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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: BiocBookDemo
Commit: 45ac12ecff53c2ef7ea22c123f9d4ecfc5151408
Author: Jacques <jacquesserizay@gmail.com>
Date: 2026-09-04 23:33:51 +0200
Commit message:

 bump to 1.11.1
Package: BiocBookDemo
Commit: f62a453792b89f611ef62dbde4d0e8014d0d23ea
Author: Jacques <jacquesserizay@gmail.com>
Date: 2026-09-04 22:51:35 +0200
Commit message:

 fix: python code chunk styling
Package: BiocBookDemo
Commit: d0ebc71142a96f083228fdfd3f92f3f63e79f1c9
Author: Jacques <jacquesserizay@gmail.com>
Date: 2026-09-04 22:37:29 +0200
Commit message:

 fix: deeptool call
Package: BiocBookDemo
Commit: 214a0f6f1e70408e257c52e7753fc222f9a853c7
Author: Jacques <jacquesserizay@gmail.com>
Date: 2026-09-04 22:16:45 +0200
Commit message:

 fix: cooler calls
Package: BiocBookDemo
Commit: f3ab969763d74b832b2a39e702cb890603860606
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-09-04 15:31:53 +0200
Commit message:

 deps: add remotes entry for js2264/BiocBook
Package: BiocBookDemo
Commit: 9b22b0a5111b436e83eb7619f5df405d48f81292
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-09-04 14:55:06 +0200
Commit message:

 feat: try python chunks
Package: BiocBookDemo
Commit: 5ec6cc57d053215a555b2df43b11cd8e811afcd3
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-09-04 13:37:33 +0200
Commit message:

 ci: install remotes
Package: BiocBookDemo
Commit: ca6e15e72a8a688d06a288d108ecce45644c7c29
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-09-04 12:35:49 +0200
Commit message:

 fix: enable pdf
Package: BiocBook
Commit: 562ccc635b0c10de5985680723cd8a7e069b3700
Author: Jacques <jacquesserizay@gmail.com>
Date: 2026-09-04 23:07:54 +0200
Commit message:

 bump to 1.11.1
Package: BiocBook
Commit: ab1ec74767b683b2f58ae06f5b8be0e2befa3377
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-09-04 17:08:38 +0200
Commit message:

 fix: update documentation
Package: BiocBook
Commit: 322a1b2503af44afe551ea32e3191e2df1685fb8
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-09-04 16:24:51 +0200
Commit message:

 doc: enhance doc for Python integration with setup_python and micromamba support
Package: BiocBook
Commit: 035b6e614b14ce7659ae27d6118f8e6715ae5912
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-09-04 15:31:12 +0200
Commit message:

 fix: move reticulate from Suggests to Imports
Package: BiocBook
Commit: ae57e24ff22aca7fbee763e3a83d24b0388a8ccc
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-09-04 15:26:59 +0200
Commit message:

 feat: add support for Python chapters and micromamba integration
Package: BiocBook
Commit: 45db39041157e59e95fc5cc09126ab85bae05845
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-09-04 15:21:06 +0200
Commit message:

 feat: add page body directly from function call
Package: splicelogic
Commit: b78a80ffefe2fc5ce6be14611497113c4b3433ae
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-04 15:31:58 -0400
Commit message:

 Version bump to 1.1.4
Package: splicelogic
Commit: da080e700961eb07a85b7106f928a39a3c33b927
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-04 15:31:19 -0400
Commit message:

 update news to 1.1.4 and add renamed functions
Package: splicelogic
Commit: 6dd72f9595b7d75f982eeb3c1fedb65c0fbf792b
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-04 15:28:06 -0400
Commit message:

 rename alternative splice site functions for clarity and update documentation
Package: splicelogic
Commit: c612e3086961632efdad3d408c3b3b64ea28e3dc
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-04 14:55:36 -0400
Commit message:

 update news for version 1.1.3
Package: splicelogic
Commit: 3e2c8147ebd134e9109787fc23420a489b1e57ff
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-04 14:53:06 -0400
Commit message:

 Version bump to 1.1.3
Package: splicelogic
Commit: c4c1bac824dfdaadb01bf34a19690b7201ef6414
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-04 14:27:04 -0400
Commit message:

 update README
Package: splicelogic
Commit: 86c9d38b5476ddc39683fca6ff4fb00f42f68b61
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-04 14:22:13 -0400
Commit message:

 vignette updates and reorganization
Package: splicelogic
Commit: 615a016eb5798831da3f245ae496b071ce3c89d9
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-04 14:20:01 -0400
Commit message:

 Update documentation for 'type' parameter in find_events functions
Package: splicelogic
Commit: 43a3af54ad7a36e26980ee20c0cf11a5df55d42f
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-03 22:03:26 -0400
Commit message:

 Enhance documentation and include alternative transcription start and end site detection
Package: splicelogic
Commit: 603a49df90592a0b482b715b935157afe3991807
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-03 22:03:01 -0400
Commit message:

 Add 'coord_sig' to globalVariables in mock data generation functions
Package: splicelogic
Commit: cd0834b71bdfb74904c0deb2bf2fae7e56375a5f
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-03 21:55:17 -0400
Commit message:

 lowercase functions find_atss and find_ates
Package: splicelogic
Commit: a1b5afed7f099009fbac1328db505029b0b46471
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-03 21:31:17 -0400
Commit message:

 update documentation
Package: splicelogic
Commit: b76726731744ee32f08360dcddabfe728a276cbc
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-03 21:29:36 -0400
Commit message:

 Add functions for alternative transcription start and end site detection with tests
Package: splicelogic
Commit: c5d76e542805cde079361068ccc2830f5ebe4846
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-03 21:20:50 -0400
Commit message:

 Add functions for alternative transcription start and end site detection
Package: splicelogic
Commit: ea74b27d9d516af98941aa0f0f8bb09ea39baf5d
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-09-03 14:48:16 -0400
Commit message:

 allow a3ss and a5ss to happen in same exon and avoid misslabeling in first and last exons
Package: splicelogic
Commit: 13f259a9eaaf4dde27098a2d61db82d04a1eeb97
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-31 16:35:03 -0400
Commit message:

 Add strand argument to create_mock_data documentation and examples
Package: splicelogic
Commit: ded70e04a2ec68c5843b7b49f11cded4ea6ca7d3
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-31 16:34:36 -0400
Commit message:

 support & tests for minus-strand data handling in event detection functions and mock data generation
Package: splicelogic
Commit: 95da67951f7343d4569e631154d173925c043748
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-31 16:25:06 -0400
Commit message:

 Add support for strand-specific a5ss/a3ss detection in find_alt_ss and corresponding tests
Package: splicelogic
Commit: 3b91fd3c880316cdd6bef5ec824fecf35a78db3a
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-27 16:47:45 -0400
Commit message:

 remove gene_id column for visibility
Package: splicelogic
Commit: 0ba1f8cddb72c4e4a1f4fe4028640c14dd539cbe
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-27 16:44:06 -0400
Commit message:

 Clarify documentation on upstream DTU methods in vignette
Package: splicelogic
Commit: 028938c48a99e2b8aba5eeae4ef9911a4a9bbf7d
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-27 16:33:12 -0400
Commit message:

 Enhance documentation for `find_*()` functions in vignette
Package: splicelogic
Commit: 30444b66c4158a1fd6f91c01cd96363b102d47bc
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-27 16:22:05 -0400
Commit message:

 Update mock data generation script and files for exon_id
Package: splicelogic
Commit: 5dc7c080aa24ac66a6cf871ffe3aecf98b36ade9
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-26 13:56:58 -0400
Commit message:

 fix the bug
Package: splicelogic
Commit: b04e42bd0dabccd6e384187f77034944a162b70b
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-26 13:31:08 -0400
Commit message:

 one more tweak
Package: splicelogic
Commit: 4948fe1b50796f3d2cf3a748c1e3b409a3328945
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-26 13:20:29 -0400
Commit message:

 some vignette tweaks
Package: splicelogic
Commit: f0c12e7109c04df3b17af46ea32bc951d113f321
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-08-26 12:11:08 -0400
Commit message:

 tweak to the README
Package: splicelogic
Commit: e92abf0c08daa93a2da0e18cf6977aabf25ed5fc
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-21 17:24:46 -0400
Commit message:

 Update installation instructions
Package: splicelogic
Commit: dba60f4b6ef6bff6764a12b7ccc4e4a3240326a4
Author: Beatriz Campillo <beatrizcampillo29@gmail.com>
Date: 2026-08-21 17:20:43 -0400
Commit message:

 Update README title for clarity
Package: splicelogic
Commit: 66336cb1f052b5843babf699ae819cd7501620bf
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-21 17:18:48 -0400
Commit message:

 fix library(splicelogic) call
Package: splicelogic
Commit: 6a21745dbbbb1504abb2f8ef26388f19365e0ff6
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-21 17:11:30 -0400
Commit message:

 Update README to clarify splicelogic functionality for transcript sets
Package: splicelogic
Commit: 9a8e22ef7a82941e7a8d4b88a5f21ca1f1fedf2e
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-21 17:08:00 -0400
Commit message:

 Big reorganization and include example for transcript sets
Package: splicelogic
Commit: ba05881b0b4001b799a6d4594a385a068592ff66
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-21 17:01:17 -0400
Commit message:

 comment fix
Package: splicelogic
Commit: e4d0fe8207a5f0327b13167e24cb30d872eb719c
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-21 16:46:36 -0400
Commit message:

 Add mock data generation script and corresponding exon files
Package: splicelogic
Commit: cd746588c7e6c505d6123aebe064dc38cae4c721
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-20 16:09:32 -0400
Commit message:

 Add test for find_mxe to ignore overlapping middle exon as MX candidate
Package: splicelogic
Commit: 328178ef785a742a5e4ea04c24f5c5b833c26f03
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-20 16:09:17 -0400
Commit message:

 Fix: improve filtering logic for mxe to avoid FP
Package: splicelogic
Commit: d2f50d2826b0c752740660ef0c64cd9ddcdb3394
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-10 15:01:00 -0400
Commit message:

 Add tests for exon_rank validation in preprocess function
Package: splicelogic
Commit: 8e24c5c057f1f8cb9142d277d54b3a486a0a8678
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-10 14:54:47 -0400
Commit message:

 Add cds_mock_data and test for skipped exon detection in cds
Package: splicelogic
Commit: 784a5a411ebd0d9ebfc4f71104dce7a27cb8dace
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-10 14:52:43 -0400
Commit message:

 Fix:  check_exon_rank function to ensure consecutive exon ranks within transcripts in input
Package: splicelogic
Commit: cb4769ea24bdce6954d34123af07f730da4342d3
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-08-07 10:25:12 -0500
Commit message:

 Fix: update internal flag calculation to correctly handle exon ranks not starting at 1
Package: splicelogic
Commit: 2c0f9bf996a709bb92abbbe968bdda9e27321151
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-07-28 15:04:44 -0400
Commit message:

 adding sim_event column for sim event generators
Package: splicelogic
Commit: b9ae62f270dc46cd6482df90e455aaf9a6179573
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-07-28 11:58:18 -0400
Commit message:

 Fix: count isoforms not exons when selecting candidates by splitting positive exons by transcript; add testing
Package: splicelogic
Commit: b8e0f54931162106cd09431e797ac9db89e5c191
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-07-27 17:41:57 -0400
Commit message:

 Fix: count_overlaps() by renaming seqnames to gene_id for accurate gene-specific overlap counting
Package: splicelogic
Commit: f257e4cf36cefd2991f9b321870a315d471f8337
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-07-27 13:04:09 -0400
Commit message:

 fixing the per gene event in generate_se
Package: splicelogic
Commit: ab22ca47e35aeb030b15902a887e060591c4d125
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-07-27 12:10:35 -0400
Commit message:

 per-gene coordinate offset now scales with n_exons_per_tx
Package: splicelogic
Commit: a24951b26bd4b076657422951774f8127d5b7177
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-07-27 11:56:47 -0400
Commit message:

 supressing some select() messages
Package: splicelogic
Commit: 1ebe730ed7e54affaf96bb5c80fa2f4a7fe2f03f
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-07-27 11:36:34 -0400
Commit message:

 Add alias functions
Package: splicelogic
Commit: 4bf370c0fbf4401946238cd1ee02a4511d79b9b6
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-05-19 17:55:25 -0400
Commit message:

 suppress msg
Package: splicelogic
Commit: 0f87d488db71ea33251d9f786731f2be20aa72c6
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-05-19 17:43:30 -0400
Commit message:

 fix pipe
Package: splicelogic
Commit: 401821432a62badb4fab6163e8bb2289a3597eca
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-05-19 17:43:21 -0400
Commit message:

 fix pipe
Package: splicelogic
Commit: 3a75b309a9bae20d45074f7832f684443d4e3a25
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-05-19 12:47:42 -0400
Commit message:

 updating docs for get_seq
Package: splicelogic
Commit: 57a21a0460746c4056c05521f8476fd4b5367187
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-05-19 09:51:12 -0400
Commit message:

 fix back
Package: splicelogic
Commit: 5931f89c6a779085ab4d0dbecf2afe088d4bd523
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-05-19 09:44:11 -0400
Commit message:

 Merge branch 'devel' of github.com:thelovelab/splicelogic into devel
Package: splicelogic
Commit: 5044fdc58ba7432a7a59328a44d304e16840a2ac
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-05-19 09:44:10 -0400
Commit message:

 small vignette tweaks
Package: splicelogic
Commit: 6f63ec20d84d765ce0f9140d7f78a8fa813b5156
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-05-19 09:25:58 -0400
Commit message:

 add get_seq() reference
Package: splicelogic
Commit: 9f8118bef9d1e54a0cd3ddad38dbbfe54ae5ecfe
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-05-18 22:53:29 -0400
Commit message:

 remove check from examples in get_seq documentation
Package: splicelogic
Commit: 0075a49906ed274720ce5041839976fc0bfdb603
Author: beamimc <beatrizcampillo29@gmail.com>
Date: 2026-05-18 22:51:16 -0400
Commit message:

 add get_seq function to extract sequences from GRanges
Package: splicelogic
Commit: c6d723cbfc329cf9832cccc721c14deb88afb902
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-05-18 17:18:47 -0400
Commit message:

 some tweaks to the vignette text
Package: SAIGEgds
Commit: 12a60aa0fd7fcff3041fd8aa5845df028bdf4162
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-09-04 13:59:39 -0500
Commit message:

 new survial analysis
Package: scpdata
Commit: f42b85c6bd52be8e9aed352d000c10549d0cd3cb
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-09-04 13:46:05 +0000
Commit message:

 Merge pull request #40 from leopoldguyot/master

Add zenodo path for wu2026
Package: scpdata
Commit: 725c98fe87f4e47abcdf7b38534cdca502c6c1ae
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-09-03 17:42:26 +0200
Commit message:

 update data location
Package: scpdata
Commit: 57c0a9e5df9bbdf64b60a2d5f34338187563b741
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-09-03 17:38:26 +0200
Commit message:

 add data to zenodo
Package: scpdata
Commit: 9fdd0ae45c0650b0402ea32787145435fe97f3e3
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-09-03 15:31:46 +0200
Commit message:

 Update version and NEWS + fix make-data table
Package: scpdata
Commit: 1dee3215410ed2bc7ea1aac53015c68e89269a53
Author: Léopold Guyot <leopold.guyot13@gmail.com>
Date: 2026-09-03 15:25:43 +0200
Commit message:

 Merge branch 'master' into master
Package: scpdata
Commit: 44b5d73969044f7410f821a6d7772bf1f39b3816
Author: Léopold Guyot <leopold.guyot13@gmail.com>
Date: 2026-04-27 15:58:29 +0200
Commit message:

 Merge branch 'UCLouvain-CBIO:master' into master
Package: scpdata
Commit: 3578e0d9de4959a29b8541f11c0e9eabed59b5a8
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-04-27 15:58:11 +0200
Commit message:

 change data path to zenodo
Package: BiocCheck
Commit: d12d0480ea16c2391709df6d010b2c6326d932ad
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-09-04 12:03:48 -0400
Commit message:

 Add BiocType as acceptable Description field
Package: BiocCheck
Commit: ca5c23e019dd695b7a5e29286f593a0e9b13639a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-07-27 11:07:54 -0400
Commit message:

 version bump 1.49.30
Package: BiocCheck
Commit: d19ace18a62d0f9b2f536eeaa0cdc489cdb3df7c
Author: Jeroen Ooms <jeroenooms@gmail.com>
Date: 2026-07-27 10:20:06 +0200
Commit message:

 Allow RemoteRef, RemoteUrl, RemoteSha, etc used by R-universe.
Package: spammR
Commit: 6a00912bf80a805a7ae7479870a722c1b7e303d3
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-09-04 08:54:58 -0700
Commit message:

 bumping version
Package: ramr
Commit: 6be608986bda9d0f39f48f3610ba0200ae9f5769
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2026-09-04 16:53:24 +0200
Commit message:

 correct measure.vars
Package: ramr
Commit: 93026620b156d9bce60834a6adc5d318ef37bec3
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2026-09-04 16:44:17 +0200
Commit message:

 mcols to S4Vectors
Package: ramr
Commit: 8c7fb8f577344439a98054f0f327586a2b81002f
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2026-09-04 16:24:09 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: ramr
Commit: 28a33b2ed0f227a6709d4403f8feeedb573cd27b
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2026-09-04 16:20:57 +0200
Commit message:

 non-ASCII fix
Package: ramr
Commit: e949322cd76e8c906a2ac295a86aa30aa3e0f6e5
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2026-09-04 16:19:05 +0200
Commit message:

 fresh flow
Package: exploreSE
Commit: e15d7f5711b8437f37d434b29281e07043605672
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-09-04 11:16:54 +0200
Commit message:

 buf fix in .de_results
Package: exploreSE
Commit: 48c7d194fc4a3efcc5c36e838b09cc7407196823
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-09-04 11:10:50 +0200
Commit message:

 excluded NS from the hitlist
Package: OmniAgeR
Commit: 21c6cec316fffeeb4ffd22257e8282e8443a7a1e
Author: Zhaozhen Du <duzhaozhen@inspur.com>
Date: 2026-09-04 17:09:39 +0800
Commit message:

 Address Bioconductor review comments
Package: alabaster.mae
Commit: 32fd9aad7dfa676c8b28d386b69978cc8a494401
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-04 19:04:42 +1000
Commit message:

 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.
Package: OmniAgeRData
Commit: f5c64ca486ab428571f06c75c6857cedb31f5263
Author: Zhaozhen Du <duzhaozhen@inspur.com>
Date: 2026-09-04 16:54:10 +0800
Commit message:

 Fix value documentation for clock resources
Package: alabaster.files
Commit: c1b99b888836f6ece95eb792f78eea844e5b5600
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-04 18:51:26 +1000
Commit message:

 Added NEWS, updated LICENSE, fixed doclinks and roxygen warnings.
Package: alabaster.files
Commit: 8d5c2c111ff41ad86e8533ea11a3137432c927bb
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-04 18:36:11 +1000
Commit message:

 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.
We also deprecated the various Wrapper classes in favor of FileReference.
Package: canceR
Commit: 92939cd570eb107c6ea9b74b2df3c79effbbee8c
Author: kmezhoud <kmezhoud@gmail.com>
Date: 2026-09-04 09:31:04 +0100
Commit message:

 add pandoc dependency and omit warning caused by @usage tag
Package: alabaster.bumpy
Commit: bf0a372898af6a40e026bb6e6ea6ee3d0eb24cf8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-04 18:08:49 +1000
Commit message:

 Fixed license, added NEWS.
Package: alabaster.bumpy
Commit: 41522ed6718e831e7c92bafb5c27e7aff821b272
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-04 18:02:32 +1000
Commit message:

 Officially deprecate the stageObject(), loadObject() methods.

Almost everyone should already be using saveObject and loadObject anyway.
Package: OmniAgeRData
Commit: 11f63325fb520fa9923c05b4d696a902a803c593
Author: Zhaozhen Du <duzhaozhen@inspur.com>
Date: 2026-09-04 15:37:53 +0800
Commit message:

 Add resource licensing information and update documentation
Package: alabaster.matrix
Commit: b1ca9185cdfe42bd0fb08cf7e4244118dbe1b886
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-04 16:19:00 +1000
Commit message:

 Fleshed out NEWS with the latest changes.
Package: alabaster.matrix
Commit: 35c2056594c30b172a237e0ce9dbfa8e007b6407
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-04 16:10:47 +1000
Commit message:

 Officially deprecated functions associated with stageObject/loadObject.

Almost everyone should already be using saveObject and readObject anyway.
Package: alabaster.base
Commit: e63144a8f66516989b797494b2d51eda37ce854c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-04 16:04:23 +1000
Commit message:

 Updated NEWS with the deprecation notice.
Package: alabaster.base
Commit: 64d4495c070a3f12cb2e26b35de0996170321922
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-04 14:02:44 +1000
Commit message:

 Officially deprecate all functions for stageObject/loadObject.

We want to push folks to saveObject/readObject, though hopefully they're
already there, given that we've soft-deprecated stage/load for a long time.
Package: edgeR
Commit: 4a090edefd1379ec471ea81cb84fee50a30c3505
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-09-04 15:30:39 +1000
Commit message:

 edgeR 4.99.3
- New argument `impute.eff.len` for catchSalmon() and catchSalmonWithGencode().
- Moderated gene lengths from catchSalmonWithGencode() are now moderated more strongly towards gene average.
- All catch functions store matrix of effective lengths, now called `effective.length`.
- Annotation columns from catch functions now called AveEffLen, Max2MinEffLen instead of AveTxLength, Max2MinTxLength.
- Bug fix to catchRSEM() to store sample-specific tx lengths. Previously just storing those for first sample.
- Expanded help for catch functions.
Package: QFeatures
Commit: c4b3bb93ec0b824a52d2f20ea05d5b15a26d7c52
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-09-03 20:29:47 +0200
Commit message:

 add pkgdown topic
Package: QFeatures
Commit: 05a7fffbb96a52b4020910785736b07a840b539c
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-09-03 15:44:16 +0000
Commit message:

 Merge pull request #263 from leopoldguyot/aggregateSamples

Implementation of aggregateSamples
Package: QFeatures
Commit: 053108deed33feedd4a1bd96abcbfcc60f6949d2
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-09-03 17:17:51 +0200
Commit message:

 add ORCID
Package: QFeatures
Commit: 3f15be698ea763fe134e7f18a9014e3587782666
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-08-27 16:48:20 +0200
Commit message:

 replace moreFUN by fixed aggsd and aggcounts extra assays
Package: QFeatures
Commit: ed02bdf51f14182e2339dc8c6931a397147c80c5
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-08-19 16:45:06 +0200
Commit message:

 add extra parameters for setAs
Package: QFeatures
Commit: 1cb5eae9f670bf9a03284b474b0e275a9599ecb7
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-08-19 11:56:49 +0200
Commit message:

 assay into set QFeatures-class.R
Package: QFeatures
Commit: 26e85fe48758876e4b568fd22120c1d89db91162
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-08-19 11:06:20 +0200
Commit message:

 rename assay into set in aggregate tests
Package: QFeatures
Commit: fe939d0b12e44e55c037925a4a22500d65cbb698
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-08-19 10:28:15 +0200
Commit message:

 rename assay by set in QFeatures-aggregation.R
Package: QFeatures
Commit: 22643f908682b99ceda7c8d14a0f391475d5ad8e
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-07-29 15:15:29 +0200
Commit message:

 add NEWS + update outdated condition
Package: QFeatures
Commit: 79a7e4bc4aaa65c0c65949ba2d02737059caf68d
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-07-29 14:46:48 +0200
Commit message:

 colData joining handled by addAssay, argument forwarding, drop factor + tests and docs
Package: QFeatures
Commit: 9b35df2522b1cb24984f8a7fa4f928f392d4b8b3
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-07-28 16:25:35 +0200
Commit message:

 add tests for aggregateSamples + styling
Package: QFeatures
Commit: 62a2eb799f0636ac77ce9ccf45323df54128c3fb
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-07-28 13:07:02 +0200
Commit message:

 enforce i and name of length one
Package: QFeatures
Commit: 8fe9d57679ba19e9551a99e72d9fdbada75b7c2e
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-06-29 17:13:34 +0200
Commit message:

 first implementation of aggregateSample
Package: spammR
Commit: 0b17c8af18ef96b4987a08af8d95c281b5c9da3a
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-09-03 11:57:06 -0700
Commit message:

 updated to address build issues
Package: spammR
Commit: 108eb55f1411a76ba8d7caff475cdf8e67bf7d71
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-09-03 11:03:26 -0700
Commit message:

 updated documentation
Package: spammR
Commit: bce77ccc76ecb490e07d57a3cec363b1996722a6
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2026-09-03 10:22:05 -0700
Commit message:

 moved to DT::datatable

Per recommendation from Vince Carey, updated vignettes
Package: exploreSE
Commit: 16e225f2af495f7c542231f519acd8044f3e1fb7
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-09-03 16:45:46 +0200
Commit message:

 added split table
Package: exploreSE
Commit: f88954b0529d15b61a689496252f8322259144f6
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-08-24 13:54:36 +0200
Commit message:

  readme update
Package: exploreSE
Commit: 8b9700aa5ccaf127bacdf6e24352105967614891
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-08-21 11:47:18 +0200
Commit message:

 updated readme
Package: exploreSE
Commit: 5f433744b4b16416fdc63a71c9cdd43407ec225b
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-08-21 11:18:01 +0200
Commit message:

 readme update
Package: exploreSE
Commit: ad413cab9e0d3634dc34452ed92f368b4749a732
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-08-21 11:12:33 +0200
Commit message:

 another readme update
Package: exploreSE
Commit: a1c9083de90f9f4a19bb945bd5fa2845ba8b21d6
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-08-21 11:01:57 +0200
Commit message:

 rereredo of readme
Package: exploreSE
Commit: b9c45c25f6ca6e04d123c24ea39a8c8ec29d0975
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-08-21 10:51:33 +0200
Commit message:

 reredo readme
Package: exploreSE
Commit: 22d9c4297261ad1d11c925411074921dd4b79276
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-08-21 10:22:59 +0200
Commit message:

 updated readme again
Package: exploreSE
Commit: d5a865c5c22c972d0b93163eefd44ee2328fd30f
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-08-21 10:11:02 +0200
Commit message:

 updated readme
Package: lcmsPlot
Commit: 5c62d07fcdb6d63e1309a440f54a93e6eb57ae3c
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2026-09-03 14:32:15 +0100
Commit message:

 feat(spectra): add mz_breaks_n option for m/z axis breaks

Expose the number of pretty breaks on the spectrum m/z axis as an
lp_spectra() option instead of a hardcoded value of 20, and bump the
package version. Also renames the internal .cd_node_col helper to
first_matching_column and trims stale xcms cross-references from a
few man pages.
Package: PostChicago
Commit: 865ba5936f89143aca8c1571d2789df12f9ac7b8
Author: Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de>
Date: 2026-09-03 14:22:08 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/PostChicago into devel
Package: PostChicago
Commit: 326117225007e3cd1ffac4f6de623403a33eec13
Author: Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de>
Date: 2026-09-03 13:31:03 +0200
Commit message:

 Add files via upload
Package: PostChicago
Commit: dd0175858b82691482f660004794194fa656413c
Author: Angelika Feldmann <angifeldmann@gmail.com>
Date: 2026-09-03 13:30:41 +0200
Commit message:

 Delete NAMESPACE
Package: PostChicago
Commit: 0f1f93a2db7f8231d6fdfd98088b44d66d1e28cd
Author: Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de>
Date: 2026-09-03 13:26:28 +0200
Commit message:

 Add files via upload
Package: PostChicago
Commit: ca928509dd971fdb9e223d3e285ca8beb48e7f47
Author: Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de>
Date: 2026-09-03 13:25:37 +0200
Commit message:

 Add files via upload
Package: PostChicago
Commit: ed66d3ae6c63d7fc43022ada000b73cd63d5f2e3
Author: Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de>
Date: 2026-09-03 13:25:16 +0200
Commit message:

 Add files via upload
Package: PostChicago
Commit: 10a61dd39e30249d0c118002b87e128e4d1959d4
Author: Angelika Feldmann <angifeldmann@gmail.com>
Date: 2026-09-03 13:23:09 +0200
Commit message:

 Delete NAMESPACE
Package: PostChicago
Commit: 0c153ea536647372a229fa1d5425409d9f45d61f
Author: Angelika Feldmann <angifeldmann@gmail.com>
Date: 2026-09-03 13:22:59 +0200
Commit message:

 Delete DESCRIPTION
Package: PostChicago
Commit: 8851f1eb7185b1c0af3465117d7f2b761caf44a8
Author: Angelika Feldmann <angifeldmann@gmail.com>
Date: 2026-09-03 13:22:45 +0200
Commit message:

 Delete vignettes directory
Package: PostChicago
Commit: 22219d3e94406115164784976e3859b781d021f3
Author: Angelika Feldmann <angifeldmann@gmail.com>
Date: 2026-09-03 13:22:27 +0200
Commit message:

 Delete man directory
Package: PostChicago
Commit: 2811ab66ed7e55ebd03993cc5344ca2d9612e500
Author: Angelika Feldmann <angifeldmann@gmail.com>
Date: 2026-09-03 13:22:01 +0200
Commit message:

 Delete inst/extdata directory
Package: PostChicago
Commit: dfafa60b7e9452e0a84e582f98179c227b78d76d
Author: Angelika Feldmann <angifeldmann@gmail.com>
Date: 2026-09-03 13:21:47 +0200
Commit message:

 Delete R directory
Package: miRSM
Commit: 702e8e3321cb2f57ac98777403afe230ccdd373d
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2026-09-03 20:07:05 +0800
Commit message:

 Update
Package: miRSM
Commit: c6462ef0f06da4879b1aba6cf7ae3f7f3356285d
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2026-07-23 16:56:54 +0800
Commit message:

 update
Package: miRspongeR
Commit: 58ede134f2904ab6b8a28077cc9d6b2e54fe3a26
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2026-09-03 19:52:45 +0800
Commit message:

 UPDATE
Package: miRspongeR
Commit: ebb69e02fe0d5d5f41c23e1ca544dd1ea0b57c60
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2026-07-23 15:41:37 +0800
Commit message:

 Update
Package: ontoProc2
Commit: f18431d2289961758a944899d775883e825f002b
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-09-03 07:08:21 -0400
Commit message:

 add ggraph/graphlayouts alternatives to onto_plot2 (Rgraphviz-free)

Introduces onto_plot2_sugiyama and onto_plot2_stress as ggplot2-based
alternatives using igraph + ggraph + graphlayouts. All visual constants
are collected in onto_plot2_params() so callers can tune appearance
without touching individual arguments. Bumps version to 0.99.32.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: cosmosR
Commit: b2ed195738479c4ad204cace37fd11ae2fd02bb8
Author: Aurelien Dugourd <dugourd@ebi.ac.uk>
Date: 2026-09-03 10:31:50 +0100
Commit message:

 fix: remove legacy DoRothEA dependency
Package: spatialFDA
Commit: 1b1c9d6f6dbf61535d3ff1a4118cc0011e03dc58
Author: mjemons <martin.emons@gmail.com>
Date: 2026-09-03 10:00:13 +0200
Commit message:

 option to apply link inverse to intercept
Package: cosmosR
Commit: 0cb316a7d6b5d472d1a5db12562e1f6cf8d072f7
Author: Aurelien Dugourd <dugourd@ebi.ac.uk>
Date: 2026-09-03 09:36:57 +0100
Commit message:

 chore: synchronize Bioconductor devel and GitHub master
Package: cosmosR
Commit: 78af5e12c9ec2bdcc71e887669c89e74c9f9c263
Author: Aurelien Dugourd <dugourd@fwytr7kc7t.windows.ebi.ac.uk>
Date: 2026-07-28 14:44:38 +0100
Commit message:

 docs: bundle MOON semantic guides
Package: cosmosR
Commit: 5e9d5552f249a67309802e0ac2e7be03cb55468f
Author: Aurelien Dugourd <dugourd@fwytr7kc7t.windows.ebi.ac.uk>
Date: 2026-07-28 13:03:48 +0100
Commit message:

 docs: make MOON skill portable
Package: cosmosR
Commit: 6d8acf8a7e11cb3a5211c17fa80c7995838a59ce
Author: Aurelien Dugourd <dugourd@fwytr7kc7t.windows.ebi.ac.uk>
Date: 2026-07-28 11:44:06 +0100
Commit message:

 docs: add COSMOS MOON pipeline skill
Package: cosmosR
Commit: 3744609402b643afe283dcf35c23069477c6fb97
Author: Aurelien Dugourd <dugourd@fwytr7kc7t.windows.ebi.ac.uk>
Date: 2026-06-04 16:30:48 +0100
Commit message:

 test push
Package: cosmosR
Commit: f260369477b4a7910692406cf2e82234d4160a14
Author: Aurelien Dugourd <dugourd@ebi.ac.uk>
Date: 2026-06-04 11:34:08 +0100
Commit message:

 Add MOON data-to-PKN mapping vignette
Package: cosmosR
Commit: 469f0fe223652f2613787a3ef116704a31d14558
Author: Aurelien Dugourd <dugourd@ebi.ac.uk>
Date: 2026-06-04 10:47:32 +0100
Commit message:

 Add perturbation and timepoint MOON guidance
Package: cosmosR
Commit: 1860432cd9b1dc78ea99fd4bf5ab84b299ebd3fb
Author: Aurelien Dugourd <dugourd@ebi.ac.uk>
Date: 2026-06-04 09:20:06 +0100
Commit message:

 Refine DNA lesion propagation guidance
Package: cosmosR
Commit: 84a2f512fdd462c1fbbdca6ed2d51de8d9c0ffd8
Author: Aurelien Dugourd <dugourd@ebi.ac.uk>
Date: 2026-06-03 17:06:08 +0100
Commit message:

 Add agent-facing MOON workflow guidance
Package: cellNexus
Commit: 9fb8d97e6a7e4e44223b9df798d050c7254ccebb
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-09-03 14:42:57 +1000
Commit message:

 Merge pull request #156 from myushen/bioccheck_dependency

remove cellxgene.census dependency in suggest
Package: cellNexus
Commit: a5f9e79c577884ee361b726586f72d70378a814a
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-09-03 14:19:16 +1000
Commit message:

 remove cellxgene.census dependency in suggest
Package: cellNexus
Commit: fa590e1ff88b9cb58a461a16bc6715892dab3d98
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-08-25 14:01:29 +1000
Commit message:

 Merge pull request #151 from myushen/guard_file_download_corruption

Guard file download corruption
Package: cellNexus
Commit: fbe84ad7af6b366d6777e4f33aa9a7410151c414
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-08-13 14:21:22 +1000
Commit message:

 NEWS
Package: cellNexus
Commit: 8c37e3215600c724402333fda5b1ce484763cf5a
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-08-13 13:46:07 +1000
Commit message:

 limit server-side parallel connections to 500 per batch
Package: cellNexus
Commit: 719dec949956a01448c437f08babe21de96e0c7e
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-08-13 11:51:03 +1000
Commit message:

 resolve half-download/corrupted files, resume download
Package: cellNexus
Commit: d49432f6579b0209f786e9cfc0ba0434d7f69088
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-08-07 15:58:44 +1000
Commit message:

 Merge pull request #148 from myushen/add_download_only_argument

add download_only argument to get_* functions
Package: cellNexus
Commit: 980a356c86b114b153f0b3dabb31479e9e44dd89
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-08-07 15:32:23 +1000
Commit message:

 add download_only argument to get_* functions
Package: jazzPanda
Commit: 8517a1854dd69c5ee389d181b3bb47b7cab75492
Author: Melody <Melody-Jin@outlook.com>
Date: 2026-09-03 12:28:28 +1000
Commit message:

 add preprint/workflowr link
Package: DuckDBGRanges
Commit: 86c1be7bda3c12a7e4c65c51b567dae60204328f
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-09-02 21:24:56 -0400
Commit message:

 docs: cleaned up the prose in the results section of the benchmarking vignette
Package: tidyprint
Commit: dccb01abb0a143257e10d91a802e3a2f02414f87
Author: Chen Zhan <chen.zhan@adelaide.edu.au>
Date: 2026-09-03 10:43:48 +0930
Commit message:

 Transfer maintainer role to Stefano Mangiola in DESCRIPTION

Chen Zhan remains author; Stefano Mangiola is now maintainer (cre).
Package: tidyprint
Commit: 4bfafe52910a208f4524f80f3e69872f9e02bbe3
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 16:31:47 +0930
Commit message:

 Merge pull request #33 from tidyomics/fix-option-overrides-cache-once-per-session

Fix option overrides cache once per session
Package: tidyprint
Commit: 44fef534f86d0b94f8fe658f399d9e2f633c97a7
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 15:55:18 +0930
Commit message:

 Update NEWS for tidyprint 1.1.1 release

Updated version number to 1.1.1 and added bug fixes.
Package: tidyprint
Commit: 4a37bfc131e69d511a14090a71170169106ff817
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 15:54:56 +0930
Commit message:

 Change version to 1.1.1 and update description

Updated version number and modified description text.
Package: tidyprint
Commit: b33d6efa8c594383ba4be63a49d55415b1bd58c7
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 13:34:10 +0930
Commit message:

 Update README.md to reflect changes in tidyprint messages and R version

- Removed outdated warnings related to package versions.
- Improved formatting of messages for clarity.
- Updated R version and platform information in the sessionInfo section.
Package: tidyprint
Commit: 9fc9cabf840875f2fb57bfcfc4eba46ef8c053d0
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 13:32:03 +0930
Commit message:

 Update tidyprint to version 1.2.0

- Fixed a subsetting bug in `print.SummarizedExperiment()` for 7-sample pasilla-shaped inputs when assay data is a `data.frame`.
- Added a regression test to ensure `show()` does not produce out-of-bounds errors.
Package: tidyprint
Commit: db22be3629a6f47fe076560977c57da16f894701
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 13:31:02 +0930
Commit message:

 Merge branch 'fix-option-overrides-cache-once-per-session' of https://github.com/tidyomics/tidyprint into fix-option-overrides-cache-once-per-session
Package: tidyprint
Commit: 81172f3647f8eb864b556ab338888d7cbe938523
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 13:28:01 +0930
Commit message:

 Update tidyprint with enhancements to message frequency control

- Introduced frequency control for messages in `tidy_message()`, allowing messages to be displayed once per R session.
- Updated `tidy_print_enabled()` to show the option-vs-cache mismatch warning only once per session.
- Added tests to verify the new message frequency functionality.
Package: tidyprint
Commit: 85d1c3f2b39d099dd28d161b2f9bdbbeb3d47045
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-08-21 13:28:01 +0930
Commit message:

 Update tidyprint with enhancements to message frequency control

- Introduced frequency control for messages in `tidy_message()`, allowing messages to be displayed once per R session.
- Updated `tidy_print_enabled()` to show the option-vs-cache mismatch warning only once per session.
- Added tests to verify the new message frequency functionality.
Package: NanoStringNCTools
Commit: 61ba4660a16cc74b77cc21ec5bad0aea68f096a0
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2026-09-02 15:40:27 -0600
Commit message:

 verison
Package: NanoStringNCTools
Commit: 2ff510a6a8e164f3eb1d84600e860f85181913a9
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2026-09-02 15:27:34 -0600
Commit message:

 Merge pull request #43 from Nanostring-Biostats/bioc_build_fail

Bioc build failure
Package: NanoStringNCTools
Commit: d42cf6ad70843e35dfa79d701c322a283521eaf4
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2026-09-02 17:33:53 +0000
Commit message:

 fix build failure
Package: PCAtools
Commit: 6da9b6856906507f734fcccfe85f341a3ed381f0
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-09-02 13:37:30 -0500
Commit message:

 NEWS update
Package: GenomicRanges
Commit: 44c311c711b9a5a5d6db070a8f3210819e4bc9de
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-09-02 11:22:01 -0700
Commit message:

 typo
Package: IFAA
Commit: 2c1c8be60d4278cefcb1aaff91afb9257364a35f
Author: Mingkai Chen <chenm1@ufl.edu>
Date: 2026-09-02 13:33:59 -0400
Commit message:

 Bump version to 1.15.1
Package: IFAA
Commit: ecdbeb6533e0286b5e0f8763125a3732bbd6c2fa
Author: Mingkai Chen <chenm1@ufl.edu>
Date: 2026-09-02 13:29:21 -0400
Commit message:

 Use HTML output for package vignette
Package: signeR
Commit: 292bfbd9049c1fec973702f3672c10653dbf2508
Author: Renan Valieris <renan.valieris@accamargo.org.br>
Date: 2026-09-02 14:06:05 -0300
Commit message:

 fix seqinfo subset error
Package: geyser
Commit: 7d8ece929adc8723d980e4519ebea66fd8f47137
Author: davemcg <mcgaughey@gmail.com>
Date: 2026-09-02 12:55:56 -0400
Commit message:

 match devel
Package: geyser
Commit: 152b7f035619f496a5d16ce060988ce6c985c767
Author: davemcg <mcgaughey@gmail.com>
Date: 2026-09-02 12:53:03 -0400
Commit message:

 Add pandoc to system req
Package: geyser
Commit: 2d8114a8942f37e8e6964e242a58557f7f90cf01
Author: davemcg <mcgaughey@gmail.com>
Date: 2026-04-07 15:44:43 -0400
Commit message:

 x y axis label fix
Package: geyser
Commit: 489b36d2cfba5c5598bfeab780ede13dedc7f5d2
Author: davemcg <mcgaughey@gmail.com>
Date: 2026-04-07 11:33:24 -0400
Commit message:

 news update
Package: geyser
Commit: d1592aed7bfefed3f3914c6b635162a21a1ddacd
Author: davemcg <mcgaughey@gmail.com>
Date: 2026-04-07 11:32:15 -0400
Commit message:

 checkbox toggles added, readme updated with custom config options explanation
Package: geyser
Commit: f9973160367ff91cffbaed38d4c990fff84a369e
Author: davemcg <mcgaughey@gmail.com>
Date: 2026-04-06 15:34:07 -0400
Commit message:

 increment version
Package: geyser
Commit: 6b5d33ce01871a58a8ea93e718d902d1f90ad261
Author: davemcg <mcgaughey@gmail.com>
Date: 2026-04-06 14:37:19 -0400
Commit message:

 fix news version numbers that got shifted with bioc release
Package: cigarillo
Commit: 5add90b609ca0ffa6e22d9d98a2ee1ca32fd902c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-09-01 17:44:59 -0700
Commit message:

 add missing package anchor to Rd \link{} target
Package: GenomicRanges
Commit: 6248364b20a9a1becdc1e50bd7ff7609ff2e4705
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-09-01 17:16:24 -0700
Commit message:

 add missing package anchors to Rd \link{} targets
Package: GenomicRanges
Commit: 6738af10b90f6c63ac29a1173d73b23ad17b7464
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-09-01 16:26:16 -0700
Commit message:

 fix unit tests
Package: BioCor
Commit: 058cb4cf3ed9d3bd8aa81a6cc95c198ed1405088
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-09-01 22:50:54 +0200
Commit message:

 Fix problems with names
Package: BioCor
Commit: fd2cb0e10580e0633036e0cdb88dc316d762b356
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-09-01 22:50:33 +0200
Commit message:

 Increase code coverage by switching to GSC
Package: BioCor
Commit: 81820e3552387ea536ed478d73c151960448bffe
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-09-01 22:08:35 +0200
Commit message:

 Fix seed
Package: BioCor
Commit: 3ffac8aac6670bac584c1a5ae01811e537473952
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-09-01 22:08:24 +0200
Commit message:

 Fix indentation for 4 spaces as Bioconductor requires
Package: BioCor
Commit: f6e3dfb2d2a363f926b1fb566680226ada1f3e12
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-09-01 21:54:12 +0200
Commit message:

 Upgrade acording to BiocCheck
Package: Biostrings
Commit: 7dc83a0cbbde5708995945a9794b3728e67f25fc
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-09-01 12:00:42 -0700
Commit message:

 Fix unit tests.

Also fix regression in as.data.frame.XStringViews() introduced at
commit 3dab5d9.
Package: CNVRanger
Commit: b58eb43709bcd75df1547d289039c66f9d5abc8a
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2026-05-14 14:24:15 -0400
Commit message:

 Add CITATION.cff (#51)
Package: edgeR
Commit: 61de2f486eebbf9332efabb11c0c80b72e334111
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-08-30 18:23:24 +1000
Commit message:

 edgeR 4.99.0

- The genewise C kernels (GLM fitting, deviances, CPM, quasi-likelihood adjustment, exact test,
diffSplice, etc.) are now parallelized with OpenMP. The number of threads is controlled by a new `
nthreads` argument on the affected functions, or globally via `options(edgeR.nthreads=)`, and defaults
to 1 (serial) so results are unchanged by default.

- The C backend for diffSplice() now exploits the bordered block-diagonal ( arrowhead) structure of the
splice design matrix, fitting the genewise null models in time linear, rather than cubic, in the number
of exons per gene. Results are unchanged. diffSplice() also gains `maxit` and `tol` arguments
controlling the genewise GLM fits.

- voomLmFit() has been removed from edgeR and is now provided by the limma package.

- New functions binQLFit() and binQLFTest() to fit quasi-binomial generalized linear models, to estimate
bias-adjusted deviances, and to test hypotheses. These functions are closely analogous to glmQLFit() and
glmQLFTest() but for paired counts and differential proportion analyses instead of regular counts and
differential abundance analyses.

- New functions binFit(), mBinOneWay(), and mBinIWLS() to fit binomial generalized models.

- New class DGEBin to store quasi-binomial generalized linear model fits.

- New function readBismark2PC() to read Bismark output into an edgeR PCList object.

- New class PCList to store paired counts, for example methylated and unmethylated reads, for the same
genomic regions.

- New argument `parent.dir` for catchSalmon(), catchSalmonWithGencode(), catchKallisto(),
catchOarfish(), and catchRSEM(), to more easily read all the samples available in a specified output
directory. New argument `sample.dirs` for catchSalmon(), catchSalmonWithGencode(), and catchKallisto(),
that replaces ` paths` and allows individual samples to be specified.

- New argument `offset.prior` for cpm(), rpkm(), catchSalmon(), and catchSalmonWithGencode() to allow
the offset matrix to be specified relative to the log(library sizes).

- sampleWeights() now accepts a DGEGLM fitted model object from glmQLFit() instead of a matrix of
adjusted unit deviances.

- Revision of all the Rd help files to add DOIs, to fix typos, and to standardize formating and American
spellings.
Package: DOSE
Commit: df6e838da2ef9c853f80be086ca343f96cbb7ad3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-08-30 15:46:18 +0800
Commit message:

 update
Package: DuckDBGRanges
Commit: 9983bb13db331b5f1616d048b37e91512af23a49
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-29 22:56:20 -0700
Commit message:

 fix: restore checkDuckDBGRanges() for GenomicRanges >= 1.65.2

GenomicRanges 1.65.2 rewrote as.data.frame.GenomicRanges(): it used
to default row.names to names(x) when not supplied, and now hardcodes
row.names = NULL internally (an explicit row.names argument is
silently discarded too), putting names(x) in a new "names" column
instead.

checkDuckDBGRanges()'s own df <- as.data.frame(expected) reference
assumed the old convention, so its row names stopped matching
as.data.frame(object)'s, which still carries real names as row names
via DuckDBDataFrame's own conversion. Not a DuckDBGRanges bug: verified
by installing the exact upstream commit and confirming
as.data.frame,DuckDBGRanges-method itself is unaffected.
Package: limma
Commit: 57a8de7296ad733ac25d3e3c01de3fdddcd0a9ae
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-08-30 10:48:25 +1000
Commit message:

 Add new files for limma 3.99.0.
Package: limma
Commit: 8f72e4736e4cee7f10b8345088d8328c689e186e
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-08-30 10:47:07 +1000
Commit message:

 30 Oct 2026: limma 3.99.0

- voomLmFit() transferred to limma from the edgeR package.
  Previously, voomLmFit() needed to call edgeR::glmFit() in order to
  identify exact zero fitted values, but voomLmFit() now calls a
  new limma C routine `poisfit` for the same purpose, removing the
  dependence on edgeR.

- For the purpose of estimating sample weights, voomLmFit() calls
  arrayWeights() with `method="reml"` if there is no loss of df due to
  exact zero fitted values and `method="genebygene"` otherwise.

- The voomLmFit help page has been expanded, while the voom and
  voomWithQualityWeights help pages now have preambles that point
  users to voomLmFit.

- voomLmFit() now gives priority to `offset` over `offset.prior` or
  `lib.size` and no longer forces the rows of `offset.prior` to add
  to zero.

- New argument `contrasts` for voomLmFit(), lmFit(), lm.series() and
  gls.series(), which converts coefficient estimates and standard
  deviations into contrast estimates and standard deviations. This
  argument provides the  same functionality as calling `contrasts.fit`
  on the output object, but with exact rather than approximate
  standard deviations.

- New argument `nthreads` for voomLmFit(), lmFit(), lm.series(),
  gls.series(), duplicateCorrelation(), .arrayWeightsPrWtsREML(), and
  arrayWeights() to enable OpenMP parallelization of genewise fits.

- C code backends for lm.series() and gls.series().

- C code backend for duplicateCorrelation(). duplicateCorrelation()
  previously called statmod::mixedModel2() to estimate genewise
  correlations, but this functionality is now absorbed into the C
  code. The new code is able to evaluate the genewise SVDs needed by
  mixedModel2() more efficiently than was possible for the univariate
  R function, resulting in substantial speed and memory improvements.

- C code backend for .arrayWeightsPrWtsREML(), which is called by
  arrayWeights() when `method="reml"` and prior weights
  are set.

- The C code for weightedLowess() is not new but has been
  revised to fit in with the new C code elsewhere.

- All the Rd pages have been checked for typos and inconsistent
  formating, especially regarding the reference lists. Reference URLs
  converted to DOIs where possible and some new DOIs added. Author
  lists converted to compact PubMed style without unnecessary
  punctuation. A few instances of British spellings converted to
  American spellings.

- Replace old statsci.org/smyth/pubs preprint URLs with
  gksmyth.github.io/pubs URLs in 05Normalization.Rd and in User's
  Guide.

- Fix documentation link in 06linearmodels.Rd.

- Expand changelog.txt entries for limma 1.0 and earlier.

- Add test files dupcor.R, gls-series-c.R, lmfit-contrasts.R,
  lm-series-c.R, and voomlmfit-contrasts.R.

- All package files now use Unix format line-endings.

- Update author order in DESCRIPTION.
Package: BioCor
Commit: e1b232499b067226ddd70255bb854214b67fb174
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-08-29 12:58:02 +0200
Commit message:

 Fix DESCRIPTION
Package: BioCor
Commit: f07961f3753047b127745eb5a6e30f8bcb588872
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-08-29 12:57:23 +0200
Commit message:

 Upgrade cff
Package: BioCor
Commit: ac77cee02064312437dd0a12c719509e88fbee60
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-08-29 12:53:43 +0200
Commit message:

 Version bump to propagate changes
Package: BioCor
Commit: d8f4130a40b0de328e14331c9cf06bf8b37f6876
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-08-29 12:53:16 +0200
Commit message:

 Update documentation
Package: BioCor
Commit: 07b7084920f9fc39f37a791db928df81fe9a242d
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-08-29 12:39:16 +0200
Commit message:

 Update style
Package: BioCor
Commit: 6d5e44f87435ca0938a1e06f900a4a8e8ad1c78a
Author: Lluís <lluis.revilla@gmail.com>
Date: 2026-08-29 12:38:34 +0200
Commit message:

 Fix lintr logical issue
Package: ontoProc2
Commit: ab2304ef1e401ce463190cbd395fff2fbbb4b768
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-08-28 23:06:41 -0400
Commit message:

 remove references to aws throughout
Package: BatchQC
Commit: e38a3459350dff7d2f41c0d27ea78c132db15401
Author: technophilic03 <leng@bu.edu>
Date: 2026-08-28 14:44:33 -0400
Commit message:

 Bump version umber to 2.9.2 for devel
Package: BatchQC
Commit: 01a30073ecc1dc3e2f708fc2ee20be758573a607
Author: Jessica <102758461+jessmcc22@users.noreply.github.com>
Date: 2026-08-25 14:45:35 -0600
Commit message:

 Merge pull request #144 from jessmcc22/devel

Updated descriptions
Package: BatchQC
Commit: d07b5b55b9d57b79dcaf2b9b9f617bbcc92eefe7
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2026-08-25 16:40:53 -0400
Commit message:

 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
Package: BatchQC
Commit: f2ab523559e05818d84dce8eb68df21023826fae
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2026-08-25 15:52:04 -0400
Commit message:

 Updated some descriptions to better support manuscript and provide info to users.
Package: BatchQC
Commit: 3346f533ff2ac23eab94980df56eafce944e7cf2
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2026-08-25 15:52:04 -0400
Commit message:

 Updated some descriptions to better support manuscript and provide info to users.
Package: BatchQC
Commit: 3793afca5df726ed28dfa7bd2b2c536d0a72feca
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2026-08-19 14:41:37 -0400
Commit message:

 Updated version to match Description file (even is for release branches)
Package: BatchQC
Commit: e300047e9d4fb1c108a6ea713159c00ff2772862
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2026-08-19 14:40:55 -0400
Commit message:

 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
Package: BatchQC
Commit: 96c1724e4386db46dd132a1e48d9cfed323c6dd6
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2026-08-19 14:39:38 -0400
Commit message:

 Added additional details about the method functionality to the function descriptions and in the vignette.
Package: scRNAseqApp
Commit: f851c9c88bc453c2ef33adf1e224c8a760a90f56
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-08-28 14:08:11 -0400
Commit message:

 Get IP from request string but not session.
Package: MultiAssayExperiment
Commit: a1764de323ff619f63ecba160e588c7beed73be2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-08-28 13:58:04 -0400
Commit message:

 version bump 1.39.1
Package: MultiAssayExperiment
Commit: e981f5e2862d218de6805faa06323973ec253913
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-08-28 13:57:10 -0400
Commit message:

 use updateObject::updatePackageObjects to update miniACC
Package: MultiAssayExperiment
Commit: cfe45dec646dea08f389efcedfb18befb138885f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-08-28 13:35:06 -0400
Commit message:

 roxygen2 fixes package docs
Package: MultiAssayExperiment
Commit: 5f3f14b436d5bc0518692cd3965870023aae6aa0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-08-28 13:34:36 -0400
Commit message:

 NAMESPACE line updates from roxygen2 v8
Package: MultiAssayExperiment
Commit: b1fcd2d684f53d6493047056384430c3b5f836f2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-08-28 13:34:04 -0400
Commit message:

 add coerce method to docs
Package: MultiAssayExperiment
Commit: 062eb8fbc6eaf6b88012a18a6f2858c32f65e5a6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-08-28 13:33:25 -0400
Commit message:

 update ref links in Rd docs
Package: MultiAssayExperiment
Commit: de9d681201b98855cbd7c61f748ab2c8af220f86
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-08-28 13:32:32 -0400
Commit message:

 add multi-line @aliases for roxygen
Package: MultiAssayExperiment
Commit: f14d285f62c59d93380a374bd1c3a9d44fb45e6d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-08-28 13:34:13 -0400
Commit message:

 use roxygen2 v8
Package: MultiAssayExperiment
Commit: 82663ca8903ff18198c43a7942bdd5a19b44c88c
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2026-04-16 18:50:00 +0000
Commit message:

 Add CITATION.cff
Package: S4Vectors
Commit: 79e0c50e8ca44ed621de69ca63b3e744c53f5d6e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-28 09:23:56 -0700
Commit message:

 Small tweaks to as.data.frame() methods for Vector and Rle objects.

Also remove a bunch of uneeded coercion methods from Rle to various base
types (they're redundant with the same methods defined for Vector objects).
Package: scrapper
Commit: 224ce0f797369612000a3650ef61264c2866d2e7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 22:24:05 +1000
Commit message:

 Optionally filter for high-quality cells in each quick*Qc.se() function.

Also report the unfiltered SE in analyze.se(), just in case users want to
examine the entire distribution of QC metrics prior to any filtering.
Package: MsBackendMetaboLights
Commit: c33fad99e6bc48c5bb9fd5ef7814e0e32393eed3
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-08-28 14:21:39 +0200
Commit message:

 Merge pull request #25 from rformassspectrometry/jomain

refactor: reduce need to load BiocFileCache for offline use
Package: MsBackendMetaboLights
Commit: e3564b3d802422f9e953116a68b50e2847a5bb13
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-08-28 13:00:15 +0200
Commit message:

 refactor: reduce need to load BiocFileCache for offline use
Package: terapadog
Commit: 1a7aef14a891ecca87e779080e518ffefdd21f62
Author: gionmattia <gionmattia@gmail.com>
Date: 2026-08-28 13:16:28 +0100
Commit message:

 added_ranks
Package: betterChromVAR
Commit: 0341160ba7e994ad6755cbba92d6f644efebeb3a
Author: plger <pl.germain@gmail.com>
Date: 2026-08-28 13:55:26 +0200
Commit message:

 fixed typo in citation
Package: betterChromVAR
Commit: 24a6eee3450ef6d0ca11d5e8d787c9a0f61e6139
Author: plger <pl.germain@gmail.com>
Date: 2026-08-28 13:44:01 +0200
Commit message:

 changed paper url to point direct to biorxiv
Package: betterChromVAR
Commit: 7ff55e0660f4c164855c5ca176c4c65389c7fc30
Author: plger <pl.germain@gmail.com>
Date: 2026-08-28 13:41:11 +0200
Commit message:

 Merge branch 'devel' of github.com:plger/betterChromVAR into devel
Package: betterChromVAR
Commit: d34d3b7c8bfd8e2ec83d37105ff227e4ab1ece98
Author: plger <pl.germain@gmail.com>
Date: 2026-08-28 13:40:53 +0200
Commit message:

 added references to the preprint
Package: betterChromVAR
Commit: d7916f7fbe6138323e667edfca72957d7ffe0956
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2026-08-21 14:45:36 +0200
Commit message:

 Split BiocManager install calls for clarity
Package: betterChromVAR
Commit: 649881272514ddf03d34e5eff3860bce8102ed3f
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2026-08-21 14:33:20 +0200
Commit message:

 Add Biobase to BiocManager install list
Package: betterChromVAR
Commit: 9abd6bb633c66287af26228c50336a11ca14ff43
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2026-08-21 14:17:56 +0200
Commit message:

 Change check pkg installation to BiocManager
Package: OSCA.multisample
Commit: 6984d54a2143230e7d2bfe835d1e1379f3632754
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2026-08-28 08:58:34 +0100
Commit message:

 Merge pull request #20 from OSCA-source/stripped

Stripped out all content and replaced with redirects to scrapbook.
Package: OSCA.multisample
Commit: 1fc1562368a1c0b2b9530269cd38dea607005531
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 16:04:09 +1000
Commit message:

 Removed unnecessary GHA.
Package: OSCA.multisample
Commit: 386ef6f9b10500cb49e2838e1311ee81f78a1ae5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 15:59:48 +1000
Commit message:

 Replaced all chapters with redirects to scrapbook.
Package: SingleR
Commit: f550f73f67c2b8e0a234f05039c6166ba44ab104
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 14:25:08 +1000
Commit message:

 Updated C++ bindings for find_classic_markers.
Package: assorthead
Commit: caf3a73117c673b9f613bec040c4927c76f37fee
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 14:26:32 +1000
Commit message:

 Update the version of singler_classic_markers.
Package: DuckDBDataFrame
Commit: 1b797dfe5b363d0154fabf624a3af9b97868a69f
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-27 16:07:28 -0700
Commit message:

 fix: reverted the previous fix
Package: VDJdive
Commit: 819f671011374f336f7597c9f70a6fa9a8d6e1fc
Author: Kelly Street <street.kelly@gmail.com>
Date: 2026-08-27 15:28:28 -0700
Commit message:

 removed compiled artifacts
Package: DuckDBDataFrame
Commit: e0324474831ec2a28395954e658a19de518a80bc
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-27 14:32:13 -0700
Commit message:

 fix: the previous fix
Package: DuckDBDataFrame
Commit: b05e881461dce0f08dec627ed338406398435cd4
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-27 14:13:14 -0700
Commit message:

 fix: dim-table partition pruning used positional indexing on keycol values (0.99.26)

.filter_tblconn()'s dimtbl[set, , drop = FALSE] indexed a dimension table
by a keycol's raw stored values, but a numeric index in R is always
positional (row number), not a value lookup. This was silently wrong
whenever a key's value differs from its row position in the dim table --
exactly the shape a DuckDBTable/DuckDBArray shard (a subset of a larger
dataset's keys) takes, which is what dimtbls-based partition pruning
exists to optimize.
Package: scRNAseqApp
Commit: e512f606db4d8b49a4819b86e1f52753de18599f
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-08-27 12:39:23 -0400
Commit message:

 Fix the bug for splash screen.
Package: methodical
Commit: 92fa1369c1b6b5c34470019a41c298343a2cebce
Author: Richard Heery <richardheery@gmail.com>
Date: 2026-08-27 17:25:10 +0100
Commit message:

 update
Package: assorthead
Commit: cfb13bd090130480c7f7543df9a8e4905d3fdbc8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 02:15:33 +1000
Commit message:

 Updated the vendored version of knncolle.
Package: BiocSingular
Commit: 8544ac52d53b7bb2149fed8268a99484a606c18e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 01:57:31 +1000
Commit message:

 Bumped version and date, re-run roxygen.
Package: BiocSingular
Commit: 16a8dd7f0a85c0e6df32a472e3e6cb7ec24ebbef
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 01:33:22 +1000
Commit message:

 Replace most of our custom C++ functions with tatami.* utils from beachmat.

Also refactor the compute_scale() implementation to improve work-sharing upon
parallelization, at the cost of some small floating-point differences depending
on the number of threads. This aligns with the policy in the new tatami_stats.

Also switch the edge cases to report NaNs instead of NA_real_. The former is
more appropriate as the statistics are invalid, not missing.
Package: miaViz
Commit: 33a50dc49f455a62695592fbb4d8d5806dc5bc20
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2026-08-27 18:39:01 +0300
Commit message:

 Update plotAbundance defaults for showing sample grouping (#232)
Package: msa
Commit: c07a1e4fa646df33b5094a1cb30705abf690f524
Author: UBod <ulrich@bodenhofer.com>
Date: 2026-08-27 17:18:20 +0200
Commit message:

 some updates and corrections; version number bumped to 1.45.6
Package: beachmat
Commit: c6b2b5b65620ac89ee5058b3ba93b9cb289e7d94
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 01:13:05 +1000
Commit message:

 Docfixes for some soft-deprecated functions.
Package: beachmat
Commit: e5192e337743d9efa3f9fba91d10635fb3a722ea
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 01:00:06 +1000
Commit message:

 Added the tatami.variances() function for quick dimwise variances.
Package: scRNAseqApp
Commit: 9dec50101b96f552c68e16cbab2fd7fcd16889e9
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-08-27 11:01:01 -0400
Commit message:

 Fix a bug for splash screen
Package: scuttle
Commit: d3476eb0833aaa38cd59b2db3c941c38fc64677b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-28 00:25:15 +1000
Commit message:

 Updated bindings to the new C++ functions.
Package: scpdata
Commit: c2d8a7629773cde959000522e18f1f6995f8261c
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-08-27 12:58:23 +0200
Commit message:

 add missing leduc2025 man page
Package: geneslator
Commit: e9b59c133ff48f0d4a2d72b5b3a2862e81f5e314
Author: GMicale <gmgmicky@gmail.com>
Date: 2026-08-27 12:58:32 +0200
Commit message:

 Fixed query for KEGG pathways
Package: geneslator
Commit: 9524d78e37e75d405e431b1fedf85996be491b65
Author: GMicale <gmgmicky@gmail.com>
Date: 2026-08-27 12:38:57 +0200
Commit message:

 Fixed query for keytypes
Package: OSCA.basic
Commit: 7311fc4071852124485659738a1df71e621ae7b7
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2026-08-27 11:19:07 +0100
Commit message:

 Merge pull request #21 from OSCA-source/stripped

Replace all content with redirects to scrapbook chapters.
Package: OSCA.basic
Commit: a9d404c3bce32dafd881cdc43158e0de565f2aa7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-24 23:35:16 +1000
Commit message:

 Replace all content with redirects to scrapper chapters.
Package: MetaboDynamics
Commit: 067faf9d5333f249b9049a357612ed1be18af989
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-08-27 11:46:59 +0200
Commit message:

 version bump
Package: MetaboDynamics
Commit: 05e7b2151146ff2cef1fc2591a943e3d9baabba2
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-08-27 11:46:23 +0200
Commit message:

 corrected vignette title
Package: scrapbook
Commit: a1fc037fa7451af8afb35e15f87a8b79a9f76d40
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-27 19:13:15 +1000
Commit message:

 More streamlined wording of the normalization chapter.
Package: eisaR
Commit: 4d658f04bd930761d190d0e8a8d02f14d0da6bc2
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2026-08-27 09:38:41 +0200
Commit message:

 Merge pull request #44 from fmicompbio/test-r-devel

Adapt to upcoming changes in rbinom in R devel
Package: eisaR
Commit: 77cbce1a657307453daedba857e8d018c73ec8a0
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-27 08:35:41 +0200
Commit message:

 Disable running of devel GHA workflow
Package: eisaR
Commit: 2879a2a3b2d51697344cc100e38b0917e44271cd
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-27 07:16:18 +0200
Commit message:

 Suppress warnings instead of expecting them (to avoid failing in release R)
Package: eisaR
Commit: e07a3f29e55a8c10d2049b932b19e89cbfc690ad
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-27 06:53:04 +0200
Commit message:

 Run devel workflow also on PR to devel
Package: eisaR
Commit: 3d10f5dd6acedd1a9ee79139b35cdcd0a8cd4cdb
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-26 21:55:29 +0200
Commit message:

 Bump version
Package: eisaR
Commit: 9bda5e69929f1f340e4aba9e22927cecbf7c09c8
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-26 21:55:12 +0200
Commit message:

 Set RNGversion to 4.6 in tests to get consistent values from rmultinom
Package: eisaR
Commit: 018a8791307c7d91f83ec4130a4938aa65c159d1
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-26 21:54:37 +0200
Commit message:

 Only run R-devel checks upon request
Package: eisaR
Commit: 518bfca442950fc7c7e2973d87f111e346ac9dbb
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-26 21:26:50 +0200
Commit message:

 Fix Linux system dependencies installation
Package: eisaR
Commit: 1e150e6984569105f2c72e5bd87aa02954f3d196
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-26 20:43:36 +0200
Commit message:

 Add more configs to GHA matrix
Package: eisaR
Commit: 2a422f3c07136ce9a27397ce52e3a5b49d36cf73
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-26 20:03:54 +0200
Commit message:

 Update setup-r action version
Package: eisaR
Commit: 93eed55670fb8b71491e80363217ee5fa0d615a6
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-26 20:02:26 +0200
Commit message:

 Remove scheduled run
Package: eisaR
Commit: 1957f797e47996fd4a80b39ddb1eecd8da622c02
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-08-26 17:12:20 +0200
Commit message:

 Add GHA workflow testing on R-devel
Package: scrapbook
Commit: 4d63d107821318f91bcee9b731535d7207bb04a0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-27 16:58:27 +1000
Commit message:

 Bumped version and date.
Package: scrapbook
Commit: 260b9b4894c823f5dd0abacdd6e2a2eb99c445c8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-27 16:47:21 +1000
Commit message:

 Improved explanation of composition biases, plus minor text fixes.
Package: scrapbook
Commit: bb157ae4eacd85db91b9e4b29626f1626601cea5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-27 16:10:58 +1000
Commit message:

 Added a paragraph on dealing with composition biases in DA analyses.
Package: scrapbook
Commit: f5bf81eb70c833088794e8f9d914cd8c5177863f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-27 00:24:55 +1000
Commit message:

 Migrated the ambient contamination section from OSCA.multisample.
Package: DuckDBDataFrame
Commit: 5eec18f076aa376188ef9879905a9f957b0f2b8d
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-26 22:52:16 -0700
Commit message:

 feat: add anyNA and is.na methods
Package: AnnotationDbi
Commit: 00bc715f3ecc0d78d7794257c041d3d463766e11
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:54:04 -0700
Commit message:

 spelling
Package: SplicingGraphs
Commit: 841410fcac751fe3ce3a811b10c63644654007ae
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:52:17 -0700
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: SplicingGraphs
Commit: 7063f7a222a2e35275de15930eddaa082d9dd3ef
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:51:41 -0700
Commit message:

 spelling
Package: BSgenome
Commit: da2ce6bcbe3b850db8458bdb0d60bad5fadaea9d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:49:44 -0700
Commit message:

 spelling
Package: GenomicFeatures
Commit: 406313962cfb98d282a85728b9718f096c317bc5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:49:12 -0700
Commit message:

 spelling
Package: HDF5Array
Commit: c4132ae2db816faf0a8c93dd7fccb502aad92e5d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:40:22 -0700
Commit message:

 small tweak to long tests
Package: HDF5Array
Commit: 6d442dc8c9c01f8538fa2ad57e2f29698630a2bb
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:38:54 -0700
Commit message:

 tidy NAMESPACE
Package: HDF5Array
Commit: a73534d9963fcd1d0f5331c66815b17503a79bee
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:35:20 -0700
Commit message:

 spelling (again)
Package: HDF5Array
Commit: 2312b92cbdeff66440f34a44a66c99c54ed0de9e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:32:12 -0700
Commit message:

 Revert "spelling"

This reverts commit 6e071082859536e7a773d1f0c8a11b9e5a47fd78.
Package: HDF5Array
Commit: 008c9d5ce9eadf6470acf552dc289bb67a4748ad
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:31:41 -0700
Commit message:

 Revert "spelling"

This reverts commit 22568f16a608cb968109a42a481ba2626e253510.
Package: HDF5Array
Commit: 46678ea2217b1ad88cb21f65f759ed7ddef1d3ca
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:24:57 -0700
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: HDF5Array
Commit: 22568f16a608cb968109a42a481ba2626e253510
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:18:05 -0700
Commit message:

 spelling
Package: HDF5Array
Commit: 6e071082859536e7a773d1f0c8a11b9e5a47fd78
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:18:05 -0700
Commit message:

 spelling
Package: S4Arrays
Commit: 22cee5bc9e8025ab7a46e82e61a43e82a3379d07
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:17:40 -0700
Commit message:

 spelling
Package: updateObject
Commit: 9be97ff3556fdafe683b0818c1421443e708eca6
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:17:14 -0700
Commit message:

 spelling
Package: scRNAseqApp
Commit: c860b60511c994c173ee3e7b6e7818a42cc508b8
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-08-26 21:16:34 -0400
Commit message:

 allow user to close the splash screen.
Package: GenomicRanges
Commit: b0be93253202832f530135f732a5b8d6d9740a88
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:15:26 -0700
Commit message:

 spelling
Package: GenomicAlignments
Commit: 5ab0e428f28d6632acb2c4534e146cdeeac435c9
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:14:21 -0700
Commit message:

 spelling
Package: IRanges
Commit: 75107e286bf13c8696ea2c3962ed9cd0c7c50d48
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:13:55 -0700
Commit message:

 spelling
Package: S4Vectors
Commit: e7446f1ce8c2c88773acbbc006d7dfafcb21b625
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:07:54 -0700
Commit message:

 spelling
Package: Biostrings
Commit: e9c2456e1761818986a9f6fe342566b0e5c8c7a5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 18:01:28 -0700
Commit message:

 removing github workflows as they keep causing problems
Package: Biostrings
Commit: 3dab5d92fa32a5a6cb68f265ccd0176681975686
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 17:53:14 -0700
Commit message:

 Biostrings 2.81.7

Refactor as.data.frame.XStringSet() and as.data.frame.XStringViews().

Also revisit show() methods for XString, XStringSet, and MaskedXString
objects.
Package: IRanges
Commit: e4969215e13dd557714d6a0bc88248dcd6ae4520
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 17:49:11 -0700
Commit message:

 IRanges 2.47.5: Revisit show() method for MaskCollection objects
Package: IRanges
Commit: 36b34e09b6551cf43328359a51edd61d15f009bb
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 13:50:59 -0700
Commit message:

 more tweaks to as.data.frame.IPosRanges() and as.data.frame.IPos()
Package: GenomicRanges
Commit: 4b626b5ed07dc043df803c0974aa3e661fc45ff6
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 13:45:33 -0700
Commit message:

 GenomicRanges 1.65.3: More tweaks to as.data.frame.GenomicRanges() and as.data.frame.GPos()
Package: Seqinfo
Commit: 93f9978435ee2ff778f21368ef7d54492492de2f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 13:39:39 -0700
Commit message:

 Seqinfo 1.3.2: Another tweak to as.data.frame.Seqinfo()
Package: scRNAseqApp
Commit: d2cff64852449c260c6d6aa03016f1f969d79ba5
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-08-26 16:33:45 -0400
Commit message:

 update splash screen style.
Package: IRanges
Commit: 41524d507cefefd7657cc15660baf5edd8beed9b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 13:25:59 -0700
Commit message:

 more tweaks to as.data.frame.IPosRanges() and as.data.frame.IPos()
Package: IRanges
Commit: 3ea56ddef61e988bcf3bf87d14f0c2440994c462
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 13:17:43 -0700
Commit message:

 IRanges 2.47.4: Fix handling of names and mcols in ranges() method for Views objects
Package: Seqinfo
Commit: ad77d503ccfafa779e92e483a71350f8ef3d01b4
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 11:12:52 -0700
Commit message:

 one more tweak to as.data.frame.Seqinfo()
Package: IRanges
Commit: 0233e68b34b31029d97e35caaf841eed1ba54363
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 10:54:50 -0700
Commit message:

 more tweaks to as.data.frame.IPosRanges() and as.data.frame.IPos()
Package: S4Vectors
Commit: 61ed37f650b7391534e1a9a032335350ce420a93
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 10:51:22 -0700
Commit message:

 another tweak to as.data.frame.DataFrame()
Package: GenomicRanges
Commit: a6269257dc2a876c6907c857b7f61fba14e55ade
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 10:47:42 -0700
Commit message:

 GenomicRanges 1.65.2: Small tweaks to as.data.frame.GenomicRanges() and as.data.frame.GPos()
Package: DuckDBArray
Commit: 4aae0acc188206b6e334fca1d9205514f39420ba
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-26 10:34:14 -0700
Commit message:

 fix: correct integer64 handling in DuckDBArraySeed, fix writeCoordArray() docs (0.99.8)

Bug report on writeCoordArray()/DuckDBArray() surfaced two issues:

- Constructing a DuckDBArray/DuckDBArraySeed/DuckDBMatrix over a genuinely
  BIGINT/HUGEINT-typed value column crashed with "vector: cannot make a
  vector of mode 'integer64'". coltypes() reports "integer64" for such
  columns, and 9 call sites built the seed's structural fill value via
  vector(coltypes(...), 1L), which errors because "integer64" isn't a valid
  vector() mode. Replaced with a shared .coltypeFillVector() helper.

- Fixing that crash surfaced a second, more serious bug: as.matrix() /
  extract_array() on a successfully-constructed integer64-valued
  DuckDBArray silently returned garbage values (e.g. 4.94e-324 instead of
  1) instead of erroring. array() and [<- are class-blind and operate on
  the underlying double storage only, so an integer64-classed datacol value
  (the standard construction path opens its connection with bigint =
  "integer64", see acquireDuckDBConn()) never goes through bit64's
  as.double.integer64() conversion and its raw 64-bit pattern gets copied
  in as-is. rowSums()/rowCounts() were unaffected (SQL-computed, not
  R-side materialized). extract_array(), extract_sparse_array(), and the
  COO fast path (.collectCOO()) now normalize any integer64-classed
  datacol value to plain double at the point it's materialized from the
  database (.dropInteger64()), consistent with how DuckDBArray already
  treats integer64 everywhere else.

- DuckDBArraySeed's fill slot is now "ANY" (was "atomic"), with validity
  enforced via is.atomic() instead of the slot's formal class, so a genuine
  integer64 fill value is accepted without needing a class union that names
  "integer64" -- which triggered a bit64-related warning at install/build
  time, since bit64 registers integer64 via setOldClass() but never calls
  exportClasses(). bit64 is no longer an import of this package.

- writeCoordArray()'s arrowtype/max_dim docs now correctly describe the
  DuckDBArray fast-path method: unlike the ANY method, which infers the
  narrowest type from the data (or from dim(x) for index columns) when
  these are NULL, the DuckDBArray method takes the source's existing
  declared column type as-is, with no data-driven narrowing.

Full test suite: 0 failures. R CMD check: 0 errors, 0 warnings (2
pre-existing, unrelated NOTEs).
Package: S4Vectors
Commit: d6cc3bb14469380fba2d03698d82615c103d7fc3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 10:19:38 -0700
Commit message:

 S4Vectors 0.51.9: One more tweak to as.data.frame.DataFrame()
Package: Seqinfo
Commit: 2c09ad5381b033458636a59b919e6959e37dbfc4
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-26 09:31:30 -0700
Commit message:

 Seqinfo 1.3.1: Minor tweaks to as.data.frame.Seqinfo()
Package: MOFA2
Commit: 4a102f2b491ab600738ddf693a70f0baf032ca68
Author: Jan Sprengel <janlsprengel@gmail.com>
Date: 2026-08-26 15:21:02 +0200
Commit message:

 increment minor version to 1.23.2
Package: MOFA2
Commit: fd80044229b91e8cedad90160a5b7a3759bc3829
Author: Jan Sprengel <janlsprengel@gmail.com>
Date: 2026-08-20 15:41:24 +0200
Commit message:

 run_mofa(): relax warning for patch versions ahead
Package: MOFA2
Commit: 90fbbae10b32e38fafa2a4450eb2e23b9c0a0dd5
Author: Jan Sprengel <janlsprengel@gmail.com>
Date: 2026-08-26 10:55:48 +0200
Commit message:

 bump mofapy2 version to 0.7.5, reformulate run_mofa() docs
Package: MOFA2
Commit: eeb3ab8f0383eb268b8900bdeea2194bd705db9e
Author: Jan Sprengel <janlsprengel@gmail.com>
Date: 2026-08-20 17:03:26 +0200
Commit message:

 increment mofapy2 version to 0.7.4
Package: MOFA2
Commit: 3c0d58025e6abf506f5347d7d0c11f96639f746a
Author: Jan Sprengel <janlsprengel@gmail.com>
Date: 2026-07-30 16:23:56 +0200
Commit message:

 update run_mofa() docs to recommend py_require(), pin version in vignettes

pin mofapy2 in examples and vignette calls of py_require
Package: MOFA2
Commit: 288df7d2c465dbaa926cf18535927111b0c3fd0c
Author: Jan Sprengel <janlsprengel@gmail.com>
Date: 2026-07-31 11:19:39 +0200
Commit message:

 CI: add Bioconductor GitHub Actions workflow

Also pin Python 3.12.10 (3.12.12 is not resolvable on the windows CI runner), switch to testthat 3rd edition and switch vignettes from basilisk to py_require()
Package: MOFA2
Commit: 2f3eb9522906baf951ace8da86eb8c0adb9a285a
Author: Jan Sprengel <janlsprengel@gmail.com>
Date: 2026-07-17 22:14:02 +0200
Commit message:

 implement plot_factor_mean_cor() QC visualiser, adjust QC warning message

implements plot_factor_mean_cor() with multi-group option, bold factor labels. Also the scope of a warning suppression is adjusted.
Package: multipointR
Commit: 2af89138ec317c161d5d0df885016bf63dd2287b
Author: Martin Emons <55688661+mjemons@users.noreply.github.com>
Date: 2026-08-26 16:28:29 +0200
Commit message:

 Enable elastic net fit for complex models with splines  (#3)

* added option for relaxed enet fit

* add requirement on glmnet for type enet fit

* adjust for the fact that all terms are zero - intercept only model

* updated vignette and various fixes
Package: PhyloProfile
Commit: 5118a80cbccd977895f17fc7a0948c7114106642
Author: trvinh <trvinh@gmail.com>
Date: 2026-08-26 09:36:57 +0200
Commit message:

 option to ignore invalid/unknown taxa; URL for pseudo taxID
Package: eisaR
Commit: 3f710e547ad31f80aaa5406e0c03889b9b84d9ff
Author: mbstadler <stadler.michael@gmail.com>
Date: 2026-08-26 09:26:10 +0200
Commit message:

 bump version to trigger a new R-universe build
Package: gdsfmt
Commit: 4ec0aeba21824461c200388caa9c3a143dbf94bb
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-08-26 02:15:52 -0500
Commit message:

 cloud update & export
Package: MsBackendMetaboLights
Commit: 582814291e7bb4040144cc3a69fb3a37aa7b734e
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-08-26 08:08:41 +0200
Commit message:

 Merge pull request #24 from rformassspectrometry/jomain

Add pause to examples
Package: MsBackendMetaboLights
Commit: aa6026ef99c5bf59e1774a6c87ed79feda3d9af4
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-08-26 07:47:32 +0200
Commit message:

 Add pause to examples
Package: scrapbook
Commit: 80cd6b605a39982b31e368fc45bc172ea1287ee1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-26 12:45:13 +1000
Commit message:

 Fixed section title for consistency.
Package: scrapbook
Commit: 7eedf6966f01ba717e66f7e0b4c94c8d5c811208
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-08-26 12:40:31 +1000
Commit message:

 Migrated a short nuclei analysis chapter from OSCA.advanced.
Package: IRanges
Commit: 28c9970cca9bcec8eec020bff6390924b0a0e583
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-25 17:29:34 -0700
Commit message:

 IRanges 2.47.3: Minor tweaks to as.data.frame.IPosRanges() and as.data.frame.IPos()
Package: S4Vectors
Commit: e4668d7b6cb34e21de42f251764d4a8d13e31824
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-08-25 17:12:56 -0700
Commit message:

 S4Vectors 0.51.8: Various tweaks to as.data.frame.DataFrame()

This fixes issue #138.
Package: DuckDBDataFrame
Commit: ddcf2f5d57058deaf061d41f07a43ecf7a6958e3
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 16:36:48 -0700
Commit message:

 fix: pair the _INCOMPLETE reader check with the directory-wrap fix
Package: DuckDBGRanges
Commit: 94ecf2a80b6b4be8cf50dc9cb0f1739ecbd1b91d
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 14:18:11 -0700
Commit message:

 fix: validate narrow()'s start/end/width request as base does

narrow() accepted four requests base refuses, and two of them returned a
range wider than the input. A supplied width fixes whichever side was
left NA, so exactly one of start/end must be NA; "width only" quietly
anchored at the start and supplying all three quietly ignored end. And
narrow() may only shrink a range (base solves with
allow.nonnarrowing = FALSE), so narrow(x, start=5, end=200) on a
101-wide range returned 104-299 instead of erroring. The widen/invert
check is per row, matching base, and costs one aggregate query.

The start/end resolution is factored into .narrow_resolve(), used both
to build the new columns and to build the validation predicate.

Review item R-G3 described this as narrow(width=w) leaving coordinates
unchanged while writing an inconsistent width. That does not reproduce:
.modify_DuckDBGRanges_datacols() recomputes end as start + width - 1
when only the width changes. The missing validation is the real gap.
All solvable forms already matched GenomicRanges and still do.
Package: DuckDBGRanges
Commit: 8adfde28d7d74dea23d8a6a61f84804f84fbf74e
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 13:54:57 -0700
Commit message:

 fix: correct the remaining element-wise set operations and distance()

punion() and pintersect() share .parallel_set_op(), which paired x[i] with
y[i] using a bare row_number() over DuckDB's undefined scan order (review
item R-G4) and coordinate-sorted its result, so result[i] was not
x[i] combined with y[i]. Pairing now goes through the recorded keycol,
matching the pgap() and psetdiff() rewrites, and the result keeps the
pairing order.

Fixing that surfaced the same defect class as R-G1 in both callers, which
base treats differently and which was not modelled at all: pintersect()
produced a negative width for a non-overlapping pair (unmaterializable)
where base returns a zero-width range, and punion() silently spanned a gap
where base errors unless fill.gap=TRUE. Neither checked seqname or strand
compatibility, so both combined ranges across chromosomes. ignore.strand,
strict.strand, and drop.nohit.ranges were all accepted and ignored.

Separately, distance() returned a number rather than NA for a pair on
different seqnames whenever either strand was '*': the strand OR-chain was
not parenthesized inside the AND, so SQL precedence let any '*' strand make
the pair valid on its own. Same hazard already documented on pgap(); the
existing test never combined a seqname mismatch with a '*' strand.

All three operations are now checked against GenomicRanges with and without
an explicit keycol; each fix was reverted individually to confirm it is
load-bearing.
Package: DuckDBDataFrame
Commit: adfaf4686e19826e596d1b0ad5d93f0328558a35
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 13:38:00 -0700
Commit message:

 fix: readParquetSchema() leak
Package: DuckDBDataFrame
Commit: 3b3a38e9cca3093d2e9052ec564e5315d92b8742
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 13:18:42 -0700
Commit message:

 fix: release the parquet file handle before renaming or unlinking

Follow-up to the mmap fix: removing the memory mapping unblocked the
in-place write but not the rename and unlink that splitParquetPart()
performs on its source. ParquetFileReader opens the file and has no
Close() method, so .findFactorColumns() left a handle live until GC, and
Windows refuses to rename or unlink a file that any handle still holds.

It now creates its own ReadableFile, passes that to ParquetFileReader,
and closes it explicitly; the returned Schema stays valid afterwards.
Confirmed by file-descriptor count: the old form leaves one handle open,
the new form leaves none. splitParquetPart() also drops its DuckDB temp
table before touching the source rather than at function exit, and the
"failed to move aside" error now names the Windows cause.
Package: DuckDBDataFrame
Commit: ad1a3e9bb7b8f3d55710c0ec1da325605bec900b
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 12:01:26 -0700
Commit message:

 fix: unmap parquet reads so in-place rewrites work on Windows

The factor-restoration path reads and rewrites each parquet file in
place, and arrow's default memory-mapped read leaves a mapping open that
Windows refuses to write over, rename, or unlink (error 1224). Staging
the write elsewhere and renaming would not help: replacing a mapped file
is blocked the same way, so the mapping itself has to go.

Fixed at three sites, not just the one in the traceback.
.restoreFactorColumns() and .findFactorColumns() both read the source
file that splitParquetPart() later renames aside and unlinks, so leaving
either mapped would simply have moved the failure downstream into the
rollback path. .findFactorColumns() switches from open_dataset(), which
cannot opt out of mapping, to ParquetFileReader$create(mmap = FALSE).
writeDuckDBTableParquet()'s sample_df read is unmapped for the same
reason, though it was not implicated here.

The splitParquetPart() half of this is a pre-existing 0.99.22 defect that
only surfaced now because that function had no test coverage until this
release. Adds a test asserting the files stay renameable and removable
after both helpers touch them.
Package: DuckDBGRanges
Commit: a4634eb0dc514478a326e28fc849d8daea18951b
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 11:54:59 -0700
Commit message:

 fix: correct psetdiff for non-overlapping, covering, and inside pairs

psetdiff() handled only edge-aligned overlaps, as its header comment
conceded. A non-overlapping pair came back wider than x, and a covering
pair came back with negative width, which is not merely wrong but
unmaterializable ("each range must have a non-negative width"). A y
sitting strictly inside x cannot be expressed as one range and base
refuses it; this returned garbage instead.

Three further defects in the same method: seqname and strand
compatibility were ignored, so ranges were subtracted across
chromosomes; ignore.strand was accepted and never used; and the result
was coordinate-sorted by .build_DuckDBGRanges()'s default ordering, so
result[i] was not x[i] minus y[i].

Pairing also moves from a bare row_number() over DuckDB's undefined scan
order to .add_keycol_indices(), matching the pgap() rewrite. That is
review item R-G4, done here because correct pairing is a precondition
for this method being correct at all; punion/pintersect still need it.
Package: flowViz
Commit: 077ee734b27398a50661e772f281368eeae324d5
Author: Mike Jiang <mike@ozette.com>
Date: 2026-08-25 11:47:51 -0700
Commit message:

 Bump version to 1.77.1
Package: flowViz
Commit: 065ecc59d52d978d4ee20af3e2bdd77a18985ce9
Author: Mike Jiang <mike@ozette.com>
Date: 2026-08-25 11:47:37 -0700
Commit message:

 Migrate parallel to parallelplot for lattice >= 0.23

lattice 0.23 removed the long-deprecated parallel() function
(replaced by parallelplot() in 0.20). setGeneric("parallel")
therefore fails at install time with:
  must supply a function skeleton for 'parallel'

Rename the generic, methods, exports, and docs to parallelplot.
Package: DuckDBGRanges
Commit: 5a9784db51058d3c90e4127a2c63e129b67f55ef
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-08-25 11:19:18 -0700
Commit message:

 fix: repair the nearest-neighbour family for row-number-keyed objects

Three stacked defects made nearest(), precede(), follow(), and
distanceToNearest() unusable on any DuckDBGRanges without an explicit
keycol, which is the default for a file-backed object. Every existing
test in this family supplies one, so none of it was covered.

.add_keycol_indices() treated the keycols slot as literal key values,
but a row-number-keyed frame stores set_row_number()'s c(NA, -n)
sentinel there; joining against it matched nothing and silently emptied
the result. It now derives the position with row_number()
instead. window_order() is deliberately avoided: dbplyr keeps that
ordering attached and re-emits it after the column has been grouped
away.

.build_nearest_single_result() subscripted with the SQL-derived index
directly, and an integer64 subscript silently yields NA for every
position.

.nearest_ddb() lacked the is.na(subj_idx) guard .distanceToNearest_ddb()
has. DuckDB's greatest() skips NULLs, so a query on a seqname with no
subject scored greatest(NULL, NULL, 0) = 0, won its own min-distance
filter, and produced a hit to a NULL subject.
 </pre>
    </div>
  
    

      Package: scRNAseqApp

      Commit: d89bc02109e271b19c586b4c991307869a421ae3

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

      Date: 2026-08-25 13:57:35 -0400

      Commit message:


	  
		
 adjust a little bit the css.
 

    

  
    

      Package: scRNAseqApp

      Commit: 1e32f964f7f3a58664072f5d40a63f784e8ea98d

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

      Date: 2026-08-25 13:27:20 -0400

      Commit message:


	  
		
 add splash screen.
 

    

  
    

      Package: DuckDBDataFrame

      Commit: cfa12fb3e564aed3178e5968a18a10aa06fbd358

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

      Date: 2026-08-25 09:49:49 -0700

      Commit message:


	  
		
 fix: prevent data loss on two DuckDBTable parquet write paths

splitParquetPart() unlinked the source file before copying the split
parts into place, discarded file.copy()'s return value, and left
overwrite=FALSE. A failed copy destroyed the only copy of the data and
returned without error. The source is now moved aside, the copy is
checked, and any failure rolls the directory back to its original
contents. A read-only target directory previously produced a silent
no-op reported as success; it now errors.

writeDuckDBTableParquet() never consulted @collevels, so its SQL COPY
flattened every factor column to VARCHAR and dropped any level unused in
the data. It now re-applies the recorded levels via the same arrow-side
fixup splitParquetPart() already used, refactored into a shared
.applyFactorLevels() helper, and does so before sample_df is read back
so the caller's schema inference sees the factors too.
 

    

  
    

      Package: maaslin3

      Commit: 4b6855d6a2f8283e1667208ab3c643d71f596426

      Author:  Will Nickols <willanickols@gmail.com> 

      Date: 2026-08-25 08:25:03 -0700

      Commit message:


	  
		
 Fix random effects handling for multiple crossed random intercepts
 

    

  
    

      Package: IFAA

      Commit: 7f243b8d985160cb53bb8c623c6ca91054f893fa

      Author:  Mingkai Chen <chenm1@ufl.edu> 

      Date: 2026-08-10 16:03:22 -0400

      Commit message:


	  
		
 Internalize HDCI routines to restore package build
 

    

  
    

      Package: scRNAseqApp

      Commit: 6f1778ebb777237397264aa6dd17e557109f3fce

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

      Date: 2026-08-25 09:17:59 -0400

      Commit message:


	  
		
 Add gene score vs gene expression modules.
 

    

  
    

      Package: scRNAseqApp

      Commit: d3ad57d7b80bcc406dbf2f0b488b412cb189810c

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

      Date: 2026-08-14 15:32:02 -0400

      Commit message:


	  
		
 fix a typo.
 

    

  
    

      Package: scRNAseqApp

      Commit: 4a473552eba18c3c3082405140ebb686da40bf85

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

      Date: 2026-08-14 13:23:18 -0400

      Commit message:


	  
		
 fix column names for fragments.
 

    

  
    

      Package: cytomapper

      Commit: 2efbbe1b58492660783b898a3c1cbf87676ecb22

      Author:  Lasse Meyer <73339780+lassedochreden@users.noreply.github.com> 

      Date: 2026-08-25 12:29:00 +0200

      Commit message:


	  
		
 Merge pull request #102 from BodenmillerGroup/bioc24_buildfix

Bioc24 fix 

    

  
    

      Package: cytomapper

      Commit: 65bc5a7969825d303d8caa708c88b01a156494b2

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-08-25 11:18:24 +0200

      Commit message:


	  
		
 Revert "fix runners for shinytest", "update runners" x2

Reverts 6206c47, 67ec23c, f6bc0d8. Back to the bioc24_buildfix branch
state as of "bioc24 fix" (064205c), before the GitHub Actions
runner/PhantomJS-caching changes.
 

    

  
    

      Package: cytomapper

      Commit: 6206c4746fd06ac28baac39f0892e8530370f1b5

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-08-25 10:30:23 +0200

      Commit message:


	  
		
 fix runners for shinytest
 

    

  
    

      Package: cytomapper

      Commit: 67ec23c4b27b6edc84e44f1babb147e4a1138cf8

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-08-25 10:06:09 +0200

      Commit message:


	  
		
 update runners
 

    

  
    

      Package: cytomapper

      Commit: f6bc0d89a4b6c34cb0363107430483fdcbb98464

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-08-24 17:14:57 +0200

      Commit message:


	  
		
 update runners
 

    

  
    

      Package: cytomapper

      Commit: 064205cfb4f488e62aee5705ef05256194b84a8f

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-08-24 16:30:33 +0200

      Commit message:


	  
		
 bioc24 fix
 

    

  
    

      Package: bluster

      Commit: ef34d956f9c1184265beef3fb868bf680ab83d17

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

      Date: 2026-08-25 18:29:59 +1000

      Commit message:


	  
		
 Cleaned up docstring warnings, bumped version and date.
 

    

  
    

      Package: bluster

      Commit: 40b38d0eef9fd2b31b728fcc000d18ce87bacd33

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

      Date: 2026-08-25 16:58:05 +1000

      Commit message:


	  
		
 Switch from scuttle/scran to scrapper for dataset setup.
 

    

  
    

      Package: bluster

      Commit: 4c7e644f89cce76561341ea6ee7ccf92ca05545d

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

      Date: 2026-08-25 16:36:33 +1000

      Commit message:


	  
		
 Migrated explanatory text from OSCA.advanced's cluster redux chapter.

Also switch to scrapper to set up the dataset in the diagnostics.Rmd.
 

    

  
    

      Package: bluster

      Commit: ce7ac0a3deaf212f86c90c9463bcb515b0ebd657

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

      Date: 2026-08-25 15:28:35 +1000

      Commit message:


	  
		
 Tidied up pairwiseRand manpage.
 

    

  
    

      Package: msa

      Commit: 2e9a9e9728455d7c097f7f7f8c9ee66d5429e14f

      Author:  UBod <ulrich@bodenhofer.com> 

      Date: 2026-08-25 10:07:18 +0200

      Commit message:


	  
		
 updated vignette; version number bumped to 1.45.5
 

    

  
    

      Package: MsBackendMetaboLights

      Commit: f49c8bc69d49d62c988a85a5a55389a586950592

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

      Date: 2026-08-25 09:05:17 +0200

      Commit message:


	  
		
 Update README
 

    

  
    

      Package: MsBackendMetaboLights

      Commit: fdfed26db27a8c5b3fb4c9fe4602898c62857eb5

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

      Date: 2026-08-25 08:39:00 +0200

      Commit message:


	  
		
 Fix installation instructions and add 4 second breaks to unit tests
 

    

  
    

      Package: MsBackendMetaboLights

      Commit: 798de387ad331d8e097fbedad942367eb77abf5e

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

      Date: 2026-08-25 08:20:12 +0200

      Commit message:


	  
		
 small updates in NEWS and README
 

    

  
    

      Package: MsBackendMetaboLights

      Commit: bbaddc706e3ee49efd1983e0616578518cc8f164

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

      Date: 2026-08-24 09:01:32 +0200

      Commit message:


	  
		
 Update roxygen version
 

    

  
    

      Package: scrapper

      Commit: 985ad210f9f2b964dcd072ddc4a2bed302d0caef

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

      Date: 2026-08-25 11:27:58 +1000

      Commit message:


	  
		
 Vignette is now a stub that redirects to the book.

No point having a poor man's duplicate of the documentation when we could just
point users to the real deal and save ourselves some build time.
 

    

  
    

      Package: drugTargetInteractions

      Commit: a95ecf0aec40f8aadec98ee09258d4371b359392

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

      Date: 2026-08-24 21:19:29 -0700

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: drugTargetInteractions

      Commit: 93058dc4cc5b0f8350481e46fe2ae40d1b173eea

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

      Date: 2026-08-24 21:16:28 -0700

      Commit message:


	  
		
 Add buildMoaMasterTable(): enumerate the drugs that have a mechanism

assembleMoaTable() shapes whatever queryDrugTargets() was asked for, so
you have to name the drugs going in. There was no way to ask which drugs
have a mechanism at all.

A mechanism belongs to the drug, not to a drug-target edge, and the
difference is not academic. Measured against the real sources: 1,470 of
the Broad Hub's 6,855 drugs with a mechanism name no target gene (21%),
as do 329 of ChEMBL's 5,727 (6%). Roughly two thousand annotated drugs
are therefore unreachable from buildGenomeWideDrugTargetTable(), which is
anchored on genes - "c-Myc inhibitor", "polyamine biosynthesis
inhibitor", "Radiotherapy agent" and so on.

Sweeps the two sources that can be enumerated: ChEMBL's /mechanism is a
pageable collection (7,561 records, ~8 requests) and the Broad Hub is
already local SQLite. The whole table is 14,723 rows over 12,582 drugs
and 3,263 mechanisms in about a minute. Open Targets carries real MOA too
but its GraphQL has no clean enumeration path and its drug annotations
derive largely from ChEMBL, so it stays with queryMoa().

Two data details that would otherwise mislead:

- The Broad Hub packs up to 6 mechanisms into one "a | b" string, for 493
  drugs. Splitting them turns 1,612 apparent mechanisms into 1,294 real
  terms; without it, 318 of the "distinct MOAs" are combinations.
- ChEMBL records "Unknown" as the mechanism for 228 rows. Dropped by
  default as a placeholder; includeUnknown = TRUE keeps them.

Sources are kept side by side, not merged: drug_id is a ChEMBL id on
ChEMBL rows and the Hub's own drug name on Broad rows. They also word
mechanisms at different granularity - ChEMBL names the isoform
("Carbonic anhydrase VII inhibitor") where Broad names the family
("carbonic anhydrase inhibitor") - so only 7 of 3,263 terms are shared
verbatim, and 102 after lower-casing. Documented, since it decides
whether grouping the column across sources means anything.

Every count reconciles against independent raw measurements of both
sources. New .dtiPageAll() for unfiltered collection paging, beside the
existing .dtiBatchGET(). Vignette section 7 gains "A Master Table of
Mechanisms". test-moaTable.R 57 -> 90 with the network on, the Broad half
network-free against a synthetic SQLite.
 

    

  
    

      Package: drugTargetInteractions

      Commit: 05e656c64d1f073c2c0fb29fd6391de68dbd7c0b

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

      Date: 2026-08-24 20:48:20 -0700

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: drugTargetInteractions

      Commit: 845f69b2a455d6b1885d5f5cc1e17e80e96be3ba

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

      Date: 2026-08-24 20:45:45 -0700

      Commit message:


	  
		
 Reject an unrecognised source or column instead of silently dropping it

match.arg(several.ok = TRUE) drops any value it cannot match as long as
at least one other value does, and its matching is case-sensitive. So

  sources = c("chembl", "dgidb", "opentargets", "ttd", "broad", "GtoPdb")

built a five-source table with no error, no warning, and no gtopdb
element in the result - the mis-cased name simply vanished. Passing
gtoPdbDbPath did not help, because the requirement check runs after
match.arg has already discarded the name.

queryDrugTargets() already validated its own sources with an explicit
%in% check; the three match.arg(several.ok = TRUE) call sites were the
outliers. All now use .dtiMatchSet(), which errors on anything
unrecognised and, when a value differs only in case, says which name was
meant - every accepted name is lower-case:

  'sources' does not recognise: GtoPdb. Did you mean "gtopdb"? These
  names are lower-case. Expected any of: chembl, dgidb, opentargets,
  ttd, broad, gtopdb.

Covers buildGenomeWideDrugTargetTable(sources), combineDrugTargets(columns)
and mergeDrugTargets(by). Exact matching replaces match.arg's partial
matching, which is the same trade queryDrugTargets() already made.
 

    

  
    

      Package: RBPEqBind

      Commit: e1f34337a3adf282f7e6ccd152753bf194ec2b84

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-08-24 22:29:26 -0400

      Commit message:


	  
		
 Bump version to 0.99.4 and refine parallel architecture
 

    

  
    

      Package: VDJdive

      Commit: 74f33a6f30ed7ba27bf714fa699e020a57a500b5

      Author:  Kelly Street <street.kelly@gmail.com> 

      Date: 2026-08-24 16:45:04 -0700

      Commit message:


	  
		
 reran Rcpp::compileAttributes()
 

    

  
    

      Package: gDRcore

      Commit: 0901d750ecc307af97f90cb717aed7a18db4e230

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

      Date: 2026-08-24 13:26:34 +0200

      Commit message:


	  
		
 Merge pull request #206 from gdrplatform/GDR-3542

feat: add get_period_timepoints() listing the measurements in each growth-rate window 

    

  
    

      Package: gDRcore

      Commit: 0c2b2ff294cc0ea4a92d6db8b7db4bc629961e46

      Author:  Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com> 

      Date: 2026-08-20 11:52:04 +0200

      Commit message:


	  
		
 refactor: extract .assert_periods() and cover the default lfc_assay path
 

    

  
    

      Package: gDRcore

      Commit: 1e23f5ac51179e9951e1be2df07912aaddfcae15

      Author:  Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com> 

      Date: 2026-08-19 14:18:44 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into GDR-3542

# Conflicts:
#	DESCRIPTION
#	NEWS.md
 

    

  
    

      Package: gDRcore

      Commit: 71f2ec036923ebbde7eb22aed7347975c1cd4814

      Author:  Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com> 

      Date: 2026-08-19 12:50:44 +0200

      Commit message:


	  
		
 feat: add get_period_timepoints() listing the measurements in each growth-rate window
 

    

  
    

      Package: lineagespot

      Commit: 1c3132ac4f90d93c26f53f0e17c2ee2858ff2545

      Author:  Theodoros Katzalis <thodkatz@gmail.com> 

      Date: 2026-08-24 11:04:33 +0300

      Commit message:


	  
		
 Remove outdated outbreak api

add ci to replicate the bioconductor pipeline and bump versioning to 1.17.1
 

    

  
    

      Package: lineagespot

      Commit: 13b0d6100e5302342df581c2c290be20032d9bd3

      Author:  Theodoros Katzalis <thodkatz@gmail.com> 

      Date: 2026-08-20 15:35:55 +0300

      Commit message:


	  
		
 Bump DESCRIPTION to 1.17.1
 

    

  
    

      Package: lineagespot

      Commit: 3144e41c683375d856d8737a37f795d3a5867e75

      Author:  Theodoros Katzalis <thodkatz@gmail.com> 

      Date: 2026-08-20 15:13:56 +0300

      Commit message:


	  
		
 remove outdated outbreak.info api

we can't get lineages from outbreak api since it has reached end of life, so we have removed it. Lineages currently can be only local - offline
 

    

  
    

      Package: lineagespot

      Commit: 1a04c30d49bbe4828eda3188839103308f58fdc5

      Author:  Theodoros Katzalis <thodkatz@gmail.com> 

      Date: 2026-08-20 14:50:03 +0300

      Commit message:


	  
		
 use auto-generated bioconductor workflow

replaces our custom workflow, and uses the official one, replicating the actual pipeline on bioconductor
 

    

  
    

      Package: lineagespot

      Commit: 1da929573143a6b9bcc1089fd0048b8c9126fa69

      Author:  Theodoros Katzalis <thodkatz@gmail.com> 

      Date: 2026-08-05 15:58:00 +0300

      Commit message:


	  
		
 use dual license file convention
 

    

  
    

      Package: lineagespot

      Commit: 93137be3c7f7d39375c214db7284eccec2dddc3b

      Author:  Theodoros Katzalis <thodkatz@gmail.com> 

      Date: 2026-08-05 15:45:01 +0300

      Commit message:


	  
		
 add ci to test build in bioconductor containers
 

    

  
    

      Package: methylclockData

      Commit: 98e411af857b56ca01ddb539b6b08adb86da71d2

      Author:  dpelegri <43083225+dpelegri@users.noreply.github.com> 

      Date: 2026-08-24 09:59:13 +0200

      Commit message:


	  
		
 Add the coefGarma resource and bump to 1.21.3

The Garma & Quintela-Fandino (2024) cross-platform age clock needs one new ExperimentHub resource. metadata_v2026_08b.csv (with its make-metadata script) points to the new version of the Zenodo deposit (record 22069904,
verified by download); get_coefGarma() joins the accessors, pending its ExperimentHub id. The 28 resources from the previous round are unchanged.
 

    

  
    

      Package: MetaboDynamics

      Commit: 42de4d6a3457843d3abb624968a3b4ab491de987

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-08-24 09:22:18 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: MetaboDynamics

      Commit: 23a33c72d72db8b100ad015fde911b183b665a11

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-08-24 09:21:56 +0200

      Commit message:


	  
		
 bug fix: Guide to prior settingp
 

    

  
    

      Package: scrapper

      Commit: dc2904c751ede19a63e91e879a43cbf11e98c6b5

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

      Date: 2026-08-24 15:53:08 +1000

      Commit message:


	  
		
 Avoid clang errors from alias template class deduction.
 

    

  
    

      Package: gDR

      Commit: 2fd929fb761bc1f5dfcb55db79dc905dc1fb6824

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

      Date: 2026-08-24 07:48:39 +0200

      Commit message:


	  
		
 Merge pull request #61 from gdrplatform/GDR-3530

chore: align DESCRIPTION date with NEWS entry 

    

  
    

      Package: gDR

      Commit: 65f284e0abfa8ebb6b84ea7beb98ff5990e0e596

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

      Date: 2026-08-18 08:26:51 +0200

      Commit message:


	  
		
 chore: align DESCRIPTION date with NEWS entry
 

    

  
    

      Package: drugTargetInteractions

      Commit: a93caef2962ddcae9772013ab8c176e07ff1cd89

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

      Date: 2026-08-23 21:38:38 -0700

      Commit message:


	  
		
 Ignore vignette render artifacts

rmarkdown::render() leaves a ~1MB html plus a ~1MB knitr cache in
vignettes/, so every render ended with a manual cleanup to keep the tree
clean. Nothing tracked matches these patterns, so nothing is hidden
retroactively.

Scoped to vignettes/ rather than a bare *.html on purpose: gh-pages keeps
the published page as a root-level index.html and has no .gitignore of
its own, so an unscoped rule would silently make the next publish a no-op
if this file ever reached that branch.
 

    

  
    

      Package: drugTargetInteractions

      Commit: cdc5557d74f597a957220cc087d558f1a54c82ce

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

      Date: 2026-08-23 21:32:13 -0700

      Commit message:


	  
		
 Warn about the symbols given, not about the whole HGNC snapshot

buildHgncSymbolMap() warned "1268 old symbol(s) map to more than one
current symbol" on every call. That count describes the HGNC snapshot -
it is the same 1268 whatever you are translating - so every caller got it
regardless of relevance. Translating FGFR1 warned about 1268 genes, none
of them FGFR1.

The vignette showed the cost: four copies of that warning, in chunks
querying only genes that are not ambiguous at all. Suppressing it there
would have hidden a wrong warning rather than fixed it.

normalizeGeneSymbols() now reports the ambiguities the symbols it was
given actually run into, names them, and scopes attr(., "ambiguous") to
those. A symbol that is already current is passed through untouched and
can never be ambiguous, so the common case is silent. addCommonIds() and
normalizeGeneSymbols() build their map with warn = FALSE; a direct
buildHgncSymbolMap() call still reports the snapshot-wide count, which is
meaningful when the map itself is what you asked for.

Verified by re-rendering: the vignette now has 0 warnings and 0 errors
across all 151 chunks, against 4 before. The full suite is warning-free
too (was 2 "expected" warnings), FAIL 0 ERROR 0 SKIP 86 PASS 408.
 

    

  
    

      Package: drugTargetInteractions

      Commit: c968b7b2e1b4d4947009e759a4d8585f63a44f35

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

      Date: 2026-08-23 21:13:59 -0700

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: drugTargetInteractions

      Commit: e09215a23e80e7663c5bc4c1c67d6c3e1634122f

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

      Date: 2026-08-23 20:48:39 -0700

      Commit message:


	  
		
 Carry gene identity once in mergeDrugTargets, and select columns by concept

Two things this function got wrong for a genome-wide build, neither of
which changes what placing sources side by side means.

The identity block was repeated once per source. A build tags every
source's rows with the same gene, so the output carried chembl_symbol,
dgidb_symbol, opentargets_symbol and ttd_symbol all reading ADRA1A, and
four more columns all reading ENSG00000120907 - 8 of 61 columns spent
restating what the key already determines. It is now collapsed like any
other column but emitted once, beside the key: 61 columns become 55.
Keyed on a gene each cell holds one value; keyed on a compound, symbol
holds every gene that drug hits, which is the honest answer rather than
an arbitrary winner.

Selecting a column meant knowing all six names for it. Reaching FGFR1's
drugs took columns = c("Drug_Name", "drug_name", "DrugName",
"pert_iname", "ligandName"). `columns` now also accepts a shared name
from the mapping table, so "drug_name" selects whatever each source calls
it. Source-native names still work unchanged, and the two forms mix. The
columns still come back one per source - this view exists to compare what
each source says, so it deliberately does not merge them.

Also documents a trap the genome-wide data exposed: n_sources counts the
sources that returned a row, not the sources that found a drug. A build
queries every gene everywhere, so 18,778 of 19,296 genes have a row from
all four sources while only 1,025 have a drug in all four, and 14,710
have none anywhere. Test the cells, not n_sources.

The hgnc_id clobbering this function also had needed no work here - it
routes through addCommonIds(), so the previous fix covered it.
 

    

  
    

      Package: drugTargetInteractions

      Commit: 2a17f690a972c193eb7da44af363f2283a7a6837

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

      Date: 2026-08-23 18:27:18 -0700

      Commit message:


	  
		
 Add a user-editable column map, and assemble a genome-wide build with it

buildGenomeWideDrugTargetTable() returns one table per source, each with
that source's own columns. Stacking them needs two things: columns
holding the same content under different names aligned onto one column,
and columns belonging to one source carried through as their own.

combineGenomeWideDrugTargets() does that. The identity block (hgnc_id,
symbol, ensembl_gene_id, QueryIDs) is emitted verbatim and never
recomputed - see the previous commit for why. Canonical columns are
character throughout, since sources sharing a concept do not share a
type; each source's own columns keep theirs, since each belongs to
exactly one source and nothing has to be reconciled.

Which columns hold the same content now lives in a table the user can
see and edit. drugTargetColumnMap() returns it as a plain data.frame,
and .dtiCuratedColumnMap is the single source of truth:
.dtiCombineColMap is derived from it, with a test asserting the
derivation reproduces the old hardcoded list exactly, so the map a user
edits and the map combineDrugTargets() applies cannot drift apart.

Curated groups grow from 3 to 8, each checked against real values first:
mechanism (free text naming the target, as against action's bare label -
TTD's MOA is a bare label and stays in action), target_uniprot,
pubchem_cid, max_phase and indication. max_phase is deliberately lossy
and documented as such: ChEMBL a number -1..4, Open Targets PHASE_3, TTD
and the Broad Hub Approved. Broad's moa is the one native column feeding
two canonical columns, which the map allows on purpose.

The map can also be generated from a build, but only as a draft.
Matching column names after normalising case and punctuation proposes
opentargets:drug_id with ttd:DrugID, which are a ChEMBL identifier and a
TTD-internal one - aligning them would fabricate identity. It equally
misses groups sharing no name at all, such as approved_symbol/gene_name/
GeneName. So proposals come back inactive and are inert until someone
turns them on.

Verified on a full 212,827-row build: 212,827 rows out, 41 columns,
hgnc_id complete and every value kept as supplied, per-source row counts
identical to input, canonical columns identical() to their native
source column, and no native column carrying a value outside its own
source's rows.
 

    

  
    

      Package: drugTargetInteractions

      Commit: bf7d06fe279bbd80bc9dd4af07beb5b43a93764c

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

      Date: 2026-08-23 18:26:47 -0700

      Commit message:


	  
		
 Keep an hgnc_id a caller already established instead of re-deriving it

addCommonIds() overwrote hgnc_id unconditionally, which is wrong for any
table that already carries one. buildGenomeWideDrugTargetTable() tags
every row with the HGNC gene it queried *from*, so that column is
complete by construction; recomputing it from the identifiers a source
echoes back is strictly worse, and sometimes simply wrong.

Measured on a four-source genome-wide build, first 2000 rows per source:
re-derivation recovers 497/2000 ChEMBL rows (many UniProt accessions name
more than one gene, so NA is the honest answer), 1306/2000 for Open
Targets, 1670/2000 for TTD - and moves 98 of TTD's rows to the wrong gene
outright. Rows queried as ADRA1A come back as HGNC:280, which is ADRA1D:
ADRA1A is also a previous symbol of that gene, and the ambiguity
tie-break picks alphabetically. A tie-break that is reasonable when there
is nothing better becomes a silent corruption when there is.

Now only the gaps are filled. gene_symbol/target_uniprot follow the key
that was kept, which incidentally fills ChEMBL's otherwise-NA gene_symbol
offline - that previously needed resolveGeneSymbol = TRUE and a network
round trip.
 

    

  
    

      Package: mobileRNA

      Commit: 49137e2b494b71e047939aa0bff147715ee86794

      Author:  Katie Jeynes-Cupper <katie.jeynescupper@gmail.com> 

      Date: 2026-08-23 21:26:31 +0100

      Commit message:


	  
		
 corrections

version control numvering issue lol
 

    

  
    

      Package: mobileRNA

      Commit: 2944bf1232044f66c16527eb1e1b3fc158e9af34

      Author:  Katie Jeynes-Cupper <katie.jeynescupper@gmail.com> 

      Date: 2026-08-23 21:24:47 +0100

      Commit message:


	  
		
 corrections to version control
 

    

  
    

      Package: mobileRNA

      Commit: 41aad760b2851d91878eddeeabd1ebba972f6e15

      Author:  Katie Jeynes-Cupper <katie.jeynescupper@gmail.com> 

      Date: 2026-08-23 21:23:25 +0100

      Commit message:


	  
		
 Merge branch 'devel' of github.com:KJeynesCupper/mobileRNA into devel

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md
 

    

  
    

      Package: mobileRNA

      Commit: dd2a2941eb09ff726deab522dd2c9b7f92a9b709

      Author:  Katie Jeynes-Cupper <katie.jeynescupper@gmail.com> 

      Date: 2026-08-23 21:22:48 +0100

      Commit message:


	  
		
 version control
 

    

  
    

      Package: mobileRNA

      Commit: 610b846dec780ad644c34a5a34ea35382d520c85

      Author:  Katie Jeynes-Cupper <katie.jeynescupper@gmail.com> 

      Date: 2026-08-23 15:31:45 +0100

      Commit message:


	  
		
 baymobil integration

Integrated baymobil, and removed simDesign (causing loading error). 

    

  
    

      Package: mobileRNA

      Commit: 41ab229c9dc6b9d24fcb469641115086afdd1a1b

      Author:  Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com> 

      Date: 2026-03-03 20:58:23 -0600

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: mobileRNA

      Commit: ed1157b28b535adf99642472e0e554e65f6069e3

      Author:  Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com> 

      Date: 2026-03-03 12:24:23 -0600

      Commit message:


	  
		
 Update R-CMD-check.yaml 

    

  
    

      Package: mobileRNA

      Commit: 3882409fab672a722fea9d53e1e88c71070e0b05

      Author:  Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com> 

      Date: 2026-03-03 11:49:28 -0600

      Commit message:


	  
		
 Update R-CMD-check.yaml 

    

  
    

      Package: mobileRNA

      Commit: 8b80071012fa6777675cab169280c23963a6b1a3

      Author:  Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com> 

      Date: 2026-03-03 11:47:56 -0600

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: mobileRNA

      Commit: c4bb6f3f3e64f37d2a41232d5b3519a3b646250d

      Author:  Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com> 

      Date: 2026-02-27 13:06:42 -0600

      Commit message:


	  
		
 Update _pkgdown.yml 

    

  
    

      Package: mobileRNA

      Commit: 167279072541c6b647c9cf92118ea177b2f8ef6d

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-10-23 12:16:01 -0500

      Commit message:


	  
		
 version control 

    

  
    

      Package: mobileRNA

      Commit: dc1d838d8e820f8abbf8f687dd8beb70b434c696

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2026-02-27 12:39:45 -0600

      Commit message:


	  
		
 update-version-mk 

    

  
    

      Package: mobileRNA

      Commit: 1a3e4ba750d3ae601405af1deae5352938bd2e8d

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2026-02-27 12:21:13 -0600

      Commit message:


	  
		
 mobile_sRNA_import_update

Fixed bug that prevent mobile sRNA data being loaded into R 

    

  
    

      Package: mobileRNA

      Commit: a0955c4e64df214396e262e117c728141d8affd8

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-11-18 16:48:20 -0600

      Commit message:


	  
		
 contact-update
 

    

  
    

      Package: mobileRNA

      Commit: 9f3e7416aa56cb7ea72454f33b72b0620a01d6d1

      Author:  Katie Jeynes-Cupper <katie.jeynescupper@gmail.com> 

      Date: 2026-08-23 16:50:07 +0100

      Commit message:


	  
		
 Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md
 

    

  
    

      Package: mobileRNA

      Commit: 09119fa8de8abe4c004d7d47934140d620204d61

      Author:  Katie Jeynes-Cupper <katie.jeynescupper@gmail.com> 

      Date: 2026-08-23 15:31:45 +0100

      Commit message:


	  
		
 baymobil integration

Integrated baymobil, and removed simDesign (causing loading error).
 

    

  
    

      Package: mobileRNA

      Commit: 1f721799a7e9b1fe6e255e3d56f9f147182e2b9e

      Author:  Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com> 

      Date: 2026-03-03 20:58:23 -0600

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: mobileRNA

      Commit: f819c5ea875f950077d517b5e4bf98a3eea79051

      Author:  Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com> 

      Date: 2026-03-03 12:24:23 -0600

      Commit message:


	  
		
 Update R-CMD-check.yaml 

    

  
    

      Package: mobileRNA

      Commit: ad7187067c24187246fef7e0a18a36c7a5231f0c

      Author:  Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com> 

      Date: 2026-03-03 11:49:28 -0600

      Commit message:


	  
		
 Update R-CMD-check.yaml 

    

  
    

      Package: mobileRNA

      Commit: 6f53c59ded620909b657d3f39061dbf0b7cee378

      Author:  Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com> 

      Date: 2026-03-03 11:47:56 -0600

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: mobileRNA

      Commit: cb4f0aa6e37f2606b677a5baae7201422cb14b2d

      Author:  Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com> 

      Date: 2026-02-27 13:06:42 -0600

      Commit message:


	  
		
 Update _pkgdown.yml 

    

  
    

      Package: mobileRNA

      Commit: c5a7a39f8ec1c2ca49fd13b61b48e5f9b5a56623

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2026-02-27 12:39:45 -0600

      Commit message:


	  
		
 update-version-mk
 

    

  
    

      Package: mobileRNA

      Commit: 8a03e5b40ee534177f0c53f6c6815e82b92fb7ad

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2026-02-27 12:25:59 -0600

      Commit message:


	  
		
 Merge branch 'main' of https://github.com/KJeynesCupper/mobileRNA
 

    

  
    

      Package: mobileRNA

      Commit: b39d9baa6c2a3c35b631136458d177738e4976af

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2026-02-27 12:21:13 -0600

      Commit message:


	  
		
 mobile_sRNA_import_update

Fixed bug that prevent mobile sRNA data being loaded into R
 

    

  
    

      Package: mobileRNA

      Commit: 9b1f8488950234e5710804e71abac1f55785138d

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2026-01-12 18:40:46 -0600

      Commit message:


	  
		
 Bump patch version to 1.6.1
 

    

  
    

      Package: mobileRNA

      Commit: 13a09409420a76a588153324512830c8acaec074

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-11-18 16:50:13 -0600

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/KJeynesCupper/mobileRNA

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md
 

    

  
    

      Package: mobileRNA

      Commit: 74c565b943b186dd864f416a210769bb3135cd0f

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-11-18 16:48:20 -0600

      Commit message:


	  
		
 contact-update
 

    

  
    

      Package: mobileRNA

      Commit: 00bf8fe986a43796f3035cafe734a87fa249541f

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-10-23 12:16:01 -0500

      Commit message:


	  
		
 version control
 

    

  
    

      Package: geneslator

      Commit: b6ea241cf1c7e90c447d61bc6f918cdbabd04e94

      Author:  GMicale <gmgmicky@gmail.com> 

      Date: 2026-08-23 10:49:14 +0200

      Commit message:


	  
		
 Fixed queries to KEGG db
 

    

  
    

      Package: RBPEqBind

      Commit: 569d691fd8a79478cf5c43493c90df2dffcf806a

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-08-22 19:04:05 -0400

      Commit message:


	  
		
 Bump version to 0.99.3 and clean up dependencies for Bioconductor review
 

    

  
    

      Package: RBPEqBind

      Commit: 0b9c6f4970d63525f52066ee0afd09eb91cca408

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-08-22 19:03:59 -0400

      Commit message:


	  
		
 Add extdata provenance script, update README BiocManager install, and refine vignette
 

    

  
    

      Package: RBPEqBind

      Commit: f3d440379d41d209e02dad76694f603f5c78d5a1

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-08-22 19:03:54 -0400

      Commit message:


	  
		
 Implement scale-invariant log solver, fix peak edge background, and add invariant tests
 

    

  
    

      Package: RBPEqBind

      Commit: f70e67df3777e058c7a09d0fafd80a8c87f1e5e5

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-08-22 19:03:45 -0400

      Commit message:


	  
		
 Harmonize JSON export, integrate rtracklayer for BED export, and update palette
 

    

  
    

      Package: RBPEqBind

      Commit: 02565f7bdce6f602d6c15c1effadbec0298cdf6f

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-08-22 19:03:38 -0400

      Commit message:


	  
		
 Refactor simulation with future.apply parallelization, add k-mer checks, and regex docs
 

    

  
    

      Package: igvShiny

      Commit: d5bca1f423b6607074d33d438e27ed15190361ef

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

      Date: 2026-08-22 20:39:28 +0200

      Commit message:


	  
		
 fix: remove a session's track files when the session ends (#173)

* fix: remove a session's track files when the session ends

Every loader that writes into the served tracks directory left the file
behind for the lifetime of the R process. Harmless interactively, where
the directory sits under tempdir(), but a deployed app keeps one process
across many user sessions, and TRACKS_DIR may point outside tempdir(),
where nothing removes them at all. A bam export or a cram copy is
gigabytes per load.

The six loaders holding a session now name their file through
.trackFile(), which collects the paths in session$userData and registers
a single onSessionEnded() hook to unlink the set. The bam index
rtracklayer writes next to its output is registered the same way.

The two write sites without a session in hand - the custom-genome copies
in igvShiny() and the GWASTrack constructor - are unchanged.

Closes #152

* docs: finish the session parameter description on .stageTrackFile

* docs: point agents at a local CLAUDE.md when one is present 

    

  
    

      Package: Rarr

      Commit: 4a6e9871f491e4e10ba1d8ce72071111ba9207d4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-22 00:06:19 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: 0d0a41e068f8f517b036a56818661d91597118e4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-22 00:05:49 +0200

      Commit message:


	  
		
 Ensure chunk get indexed when out of order with full length
 

    

  
    

      Package: Rarr

      Commit: 6321417aedb60ff4c301b25bf743844c3060671c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 14:03:54 +0200

      Commit message:


	  
		
 Use RAW_RO() where possible
 

    

  
    

      Package: Rarr

      Commit: 5c33c2a106fe335160064ac0dffcc77ba2844a3f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 19:06:50 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: 1811ace32424740077592b0dc4510f6d1e435d48

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 22:46:16 +0200

      Commit message:


	  
		
 Support scalar case in is.compact
 

    

  
    

      Package: Rarr

      Commit: 46d5bfdc269222ee1615fcfe32f97791ad337fa7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 22:56:48 +0200

      Commit message:


	  
		
 Restore FIXME comment
 

    

  
    

      Package: Rarr

      Commit: abd7a68172103a99df1a6db2e2df3a6ccf72d7f2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 19:30:16 +0200

      Commit message:


	  
		
 Factor out + 1L
 

    

  
    

      Package: Rarr

      Commit: ff24a58d918965ee436fc02b059256e27c5bcd43

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 19:23:29 +0200

      Commit message:


	  
		
 Use rapply()
 

    

  
    

      Package: Rarr

      Commit: 9b565eda08d2dec66bb604df235122fec6cd2ba0

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 18:13:40 +0200

      Commit message:


	  
		
 Leverage ALTREP on eligible dimensions when reindexing
 

    

  
    

      Package: Rarr

      Commit: 9824d062d35421b56aa369ee96988252da675bb0

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 17:34:01 +0200

      Commit message:


	  
		
 Do not compute quotient and remainder in two separate loops
 

    

  
    

      Package: Rarr

      Commit: 9c8e7385be4b95aba0c91761858658557b1847ec

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 16:23:22 +0200

      Commit message:


	  
		
 Address identity transpose case early
 

    

  
    

      Package: Rarr

      Commit: de09cc7e8b2a576895dcbfab8a179b051fc6b5b1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 15:59:49 +0200

      Commit message:


	  
		
 Make 1D-like identity case implicit in transpose codec
 

    

  
    

      Package: rhdf5

      Commit: 1682d4b493d0ddc9e46cba78a141b780bb8390e8

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 22:25:23 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: ae839a3b4c258cb6919300f28b2bc0b93b5693f7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 23:34:42 +0200

      Commit message:


	  
		
 Make alternative explicit in deprecation warning
 

    

  
    

      Package: rhdf5

      Commit: 99f117b166feb0d28879a6b1bc8c7f101403298d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 22:24:22 +0200

      Commit message:


	  
		
 Restore as.na attribute for now
 

    

  
    

      Package: rhdf5

      Commit: 15c5e4237b150d11ccddb9c399d378ff2c491871

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 15:26:54 +0200

      Commit message:


	  
		
 Set Hugo as aut
 

    

  
    

      Package: TSSr

      Commit: bba29ddb31aa3bcc5c8e1a4276224de759b5b7ea

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-21 15:41:36 -0500

      Commit message:


	  
		
 Merge Bioconductor devel history for TSSr 0.99.21
 

    

  
    

      Package: TSSr

      Commit: 41bc18a8aa1f76ed8e2c1f6ff7699575c7ee9632

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-21 14:55:38 -0500

      Commit message:


	  
		
 Align vignette text with analysis output
 

    

  
    

      Package: TSSr

      Commit: b2cc5da42adff75ebce8c5cdd358808957b41907

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-21 14:19:47 -0500

      Commit message:


	  
		
 Revise vignette with end-to-end input workflow
 

    

  
    

      Package: TSSr

      Commit: 1fd29d2ec88b7a358683d83e4e0c5c49cfa6f259

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-21 12:41:47 -0500

      Commit message:


	  
		
 Document pipeline and expose DESeq2 fit type
 

    

  
    

      Package: TSSr

      Commit: b90a01f34276ff26b00a54e3b693128d161ca07e

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-21 07:57:31 -0500

      Commit message:


	  
		
 Close remaining review validation gaps
 

    

  
    

      Package: TSSr

      Commit: 876a27e2dab02ee1f4677d2d5c4ba5118c39eb7a

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-21 06:40:05 -0500

      Commit message:


	  
		
 Expand vignette workflow context
 

    

  
    

      Package: TSSr

      Commit: 4f85fff8b495b0ff48a12834bec3a5bfb2e60804

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-21 05:05:05 -0500

      Commit message:


	  
		
 Address Bioconductor review feedback
 

    

  
    

      Package: TSSr

      Commit: e2739767956c57b3976dfd69f4eb62ce5577cd42

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-05 09:43:18 -0500

      Commit message:


	  
		
 Remove automatic GitHub Bioconductor CI

Remove the provisional push- and pull-request-triggered GitHub Actions
workflow. It was added without being part of the requested validation plan and
spent most of its wall time downloading a complete Bioconductor dependency
stack into a fresh container. That behavior neither reproduced the
pre-installed Single Package Builder environment nor added useful coverage
beyond the pinned Linux server checks already used for this submission.

Deleting the workflow also prevents routine branch pushes from launching
long, network-dependent jobs with little diagnostic value. This commit does
not remove or skip any package example, unit test, vignette, R CMD check, or
BiocCheck step, and it changes no package implementation. Linux validation
continues explicitly in the fixed Bioconductor Docker image recorded in the
project reports, while official platform results remain the responsibility of
SPB after a Bioconductor repository push.

 

    

  
    

      Package: TSSr

      Commit: d89aa85ec64b381aeed86f666e7f1ebed43068d4

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-04 16:32:15 -0500

      Commit message:


	  
		
 Allow cold Bioconductor CI dependency installs

Increase only the provisional GitHub Actions job timeout from 45 to 60 minutes.
The workflow starts from an ephemeral Bioconductor devel container and must
download and install Depends, Imports, and Suggests before package build or
check begins; that cold setup exhausted the original job budget before it
could provide a package result.

This commit changes no package source, dependency declaration, example, test,
or R CMD check setting. It is a workflow-infrastructure adjustment intended to
separate dependency provisioning time from the package's own check time. The
automatic workflow is removed in the following commit after review determined
that repeated cold installation did not model the pre-provisioned SPB
environment closely enough to justify its time and network cost.

 

    

  
    

      Package: TSSr

      Commit: 5b2c994900eeb31b10f9273e143f3c4f7cb44993

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-04 15:54:43 -0500

      Commit message:


	  
		
 Reduce SPB runtime and add provisional Linux devel CI

Reduce repeated work after the Bioconductor Single Package Builder completed
R CMD check in 566 seconds, leaving too little margin below the ten-minute
limit. Keep every public function under real execution while replacing
unnecessarily repeated full exampleTSSr pipelines with the bundled 100-row,
four-sample, two-strand TSStable fixture or with already-computed upstream
slots. Each example and test still recomputes the function it is intended to
exercise; no skip condition, dontrun block, donttest block, or eval=FALSE path
is introduced.

Update clusterTSS(), consensusCluster(), shapeCluster(), and
exportClustersToBed() examples to construct and run a compact workflow through
the public API. Refactor workflow tests to use a balanced 1,000-row subset for
clustering, and remove redundant upstream recomputation from downstream
analysis tests. Regenerate the affected Rd files and advance the development
version to 0.99.20 with a NEWS entry that records the behavioral and timing
changes.

Add a provisional GitHub Actions workflow based on the Bioconductor devel
container to install declared dependencies, build the source tarball, run
R CMD check --no-manual --timings, and retain failure artifacts. This workflow
was an exploratory local guard and is removed in a later commit after its cold
dependency setup proved unrepresentative of SPB.

In the pinned Linux Bioconductor container, no example takes more than five
seconds and R CMD check --no-vignettes --no-manual decreases from 566 to 421
seconds while all 1,000 test assertions continue to run.

 

    

  
    

      Package: TSSr

      Commit: 68fc7fabbc55c81aa35657810c0513ab16659661

      Author:  JohnnyChen1113 <1020607557@qq.com> 

      Date: 2026-08-04 15:54:33 -0500

      Commit message:


	  
		
 Make cluster quantiles deterministic across platforms

Fix a cross-platform reproducibility failure in the 10th- and 90th-percentile
boundaries used for tag clusters and consensus clusters. The previous strict
comparison, cumsum(tags) > fraction * sum(tags), could choose adjacent genomic
positions when a cumulative sum landed on the threshold within approximately
one double-precision rounding unit. The observed SPB difference changed a
discrete cluster boundary by three bases even though the underlying values were
mathematically equal.

Introduce .firstCumulativeFractionIndex() with a scale-aware tolerance based on
machine epsilon, vector length, target magnitude, and cumulative-sum magnitude.
Treat a cumulative value equal to the requested fraction within that tolerance
as having reached the threshold. Apply the helper consistently to forward and
reverse boundaries in tag clustering and in both consensus-cluster execution
paths. This implements the documented interval semantics of containing at
least 80% of cluster signal and preserves the published macOS-side behavior.

Add public-workflow tests for exact-threshold inclusion, invariance under
positive signal scaling from 1e-6 to 1e6, and consensus-cluster behavior.
Discrete coordinates and table fields remain exact; only aggregate floating
tag sums use a 1e-12 comparison tolerance.

Regenerate exampleTSSr with the deterministic rule. One control cluster moves
its lower boundary from 123531 to 123502 and its interquantile width from 16 to
45, with the corresponding promoter-shape score update. Assigned clusters,
enhancers, differential expression, TAG tables, and promoter shifts remain
unchanged.

 

    

  
    

      Package: ProteinBatcher

      Commit: 1c6df35e6b9a0f0f333f23521ff00b7bd5ff508f

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-08-21 18:59:35 +0200

      Commit message:


	  
		
 0.99.7: optional annotation columns, configurable block_var, mzTab dispatch fix, contrast naming fix, DESCRIPTION/NAMESPACE sync
 

    

  
    

      Package: ProteinBatcher

      Commit: 0947a727ef1879f022bdc459018091114854098a

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-07-20 16:04:15 +0200

      Commit message:


	  
		
 Update to read .SDRF format for experimental results design
 

    

  
    

      Package: ProteinBatcher

      Commit: 7299cde412fb5210b812b7c95de79d2053eda248

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-07-20 16:03:24 +0200

      Commit message:


	  
		
 Incorporating .SDRF format for experimental design matrix
 

    

  
    

      Package: methylclockData

      Commit: f0e667d69b4ad6150cc5ce6dc61bee9aa56fb1cb

      Author:  dpelegri <43083225+dpelegri@users.noreply.github.com> 

      Date: 2026-08-21 18:25:16 +0200

      Commit message:


	  
		
 Fill in the ExperimentHub ids EH10460-EH10487 and bump to 1.21.2

The hubs team loaded the 28 resources into the production database and assigned EH10460-EH10487. Each accessor now carries its id instead of the EH_PENDING placeholder.

Metadata updated to the form the hubs team requested: Location_Prefix is https://zenodo.org/ and the rest of the path moved to RDataPath, matching their correction.

LICENSE reduced to the YEAR / COPYRIGHT HOLDER template R expects; the full MIT text moves to LICENSE.md, kept out of the build.
 

    

  
    

      Package: scrapper

      Commit: a31dbc034c8de03f434020ed917f4b37d018bfe8

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

      Date: 2026-08-22 02:09:07 +1000

      Commit message:


	  
		
 Bumped version and date, rebuilt namespace.
 

    

  
    

      Package: scrapper

      Commit: bed70e7e72f100a23692c8a36b4c34e05b398299

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

      Date: 2026-08-22 00:48:06 +1000

      Commit message:


	  
		
 Update C++ bindings for the latest libraries in assorthead.

The biggest user-visible change is that the number and ordering of factor
levels are now respected in any group= or block= argument. This is possible via
the the new num_groups/num_blocks= arguments in the C++ functions.

Also added some explicit tests for .transformFactor().
 

    

  
    

      Package: biomaRt

      Commit: 2b496cbf6d73c2573d2ed57027287e652db0ec4c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 18:04:10 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: biomaRt

      Commit: 79aa423c07dcde35f8912dcb377a70b1701514aa

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 18:03:57 +0200

      Commit message:


	  
		
 Document setEnsemblSSL() removal
 

    

  
    

      Package: biomaRt

      Commit: 4b8b60157f4fbca9575d831043bb52d1f1f89935

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 18:02:58 +0200

      Commit message:


	  
		
 Remove SSL modification recommendation from vignette
 

    

  
    

      Package: biomaRt

      Commit: 3d8555fac60f64e11f9b15619457e26ce1d4f2af

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 17:13:40 +0200

      Commit message:


	  
		
 Prepare deprecation of SSL settings modification
 

    

  
    

      Package: biomaRt

      Commit: 0aeaaa4b73ac0efd96afadb27b0affc9b7dd6ea4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 16:50:39 +0200

      Commit message:


	  
		
 Rename for mock test
 

    

  
    

      Package: biomaRt

      Commit: 5f9b4a03001392421d6b7967a14c8964d5c5df7c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 16:24:29 +0200

      Commit message:


	  
		
 Do not eval HTTP 500 chunk for now
 

    

  
    

      Package: biomaRt

      Commit: 0b4f42efacfd0a7f18f84b879613479b439ca2cc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 16:15:27 +0200

      Commit message:


	  
		
 Remove Collate
 

    

  
    

      Package: biomaRt

      Commit: b4833d79378afc91af45a9b252a4239272df195d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 11:27:01 +0200

      Commit message:


	  
		
 Leverage dynamic dots in req_url_query()
 

    

  
    

      Package: biomaRt

      Commit: 67ae68a0e50ffc5c750b638d0e783aa77ab62e61

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 11:11:15 +0200

      Commit message:


	  
		
 Factor out guess port util
 

    

  
    

      Package: biomaRt

      Commit: 36a303de4466d11f03fa5d12cb3fe81cdddbfc18

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 10:55:46 +0200

      Commit message:


	  
		
 Simplify sep definition
 

    

  
    

      Package: biomaRt

      Commit: 4bbb85a9e2aa8bc4a38f4cdec6527bfcd4b81dba

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 10:51:36 +0200

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: biomaRt

      Commit: 25f932f1f1e81928534d8a4ec86a8d7a1a20b9ca

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 10:51:26 +0200

      Commit message:


	  
		
 Reduce duplication by moving code to bmRequest()
 

    

  
    

      Package: biomaRt

      Commit: f4764a53d5b490818291eb18e263aa21d611a370

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 17:06:39 +0200

      Commit message:


	  
		
 Silence namespace linter
 

    

  
    

      Package: biomaRt

      Commit: 8a34a0a6effe742acb8a9cf41fe081fd0743d50c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 16:09:51 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: biomaRt

      Commit: e56b60e3463a645a62e37f1286a6775ec1dd3377

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 16:09:02 +0200

      Commit message:


	  
		
 Document all changes in NEWS
 

    

  
    

      Package: biomaRt

      Commit: 01240962a41bc72483703d950ca4233a1f083920

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 16:02:56 +0200

      Commit message:


	  
		
 Use standard workflow
 

    

  
    

      Package: biomaRt

      Commit: c23d02862e906fef32870ae097cd62d4fcd1762e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 16:01:11 +0200

      Commit message:


	  
		
 Run vignettes on CI
 

    

  
    

      Package: biomaRt

      Commit: 1fbd4191c9031b7a8791cbae9447863dab5e815d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 15:20:58 +0200

      Commit message:


	  
		
 Small docs tweaks
 

    

  
    

      Package: biomaRt

      Commit: 019cda97409249c860985aa2d7853726e8021d89

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 15:18:32 +0200

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: biomaRt

      Commit: ad7155beea1a6a1b07caf6afe2ea0bb793e1cfd4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 15:00:22 +0200

      Commit message:


	  
		
 Add dataset to pkgdown reference index
 

    

  
    

      Package: biomaRt

      Commit: 7c354a4bbde40997af8645fff89d35535524f65b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 14:59:54 +0200

      Commit message:


	  
		
 Exclude data-raw/ from lintr config
 

    

  
    

      Package: biomaRt

      Commit: 1d9901cce2b6eb2ea3c05d62fc52a88e986bd015

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 14:50:01 +0200

      Commit message:


	  
		
 Fix test
 

    

  
    

      Package: biomaRt

      Commit: 961d0c4d8d85bc78fe1fef292e7a2df5d4b52dfc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 14:49:57 +0200

      Commit message:


	  
		
 Use local archive cache in .constructEnsemblURL()
 

    

  
    

      Package: biomaRt

      Commit: b6259f1c9ffc963cdb3559ce96cf97146487c0ce

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 14:45:05 +0200

      Commit message:


	  
		
 Add local ensembl_versions to listEnsemblArchives()
 

    

  
    

      Package: biomaRt

      Commit: 8baaa9168f2185232b765d0bed1c6d536951c803

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 14:28:12 +0200

      Commit message:


	  
		
 Add local version <-> release data map
 

    

  
    

      Package: biomaRt

      Commit: 1df52d4328b981838db150d8fce025b28886b04c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-13 20:03:10 +0200

      Commit message:


	  
		
 Simplify mart short name lookup
 

    

  
    

      Package: biomaRt

      Commit: 5b5badbce9ffb4a1b31cd6c5f7dc84330528a665

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 11:00:47 +0200

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: biomaRt

      Commit: 38bd21d301b562849d460ae67e16797750a53dd1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 10:15:44 +0200

      Commit message:


	  
		
 Default to jun2026 archive
 

    

  
    

      Package: biomaRt

      Commit: 42909dfe9cf2596433e80b2f68f19a9bdc9e7e21

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-21 08:34:06 +0200

      Commit message:


	  
		
 Avoid redirect from archive
 

    

  
    

      Package: biomaRt

      Commit: 0f7b30e60051e3894c95670fd33841bdbc477848

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 19:58:50 +0200

      Commit message:


	  
		
 Remove unused function
 

    

  
    

      Package: biomaRt

      Commit: 3c563e0ef5b4c2d7626054535b8f84f7048981f4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 22:49:58 +0200

      Commit message:


	  
		
 Avoid createHash step is not using cache
 

    

  
    

      Package: biomaRt

      Commit: 4725a825bc005fdd137f935aa0aaa4945034576c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-20 20:03:12 +0200

      Commit message:


	  
		
 Do not force redirect to base ensembl site
 

    

  
    

      Package: carnation

      Commit: 1ac0ba123c09a1f207c2e6862c912a9aa14809d1

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-08-21 11:40:16 -0400

      Commit message:


	  
		
 Merge pull request #34 from NICHD-BSPC/v1.1.1

## minor planned release (v1.1.1):

### various bug fixes

- The pca plot was breaking if multiple coloring variables were selected. This was handled by wrapping a condition inside an `if()` statement in `all()`.
- For a dataset with multiple pattern analyses, switching between them was refreshing the plot with an incorrect set of clusters. This was because of race conditions - the set of clusters to be shown was not updating in time before the plot was refreshed. The fix was to set a data load flag for initial plotting, and having the plot wait for a `refresh` for subsequent updates.
- The scatter plot module was not correctly resetting clicked genes when loading a new dataset. Now the selected genes (and other) cache is correctly reset during data load.
- Pattern plot & gene plot x-axis levels (bucket list) were not updating on initial load. This was fixed by updating the reactive values with the initial set of x-axis levels during the initial data load, without depending on an observer cascade.
- The visible (plotly) gene plot and downloaded versions were not matching because of different ways of handling boxes and data grouping between `plotly` and `ggplot2`. This is now fixed.
 
### minor feature updates:

- Some gene plot settings are reorganized for better visibility. Specifically, the settings dropdown now has a *sample settings* group which includes `normalization` - relocated from `More options`, and a *plot options* group listing x-axis variable, coloring variable, faceting variable along with `free y axes` - relocated from `y-axis settings`.
- The gene plot now has a `box position` input to choose between dodged or overlapping boxes.
- The summary table in the `DE analysis` module, now has a `dds_object` column to show which `dds_list` object was used for the contrast. 

    

  
    

      Package: carnation

      Commit: ec60c368689e39c126d53ae505b658dda999a071

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-08-21 11:14:42 -0400

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: carnation

      Commit: 15d8a9244a5eaa5d74467ccb46e609aedffe4b05

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-08-21 11:13:42 -0400

      Commit message:


	  
		
 add action to sync r4.3 w devel
 

    

  
  


</div>

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