

 Added barplot function. Addtions to code, test, vignette, and autogenerated roxygen2 files
Package: spammR
Commit: afdee1247f790d069c79c300ce60a9913592bb01
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-03-10 15:11:23 -0700
Commit message:

 Merge branch 'bioc-resub' of https://github.com/PNNL-CompBio/spammR into bioc-resub
Package: spammR
Commit: 9b7b3c25606700e47600c13910c632a67d5cdc66
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-03-10 14:45:59 -0700
Commit message:

 added package level documentation
Package: spammR
Commit: 03679afa1cc7d7ebfdaefb02ac03efd30b1f2f12
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-03-10 14:34:45 -0700
Commit message:

 added changes required for bioC submission
Package: spammR
Commit: 2d3ece9172493d475204887d0270b639cec3b5b1
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-02-16 12:40:33 -0800
Commit message:

 fix to SampMin imputation

Imputation value writing was handled row by row in the proteomics data, which was incompatible with how Sample Minimum imputation data is calculated. Fixed imputed value assignment method for SampMin to fix that problem.
Package: spammR
Commit: 07662dd0d21d70dc2992863ebac5178ac25816af
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-16 15:22:03 -0800
Commit message:

 added more to vignette
Package: spammR
Commit: f313808e27dbac648bf3cf398c162f630a939d2c
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-07 20:07:30 -0800
Commit message:

 updated documentation
Package: spammR
Commit: cd86d324d69ab2d522d5133572e28e3102c41e5d
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-06 13:33:51 -0800
Commit message:

 updated gradient test with z test
Package: spammR
Commit: c69c6f80fcecf18d3391beb8f98bfe2d6399bd1d
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-05 08:13:03 -0800
Commit message:

 Added new readme and github actions to build
Package: spammR
Commit: 28bb706dfbf0885099f02099a1c0c3e9a1b22a87
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-02-03 11:40:41 -0800
Commit message:

 fixed typos & changed KO differential expression and Pathway enrichment analysis after fixes to calc_spatial_diff_ex.R
Package: spammR
Commit: 260769ca509601a707368ef6d42d2a7717fce601
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-02-02 14:38:11 -0800
Commit message:

 added additional check to log transformation of data to ensure that log transformation only happens for non count based data
Package: spammR
Commit: e3ff78979ab303cced90fcba8bd503a675d91d88
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-01-29 10:36:29 -0800
Commit message:

 added `sort.by = "none"` to `limma::topTable()` call in `calc_spatial_diff_ex.R` such differential expression results and SPE gene list are in the same order for merging. Also clarified comment in code explaining why we don't sort.
Package: spammR
Commit: 8a38d0f7279d472cfa853c6dd9099f10dbc7c7db
Author: pham259 <jennifer.pham@pnnl.gov>
Date: 2026-01-26 12:13:09 -0800
Commit message:

 add catalog-info.yaml file for forge catalog
Package: spammR
Commit: e41d1bc04021542a95da62c7a7fb7a4ff6de3845
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-01-22 14:15:17 -0800
Commit message:

 renamed imputation method from 'sampMin' to 'samp_min' to align with style guide and updated function doc string
Package: spammR
Commit: 5f9dfc119883b6d43ccc50ac04cb173ac248081d
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-01-19 10:45:48 -0800
Commit message:

 add sampMin (sampleMinimum) to imputation methods
Package: spammR
Commit: 541217e0f37256d8c5710b2d5405af39c7492b00
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-03-10 14:45:59 -0700
Commit message:

 added package level documentation
Package: spammR
Commit: 0ed97d973e84c589bf360e927d67642329fe8e94
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-03-10 14:34:45 -0700
Commit message:

 added changes required for bioC submission
Package: spammR
Commit: 4a34a4ccf9793d7754de0690cee7b00a145d3148
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-16 15:22:06 -0800
Commit message:

 Merge branch 'main' of https://github.com/PNNL-CompBio/spammR
Package: spammR
Commit: 4579c61b5015fc0df98becea4c82ee0689c51b8f
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-16 15:22:03 -0800
Commit message:

 added more to vignette
Package: spammR
Commit: 1b57682638568ffd35c4b92187706cfd0d18d8a5
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-16 12:49:56 -0800
Commit message:

 Merge pull request #83 from PNNL-CompBio/sample_min_fix

fix to SampMin imputation
Package: spammR
Commit: d0e6df38e540cdf15ef05e0f6f397a74ce3a1e3a
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-02-16 12:40:33 -0800
Commit message:

 fix to SampMin imputation

Imputation value writing was handled row by row in the proteomics data, which was incompatible with how Sample Minimum imputation data is calculated. Fixed imputed value assignment method for SampMin to fix that problem.
Package: spammR
Commit: 337815e378c48a7503ddd177d993e326f1c6af6c
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-07 20:07:30 -0800
Commit message:

 updated documentation
Package: spammR
Commit: fb66c4520d5ea799952bfd5a43a8688837debbc7
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-06 13:33:51 -0800
Commit message:

 updated gradient test with z test
Package: spammR
Commit: a4a29ca50c52b822df061a1c1b93175671c6ed91
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-05 08:13:03 -0800
Commit message:

 Added new readme and github actions to build
Package: spammR
Commit: 8502eacdae7a0667c1138bc5ef4cca7a81a7d22f
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-03 12:10:55 -0800
Commit message:

 Merge pull request #81 from PNNL-CompBio/spatMicrobiome_fixes

spatMicrobiome fixes
Package: spammR
Commit: c57f420c2757d8aeb655b85d69358e4862541fe7
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-02-03 11:40:41 -0800
Commit message:

 fixed typos & changed KO differential expression and Pathway enrichment analysis after fixes to calc_spatial_diff_ex.R
Package: spammR
Commit: 1fe0a475ff96154a9c15a3edc702bc8cce3ca4bd
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-02-03 11:27:11 -0800
Commit message:

 Merge pull request #80 from PNNL-CompBio/79-count-based-differential-expression-get-log-transformed

fix to disable log transformation if dealing with count based data in differential expression. 

Nice catch!
Package: spammR
Commit: 11c316f63fdaf50711d87e4a4b622063869f0a32
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-02-02 14:38:11 -0800
Commit message:

 added additional check to log transformation of data to ensure that log transformation only happens for non count based data
Package: spammR
Commit: 697d8da2bb8ae46886968194bc262b0b48f81b65
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-01-29 12:31:29 -0800
Commit message:

 Merge branch 'main' of https://github.com/PNNL-CompBio/spammR
Package: spammR
Commit: 7767b3a988abc8b4bf77b48b7bf051e3ce56bb42
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-01-29 12:31:26 -0800
Commit message:

 updated spatial vignette to account for new diffex bug fix
Package: spammR
Commit: ed5d1eadc8c1d091866a10eec0c2cc401d7b17da
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-01-29 11:40:54 -0800
Commit message:

 Merge pull request #78 from PNNL-CompBio/75-differential-expression-results-and-associated-proteins-not-aligned-correctly-in-calc_spatial_diff_ex-results

fix to calc_spatial_diff_ex
Package: spammR
Commit: c29a800676202ba1fe1d89d1e69423e6375f7c55
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-01-29 11:40:34 -0800
Commit message:

 Merge pull request #76 from PNNL-CompBio/feat/forge-catalog

add catalog-info.yaml file for forge catalog
Package: spammR
Commit: ad1354bb8c78b96b0b01cb999d3e73585e828c37
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-01-29 11:40:18 -0800
Commit message:

 Merge pull request #74 from PNNL-CompBio/imputation

MinSamp imputation method
Package: spammR
Commit: 6ca61c7b2d2ae7e87827ea2858b67d9ceb610aae
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-01-29 10:36:29 -0800
Commit message:

 added `sort.by = "none"` to `limma::topTable()` call in `calc_spatial_diff_ex.R` such differential expression results and SPE gene list are in the same order for merging. Also clarified comment in code explaining why we don't sort.
Package: spammR
Commit: b18d3ba8891dfa8752ddb9213ba2bcdd0f4bab37
Author: pham259 <jennifer.pham@pnnl.gov>
Date: 2026-01-26 12:13:09 -0800
Commit message:

 add catalog-info.yaml file for forge catalog
Package: spammR
Commit: fe9d26433afcb432467118db2928e06953cb7732
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-01-22 14:15:17 -0800
Commit message:

 renamed imputation method from 'sampMin' to 'samp_min' to align with style guide and updated function doc string
Package: spammR
Commit: ce5f97efe691ecf1cd11743d195533ffe4a2222b
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2026-01-19 10:45:48 -0800
Commit message:

 add sampMin (sampleMinimum) to imputation methods
Package: imageTCGAutils
Commit: ec7a5a8b5e711740ce454c9c352d2f614d15e1cf
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-10 15:58:41 -0400
Commit message:

 version bump 0.99.17
Package: imageTCGAutils
Commit: 6469342aa93f799f7a7d7fd71f8258eb9115de21
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-10 15:56:37 -0400
Commit message:

 import utils head
Package: imageTCGAutils
Commit: b3ea13304754a8fa1b4a7d04f2d95919c3ba1fb1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-10 15:56:11 -0400
Commit message:

 remove access_key and secret_key mentions
Package: imageTCGAutils
Commit: 5f07cdf4dbc59519db7db7b2034d6ce088789b34
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-10 15:52:28 -0400
Commit message:

 build ignore *_files folder
Package: imageTCGAutils
Commit: 35cb9754d51f733b692bc406d25a7f9a9f9b4fc8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-10 15:50:55 -0400
Commit message:

 version bump 0.99.16
Package: imageTCGAutils
Commit: 7fe0b6ee51aef0711bf29f79496b5c2bc8fd66e3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-10 15:50:50 -0400
Commit message:

 update .Rbuildignore
Package: imageTCGAutils
Commit: 5f94939ebd5c1bc08e820813da9a1079dc079d4c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-10 15:48:31 -0400
Commit message:

 version bump 0.99.15
Package: imageTCGAutils
Commit: 589339ed49539a5ad41313e54eee4cfcb4dfb373
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-10 15:48:26 -0400
Commit message:

 doc fix: default is geojson for listHoverNet
Package: imageTCGAutils
Commit: c9374ea09078c25f9a3b1f23751c36392359755a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-10 15:47:56 -0400
Commit message:

 update unit test to aws s3 file list
Package: imageTCGAutils
Commit: af4a63c9460cacdcf6514cb0bcb5379a57a39a4a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-10 15:45:44 -0400
Commit message:

 use paws to list files from s3 type bucket
Package: proBatch
Commit: 18d59ea5597ede2f0b43cb3499b1fc868872b6c5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2026-03-10 19:34:22 +0100
Commit message:

 Bump version
Package: proBatch
Commit: f9714c22c2bed822294e418ff8651947ea7208a7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2026-03-10 19:27:08 +0100
Commit message:

 Add export for plot_PVCA.df and update function parameters in documentation
Package: proBatch
Commit: 0e9dff2911031b5d7c204632c7af4b77821c3153
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2026-03-10 19:08:03 +0100
Commit message:

 Update .Rbuildignore and .gitignore to include additional vignettes and output files
Package: proBatch
Commit: 7332ae13c73e5184045ea0dd72f9c5d0fe878719
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2026-03-10 18:28:10 +0100
Commit message:

 Refactor PVCA plotting functions and update documentation for consistency
Package: proBatch
Commit: c9f5a938e98dc061e7c3744e65860a03c1d48339
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2026-03-10 18:06:42 +0100
Commit message:

 Add BiocStyle to output format in vignettes and update Imports in DESCRIPTION
Package: proBatch
Commit: 2343558db56611b26963b145a753c7bb28690ea9
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2026-03-10 18:01:16 +0100
Commit message:

 Remove unnecessary blank lines in test files
Package: proBatch
Commit: 0584b25340b0f37e72de4f0802cb21af9a849b40
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2026-03-10 18:01:09 +0100
Commit message:

 Remove unnecessary blank lines in auxiliary and date_conversion scripts
Package: proBatch
Commit: 091eb51a953440967a71692a0ae55c9e91d8d061
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2026-03-10 17:57:28 +0100
Commit message:

 Update .gitignore and .Rbuildignore to include additional files; refine documentation links in R scripts and vignettes
Package: proBatch
Commit: 2252aa3030038c6312f4e9f4b67eccf28dd96d00
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2026-03-10 17:13:33 +0100
Commit message:

 Update .gitignore to exclude additional cache files and figures from vignettes
Package: Rhdf5lib
Commit: e2d0017a0fc88c4222119c974fcb4c8e8d69b5cd
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 17:35:16 +0100
Commit message:

 Run devtools::document()
Package: Rhdf5lib
Commit: cc8254504ab7dc116424e2dbe2b41cb085ef6b0d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 17:30:50 +0100
Commit message:

 Add noRd to .getDynamicLinks() and .getSzipLoc()
Package: scRNAseqApp
Commit: 7a8153a1ff23003907a38dba3338582ce4dee2fa
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-03-10 12:06:06 -0400
Commit message:

 Add 'add' and 'delete' method for lasso.
Package: Rhdf5lib
Commit: 8d39845ecf132fd5b41bcc156c1741bb26e64d2d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 15:28:27 +0100
Commit message:

 Bump version
Package: Rhdf5lib
Commit: 495dc6da1d09ad308525de17124c274963d454ca
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 15:28:10 +0100
Commit message:

 Restore ros3 support
Package: Rhdf5lib
Commit: e5d224efdb3512af15e3d6c0fd84bc8e5867bb1d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 14:57:23 +0100
Commit message:

 Bump version
Package: Rhdf5lib
Commit: 79d35dad0ad315969896bd66f79dec82da000b51
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-09 10:27:00 +0100
Commit message:

 Mention switch to CMake in NEWS
Package: Rhdf5lib
Commit: 1ee1d8f72e66b419d746f8b6b39a980cd4288f54
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-09 10:04:26 +0100
Commit message:

 Reactivate ros3 support
Package: Rhdf5lib
Commit: a758732978720d92d8822ea4f09ff911a38e2524
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-06 15:47:23 +0100
Commit message:

 Disable ROS3 for now
Package: Rhdf5lib
Commit: 4dfdf6ecd9b4c85c7fa94c116e750b45cc2cc9c2
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-27 10:48:19 +0100
Commit message:

 Remove windows specific step
Package: Rhdf5lib
Commit: 3e6e2037ad1aff6c0e467c0a4639b2eeaf4899af
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-27 10:47:29 +0100
Commit message:

 Install openssl on macOS 15
Package: Rhdf5lib
Commit: 2083acfa78bcc5cf4ff28bc9f1cd3d21d6f20b8e
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-26 11:27:27 +0100
Commit message:

 Port over https://github.com/HDFGroup/hdf5/commit/e84e5ee4672e22753a4d3d600dca2d5291953d78
Package: Rhdf5lib
Commit: 7a153add99e060e11f7e3c584bfae0dcad15cd8d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-26 10:46:46 +0100
Commit message:

 Add _build_ folders to cleanup
Package: Rhdf5lib
Commit: 28c36dc8c2336f6b4ecb6f98362ba5d497e9e518
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 14:59:22 +0100
Commit message:

 Let linguist know which files are vendored
Package: Rhdf5lib
Commit: 65f2ba7dee2dc19ad9499a1b84e96b5dd2299e0c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 14:57:16 +0100
Commit message:

 Update HDF5 copyright location
Package: Rhdf5lib
Commit: d4bcf7ba0a56310c920a575f9df1409a30a035c4
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 14:50:40 +0100
Commit message:

 Add note about non standard systems
Package: Rhdf5lib
Commit: cd60db346c99aa984299f068fcc7e7cbdffbea71
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-24 15:30:27 +0100
Commit message:

 Remove outdated vignette
Package: Rhdf5lib
Commit: 210db98215a12c5a35888b2e79e24d5206295aea
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-24 12:12:43 +0100
Commit message:

 Update pkgconfig() to work with CMake compilation
Package: Rhdf5lib
Commit: 544f30a8ffabf007bfcd3fde0425b4368d4a36da
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-23 12:28:05 +0100
Commit message:

 Get lib version from settings file

Co-authored-by: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Package: Rhdf5lib
Commit: a18f248432cca53d22231819b4e6665497e1a64b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-21 11:11:46 +0100
Commit message:

 Add comment about strip-components
Package: Rhdf5lib
Commit: c2683d163999452a6fa230910b2b3adaf562cd2c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-21 11:09:34 +0100
Commit message:

 Add patching script
Package: Rhdf5lib
Commit: 510f39d460baaf22fc78172d9a023b56d1c0a735
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-20 18:04:46 +0100
Commit message:

 Ignore build folders and result
Package: Rhdf5lib
Commit: 1f86b73394670946f96c979fa20acc9d4e8d71f7
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-20 17:02:13 +0100
Commit message:

 Compile with biocmake

Co-authored-by: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Package: Rhdf5lib
Commit: f17296297516d95b29dec3230f3bed3492b7ad1c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-20 17:11:28 +0100
Commit message:

 Add vendored copy of the libraries
Package: Rhdf5lib
Commit: 14a423b9298ab78f5c2a0dcf0fe81b325c36e232
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-19 13:31:36 +0100
Commit message:

 Create bash scripts to download copies to vendor

Co-authored-by: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Package: Rhdf5lib
Commit: a9a604d95440d596e8246cdff973b7e067e9fbb8
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 17:11:12 +0100
Commit message:

 Avoid artifact name clashes
Package: Rhdf5lib
Commit: 8e6a441e23d8fcbdd73a1198e51d939dc41f9883
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 16:36:09 +0100
Commit message:

 Install tinytex manually
Package: Rhdf5lib
Commit: 8f05f9aa386e1a55ae5dcdf13aab3e49ae77b3e0
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 16:30:29 +0100
Commit message:

 Do not systematically run on all pushes

The previous setup also duplicates runs in PRs.
Package: Rhdf5lib
Commit: 7beda792047cc7c5224bca1e1799f01ec00c9b24
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 15:11:03 +0100
Commit message:

 Add cache option to differentiate between archs
Package: Rhdf5lib
Commit: db96ba57591c777b67274dc286aad48ccb64d352
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 15:06:36 +0100
Commit message:

 Remove mention of missing branch
Package: Rhdf5lib
Commit: 4952aab609dba69a4dbac5c8adc8872988f1048b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 15:06:17 +0100
Commit message:

 Update windows runner
Package: Rhdf5lib
Commit: 475115b93dce434848c2b3a5bfa3c85da30ef664
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 15:05:45 +0100
Commit message:

 Remove unnecessary workflow steps
Package: Rhdf5lib
Commit: 19dd8cafb6bbdd672be4f18b7fff04f9048f83c5
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 15:04:41 +0100
Commit message:

 Fold arm64 workflow into main workflow
Package: Rhdf5lib
Commit: f64c061b2a9d1a46da582085e092645482b25228
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 16:28:15 +0100
Commit message:

 Remove docType package

As recommended by roxygen deprecation warning
Package: Rhdf5lib
Commit: 799348be3022d44f0841b5510728a10e48b8ec48
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-23 12:41:03 +0100
Commit message:

 Update pkg level documentation
Package: SingleCellExperiment
Commit: 7cefd3266c59c1b7ad0afefbd7317d2e478a2529
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-11 00:41:13 +1100
Commit message:

 Raise a warning if i= is specified in counts() and friends.

Previously, if someone (probably accidentally) specified i= in counts(), it
would get silently forwarded to the next argument in assay(). This usually
didn't cause obvious problems as the next argument was withDimnames= and the
value would just be treated as a boolean.

Now, we catch any i= argument explicitly and warn users that they're not
getting the assay that they requested.
Package: fourSynergy
Commit: c3c033aeb179c62ffd89223934fce7a3865321c8
Author: swind <swind@uni-muenster.de>
Date: 2026-03-10 13:12:08 +0100
Commit message:

 add extdata description
Package: fourSynergy
Commit: 7c4c51aae9129cbeef62e057f34425df61f179e2
Author: swind <swind@uni-muenster.de>
Date: 2026-03-10 12:55:59 +0100
Commit message:

 add extdata description
Package: PhyloProfile
Commit: 6a59eabae6f64a30626ca9280596123a900babe3
Author: trvinh <trvinh@gmail.com>
Date: 2026-03-10 12:30:58 +0100
Commit message:

 fixed modalDialog gene name and category
Package: MsCoreUtils
Commit: 5b8d18ed663b6ad0301e9a6401f522c3e16e123d
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-03-10 11:26:38 +0100
Commit message:

 Merge pull request #142 from rformassspectrometry/jomain

Distance (similarity) functions to optionally report the number of peak pairs on which score was calculated
Package: MsCoreUtils
Commit: 866bab57c84cb122647a4793f7010ca575d40299
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-10 07:23:55 +0100
Commit message:

 refactor: distance functions to report number of matched peaks

- Refactor the distance/spectra similarity functions to report in addition the
  number of matched peaks (if new parameter `matchedPeaksCount = TRUE`). See
  also issue #350. In brief, this allows more advanced similarity functions such
  as the modified cosine (`gnps()`) to report the number of peak pairs on which
  the score was calculated.
Package: MsCoreUtils
Commit: 53b1c686b9f8d67b51ae52be5110e6b759544ffb
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-09 15:48:01 +0100
Commit message:

 tests: add additional checks for rbindFill
Package: rhdf5
Commit: ce8f5ad789e32e5ccea01eb9c826751c0d5fc340
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 10:20:38 +0100
Commit message:

 Bump version
Package: rhdf5
Commit: 54712124809549711d0f9ab8674801bc6cdb96a2
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 10:20:21 +0100
Commit message:

 Mention h5version Rhdf5lib change in NEWS
Package: rhdf5
Commit: 1e371a472bbe0d047812ff99f2c582356978080c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 10:16:49 +0100
Commit message:

 Show Rhdf5lib version in h5version()
Package: rhdf5
Commit: 5fc9c281054ccb2d536bf699d3bd90f2e310cab7
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 10:10:43 +0100
Commit message:

 Add NEWS about rchk and ARM in GHA
Package: rhdf5
Commit: 375b413f3b859535b79a6bf34ead76dcfa46b3ac
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-10 08:34:44 +0100
Commit message:

 Add manual trigger for R CMD check workflow
Package: rhdf5
Commit: 7d3a552d99b8bb85ac1a77af8ab6f9815d4a7be7
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-09 14:29:04 +0100
Commit message:

 Add CI runners for more arm OS
Package: RNAshapeQC
Commit: 413f587ee531b090bd3b83fb3c6fa9ca6f7ac347
Author: Miyeon Yeon <sqr.yeon@gmail.com>
Date: 2026-03-10 03:12:33 -0500
Commit message:

 Update vignette to demonstrate SummarizedExperiment workflow (Bioconductor/Contributions#4054)
Package: RNAshapeQC
Commit: 0667273f82af31ee76971d7cc412a101c1635619
Author: Miyeon Yeon <sqr.yeon@gmail.com>
Date: 2026-03-06 11:04:51 -0600
Commit message:

 Update vignette documentation
Package: gCrisprTools
Commit: 8c620d1eecfe009bcef06548b47e88e7756ec2a3
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-03-09 15:46:22 -0700
Commit message:

 pushing to new version
Package: Pirat
Commit: 7bb7b71f18abd182553318a3826df3e60def4f43
Author: Lucas Etourneau <38471671+Lucas-Et@users.noreply.github.com>
Date: 2026-03-09 15:40:32 -0700
Commit message:

 Update version to 1.5.8

Bump version from 1.5.7 to 1.5.8 in DESCRIPTION file.
Package: Pirat
Commit: 951e2e3e05a211872e40cd6e9bdc76a73722d971
Author: Lucas Etourneau <38471671+Lucas-Et@users.noreply.github.com>
Date: 2026-02-26 11:21:31 -0800
Commit message:

 Fix citation
Package: Pirat
Commit: 2f99d9e19b07bcd78c4e7ddb5a21bfe998df30dd
Author: Lucas Etourneau <38471671+Lucas-Et@users.noreply.github.com>
Date: 2026-02-26 11:21:08 -0800
Commit message:

 Change citation

Added a new article citation on penalized likelihood optimization for missing value imputation in proteomics, along with an abstract and other relevant details.
Package: Rarr
Commit: 4141e839ecb8370a055ca9cb369a0433c882f47e
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-09 19:43:51 +0100
Commit message:

 Bump version
Package: Rarr
Commit: bdf339583fca844ce49dc51ad1e21d8eb2b90797
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-09 19:43:35 +0100
Commit message:

 Mention C API update in NEWS
Package: Rarr
Commit: bba6fe1159e79094268d65e18a3d27da2705949c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-09 19:38:24 +0100
Commit message:

 Use r-devel for all workflows
Package: Rarr
Commit: 25f0bc219459a69a36d959539a008bcdf7968920
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-09 14:42:21 +0100
Commit message:

 Pass r-version to touchstone/actions/receive
Package: Rarr
Commit: fda9c3596baede3a44fe33942c853abf070561ec
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-09 14:25:19 +0100
Commit message:

 Update touchstone
Package: Rarr
Commit: d2e070552a875e37fa26857b3908232e5a132fed
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-09 14:00:07 +0100
Commit message:

 Use r-devel for benchmarks
Package: Rarr
Commit: 56b228b470a2102e770734449802edaa5047d404
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-09 13:57:14 +0100
Commit message:

 Check compression benchmarks
Package: Rarr
Commit: b46dd484d3e139545dd943103930dbde6faeb6db
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-09 13:54:30 +0100
Commit message:

 Use official resizeVector C API
Package: Rarr
Commit: 63d056501a27a7edc4c423572bdd550eeb0e879a
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-16 13:46:41 +0100
Commit message:

 Update conformance action
Package: Rarr
Commit: 4af8881f7c63da6190525145b157876f7c68eba1
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-13 19:56:05 +0100
Commit message:

 Remove unused workflow
Package: Rarr
Commit: b8ca7dd184640ff65985c4d28c47a32b30e52a30
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-13 11:35:10 +0100
Commit message:

 Install package for conformance CI
Package: Rarr
Commit: dedce0676f0e2d174018c7fcab36a3531692a394
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-11 16:54:37 +0100
Commit message:

 Bump version
Package: Rarr
Commit: 3d3aa2ef6420fb52e996f9811a85ccbc45d7773d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-11 16:53:26 +0100
Commit message:

 Document default compression change
Package: Rarr
Commit: 1b323845c77c7082ba705ed5e9fecc22c88e72d7
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-10 20:53:29 +0100
Commit message:

 Set zstd as default compressor
Package: Rarr
Commit: 94ca972901f4c258bf721cd52be5b37d28564627
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2026-02-09 14:09:38 +0100
Commit message:

 Exit early on integer(0) index

Co-authored-by: Hervé Pagès <hpages.on.github@gmail.com>
Package: Rarr
Commit: 9fc563d8238d6177d440aa39af3c0cdade7b091e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2026-01-31 21:44:07 +0100
Commit message:

 Fix integer(0) indexing

Fix #112
Package: Rarr
Commit: 9e2d3baa8faf71578d090b0a0a2edea13696ee7d
Author: Artür Manukyan <artur-man@hotmail.com>
Date: 2026-01-31 20:03:22 +0100
Commit message:

 Set simplifyVector = FALSE in fromJSON()

For consistency across S3 and local files, as read_json() defaults to simplifyVector = FALSE
Package: Rarr
Commit: 3f1039c998c6c56b1e482d3b0625a5934cf4bf53
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2026-01-30 09:39:12 +0100
Commit message:

 Remove cron job from conformance CI
Package: Rarr
Commit: 720fce81c702df89b905dd2af112ab7cc6dd8c2d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2026-01-27 17:10:59 +0100
Commit message:

 Skip file size checking in BiocCheck
Package: Rarr
Commit: d1a057aaf2289300408ed4b9c0b6a7d87d032ebc
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2026-01-27 15:34:08 +0100
Commit message:

 Document return value for writeZarrArray()
Package: Rarr
Commit: 08264774f37888ca4a54d85a2b0afd5bb8beae7f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2026-01-27 15:25:19 +0100
Commit message:

 Add return value to write_zarr_attributes()
Package: Rarr
Commit: f21d48ddae77b2f53fcc0c860a54c6ad417abbfd
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2026-01-27 15:16:04 +0100
Commit message:

 Do not let BiocCheck warnings pass unnoticed
Package: Rarr
Commit: 5386fd4d1670a5f5d9546c9579aef777e4c2ec27
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2026-01-22 14:07:35 +0100
Commit message:

 Use asplit() to convert array to list
Package: Rarr
Commit: 5cee6e60ecb4dc9d3e4723e6f5d1131b96ec8a68
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2026-01-22 14:01:38 +0100
Commit message:

 Re-use .generate_chunk_indices() function in update_ pathway
Package: Rarr
Commit: 0d611c8c75e5e3687262dc3367b7069dac27cc5a
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2026-01-22 13:45:48 +0100
Commit message:

 Replace Map() by mapply()
Package: miaViz
Commit: 7c01c0cf1ceca4de9f733c20eff49e7d01a99d64
Author: Tuomas Borman <tvborm@utu.fi>
Date: 2026-03-09 22:52:13 +0200
Commit message:

 Fix unit tests related to internal changes in ggplot2
Package: AnVILVRS
Commit: 9d57c9696b6b08e16fa77812f93d26c11f62c5e8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-09 16:43:05 -0400
Commit message:

 version bump 0.99.14
Package: AnVILVRS
Commit: e63389fa8531d3876a12565fcf7e1c4442a8b574
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-09 16:30:25 -0400
Commit message:

 session info is unnumbered in TOC
Package: AnVILVRS
Commit: d07fe453143eb3c623f95eb7834e877f07057c11
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-09 16:30:04 -0400
Commit message:

 add missing chunk labels
Package: AnVILVRS
Commit: 4c01df2cfa4de51172f8e9bfbd0e004d377220d4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-09 16:28:15 -0400
Commit message:

 add URL and BugReports fields
Package: plotGrouper
Commit: 026daf98a3f2b18039306101c66aa89edeb8affe
Author: John Gagnon <john.gagnon@gvt1inc.com>
Date: 2026-03-09 13:58:27 -0400
Commit message:

 update: update scripts to use modern tidyr and dplyr functions
Package: postNet
Commit: d7406bc81c663beda2d64686fd5184ad0334dbab
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-09 17:07:22 +0000
Commit message:

 KS
Package: gCrisprTools
Commit: c60f3bb2173a172b24fba26e99c6b5e4daf68c9e
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-03-09 09:16:01 -0700
Commit message:

 ready for Bioc push
Package: gCrisprTools
Commit: c7392bb8de868a3889752215745ee9d548beeefa
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-03-02 08:35:25 -0800
Commit message:

 resolve merge conflicts
Package: gCrisprTools
Commit: 0810de717cbae20c24f353004714c3b6d66b2657
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-03-02 08:33:26 -0800
Commit message:

 version bump
Package: gCrisprTools
Commit: fddb2c4b5c2fb3615412e83b5d7a2d112bff1ac1
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-28 10:01:47 -0800
Commit message:

 version bump
Package: gCrisprTools
Commit: b6b43ef8408eaae087f33147280486171b87b45a
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-28 10:01:47 -0800
Commit message:

 version bump
Package: gCrisprTools
Commit: fc67f83a1c4d0b81f596589bda1819ec4fe7509f
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 21:37:35 -0800
Commit message:

 merge with upstream

Merge remote-tracking branch 'upstream/devel'

# Conflicts:
#	DESCRIPTION
Package: gCrisprTools
Commit: 36063d210f7a3176c10d28091c06e3e9a74894cb
Author: Russell Bainer <50212033+RussBainer@users.noreply.github.com>
Date: 2026-02-27 21:29:03 -0800
Commit message:

 Merge pull request #31 from RussBainer/bioc-prep

Rename se.Rdata to se.RData
Package: gCrisprTools
Commit: daa29c1c7dc9be199786cee4f4508af52a900510
Author: Russell Bainer <50212033+RussBainer@users.noreply.github.com>
Date: 2026-02-27 21:28:24 -0800
Commit message:

 Rename se.Rdata to se.RData
Package: gCrisprTools
Commit: d706f84f0fb79bf034219e2d810da6ab5e7840ce
Author: Russell Bainer <50212033+RussBainer@users.noreply.github.com>
Date: 2026-02-27 18:23:02 -0800
Commit message:

 Merge pull request #30 from RussBainer/bioc-prep

Bioc prep
Package: gCrisprTools
Commit: 946796cac45527e1e1135d7dcd52d0f6d9b46a2f
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 17:19:23 -0800
Commit message:

 completed preprocess fit upgrade.
Package: gCrisprTools
Commit: a315103fce61459ff2d366be0c44e96d7c713958
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 15:24:00 -0800
Commit message:

 refine declared dependencies
Package: gCrisprTools
Commit: 775da621261764ae3f99b904bc2f66bf25c824c7
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 14:08:06 -0800
Commit message:

 update method import for SE
Package: gCrisprTools
Commit: adafcd6218ec133eb5ac30ae05b5bc4b751b42a8
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 09:29:44 -0800
Commit message:

 Add additional packages to DESCRIPTION
Package: gCrisprTools
Commit: 40999485e130abd3c9b34bee9d6baee61a35a7be
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 09:25:43 -0800
Commit message:

 switch to better roxygen tags
Package: gCrisprTools
Commit: f1b45564e145b2e8834c9db50229e4b1bb648064
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 09:15:27 -0800
Commit message:

 update to correct se data type
Package: gCrisprTools
Commit: 636f1c1e4fa5ec3540688a648792c5919a7fa87d
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 09:09:02 -0800
Commit message:

 Fix normalization bug
Package: gCrisprTools
Commit: 641d11ccded611ab4b5e5bf703f32924099b01c1
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 08:22:02 -0800
Commit message:

 Update doctype and other roxygen tags
Package: gCrisprTools
Commit: 80578a29bf349aeade6855983ef10b5fbc4a3e43
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 07:51:51 -0800
Commit message:

 Add binding for colMedians
Package: gCrisprTools
Commit: 386a8cc0c8c38875893a7fc418c020ca344ffbf0
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 07:41:40 -0800
Commit message:

 Update to reflect current role at Eikon
Package: gCrisprTools
Commit: c1f6f19c9fab15fb0700529f457c4d2aad358739
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 07:35:56 -0800
Commit message:

 Adding docs for new functions/data
Package: gCrisprTools
Commit: 62d3f34c4cd67a2da639c22de2ba88249ca95dbb
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 07:34:38 -0800
Commit message:

 Annotate SE data
Package: gCrisprTools
Commit: 6ebc173ac3170b25281f5d0c6eb7457075f7e4de
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-02-27 07:31:04 -0800
Commit message:

 fix bindings calls
Package: gCrisprTools
Commit: 46d04a36a391199f2b0ebdc09a863402ce07405e
Author: Russell Bainer <50212033+RussBainer@users.noreply.github.com>
Date: 2025-05-21 18:24:52 -0500
Commit message:

 Merge pull request #26 from RussBainer/tiling-screen-updates

Tiling screen updates
Package: gCrisprTools
Commit: afc40e2a4618cfbbeb6d0a14fcc4747605a37979
Author: Russell Bainer <rbainer@lighthorsetx.com>
Date: 2025-05-21 16:04:33 -0700
Commit message:

 add normalizeGenewise
Package: gCrisprTools
Commit: 588c12ab17ded3cd98ec7a0bb63e08e22f161cfa
Author: Russell Bainer <rbainer@lighthorsetx.com>
Date: 2024-01-06 13:38:49 -0800
Commit message:

 roxygenized
Package: gCrisprTools
Commit: 4fb6db2127ea32e2cd8162fec693e4026845d2a1
Author: Russell Bainer <rbainer@lighthorsetx.com>
Date: 2024-01-04 17:28:40 -0800
Commit message:

 improve error message in ct.prepareAnnotation
Package: gCrisprTools
Commit: 9b4dd8421677561c57d6e7ead600cf386e4d2dbc
Author: Russell Bainer <rbainer@lighthorsetx.com>
Date: 2023-12-28 17:44:51 -0800
Commit message:

 Pause before roxygenization
Package: gCrisprTools
Commit: 079f2067a4a2b9e06b0ab4045e4531a00679e75f
Author: Russell Bainer <rbainer@lighthorsetx.com>
Date: 2023-12-28 16:47:06 -0800
Commit message:

 create ct.extractSE
Package: gCrisprTools
Commit: e00cbd8c14f0ddddf136d06dc6ab96a8d65cb73d
Author: Russell Bainer <rbainer@lighthorsetx.com>
Date: 2023-12-21 11:09:37 -0800
Commit message:

 Update DESCRIPTION
Package: gCrisprTools
Commit: 4d7e5541992f04eed79092132929e81e9a2ecb25
Author: Russell Bainer <rbainer@lighthorsetx.com>
Date: 2023-12-20 14:57:04 -0800
Commit message:

 suppress gRNA sorting in ct.viewGuides
Package: GenomicPlot
Commit: d745253227264392b353d2b11e7cae16cd092bfc
Author: shuye2009 <shuye2009@gmail.com>
Date: 2026-03-09 11:50:09 -0400
Commit message:

 Update to version 1.9.3 - remove old tarball
Package: GenomicPlot
Commit: 557dc8591786e338b78d3182ae83d16b66a94b92
Author: shuye2009 <shuye2009@gmail.com>
Date: 2026-03-09 11:17:43 -0400
Commit message:

 Bump version to 1.9.3 and add Seqinfo to package imports
Package: SingleR
Commit: de25043a9befcd12babaa1c04968bd543face1c2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-10 02:14:09 +1100
Commit message:

 Pass along additional arguments to scoreMarkers in plotMarkerHeatmap.
Package: scrapper
Commit: f6f0e94b5ec0e1874ecc4007a3b37125718deed6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-10 01:55:44 +1100
Commit message:

 Docfix for aggregateColData for 1-based indices.
Package: rhdf5
Commit: f651ac2b9cf5deffb7116452aff40ddc72f6d007
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-09 15:04:29 +0100
Commit message:

 Remove outdated TODO

Fixes #202
Package: rhdf5filters
Commit: 98bdffb92537e44e12463c9728e1bc30e0628e72
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-09 16:18:26 +0100
Commit message:

 Revert "Test r-lib action for R CMD check"

This reverts commit 1c815e4a39bfb24c365ead993b9e1527220beb0b.
Package: rhdf5filters
Commit: b1d5c324ce165b59d3d426bf5abf5fa8af7715f0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-09 10:45:05 +0100
Commit message:

 Skip snappy test on intel mac
Package: rhdf5filters
Commit: 9f971c324284d299217b6512238b74c139efe743
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-09 10:18:46 +0100
Commit message:

 Remove C23 step
Package: rhdf5filters
Commit: 948fb1d3f2ea0f637dd9396e13007b62a56a0d54
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-09 10:18:24 +0100
Commit message:

 Add info arg in expect_identical()
Package: rhdf5filters
Commit: 13bc41d806b25435465a3696ec915ff1fac131c7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-08 22:47:01 +0100
Commit message:

 Test r-lib action for R CMD check
Package: rhdf5filters
Commit: 916ebb18c2c2a12559910ce482b0f88137519dee
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-07 21:05:06 +0100
Commit message:

 Use macos-15-intel as mac intel runner

See https://github.blog/changelog/2025-09-19-github-actions-macos-13-runner-image-is-closing-down/
Package: rhdf5filters
Commit: 1c3268013289b793471e3b13e295a7a62ce23848
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-07 19:24:44 +0100
Commit message:

 Update actions & simplify workflow
Package: rhdf5filters
Commit: 856c33cc6a91fe7bca7762dc3086e21203c669be
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-08 17:40:45 +0100
Commit message:

 Move from tinytest to testthat
Package: rhdf5filters
Commit: aaae10598dbc30654396136a4efccc1a680d7e09
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-07 13:19:01 +0100
Commit message:

 Fix typo
Package: SEMPLR
Commit: 5d0ce71070ed7c1eb062776ea6f12bc65cdbf637
Author: Grace Kenney <kenney.grace6@gmail.com>
Date: 2026-03-09 09:51:04 -0400
Commit message:

 resolve merge conflict in README
Package: SEMPLR
Commit: 4e695058cec8820cad3a065eea46072a9a8892b5
Author: Grace Kenney <kenney.grace6@gmail.com>
Date: 2026-03-09 09:50:02 -0400
Commit message:

 resolve NEWS merge conflict
Package: SEMPLR
Commit: 0a80fa597ca979049fd4dbe82bb46444faa55642
Author: Grace Kenney <kenney.grace6@gmail.com>
Date: 2026-03-09 09:45:25 -0400
Commit message:

 version bump
Package: SEMPLR
Commit: 40faa276de08eca2b124986669b4920a4cfcfea4
Author: Grace Kenney <kenney.grace6@gmail.com>
Date: 2025-10-22 16:26:03 -0400
Commit message:

 update logo and news file
Package: goatea
Commit: 9d9e555961581a79da3e3a0638714d0d31636f1b
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-09 14:30:13 +0100
Commit message:

 v1.1.6: updated vignettes and added pkgdown docs, added manuscript example data, fixed bugging code
Package: postNet
Commit: f235836c55f24328e56d30fee12afc1e14f08fb2
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-09 12:36:14 +0000
Commit message:

 KS
Package: CATALYST
Commit: b91b3eda7ebd387551b303b567baf3618d87a564
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-09 12:10:35 +0100
Commit message:

 update exports
Package: CATALYST
Commit: 4f45e2067c284bc1f5a6ee93a6993987d0a045f4
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-09 12:10:24 +0100
Commit message:

 fix doc typo
Package: CATALYST
Commit: 8440b2e4a79b1cb89109c2c99c6e0442067e0b85
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-09 09:31:46 +0100
Commit message:

 omit purrr
Package: CATALYST
Commit: 51f77e2a035af9856cc94346107dedc8223d2a74
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-09 09:02:38 +0100
Commit message:

 v1.35.2
Package: CATALYST
Commit: f3c52c724e41d7b438e97aaba8434b727f3782d8
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-09 09:00:03 +0100
Commit message:

 omit data.table
Package: CATALYST
Commit: 09c7fe09fc57bf1ce71fa47562642b15a1cf5e4d
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-20 20:53:13 +0100
Commit message:

 v1.34.1
Package: CATALYST
Commit: ffa208e4c82ed390eca5cafccef74ee41a2fe5a4
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-02 08:11:16 +0100
Commit message:

 Bioc 3.22 release version bump
Package: CATALYST
Commit: 0328effdbe7fb81065f7dfb7f3f5ce4251d42ae5
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 22:27:34 +0200
Commit message:

 fix #424 on release
Package: CATALYST
Commit: 64e8b8e1d235a2a3117d43dfb7fae7405fe3c8f7
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 22:09:59 +0200
Commit message:

 bug fix
Package: CATALYST
Commit: 3ffeed106deb4fed4c94712d0e9e52146ba39533
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 21:45:05 +0200
Commit message:

 drop caching
Package: CATALYST
Commit: 94f1fdc64d3f63a0501c699f920306b444706545
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 21:27:44 +0200
Commit message:

 update GHA
Package: CATALYST
Commit: db9f0df48b4aa25421f1b93cd4e0162b4d254977
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 21:27:19 +0200
Commit message:

 version bump
Package: CATALYST
Commit: 71122df74e34d591f69da6a83390c91ee846dbbc
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 21:27:12 +0200
Commit message:

 prettify code formatting
Package: DeeDeeExperiment
Commit: 9af13843acb71c1e8d8ce375bc99964ec0f160a7
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2026-03-09 11:15:32 +0100
Commit message:

 update the pkg version
Package: DeeDeeExperiment
Commit: 94a22db6f3820f6b67f2e1051a8075b86a84f89e
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2026-03-09 11:15:00 +0100
Commit message:

 updating vignette
Package: rhdf5
Commit: 002c24cffa5d6db432e224506f142ce07f5ec4c3
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-09 10:37:42 +0100
Commit message:

 Bump version
Package: rhdf5
Commit: 41acb4d0f723562be55cf44aa35efbb68a66ad69
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-09 10:37:24 +0100
Commit message:

 Add NOTE about deprecation warning
Package: rhdf5
Commit: aa562358984631e1339a71207726f861b671fde3
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-07 09:10:51 +0100
Commit message:

 Add actual deprecation warning to H5Pcreate(native = )
Package: rhdf5
Commit: 2c9a76c8d2f7308522f1fcdafb202daa19c747e9
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-25 13:02:05 +0100
Commit message:

 Remove unnecessary PROTECT()s
Package: rhdf5
Commit: b76959a007acdefe1d93d49f53ec7e7537f29bf7
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2026-02-25 08:24:30 +0100
Commit message:

 Fix formatting of message in h5create.R
Package: rhdf5
Commit: 5d50810c97b700bb8e76a19ef8137ada3fb6542e
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-19 16:13:32 +0100
Commit message:

 Add .venv/ to Rbuildignore
Package: rhdf5
Commit: d6cf6df5f37d62a20a945d08d5a954d2ff69e817
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-17 13:08:28 +0100
Commit message:

 Fix multicore R CMD check warning
Package: rhdf5
Commit: 4558af20bbc90fd47ee857e5e6fe63219b08fb25
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-02-11 16:33:56 +0100
Commit message:

 Switch pkgdown to bootstrap 5
Package: SingleR
Commit: a5acd72b6cde37b8cbc0ddd12b4dc392337a1b3d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-09 17:04:12 +1100
Commit message:

 Bumped version and date, updated NEWS.
Package: SingleR
Commit: f99ac7f09e177b0055f3274984cfbf9e4f58c985
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-09 14:26:58 +1100
Commit message:

 Added average= and center= options for plotMarkerHeatmap.

The former is useful when there's too many cells and we want to compact the
plot; the latter is useful if the expression is too variable across markers.

Also mention that we only accept a result DataFrame for a single reference.
Package: SingleR
Commit: cda4915bdbaac5b3c85fc2336ad32296692fecae
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-09 11:43:49 +1100
Commit message:

 Support block= in getClassicMarkers.

This is more consistent with how blocking is applied for scoreMarkers when all
samples exist in a single matrix. It also allows us to pass the blocking factor
in de.args= when training, regardless of the choice of de.method=.
Package: BamScale
Commit: 0098c6273cd3bfdf235c325e7ed5daa4fe95fdef
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-09 13:43:15 +1100
Commit message:

 Increment version number to 0.99.3
Package: BamScale
Commit: 5e0dbf593147709170edc23a9bfacbc0b9a02ec9
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-09 13:42:44 +1100
Commit message:

 remove citation entry
Package: BamScale
Commit: f9d96eec66d59cc98387063c7490f1c3af2f65ee
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-09 13:42:30 +1100
Commit message:

 update gitignore
Package: BamScale
Commit: ee3b73945c510dcdbc740d1cdbb58cbfbeb6d6de
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-09 13:32:41 +1100
Commit message:

 Increment version number to 0.99.2
Package: BamScale
Commit: 273e3f1ea58be50bc9015a2bc4ea91b4a3bf556a
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-09 13:19:26 +1100
Commit message:

 Increment version number to 0.99.1
Package: TPP
Commit: ac3dc359af1eb3c3689ae04167cc51572d3fef88
Author: Dorothee Childs <childs@embl.de>
Date: 2026-03-09 00:32:08 +0100
Commit message:

 bump version
Package: TPP
Commit: 8b1f3cde725c750761e920f00e30310e515158f5
Author: Dorothee Childs <childs@embl.de>
Date: 2026-03-09 00:31:10 +0100
Commit message:

 Update NEWS
Package: TPP
Commit: 3cafe59177afbd871a74bf924c6cca7894d17964
Author: Dorothee Childs <childs@embl.de>
Date: 2026-03-09 00:30:01 +0100
Commit message:

 Remove foreach parallel loop from CCR and Plot functions; replace with sequential purrr::map for better maintainability.
Package: TPP
Commit: 9a7080194fa2111b434d6b1976b802882eef9e95
Author: Dorothee Childs <childs@embl.de>
Date: 2026-03-09 00:20:11 +0100
Commit message:

 Fix ggplot2 aes_string() deprecation warning by adopting tidy evaluation with aes() and rlang::sym()
Package: TPP
Commit: 3831c0c5bb4ebfdf44ac528c73928c31b9caafcb
Author: Dorothee Childs <childs@embl.de>
Date: 2026-03-08 23:04:37 +0100
Commit message:

 Remove foreach parallel loop from spline fitting; replace with sequential purrr::map for better maintainability.
Package: TPP
Commit: 9a40be6c7e2d9c457b59d5e284f31c69e18cd8ab
Author: Dorothee Childs <childs@embl.de>
Date: 2026-03-08 23:02:46 +0100
Commit message:

 Set global option to avoid deprecated dplyr::tbl_df() in biobroom dependency
Package: omicsViewer
Commit: aed5106d75978551b34a893d320110008617392a
Author: mengchen18 <mengchen18@gmail.com>
Date: 2026-03-08 20:19:25 +0100
Commit message:

 fix: resolve Bioconductor build warnings and notes
Package: CrcBiomeScreen
Commit: 1fa4a6a98cf099263aa35c318294281536852951
Author: Chronostasis <82665896+iChronostasis@users.noreply.github.com>
Date: 2026-03-03 11:46:40 +0000
Commit message:

 Merge pull request #4 from Dragon96pl/devel

Proposed fix R CMD CHECK errors
Package: CrcBiomeScreen
Commit: f65358abaee0102fd404953f7d52127288d101e3
Author: Damian Czopek <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-02-02 03:48:05 +0100
Commit message:

 Ensure output directory exists and update save path

Added output directory parameter to model evaluation functions and ensured the directory exists before saving results.
Package: CrcBiomeScreen
Commit: bb039f7c3c657b30a20b04fe045a8836623c6d9d
Author: Damian Czopek <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-02-02 03:30:40 +0100
Commit message:

 Update documentation for CrcBiomeScreen class

Added documentation for CrcBiomeScreen class.
Package: CrcBiomeScreen
Commit: 888c9a8b8207b44ea0d2afacd81b3fb232723a0a
Author: Damian Czopek <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-02-02 03:27:30 +0100
Commit message:

 fix object in  getModelData

Fixed an 'object not found' error in the getModelData example code by replacing the undefined CrcBiomeScreenObject with the correct toy_obj variable. This resolves the build failure occurring during the package check execution.
Package: CrcBiomeScreen
Commit: bcf4e02f038ae77a7d5eac05f71968dcacfdfc2a
Author: Damian Czopek <36973370+Dragon96pl@users.noreply.github.com>
Date: 2026-02-02 03:23:52 +0100
Commit message:

 Document outdir parameter in EvaluateModel function

Added parameter documentation for output directory.
Package: scrapper
Commit: d87b5fbdd8f84d9ee5a390601cd53dd4ddf79549
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-09 01:26:43 +1100
Commit message:

 Remove dependencies on Matrix and related packages.

In particular, we switch from colSums to tatami.column.sums when normalizing
without size factors. This also allows us to parallelize the calculation.
Package: Voyager
Commit: 771242af677586bf766f8d7225df992a44db371b
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2026-02-19 12:46:09 -0500
Commit message:

 Version bump for wayfarer
Package: Voyager
Commit: 9cbecdfef73b2529c6ab1d52853fa685a9e23879
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2026-02-19 12:44:37 -0500
Commit message:

 Added plotBivariate
Package: Voyager
Commit: e807e44b9d491f9f68f9e41350aa125641f9e8c5
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2025-12-01 15:58:20 -0500
Commit message:

 Reloaded matrix woe
Package: Voyager
Commit: a0e666e99b9052235e1da20096db135f7848689e
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2025-12-01 15:58:02 -0500
Commit message:

 Deal with #56
Package: ggcyto
Commit: 3e26b158a45ecad31155583b65603185ca6a1ddf
Author: Mike Jiang <mike@ozette.com>
Date: 2026-03-07 16:26:26 -0800
Commit message:

 bump version to 1.39.3
Package: ggcyto
Commit: e384570895696ed11cab1747d0bfed7ebcf54447
Author: Mike Jiang <mike@ozette.com>
Date: 2026-03-07 16:21:03 -0800
Commit message:

 Replace deprecated aes_q()/aes_string() with aes(iessym())

Replace all deprecated ggplot2 aes_() family calls with modern
tidy evaluation idioms using aes() + rlang::sym():

- autoplot.R: aes_q(x = as.symbol(x)) -> aes(x = iessym(x))
- ggcyto.R: aes_string(label = "value") -> aes(label = iessym("value"))
- ggcyto.R: add sym to @importFrom rlang
- ggcyto.R: update roxygen example to use iessym() instead of aes_string()

Fixes #112
Package: spoon
Commit: ba475a18644c8dd61c6dd901840ea2b9e7425e26
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2026-03-07 13:01:05 -0500
Commit message:

 update
Package: spoon
Commit: 03e345d84869d3bf3319028703ffa3731826c945
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2026-03-07 12:58:44 -0500
Commit message:

 add pub citation
Package: iscream
Commit: 1d85ebb991560ba97abf3c22c24f063708d1107d
Author: James Eapen <james.eapen@vai.org>
Date: 2026-02-23 12:50:15 -0500
Commit message:

 chore(DESCRIPTION): bump version
Package: iscream
Commit: 56912817f25978b99537cdc6a7d3ae72b569687a
Author: James Eapen <james.eapen@vai.org>
Date: 2026-02-23 14:00:56 -0500
Commit message:

 chore(NEWS): update
Package: iscream
Commit: 1fb2253343928ee8f459e7bb8498a1ef8d6aa610
Author: James Eapen <james.eapen@vai.org>
Date: 2026-02-23 12:49:15 -0500
Commit message:

 refactor(verify_files): use && and !all instead of any(!)
Package: iscream
Commit: 78aab14e374276e2e5cc64dffbe4defc538eea0e
Author: James Eapen <james.eapen@vai.org>
Date: 2026-02-23 12:46:03 -0500
Commit message:

 fix(verify_files): correctly check length of missing_files
Package: iscream
Commit: 7a0c62ba93f88b89094434e46c5841c03de5fb64
Author: James Eapen <james.eapen@vai.org>
Date: 2026-02-23 12:45:33 -0500
Commit message:

 fix: use inherits instead of %in% class
Package: iscream
Commit: 8f760127aa1824d4534f503c2a98be0cdd8ee652
Author: James Eapen <james.eapen@vai.org>
Date: 2026-02-20 15:03:23 -0500
Commit message:

 chore(flake): flake update
Package: iscream
Commit: 73076e13dff2b789a1d0feecdb4afbecb06c2d1d
Author: James Eapen <james.eapen@vai.org>
Date: 2026-02-20 13:58:04 -0500
Commit message:

 chore(flake): clean up and organize the Suggests, rDevDeps
Package: iscream
Commit: 1086dbd8931715a9c1aaecbeed1d9cdb9fa4a6cc
Author: James Eapen <james.eapen@vai.org>
Date: 2026-02-20 13:56:23 -0500
Commit message:

 chore(flake): clean up, pass buildInputs correctly

correctly passing native vs propagatedBuildInputs, rename lists
accordingly

the devShells buildInputs aren't needed since its gets it from
inputsFrom and dev shell tools go in packages
Package: iscream
Commit: 2c4070b15e11c669144471918303edb68bd71536
Author: James Eapen <james.eapen@vai.org>
Date: 2025-12-08 13:55:36 -0500
Commit message:

 chore(DESCRIPTION): bump version
Package: iscream
Commit: 7de6990d9a799ae147824c38dfef0089c034d8e0
Author: James Eapen <james.eapen@vai.org>
Date: 2026-01-08 10:37:49 -0500
Commit message:

 test(summarize_regions): update tests with pstddev
Package: iscream
Commit: 6e717075232292394c07b1df219d14a44d32da6e
Author: James Eapen <james.eapen@vai.org>
Date: 2026-01-08 10:27:55 -0500
Commit message:

 feat(summarize_regions): add population standard deviation
Package: iscream
Commit: e541bca53da07e3f1f641e45dc6069cb10173764
Author: James Eapen <james.eapen@vai.org>
Date: 2025-12-29 16:31:42 -0500
Commit message:

 docs(summarize_regions): add GRanges mcol as feature_col input

Its in the details but to more clearly say that granges with features as
mcols are allowed
Package: iscream
Commit: be07e19acf9c21a042d342b3bec51d31074cff00
Author: James Eapen <james.eapen@vai.org>
Date: 2025-12-29 16:32:58 -0500
Commit message:

 chore(NEWS): format functions so they're linked
Package: iscream
Commit: e4d2f5bb8a3aeb2bf57494c14203c600ca899765
Author: James Eapen <james.eapen@vai.org>
Date: 2025-12-29 15:50:43 -0500
Commit message:

 chore(NEWS): update
Package: iscream
Commit: 2d03348f43b6f814b996e92bd060ec855d17ecf2
Author: James Eapen <james.eapen@vai.org>
Date: 2025-12-29 15:14:33 -0500
Commit message:

 docs(vignettes): fix missing 'uses'
Package: iscream
Commit: e6f4fcecf747c771d1810d78d02790101e3390bc
Author: James Eapen <james.eapen@vai.org>
Date: 2025-12-29 15:06:00 -0500
Commit message:

 docs(vignettes): knit performance vignette
Package: iscream
Commit: d1b28b5c0490d45ae9ed0da4bb785e1348c6cb8d
Author: James Eapen <james.eapen@vai.org>
Date: 2025-12-29 15:04:00 -0500
Commit message:

 docs(vignettes): explicitly load SummarizedExperiment
Package: iscream
Commit: 51351c96f7e4ea35b28d4da09762c3dfd63e79ca
Author: James Eapen <james.eapen@vai.org>
Date: 2025-12-29 15:03:27 -0500
Commit message:

 docs(vignettes): reduce funs used to fit width without overflow
Package: iscream
Commit: 7222e24584d83d4daef8cd58d9a5e8a1271cb85d
Author: James Eapen <james.eapen@vai.org>
Date: 2025-12-29 15:52:37 -0500
Commit message:

 docs(vignettes): read genes names