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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: cicero
Commit: 2cc70b941c97b890327d761ede0c238e54e4c2c0
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 22:35:53 +0100
Commit message:

 update deprecations
Package: MsDataHub
Commit: 1d997f090ffd167f1f255de5ac283f38a6cff498
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-03-18 21:03:02 +0100
Commit message:

 Merge pull request #13 from rformassspectrometry/jomain

docs: add descriptions of new data sets to vignette
Package: MsDataHub
Commit: f028d65bb112711bf003f3512ac15775cf36dfd9
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-18 07:59:28 +0100
Commit message:

 docs: add descriptions of new data sets to vignette

- Add description for the newly added data sets to the vignette (issue #12).
Package: wiggleplotr
Commit: ce7c8daf78df4d218ef0101acfc8c63aab5fbce6
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2026-03-18 21:13:26 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/wiggleplotr
Package: wiggleplotr
Commit: 5fe9770c17da9c0efd58cc5c275340865b94f8a4
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2026-03-18 21:02:54 +0200
Commit message:

 Merge pull request #27 from kauralasoo/parquet_coverage

Add support for parquet coverage files and fix deprecated dplyr syntax
Package: wiggleplotr
Commit: ede9fec086f9639ea80c5309f3bb68d4f0efb9ce
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2026-02-10 09:57:51 +0200
Commit message:

 Replace deprecated dplyr and ggplot2 syntax.
Package: wiggleplotr
Commit: 63840336a9fe0fe6f391df71588169cf18bb3fac
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2025-12-30 15:10:20 +0200
Commit message:

 Sort parquet file after reading it in
Package: wiggleplotr
Commit: b5f497038c539a2ae8121b3034627eae302e3dbc
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2025-11-06 23:41:22 +0200
Commit message:

 Read specific region directly from the parquet file
Package: wiggleplotr
Commit: e86c12a1a731a061316984f21630d833a4e1ba2c
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2025-11-04 17:27:47 +0200
Commit message:

 Read RNA-seq coverage from Parquet files instead of BigWig files
Package: cicero
Commit: 3a9e8f64cd4d4690dd4fd49829ea92ae837ad908
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 18:41:29 +0100
Commit message:

 version
Package: cicero
Commit: 9d04c3753b88ce64b2fe4968a54ed35d2ae129ea
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 18:33:59 +0100
Commit message:

 version bump
Package: cicero
Commit: 7e7360fe97449d0678fbf7863c835385239e8e79
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 18:25:45 +0100
Commit message:

 version bump
Package: cicero
Commit: da5bca78c156f33780811c44c30c64a3a036ddc5
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 18:22:43 +0100
Commit message:

 Merge remote-tracking branch 'origin/master'
Package: cicero
Commit: 2523a6422f1485869f9c397d276421f90ccee706
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 18:06:40 +0100
Commit message:

 workaround for monocle deprecation error
Package: cicero
Commit: 07f8731b2d2029ab774621b768b20259238ede4d
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2024-09-03 03:07:35 +0200
Commit message:

 Update runCicero.R
Package: cicero
Commit: 26b56abfc45f9722a2797d40ec8de3fd036bbbde
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2024-09-03 03:00:20 +0200
Commit message:

 Merge pull request #96 from Puriney/patch-1

Update runCicero.R
Package: cicero
Commit: 8ef1ce7fe8901f1280f2921d180b738db4e0f9ea
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2024-09-02 20:03:12 -0400
Commit message:

 Merge remote-tracking branch 'origin/master'
Package: cicero
Commit: fedf1c47fb04f57ab25ff56c210ac45fba037674
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2024-09-02 20:02:59 -0400
Commit message:

 Merge remote-tracking branch 'bioc/master'
Package: cicero
Commit: 93474c1f84c958b26ccbe6d1f7a5fe8472566bed
Author: Yun YAN <Puriney@users.noreply.github.com>
Date: 2024-02-06 12:03:45 -0600
Commit message:

 Update runCicero.R
Package: cicero
Commit: 10720b05f39b648fb023357bb5054c3ccb970b6c
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2023-05-04 19:26:02 +0200
Commit message:

 Update check-standard.yaml
Package: cicero
Commit: b1cd65ec78ef9f049e3ce7718c0c6a3d367f77da
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2023-02-27 19:39:39 +0100
Commit message:

 Update data objects
Package: cicero
Commit: f5f6799208836ef2c3964fcc1722c0119e80405e
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2023-02-26 00:23:02 +0100
Commit message:

 Merge branch 'master' of github.com:cole-trapnell-lab/cicero-release
Package: cicero
Commit: 46db306eec3a8aa1bbfde5ec9e088c94f9c20791
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2023-02-26 00:22:54 +0100
Commit message:

 update workflow
Package: cicero
Commit: ed32a7a82925b3be3cf299f04a5fd4eab9dbdc27
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2023-02-26 00:08:01 +0100
Commit message:

 Update README.md
Package: MSnbase
Commit: f6bac75e651931d922e037b39fdb0ac2fb62c074
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 18:05:17 +0100
Commit message:

 bump version
Package: MSnbase
Commit: 7f1fc6ee433cff7ce85a260b20c25cb7215ff33a
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 17:00:41 +0100
Commit message:

 more fix tests and warnings
Package: MSnbase
Commit: 0301b6b3bc549e7a4d12f8fe4a239ddac6a53f60
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 13:31:39 +0100
Commit message:

 more fix tests and warnings
Package: MSnbase
Commit: 29137c4a3b1f5dfba7950dff77d75f9bb1dd1861
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 13:05:53 +0100
Commit message:

 more fix tests and warnings
Package: MSnbase
Commit: 51d2420a00429d9b7beb6905df674dede77314e4
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 13:05:31 +0100
Commit message:

 more fix tests and warnings
Package: MSnbase
Commit: 48cd6f8ce5ad50d192b37d5d947fbdd1f6e7e1cd
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 13:00:10 +0100
Commit message:

 fix tests and warnings
Package: MSnbase
Commit: 507473b9bbbc60097f6905d8e414aa9ea396534c
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-17 22:12:41 +0100
Commit message:

 use r/bioc devel
Package: scRNAseqApp
Commit: 3f56d699d88ab28c56ad64eedc64f8360182a6e0
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-03-18 12:51:46 -0400
Commit message:

 add search link for species.
Package: PolySTest
Commit: 9185a149f34d2e01e2b245d5bbb5e705af0d953e
Author: veitveit <veits@bmb.sdu.dk>
Date: 2026-03-18 17:33:06 +0100
Commit message:

 temporary version for bioconductor
Package: PolySTest
Commit: 4c9d5bf475c59fd923c237ee7ea5bb117fa7966b
Author: veitveit <veits@bmb.sdu.dk>
Date: 2026-03-18 17:32:44 +0100
Commit message:

 temporary version for bioconductor
Package: PolySTest
Commit: 582ba729dc574040627c8cc60d6d8876f032cfea
Author: veitveit <veits@bmb.sdu.dk>
Date: 2026-03-17 08:02:19 +0100
Commit message:

 more fixes
Package: PolySTest
Commit: b8f289d5e25664158036a23a23b5d961baaeb88c
Author: veitveit <veits@bmb.sdu.dk>
Date: 2026-03-17 07:30:44 +0100
Commit message:

 small fix of shiny app
Package: pathlinkR
Commit: 5adccf7adb74fb4fd39f71b592a1d302dcb16f5c
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2026-03-18 09:12:24 -0700
Commit message:

 Added argument for better font size control in plotFoldChange
Package: mzR
Commit: 22865a4d05ffc3d8d896add3c660fba08cfd93d4
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 17:12:52 +0100
Commit message:

 fix isseu #315
Package: mzR
Commit: bc55bd303fef201a5f95029d1f3d0f6d6381e23e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-03-18 17:05:15 +0100
Commit message:

 Merge pull request #317 from jorainer/jomain

Remove dependency from msdata and small bug fix in mzML import
Package: mzR
Commit: eac9debc41ad2f2f5e7293dd0c78105bad44f5a1
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-13 07:54:33 +0100
Commit message:

 Use BioC devel
Package: mzR
Commit: d679664f522c8aeebe60512ab3b720fd420eeedc
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-12 15:55:01 +0100
Commit message:

 tests: fix unit tests removing references to msdata
Package: mzR
Commit: 4fc19cb7526e28913ca610ad531a6bbef1d569ee
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-12 15:47:00 +0100
Commit message:

 refactor: load test files from MsDataHub

- Load the test files from *MsDataHub* and removing the dependency
  from *msdata*.
Package: mzR
Commit: 8c096294323cf849d4cdb4c03397d3fdd13b7497
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-02-26 14:22:29 +0100
Commit message:

 fix RcppExports
Package: mzR
Commit: 49c7fc6f225c06ec9b35f70abc41f473f0f7c7fa
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-02-26 13:44:04 +0100
Commit message:

 fix: catch potential error in spectrum id parsing
Package: mzR
Commit: fa8dd67c1d9580d53077186d9d6aaf8d6eb04f26
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-02-26 13:25:49 +0100
Commit message:

 Merge remote-tracking branch 'bioconductor/devel' into jomain
Package: mzR
Commit: 83ef5dd55222b69c8f4e483c113b5b2c8095241a
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-02-10 14:22:39 +0100
Commit message:

 First fixes for replacement msdata -> MsDataHub
Package: Voyager
Commit: fa06d54ae0aa86041eb9805d7c903e62216999c1
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2026-03-18 12:11:17 -0400
Commit message:

 Forgot that biscale is not imported but suggested
Package: MsBackendMassbank
Commit: b93ed941478757a4a4c5dbe946d44196a9ae5e59
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-03-18 15:57:48 +0100
Commit message:

 Merge pull request #61 from rformassspectrometry/jomain

refactor: used rbindlistWithRownames to combine data
Package: MsBackendMassbank
Commit: 2740db80786c0bbcbb0ba4218abbd727f8d1a220
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-18 15:39:59 +0100
Commit message:

 refactor: used rbindlistWithRownames to combine data
Package: trackViewer
Commit: f069bceca0fa73b83c9006fadf060f026867c8f0
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-03-18 10:21:14 -0400
Commit message:

 Fix the mis-match y-axis for dandelion.plot when max score is smaller than 1.
Package: trackViewer
Commit: 6c1f5eabc07d4429c35d4de05c9c92806407be66
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-03-17 16:17:37 -0400
Commit message:

 fix a typo.
Package: sfi
Commit: e0897f47b43af099b43c082b707f37253133c9b4
Author: yufree <yufree@live.cn>
Date: 2026-03-18 09:43:00 -0400
Commit message:

 bump version to 0.99.5
Package: MetaboAnnotatoR
Commit: 806e76bc7ec3fa3a1dd24cdc859c83caa6d522f3
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:35:33 +0000
Commit message:

 vignette updated after fixing the library data calls
Package: MetaboAnnotatoR
Commit: 7b42738d70ffc162399044d43fe3e69dbad4f41f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:34:43 +0000
Commit message:

 tests updated
Package: MetaboAnnotatoR
Commit: fa8f760b8a2a707fac4cbead53110adc41ad902f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:32:56 +0000
Commit message:

 examples fixed
Package: MetaboAnnotatoR
Commit: a6060d1fcfbf8f17afdc8453f7f4cf0901ba9967
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:31:57 +0000
Commit message:

 usage fixed
Package: MetaboAnnotatoR
Commit: 0d2208b3321813189519cfacf341eb1817e0ab34
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:30:32 +0000
Commit message:

 more global variables added
Package: MetaboAnnotatoR
Commit: 989dcf1461f3a420016d77a698337a0dfbbbe887
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:26:06 +0000
Commit message:

 fixed examples
Package: MetaboAnnotatoR
Commit: e16a265687881f9899b0da2e95a7113f8d49ef95
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:25:34 +0000
Commit message:

 fixed examples
Package: MetaboAnnotatoR
Commit: cbd6ac3506875df4efdff29a74667b5d518363d2
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 22:44:21 +0000
Commit message:

 documentation fixed
Package: MetaboAnnotatoR
Commit: df96e3712c1ddc9c77fb7c9e5a36ec2bb3d239ba
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 22:33:57 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: 9591233bab555548517d2ff04fa7b3aaf0c58833
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 22:31:28 +0000
Commit message:

 tabs removed
Package: MetaboAnnotatoR
Commit: 0330bfe26e0e7d0f8d338867b401486cd18a1fc4
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 22:29:16 +0000
Commit message:

 library data call corrected to avoid calling data() inside the function
Package: MetaboAnnotatoR
Commit: 97c5f2670da816de0c20b4640557aeb759a4d349
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 14:02:46 +0000
Commit message:

 small addition
Package: MetaboAnnotatoR
Commit: 28b06bac8ac042eee5004c5252cd1af4dcdbaadd
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 12:59:33 +0000
Commit message:

 default libraries loading fixed after lazy data set to false
Package: MetaboAnnotatoR
Commit: 32cbc4b84bcf90388cfb200f5029dad71caaf1b4
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 09:46:33 +0000
Commit message:

 default libraries loading fixed after lazy data set to false
Package: MetaboAnnotatoR
Commit: acf3de783f96dd4150762341133beacb0cbc6d20
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-15 17:34:29 +0000
Commit message:

 tabs removed
Package: MetaboAnnotatoR
Commit: edfa21d62dab3b9d85ff73984f9cb15bb750eec3
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-15 17:30:44 +0000
Commit message:

 Lazy data is now false
Package: MetaboAnnotatoR
Commit: c0ca4ae195fd1ad4217911388a4fba96a4eb0650
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-15 14:58:34 +0000
Commit message:

 correction in the example
Package: MetaboAnnotatoR
Commit: 3186e9c785a792cac4abc131eb9919d438ee6603
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-15 14:23:51 +0000
Commit message:

 format corrections after check
Package: MetaboAnnotatoR
Commit: 90c0879e46b82662e6f64c61a38179dbc66b5c04
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:39:52 +0000
Commit message:

 new extdata location and description
Package: MetaboAnnotatoR
Commit: 90f455fb27b65a1a549de8457de9414844e3a5fe
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:38:20 +0000
Commit message:

 extdata paths updated
Package: MetaboAnnotatoR
Commit: 17861fd2ab76c50e65bd9acebe5b2b2054230a1d
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:36:42 +0000
Commit message:

 extdata path updated
Package: MetaboAnnotatoR
Commit: a86837944c3f470e179482e3d581f8485ecb91d5
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:35:34 +0000
Commit message:

 documentation part corrected
Package: MetaboAnnotatoR
Commit: 0bed83022ecb26007ccb52ed25383ae1b8d0c0fd
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:34:21 +0000
Commit message:

 files moved to extdata
Package: MetaboAnnotatoR
Commit: ed15a3426c037e27988ccec98eadc0ad64ccc79f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:33:00 +0000
Commit message:

 corrections after testing package
Package: MetaboAnnotatoR
Commit: 3b106b35b71a659edd62a6c15a0fcc5c7151eb1b
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 11:32:16 +0000
Commit message:

 documentation corrected
Package: MetaboAnnotatoR
Commit: 3ef11f7cca18df765f805211edeaa50b9dda66d9
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 11:02:23 +0000
Commit message:

 addition to documentation
Package: MetaboAnnotatoR
Commit: 3c8d76345d7eb5a313c5fefea7237aebbca99707
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 10:44:41 +0000
Commit message:

 typo in examples corrected
Package: MetaboAnnotatoR
Commit: da35a581b39170fef5a606cf8ad1b57104817ca8
Author: Goncalo Graca <45899755+gggraca@users.noreply.github.com>
Date: 2026-03-10 09:44:53 +0000
Commit message:

 Update DESCRIPTION

New version bump after merging from Biocfixes
Package: MetaboAnnotatoR
Commit: f766fa6046b04f18b48d76cde8044cc1fcbf9c26
Author: Goncalo Graca <45899755+gggraca@users.noreply.github.com>
Date: 2026-03-10 09:43:36 +0000
Commit message:

 Merge pull request #11 from gggraca/biocfixes

Biocfixes
Package: MetaboAnnotatoR
Commit: 9fdc46bec27ffab7bb0c1475ea4eeb6ee39d4206
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:35:40 +0000
Commit message:

 tests updated
Package: MetaboAnnotatoR
Commit: aba7dae7bdff23927a389f6a5810bf828a620171
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:34:48 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: c11d4b8416f515605b458d777c820eba5676d71c
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:33:36 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: 35ecabe55cdd04db3af3f7764b9e8d6342aaf900
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:32:13 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: 98ce60de8437f5d6887dfd41101a17a65553e22a
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:30:52 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: 4f783894b0ae60d166faf0213bd8915995350067
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:30:16 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: 5e9ed869cd958500a37dde63fe72df47958c34b3
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:29:30 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: addca795f52ac4ac1aa66353bbec6d9c9845b9ee
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:28:45 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: 02e22b05e4d4a49bc73edb240072edd087607d31
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:27:56 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: 3e47f89aa2893a77cec11793721a29050c1ee9bf
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:27:08 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: 4ab3864059cfdae32d36af954a2199f3b626a15e
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:25:02 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: 586935407b9f06c3e91989b74e8cc6063b11e075
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-06 17:45:05 +0000
Commit message:

 vignette updated after function changes
Package: MetaboAnnotatoR
Commit: 25046c0b4aee5506980dcac2ee4329aa5235ba77
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-06 17:43:09 +0000
Commit message:

 implicit data directories removed and replaced by user-defined
Package: MetaboAnnotatoR
Commit: f871b350d6187f9fc4fee648899a8c10b4c84fbc
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-06 17:41:48 +0000
Commit message:

 documentation updates
Package: MetaboAnnotatoR
Commit: 4c3f45e75583b9b41be9ff4ec1fefbe2d3c17374
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:46:06 +0000
Commit message:

 importFrom added for csv functions
Package: MetaboAnnotatoR
Commit: 05879475892e959f12d28bb9eb829243b2a8a475
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:34:35 +0000
Commit message:

 corrections to the plot candidate functions
Package: MetaboAnnotatoR
Commit: 6c7e50bdc5f94c0aaa0d579ab30f7e98a4606b7f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:19:22 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: 9b0d7e2cc8e3ba98e8e7d4046344149ca2fb4d26
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:18:03 +0000
Commit message:

 new documented functions
Package: MetaboAnnotatoR
Commit: 79636b6b37934cde457dead7e8fee7b52709d4c8
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:16:06 +0000
Commit message:

 new exported function
Package: MetaboAnnotatoR
Commit: a1b0ac45a4db592fbcebf75875bf1612638eb05d
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:13:36 +0000
Commit message:

 function plotResultSpec moved
Package: MetaboAnnotatoR
Commit: e5eb40a9ed9b2c6daecb3950800565c0b507c3e2
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:11:29 +0000
Commit message:

 new exported function added
Package: MetaboAnnotatoR
Commit: c8f7967323f0d26d2f7f6b030ea26b974dbed257
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 20:26:47 +0000
Commit message:

 functions, related tests and documentation removed
Package: MetaboAnnotatoR
Commit: 76fda41737c7cd81b12cfbf085152031164a405f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 20:21:01 +0000
Commit message:

 vignette updated
Package: MetaboAnnotatoR
Commit: feb1c6c52d9697ed295561b5ece76e70ba0dd957
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 20:20:10 +0000
Commit message:

 new plotting function added
Package: MetaboAnnotatoR
Commit: e2b7fc34284cbd31df6f0f3f4210c226b45232ba
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 15:43:30 +0000
Commit message:

 vignette updated after changes in main annotation functions
Package: MetaboAnnotatoR
Commit: cbef473fb139c4e217f14038f6555d21c491877f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 15:03:16 +0000
Commit message:

 removed line that produced NA rankedResult when results was NULL
Package: MetaboAnnotatoR
Commit: 67cda578477761522934d9a73cfaa5a4f9f22c74
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 15:00:37 +0000
Commit message:

 changes to improve RC annotations results plotting
Package: MetaboAnnotatoR
Commit: 93176bff5388572c08aa047a022581cc451e18a4
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 09:25:41 +0000
Commit message:

 fixed plotting for AIF
Package: MetaboAnnotatoR
Commit: 3f345a3b1d8a02a4bc9b0c3ff7f1d3bcb2071dfe
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-04 16:13:31 +0000
Commit message:

 new function to save the results
Package: MetaboAnnotatoR
Commit: df17bd8e590c86be08bf8f14fe4c6abe78ad1b28
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-02 10:37:22 +0000
Commit message:

 small changes in the example
Package: MetaboAnnotatoR
Commit: 04d09fb0793d7bc8ff3890990691c37a01e14563
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-27 17:23:03 +0000
Commit message:

 test removed as function was removed
Package: MetaboAnnotatoR
Commit: c6c8832dd6032b5061e493061df2bf63995c3a60
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-27 17:21:24 +0000
Commit message:

 test updated to the new outputs of annotateRC
Package: MetaboAnnotatoR
Commit: 40651c7540ccdae60081f2536879f03dadc707fb
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-27 17:19:10 +0000
Commit message:

 .mzML extension added to sample name
Package: MetaboAnnotatoR
Commit: 18db8195f618a96ac8f2aee1b13e8dbc2b37b08c
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-27 17:18:25 +0000
Commit message:

 file redundant
Package: MetaboAnnotatoR
Commit: db8827fe1b865d0e8022eafe611f9fccb389dded
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-27 17:17:38 +0000
Commit message:

 outputs lists only, no files
Package: MetaboAnnotatoR
Commit: 7f91625a1a59b2b9925ee03d5b63a665e8ddffca
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-26 17:03:12 +0000
Commit message:

 adaptations to store object in workspace only
Package: MetaboAnnotatoR
Commit: ff21e3e4ee567cee11f405f0d6636638de7e9310
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-26 15:10:09 +0000
Commit message:

 all saved outputs removed
Package: MetaboAnnotatoR
Commit: aad5e04e07cd5a04f22295376df97e044681843c
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-26 10:44:51 +0000
Commit message:

 more objects added to the results list
Package: MetaboAnnotatoR
Commit: 5c53b900450d7df0b49cb235372fc574c4e5a99b
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-26 10:12:52 +0000
Commit message:

 save data suppressed
Package: sfi
Commit: c89743232bec08ba1f3e950190023fd0c43ff813
Author: yufree <yufree@live.cn>
Date: 2026-03-18 09:22:59 -0400
Commit message:

 Trigger build
Package: sfi
Commit: 5d3736fab47c6f3d948eabba1f0a72dae087aaf2
Author: yufree <yufree@live.cn>
Date: 2026-03-18 09:17:45 -0400
Commit message:

 Trigger build
Package: sfi
Commit: 942aa73f431650aab5afab39cbd4987ee56a3033
Author: yufree <yufree@live.cn>
Date: 2026-03-18 09:16:45 -0400
Commit message:

 update new function name according to review
Package: asuri
Commit: 47bc30e857a1c7de11cfa4ec04c6178ab316210f
Author: aberral <aberralgonzalez@gmail.com>
Date: 2026-03-18 12:42:05 +0100
Commit message:

 Minor fixes
Package: BamScale
Commit: f74eb1a5cb24e9560aee33c9839dbc4115f8b99c
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 22:38:21 +1100
Commit message:

 Increment version number to 0.99.6
Package: beadarray
Commit: c7ea9708ca17c975bd505ca3657a365acb7e6895
Author: markdunning <mark.dunning@gmail.com>
Date: 2026-03-18 10:53:50 +0000
Commit message:

 Reinstate BeadDataPackR to list of dependancies
Package: GSVA
Commit: 2f9c1a646fde1bb4b97b3e3c12d7c68080d5a976
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-03-18 11:49:40 +0100
Commit message:

 Bump version
Package: GSVA
Commit: 1206b3ad1ce38cddcc01898d268b61ee19cb8b1f
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-03-18 11:49:16 +0100
Commit message:

 Fixing versions >= 2.0 wrongly reported in the NEWS file, as noted in issue #261
Package: beadarray
Commit: 011450a34d53d375efe505a329fd949a8d583e80
Author: markdunning <mark.dunning@gmail.com>
Date: 2026-03-18 09:59:40 +0000
Commit message:

 Update email and versions.

Remove source file R that isn't actually referenced anywhere
Package: beadarray
Commit: 3b5574f92f5d8f937782f0289fab87364b5082c9
Author: markdunning <mark.dunning@gmail.com>
Date: 2026-03-18 09:52:40 +0000
Commit message:

 Try to remove offending broken dependancies
Package: queeems
Commit: 8200e3ea6638edce38c81d6f4beaa91659627a15
Author: thsadiq <hassan.t.sadiq@gmail.com>
Date: 2026-03-18 10:43:16 +0200
Commit message:

 Addressed Bioc Build Warnings
Package: queeems
Commit: 52091bb5ba54b1e8c5a3d8b695f18e57259b00df
Author: thsadiq <hassan.t.sadiq@gmail.com>
Date: 2026-03-18 10:27:06 +0200
Commit message:

 Addressed Bioc Build Warnings
Package: BamScale
Commit: 741ddc1a4b7de5b8a2b6e4f969045d1e99c1480f
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 14:50:56 +1100
Commit message:

 Increment version number to 0.99.5
Package: BamScale
Commit: b82209656c055bed4030cf58e8d9c4f80e4c1013
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 14:48:08 +1100
Commit message:

 README correction
Package: BamScale
Commit: 2faa484d50fbe96127427df5e3015e9538250fe0
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 14:47:47 +1100
Commit message:

 improve benchmark
Package: BamScale
Commit: a08b6a300eec58e7c0eeffc0cbde57aff7f8ada8
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 14:33:00 +1100
Commit message:

 Merge branch 'perf/compact-read-columns'
Package: BamScale
Commit: 3032787aa160c7fdea41e46fd1edad027a88f0d6
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 11:34:15 +1100
Commit message:

 Optimize bam_read with compact internal string columns
Package: carnation
Commit: fa3b19951576877f84354ce091944448ba7624ad
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-03-17 23:22:08 -0400
Commit message:

 Merge pull request #25 from NICHD-BSPC/v0.99.9

V0.99.9

- add scatter plot features
  - table can be filtered by significance
  - genes can be selected in the plot and shown in the table
  - genes can be selected in the table and added to 'Gene scratchpad'
- allow users to add pattern analysis results to carnation object using the 'Load data' -> 'New' UI
- add support for edgeR & limma
- show currently loaded dataset on 'Load data' page
- update contributors
Package: carnation
Commit: 627832fe287b768b264f1d4f453ad1c51080642a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 23:11:54 -0400
Commit message:

 version bump
Package: carnation
Commit: 4419067f0da427c4b647b8c14cd7f585b78244c0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 23:03:21 -0400
Commit message:

 pin R < 4.6 for bioc
Package: carnation
Commit: f1165d0f20bfde4674570db3490af7d7cf1e380c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 23:03:08 -0400
Commit message:

 minor formatting
Package: carnation
Commit: fc3342da801aecbfc36eaa227dd9feb859904dc5
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 22:39:14 -0400
Commit message:

 updt scatter plt test w new params
Package: carnation
Commit: d33cad9ab5a2fbb4b734117170f024e62f7ac34b
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 22:38:55 -0400
Commit message:

 use reactive to hold scatter plt src
Package: carnation
Commit: ecb3a0f58be0a57d8bf6477a08ac64d4fc52c653
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 22:25:06 -0400
Commit message:

 updt imports, NAMESPACE
Package: carnation
Commit: f10cbda97b6652d6826888e2b8d150f138e59199
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 21:43:12 -0400
Commit message:

 change github actions github install branch
Package: carnation
Commit: 93a1bfaecadd5de2a1c07659429c0b205a967ae0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 21:42:43 -0400
Commit message:

 add biocmanager install, conda install note
Package: carnation
Commit: 5957e1c7f8cadbfb26195a4850f9a6f3969373b0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 21:42:14 -0400
Commit message:

 add bioc badges, devel page
Package: carnation
Commit: b96618aba22275b5dc01c5c0cb18045b88568b1a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 16:54:45 -0400
Commit message:

 add DESeq2 column names
Package: carnation
Commit: f33543a090e79baf75378439a156408d8228f215
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 16:54:37 -0400
Commit message:

 tweak button label
Package: carnation
Commit: 1471e2874626d5ab5e0e20177e21af8947427b77
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-09 23:12:20 -0400
Commit message:

 add plotly imports to NAMESPACE
Package: carnation
Commit: 92becfc8dc3bba175e80a7f50b463a26844232e4
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-09 23:12:07 -0400
Commit message:

 add tbl & plt selection fr scatter
Package: carnation
Commit: c7d276d4ee21a505e1304906880469553c2a9500
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-09 23:11:31 -0400
Commit message:

 minor ws
Package: carnation
Commit: bf2cbaf0570310ed5604a5a94deaa06005cf5842
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-09 23:10:47 -0400
Commit message:

 set default selection type to box
Package: carnation
Commit: 14482babeb1b386b214ff8c0e331efeca15c9536
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-07 00:31:57 -0500
Commit message:

 add plotly imports
Package: carnation
Commit: ed5987abf3a9489c6602ed60e3cead93c7f5d642
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-07 00:31:32 -0500
Commit message:

 add src arg to scatter plotly plt
Package: carnation
Commit: 20c734657becb482ef65d93743c04ac551faf2eb
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 21:25:59 -0500
Commit message:

 renderdt reacts to scatter_dt
Package: carnation
Commit: c49bafbdde799436785d17719592ab19194a3ef5
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 17:21:01 -0500
Commit message:

 inc scatter plt legend char size
Package: carnation
Commit: f14b57fdcc708656ca9a47bf17a33ac99d720a28
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 17:20:50 -0500
Commit message:

 updt scatter plt docs
Package: carnation
Commit: d11ff5d39fe4fcacdf558b14786e0793f840856c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 17:17:40 -0500
Commit message:

 updt plt w gene scratchpad
Package: carnation
Commit: 12bb3797847f1b43c73ad5e214a1851b7aba148e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 17:16:45 -0500
Commit message:

 integrate tbl sel w gene scratchpad & global reset genes
Package: carnation
Commit: 0746a310211404443e0d1c235be406eb63f1c47d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 17:16:08 -0500
Commit message:

 add scatter tbl selection
Package: carnation
Commit: 63e9518d549f204174977c2d7e97dd341fcd61c8
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 16:16:00 -0500
Commit message:

 add scatter tbl filters
Package: carnation
Commit: 6da9ff6daa99589428dedfc18235c45711d79108
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:47:36 -0500
Commit message:

 mv scatter tbl to observer
Package: carnation
Commit: 2541798f3ea17e874dab72d32f15acc3905535c3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:43:31 -0500
Commit message:

 add sig column to scatter tbl
Package: carnation
Commit: 141e44dce3761787e2ed0d79021339b8f6b4d8da
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:29:13 -0500
Commit message:

 make legend entries larger
Package: carnation
Commit: 0a046495cf40c3c638e6e74ebf373ce100733065
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:29:01 -0500
Commit message:

 make scattergl by default
Package: carnation
Commit: 3fb3b9e99b7fd990c3a8c51c9a294eaadaeb2936
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:28:14 -0500
Commit message:

 split static/interactive plt outputs; switch frm renderUI to cond panel
Package: carnation
Commit: 7f9f487058d4bda8053bf0aa1cb244e4f0915e5f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:27:55 -0500
Commit message:

 always show tbl
Package: carnation
Commit: d7eda219b525707783045741686fb4b77dbc8c9d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 10:28:42 -0500
Commit message:

 fix typo
Package: carnation
Commit: 4ef27f10fd9e75143b32f1ec372bf83212afdf04
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:46:41 -0500
Commit message:

 updt NAMESPACE
Package: carnation
Commit: 762b76ffd44ba332aee5896c0a171fe123dcb226
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:44:35 -0500
Commit message:

 keep orphan dds obj
Package: carnation
Commit: 3455dc20dc35dbd6afd724668244a2970aec86f2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:43:45 -0500
Commit message:

 add degpatterns obj validator
Package: carnation
Commit: 0791b87652a785b0635ccdd3b772a116efa4099b
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:40:56 -0500
Commit message:

 add degpatterns obj via ui
Package: carnation
Commit: 1e9e7532d2da2632cad1dee1d5c33b7cc900fc28
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:40:09 -0500
Commit message:

 rm comment
Package: carnation
Commit: 1d2d905ac9c7e0b74dca9bb9392c5454cedb733d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:39:43 -0500
Commit message:

 add comment
Package: carnation
Commit: cc549a686c68808bfb0323c1548a842569a31131
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:39:05 -0500
Commit message:

 add/fix logic fr checking pre-existing paths
Package: carnation
Commit: 4b55ea9d50c5b0e321e7a4c37159267b01dea91d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:38:37 -0500
Commit message:

 rm design slot before saving
Package: carnation
Commit: cfd99b36587584c18f44fa2c6d3e4b87160f3b6d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:28:36 -0500
Commit message:

 fix typo
Package: carnation
Commit: 9419c95af6fccfde21a30f786339b214d00deebf
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:04:38 -0500
Commit message:

 mv loaded data card
Package: carnation
Commit: 3f7ae4d6fa1f8c637c1ea116cd6008d23695674c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-03 16:38:40 -0500
Commit message:

 add bioconductor shields
Package: carnation
Commit: 167f0763483f896f027452e5c354183f7fc54665
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 20:42:51 -0500
Commit message:

 pin R < 4.3.0
Package: carnation
Commit: a25bda49a49c7742756d8e306c0a9649ae4cb288
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 20:32:07 -0500
Commit message:

 add support for edgeR & limma
Package: carnation
Commit: ddaeda6a46dfe1f4b38b7f50dd6842e4de424c98
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 20:22:29 -0500
Commit message:

 add styling for card
Package: carnation
Commit: 9fb6fc47f15a94e2bbfa9ca23e0ec7328022b6d2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 16:34:34 -0500
Commit message:

 handle parent path of saved RDS being present in data areas
Package: carnation
Commit: db1d34bac719b9fb95bda1c0cb9563af61351cc2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 14:18:52 -0500
Commit message:

 rm server stuff frm README
Package: carnation
Commit: d94f525888933179b96d507d2bcb123f10b92a80
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 14:15:18 -0500
Commit message:

 check for design slot before assignment
Package: carnation
Commit: bd0aea76f245ee9c55046164f4fa19ec633a7a82
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 14:12:24 -0500
Commit message:

 show currently loaded project name
Package: carnation
Commit: b187603f6958bf81df7f0f10cc51904cf0306f8d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 13:06:03 -0500
Commit message:

 tweak function help
Package: carnation
Commit: c4fb249081acbd5628bc71a9e64bd1651d9f0ae4
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 11:09:30 -0500
Commit message:

 updt DESCRIPTION
Package: carnation
Commit: 20839a2d7ba82e574aa2ec1634c2678a533093fd
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 10:27:31 -0500
Commit message:

 updt contributors
Package: BUSpaRse
Commit: 23d0d0be1dbed95d3548c20a43cb12b4263f7417
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2026-03-17 23:20:53 -0400
Commit message:

 Merge branch 'RELEASE_3_22' into devel
Package: BUSpaRse
Commit: 444ab852abbfa0eafcbe38768e4eb3878e6357ca
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2026-03-17 23:20:31 -0400
Commit message:

 Old archives not working on the Ensembl website
Package: Rsubread
Commit: a2681547daa8a40bbc01e79e3418d097942e9126
Author: Yang Liao (Monash University) <yliao@m3v109.massive.org.au>
Date: 2026-03-18 10:02:05 +1100
Commit message:

 imporved manual
Package: clusterExperiment
Commit: 3a17003f4816b796ac601d33fc6d2f52cc843a82
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:43:28 -0700
Commit message:

 rerun documentation
Package: clusterExperiment
Commit: b82e4051fa49bf267b5077ed0d1632716cfdd7b3
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:42:20 -0700
Commit message:

 Merge branch 'claude/suspicious-antonelli'
Package: clusterExperiment
Commit: 9128cc1f1d45a5bf1d118c4e56c24f610e9bec06
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:42:01 -0700
Commit message:

 fix missing documentation
Package: clusterExperiment
Commit: 56d9563aecada310803f19ce9e1c38a38ddbdc75
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:41:19 -0700
Commit message:

 fix Rd \link{} targets missing package anchors

Add package prefixes to \link{} targets (e.g. \link[limma]{topTable}) to resolve R CMD CHECK NOTEs across clusterContrasts, getFeatures, mergeClusters, plotDendrogram, plotClustersTable, clusterSingle, makeReducedDims, and subset.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: clusterExperiment
Commit: 1fa6a8faa06afcadb97744ac0cdd4fe1df4c26d9
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:31:03 -0700
Commit message:

 bump up version
Package: clusterExperiment
Commit: c85eec8a8138d5672abac2d962e1c539f0a81c6c
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:30:48 -0700
Commit message:

 update documentation and fix tests
Package: clusterExperiment
Commit: f1a104d432f409dc9706e9aaa147c56435b54c8a
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:10:57 -0700
Commit message:

 Merge branch 'claude/suspicious-antonelli'
Package: clusterExperiment
Commit: b6048acf6fc399bd651e8dc4318598688a034ea2
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 14:51:36 -0700
Commit message:

 fix Rd documentation: replace \\itemize with \\describe where items use label/description format

Fixes 'Lost braces in \\itemize; meant \\describe?' warnings from R CMD CHECK across 19 R source files and one .Rd file.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: Rsubread
Commit: f4fb96e2a5f7e4eabc291c033c5d6eefea2278a1
Author: Yang Liao (Monash University) <yliao@m3v109.massive.org.au>
Date: 2026-03-18 08:34:57 +1100
Commit message:

 updated manual page of simReads
Package: Rsubread
Commit: 075787f019f92363d272de08f5e45ee7c54737e6
Author: Yang Liao (Monash University) <yliao@m3v109.massive.org.au>
Date: 2026-03-18 08:16:27 +1100
Commit message:

 Bumpped version number.
Package: MSnbase
Commit: 5aeafcbc637fc16aac321f0f2a7aca4a3aff3540
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-17 22:05:03 +0100
Commit message:

 fix version
Package: MSnbase
Commit: c8637c930c8b120ea2f2b441933dacd60b1e573e
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-17 22:03:58 +0100
Commit message:

 remove deps
Package: omicsViewer
Commit: 38cdd2aa8ae9a67ebeb82a3be32adab3d114b320
Author: Chen Meng <mengchen18@gmail.com>
Date: 2026-03-17 20:43:29 +0100
Commit message:

 fix: add remotes package to Dockerfile dependencies

devtools::install_github() requires the remotes package which was missing

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: imageTCGAutils
Commit: 8c58e93c6e8302da41e9a6725ad7c7d56301a0a3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-17 15:19:42 -0400
Commit message:

 version bump 0.99.19
Package: imageTCGAutils
Commit: bbac80aadf77e0f8d938c1487b6c71e50b88d3bc
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-17 15:17:03 -0400
Commit message:

 add NEWS.md file
Package: imageTCGAutils
Commit: 54e615253240575a4b76a68823bc325efd0a3f52
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-17 15:15:20 -0400
Commit message:

 stay within 80 char width
Package: imageTCGAutils
Commit: bbb5380fc899c67b70dbdadefeaaa98e5448efa3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-17 15:08:53 -0400
Commit message:

 clarify relationship with imageFeatureTCGA
Package: imageTCGAutils
Commit: 1cdff095bca1f1f424e59a25ea129828387ffbb2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-17 15:08:37 -0400
Commit message:

 fix typo in title
Package: omicsViewer
Commit: 54b64f92cc2abf643226db1107bbd9f7aa86a0fd
Author: Chen Meng <mengchen18@gmail.com>
Date: 2026-03-17 20:17:04 +0100
Commit message:

 fix: correct meta_scatter_module documentation warnings

- Add @param id, remove stale @param input/output/session (old callModule API)
- Remove misplaced code example from @param reactive_status (caused lost braces note)
- Regenerate Rd with roxygen2
- Bump version to 1.15.3

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: cosmosR
Commit: ffb736106059c3e84892bc81a292aa87ef204594
Author: Aurelien Dugourd <dugourd@ebi.ac.uk>
Date: 2026-03-17 16:51:31 +0000
Commit message:

 chore: transfer maintainer role from Attila Gabor to Aurélien Dugourd

Update Authors@R in DESCRIPTION to reflect the approved maintainer
change per Bioconductor core team request.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: plyranges
Commit: 90094094da5109e7c4551128fc69e0dacfa7f84c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-03-17 11:53:08 -0400
Commit message:

 version bump and news
Package: kissDE
Commit: bd573b4186a4668a6f3eec1d1efcc84976567269
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-17 15:21:31 +0100
Commit message:

 Clean up the README file
Package: kissDE
Commit: c1280c419572df1c5566fa439ad2557a019e8bc8
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-17 15:20:44 +0100
Commit message:

 Update version number
Package: kissDE
Commit: 78bb5c1f6e6313e1a34de276dfb6b13a5ce685b1
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-17 15:20:30 +0100
Commit message:

 Correct a field in DESCRIPTION
Package: flowSpecs
Commit: 5bcbe700272a8ed50f27bf576eb0acc89384530e
Author: Jakob Theorell <jakob.theorell@ki.se>
Date: 2026-03-17 11:14:05 +0100
Commit message:

 Bug fixes
Package: ExploreModelMatrix
Commit: d22b2d9cd2bf9e2deb2fbd900421fbea697b8d17
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2026-03-16 17:50:43 +0100
Commit message:

 version bump, 1.23.1
Package: ExploreModelMatrix
Commit: 27652e013f629658f6b6b95638893f4be0cfeffa
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2026-03-16 17:50:31 +0100
Commit message:

 fixing icon names to avoid message of (possibly dismissed?) fa icons
Package: IntEREst
Commit: 0bcab3ff70c9e30675e9f4e1382335f12fe6f741
Author: gacatag <ali.oghabian@helsinki.fi>
Date: 2026-03-17 09:54:42 +0200
Commit message:

 Removing parameters baed on defunct fucntions/params in the source packages
Package: FlowSOM
Commit: b2d43e01f25ba49809672864b9ee1ab8c4ba7de9
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2026-03-17 10:41:52 +0100
Commit message:

 Removed #include  from the C script, as this is not supported anymore, and I don't think we actually still used it.
 </pre>
    </div>
  
    

      Package: atacInferCnv

      Commit: c68116d75a0cef1fbde190e54c7a73e21fb234f5

      Author:  Konstantin Okonechnikov <k.okonechnikov@gmail.com> 

      Date: 2026-03-17 09:48:54 +0100

      Commit message:


	  
		
 Bioconductor submission fixes
 

    

  
    

      Package: atacInferCnv

      Commit: 6de546aa06d119076abede9f20cc18627174ea4c

      Author:  Konstantin Okonechnikov <k.okonechnikov@gmail.com> 

      Date: 2026-03-17 08:13:34 +0100

      Commit message:


	  
		
 Bioconductor submission fix runAtacInferCnv
 

    

  
    

      Package: DOTSeq

      Commit: b906ad56955ea91d3b8335c68d95369b4fbd74fc

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-17 15:14:35 +0800

      Commit message:


	  
		
 fix id_mapping check
 

    

  
    

      Package: scoup

      Commit: cc2e0757de802ece32830ba5ba0c06f0d3f5bda6

      Author:  thsadiq <hassan.t.sadiq@gmail.com> 

      Date: 2026-03-17 07:05:45 +0200

      Commit message:


	  
		
 Updated citation
 

    

  
    

      Package: Rsubread

      Commit: b5a6885b11b5e35f7c170973638fd9f3c8a7329b

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

      Date: 2026-03-17 15:04:55 +1100

      Commit message:


	  
		
 added the strandSpecific option to simReads()
 

    

  
    

      Package: igblastr

      Commit: d8e780657c658379ea6cfe039583d05541f606a6

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

      Date: 2026-03-16 20:13:53 -0700

      Commit message:


	  
		
 Small update to README.md
 

    

  
    

      Package: igblastr

      Commit: 15bba547fbafb9951815112a2dff1ba0402b7df7

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

      Date: 2026-03-16 19:59:00 -0700

      Commit message:


	  
		
 Relax dep on GenomeInfoDb (>= 1.47.2)
 

    

  
    

      Package: CSOA

      Commit: 57fac962a0202970065eb829ed3e297f452c9aac

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-03-17 09:36:10 +0800

      Commit message:


	  
		
 Bumped version
 

    

  
    

      Package: CSOA

      Commit: ff99e7d2666ba92451df21e503f707ef91272ff5

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-03-17 09:35:26 +0800

      Commit message:


	  
		
 Minor edits
 

    

  
    

      Package: Rsubread

      Commit: b7c6160bf692578d9626a8306a69f8c8e97bf7f6

      Author:  Yang Liao (Monash University) <yliao@m3e108.massive.org.au> 

      Date: 2026-03-17 09:36:15 +1100

      Commit message:


	  
		
 added some debug outputs
 

    

  
    

      Package: BamScale

      Commit: b24c2b768ce629243e2191660b308aac7195017c

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

      Date: 2026-03-17 07:49:34 +1100

      Commit message:


	  
		
 performance improvement
 

    

  
    

      Package: BamScale

      Commit: ce957db983dd263bfcd30ec20568fee8e85e3b1d

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

      Date: 2026-03-17 07:48:49 +1100

      Commit message:


	  
		
 Increment version number to 0.99.4
 

    

  
    

      Package: igblastr

      Commit: 43eab5dcb042185acf073fc729c001051c052955

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

      Date: 2026-03-16 13:51:19 -0700

      Commit message:


	  
		
 Add low-level utilities read_auxdata() and write_auxdata().

Also the 'auxiliary_data' argument of igblastn() can now be a data.frame
in addition to the path to a file containing auxiliary data (.aux file).
 

    

  
    

      Package: AnVILPublish

      Commit: 38c02f5d52ef40e2e7d9b6593a3718ad109afff0

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

      Date: 2026-03-16 16:08:57 -0400

      Commit message:


	  
		
 version bump 1.21.1
 

    

  
    

      Package: AnVILPublish

      Commit: 0b739f1e7b1611c8eb0b904f6084f43f4e27a6c7

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

      Date: 2026-03-16 16:08:55 -0400

      Commit message:


	  
		
 bump RoxygenNote version
 

    

  
    

      Package: AnVILPublish

      Commit: ec93f5660337bc1df6fa189aa7c4100f4031af17

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

      Date: 2026-03-16 16:08:41 -0400

      Commit message:


	  
		
 export create_workspace function
 

    

  
    

      Package: ChIPpeakAnno

      Commit: bce96ffcce846486e2625d63268d2edd9c5690db

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

      Date: 2026-03-16 15:46:26 -0400

      Commit message:


	  
		
 fix the issue for biomaRt in vignettes.
 

    

  
    

      Package: spammR

      Commit: 233efe8a8b53a6c67f75baafae20cec03e3bfc0c

      Author:  Sara JC Gosline <sara.gosline@pnnl.gov> 

      Date: 2026-03-16 12:40:04 -0700

      Commit message:


	  
		
 updated dependences
 

    

  
    

      Package: spammR

      Commit: be5b39a01be03937e72e15e3c6a770b359b08cfc

      Author:  Sara JC Gosline <sara.gosline@pnnl.gov> 

      Date: 2026-03-11 05:38:18 -0700

      Commit message:


	  
		
 added software to biocviews
 

    

  
    

      Package: Rarr

      Commit: 5ad898410c678e206f29ea6078ab741bf614f502

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 15:57:16 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: ea6042c7d3feebd51d297367473e78434f948449

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 15:56:57 +0100

      Commit message:


	  
		
 Mention DelayedArray breaking change in NEWS
 

    

  
    

      Package: Rarr

      Commit: 391d1cace6d02cb4014070c1b2eb1726b74d86c5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 15:55:00 +0100

      Commit message:


	  
		
 Remove methods dependency
 

    

  
    

      Package: Rarr

      Commit: 60c4e9f3faf77809c47924bdc235c96fe84b3bb7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 16:15:05 +0100

      Commit message:


	  
		
 Export deprecation function stubs
 

    

  
    

      Package: Rarr

      Commit: 7610fcf1ac8d497f5c1e10722dc881b13431b1a2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 14:59:09 +0100

      Commit message:


	  
		
 Use a slightly smoother deprecation process
 

    

  
    

      Package: Rarr

      Commit: 431d7b5782fdc4798c5fe9810d24a901dc2c0ad2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 10:52:28 +0100

      Commit message:


	  
		
 Relax BiocCheck check
 

    

  
    

      Package: Rarr

      Commit: 0f0de5462d0fd80fd8efc832c0974e8359d98d41

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 10:51:53 +0100

      Commit message:


	  
		
 Add more benchmarks
 

    

  
    

      Package: Rarr

      Commit: f4ceaa70d267975badda49e15507f478efcb591e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 10:32:07 +0100

      Commit message:


	  
		
 Remove all DelayedArray content

Move to the separate ZarrArray package
 

    

  
    

      Package: Rarr

      Commit: 80530bb49f99dae5567e40051743f02266c53d2a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-15 18:21:00 +0100

      Commit message:


	  
		
 Remove unused dims computation in CLI wrapper 

    

  
    

      Package: Rarr

      Commit: 6a2d5409e815e89b9117b8972403c25aef0310c1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-12 15:24:53 +0100

      Commit message:


	  
		
 Make is_signed an actual bool
 

    

  
    

      Package: Rarr

      Commit: f8f44a40f06d156b8b8c81702d6cc2bc8906e3e1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-12 15:20:02 +0100

      Commit message:


	  
		
 Add stdbool header
 

    

  
    

      Package: BiocBuildReporter

      Commit: 2a578e473b1f3a12fb4a088b1d6dadf681bbdb12

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-16 13:03:48 -0400

      Commit message:


	  
		
 Version bump and small change

 - PR from package review
 

    

  
    

      Package: BiocBuildReporter

      Commit: 68b1d73551cb410a8e81b163e10c7196d784e59f

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-16 13:02:49 -0400

      Commit message:


	  
		
 Merge pull request #4 from Bisaloo/bioc-review

Small fixes related to Bioc review 

    

  
    

      Package: BiocBuildReporter

      Commit: 716bc46fc2e8e9bb8deed80bb1682cadf5c80227

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 17:56:53 +0100

      Commit message:


	  
		
 Add BiocStyle to Suggests
 

    

  
    

      Package: BiocBuildReporter

      Commit: ebe94bc721535c3555e1b4a415b1d92500f9aaaa

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 17:52:58 +0100

      Commit message:


	  
		
 Fix package installation instructions
 

    

  
    

      Package: BiocBuildReporter

      Commit: c9499db171d48cb76b479d01e8aa4008e84a65dd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-05 19:57:42 +0100

      Commit message:


	  
		
 Fix long roxygen line
 

    

  
    

      Package: BiocBuildReporter

      Commit: 50938d3a8f3a59aeb0e6f7b37a701131db80ba6a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-05 17:36:47 +0100

      Commit message:


	  
		
 Add LICENSE.md to .Rbuildignore
 

    

  
    

      Package: VariantToolsData

      Commit: 43d49251730419601b4896783bd76b8c1f3b843e

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-16 12:28:40 -0400

      Commit message:


	  
		
 undeprecate
 

    

  
    

      Package: VariantTools

      Commit: faec495e76a27f029a845be1c3e3633da5fa245a

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-16 12:28:02 -0400

      Commit message:


	  
		
 undeprecate
 

    

  
    

      Package: LACHESIS

      Commit: 1828e01714b46df107d402b8581518db1702c5ba

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-03-16 15:46:52 +0000

      Commit message:


	  
		
 Deleted Untitled.ipynb
 

    

  
    

      Package: LACHESIS

      Commit: 0237fe4e84fadbb7f42ce174388330d2626c4423

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2026-03-16 15:45:45 +0000

      Commit message:


	  
		
 Merge pull request #129 from VerenaK90/temp_vignette_update

Vignette Update 

    

  
    

      Package: LACHESIS

      Commit: b0d357a034ca31c55b0b1df96963d8453c54f509

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-16 11:05:30 +0100

      Commit message:


	  
		
 Changes requested by Verenas review
 

    

  
    

      Package: LACHESIS

      Commit: 02002fb1c068ab768053c9496c4e95f8f631bd12

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-13 16:27:14 +0100

      Commit message:


	  
		
 stylR package
 

    

  
    

      Package: LACHESIS

      Commit: bd3f4a0700a4f45047c25111521a0eef12658467

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-13 16:23:21 +0100

      Commit message:


	  
		
 Update vignette
 

    

  
    

      Package: LACHESIS

      Commit: 5b0ada8d02b70f545ead60ff2f1ee534b7a00d72

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-13 16:20:52 +0100

      Commit message:


	  
		
 plotSurvival re-add confidence interval, adapt style to match DiseaseTraj and classifyLach, add x axis label
 

    

  
    

      Package: LACHESIS

      Commit: 19f45305e541d8e86e57424d877e060c92152339

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-13 16:18:18 +0100

      Commit message:


	  
		
 Add sage as vcf source
 

    

  
    

      Package: LACHESIS

      Commit: b2ddfa5cd37f6fcef4d13b58b5e28a368de14114

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-12 14:03:06 +0100

      Commit message:


	  
		
 Merge pull request #126 from VerenaK90/temp_plotClinicalCorrelations

Separate plotting functions, additional plots for classifyLACHESIS and plotDiseaseTrajectories 

    

  
    

      Package: LACHESIS

      Commit: f9a3b072beb2d11fb01b64d01b23f7f8ec367462

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-12 10:59:47 +0100

      Commit message:


	  
		
 Changes according to Anands review
 

    

  
    

      Package: LACHESIS

      Commit: e92ab078604638e21da17a77ef26aec602f1733f

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-03-02 13:24:31 +0000

      Commit message:


	  
		
 Updated documentation
 

    

  
    

      Package: LACHESIS

      Commit: d5d74373073da7782cccf47f7c99b735ed1ca0a7

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-03-02 13:12:50 +0000

      Commit message:


	  
		
 Reformatted lines in readVCF
 

    

  
    

      Package: LACHESIS

      Commit: aa13dbdf736832b9b334d152f87385b25083ca41

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-03-02 11:29:05 +0000

      Commit message:


	  
		
 added adjustcolor to imports
 

    

  
    

      Package: LACHESIS

      Commit: aed281f9e5724019e5a89db6f1e7d9d462cc53be

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-03-02 11:24:49 +0000

      Commit message:


	  
		
 Corrected axis scaling if max(ECA_time_mean)==0*
 

    

  
    

      Package: LACHESIS

      Commit: 6221f22db6e009724f794041c14ffea1f1b65d20

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-02-19 11:16:16 +0100

      Commit message:


	  
		
 ClassifyLACHESIS add plot 

    

  
    

      Package: LACHESIS

      Commit: 1d8b7cfba36138b15ff1c3f287a7f1aa63a797e8

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-02-19 08:52:30 +0000

      Commit message:


	  
		
 merge changes from main branch
Merge remote-tracking branch 'origin/main' into temp_plotClinicalCorrelations
 

    

  
    

      Package: LACHESIS

      Commit: e504616000fa1cf3be251f8f7e0f47a976add966

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-02-19 08:51:22 +0000

      Commit message:


	  
		
 Corrected typo (to.plot2 instead of to.plot)
 

    

  
    

      Package: LACHESIS

      Commit: 142c76e2e022c35259be40aad78ec759ce4f508d

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2026-02-19 08:49:46 +0000

      Commit message:


	  
		
 Merge pull request #127 from VerenaK90/temp_readcnv

Assign column name (A and B) to the created column 

    

  
    

      Package: LACHESIS

      Commit: 558119952c1ba85d33143d4a3d0e64c1157a2928

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-02-19 08:48:11 +0000

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into temp_readcnv
Merge changes in main into branch temp_readcnv
 

    

  
    

      Package: LACHESIS

      Commit: f5a6f17596910c240405eb884a081fecb0ab51b2

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2026-02-19 08:44:05 +0000

      Commit message:


	  
		
 Merge pull request #121 from VerenaK90/include_autosomes

There was a bug in `readCNV` when using output from ACEseq and including autosomes for male samples, which has now been corrected. 

    

  
    

      Package: LACHESIS

      Commit: c35ba35a1c946f3753ffb4c65fc752ada9c9c003

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-02-19 08:42:36 +0000

      Commit message:


	  
		
 Updated News file
 

    

  
    

      Package: LACHESIS

      Commit: c465b0c019eb24dc0491ef81666d7317dff8040a

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-02-19 08:41:34 +0000

      Commit message:


	  
		
 corrected comment
 

    

  
    

      Package: LACHESIS

      Commit: 6e25e066b05d0dedcc32d006d5b0098231b35ed4

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-02-19 08:39:53 +0000

      Commit message:


	  
		
 re-corrected R version
 

    

  
    

      Package: LACHESIS

      Commit: e10e32f09a49662adcd42472851d8172c9607769

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-02-18 16:38:10 +0000

      Commit message:


	  
		
 Each plotting function a single script. Separate function for timelines. Adjusted axes.
 

    

  
    

      Package: LACHESIS

      Commit: 606a9b93bfc84c5510feb1dc8c84efd6e6f1cea2

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-02-17 15:18:45 +0100

      Commit message:


	  
		
 Merge branch 'main' into temp_plotClinicalCorrelations 

    

  
    

      Package: LACHESIS

      Commit: 693fcbf5afc87521b98eb45a40172ac54e540cff

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-02-17 15:13:46 +0100

      Commit message:


	  
		
 Assign column name (A and B) to the created column
 

    

  
    

      Package: LACHESIS

      Commit: d71c2989077fcf14811d62aba0529d10e5db27df

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-02-12 16:58:59 +0100

      Commit message:


	  
		
 Quality check if age is before mrca and adapted cex for points and sample ids in larger cohorts
 

    

  
    

      Package: LACHESIS

      Commit: 9a072f8a689d9380e21888bf59942f789c434770

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-02-11 14:39:53 +0100

      Commit message:


	  
		
 Correlation between real-time estimation of ECA/ MRCA and age at diagnosis added as output to plotClinicalCorrelations
 

    

  
    

      Package: LACHESIS

      Commit: dee61da0c8b6e0d14e21a1f2a2b9284a0dc64361

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-02-05 15:34:25 +0000

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into include_autosomes
Get changes that were done in parallel branch
 

    

  
    

      Package: LACHESIS

      Commit: a0a2143e3e70cc74a7d3cd5eba03c315266b8e3f

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-02-05 15:34:16 +0000

      Commit message:


	  
		
 changed typo in logo
 

    

  
    

      Package: LACHESIS

      Commit: 2b3fbb88f9b2cb86602886dfd3e1499baa3fa652

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2026-02-05 15:11:35 +0000

      Commit message:


	  
		
 Merge pull request #123 from VerenaK90/temp_plotLachesis

See-through Polygon 

    

  
    

      Package: LACHESIS

      Commit: 8fa145e3968976779a6f828f02f6d0a557f80bff

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2026-02-05 09:20:47 +0000

      Commit message:


	  
		
 corrected spelling typo in Chi 

    

  
    

      Package: LACHESIS

      Commit: e0122f70dc8f8664566cca826c0565ea662785df

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2026-02-05 08:54:53 +0000

      Commit message:


	  
		
 Merge pull request #120 from VerenaK90/VerenaK90-patch-1

Update README.md 

    

  
    

      Package: LACHESIS

      Commit: b69b723db1603f09523241f0446873a9a214c7ff

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-02-05 08:53:40 +0000

      Commit message:


	  
		
 Corrected syntax to comply with data.table
 

    

  
    

      Package: LACHESIS

      Commit: 586077bf574a3ef2cd9ac3b34918db51a7031343

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-02-03 09:36:11 +0100

      Commit message:


	  
		
 Adding see-through polygon and coloring dots according to lach.col
 

    

  
    

      Package: LACHESIS

      Commit: 98d38ff974f59262cfd2071d3e6aaf2ccc2366eb

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-01-15 11:12:54 +0000

      Commit message:


	  
		
 corrected check
 

    

  
    

      Package: LACHESIS

      Commit: 7faeed9046178066a725508110cf3bbf7c9a85ae

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-01-15 11:08:52 +0000

      Commit message:


	  
		
 ensure to subset only if instances occur
 

    

  
    

      Package: LACHESIS

      Commit: 680b8bfcfe697cf018c4455367c9207d6d29fac5

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-01-15 09:57:40 +0000

      Commit message:


	  
		
 Do not filter autosomes if ignore.XY=F
 

    

  
    

      Package: LACHESIS

      Commit: 9d2e91af54e8202e46d2d9ee7a011fc6e834c916

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2026-01-13 09:48:57 +0000

      Commit message:


	  
		
 Update README.md

correct greek letter 

    

  
    

      Package: LACHESIS

      Commit: 1b94475ceac97bbc44406767d2f9a87362a4047b

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2026-01-13 09:36:18 +0000

      Commit message:


	  
		
 Merge pull request #119 from VerenaK90/temp_plotLachesis

Cumulative SNV densities at ECA ans MRCA in one 

    

  
    

      Package: LACHESIS

      Commit: 2989e0715fb7f7428b065eb67ad612c59c6e044b

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-01-12 15:44:13 +0100

      Commit message:


	  
		
 Adding a Legend
 

    

  
    

      Package: LACHESIS

      Commit: 89fe9b4119c4fd359f3345bdbde78cd1875cb3b1

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2025-12-08 15:41:17 +0100

      Commit message:


	  
		
 Cumulative SNV densities at ECA ans MRCA in one
plot for plotLachesis
 

    

  
    

      Package: LACHESIS

      Commit: a2338bc0577a04c23a718699305d16962223698a

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2025-12-08 11:44:33 +0000

      Commit message:


	  
		
 Merge pull request #118 from VerenaK90/devel

Adressing Issue #116 

    

  
    

      Package: LACHESIS

      Commit: 4500281faa3652056ccc2378591577abf170d2b5

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2025-12-04 18:04:11 +0100

      Commit message:


	  
		
 Adding italics font for plotting Driver Mutations
 

    

  
    

      Package: LACHESIS

      Commit: b47f83583c7b3805daa7308e86278b6ea2d36656

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2025-12-02 17:27:18 +0100

      Commit message:


	  
		
 Corrections accroding to Verenas suggestions
 

    

  
    

      Package: LACHESIS

      Commit: 2051ae9495034d9b1fae45494e9a9766e6bd0342

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2025-12-02 14:48:36 +0100

      Commit message:


	  
		
 Changing missing parts of [...] to [[]] and stylr package
 

    

  
    

      Package: LACHESIS

      Commit: 021790bdeb9c1760d8f536e044521914597e52df

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2025-12-01 16:33:47 +0100

      Commit message:


	  
		
 Adressing Issue #116: ggplot warnings are resolved
 

    

  
    

      Package: LACHESIS

      Commit: 7a865d9679cec8f2455efd9a89cc905861126084

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2025-11-11 08:31:51 +0000

      Commit message:


	  
		
 Merge pull request #115 from VerenaK90/devel

2nd Review 

    

  
    

      Package: BiocPkgDash

      Commit: ac4089cc03f1f086b1d8626dea80329d977647f2

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

      Date: 2026-03-16 11:39:15 -0400

      Commit message:


	  
		
 version bump 0.99.47
 

    

  
    

      Package: BiocPkgDash

      Commit: 026f67393b76d1d66886de95d30118ec01322c36

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

      Date: 2026-03-16 11:39:06 -0400

      Commit message:


	  
		
 check email is not null and non-zero char
 

    

  
    

      Package: mia

      Commit: abff00d8f5381a2fae57d8749582aa33fb61a3c1

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2026-03-16 17:35:10 +0200

      Commit message:


	  
		
 Improve Joint-RPCA (#808)

Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com> 

    

  
    

      Package: mia

      Commit: e9190adacc71775220dba9f8da181d9f21ec2218

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2026-03-06 14:56:43 +0200

      Commit message:


	  
		
 Add support for ordination results in clustering (#809) 

    

  
    

      Package: Spectra

      Commit: f5c977fed9adea16eb48d2b80cb2de2cc503ea09

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

      Date: 2026-03-16 15:49:50 +0100

      Commit message:


	  
		
 Merge pull request #381 from rformassspectrometry/jomain

feat: add rbindlistWithRownames function 

    

  
    

      Package: Spectra

      Commit: 7af652efe74278e6c84c1c32f843e24f499ce992

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

      Date: 2026-03-16 13:52:48 +0100

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: Spectra

      Commit: 5285f2da4faeaa1fd32a580f745cdfc4c9216b16

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

      Date: 2026-03-16 11:57:17 +0100

      Commit message:


	  
		
 fix: rbindlistWithRownames handles duplicated rownames
 

    

  
    

      Package: Spectra

      Commit: 32fbe869769b923bd2069bef1092e8b3887f0662

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

      Date: 2026-03-16 11:15:58 +0100

      Commit message:


	  
		
 refactor: replace rbindlist with rbindlistWithRownames
 

    

  
    

      Package: Spectra

      Commit: 383a504b1d1366611921f01460b9e2f6f571670d

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

      Date: 2026-03-16 11:00:57 +0100

      Commit message:


	  
		
 ci: install MsCoreUtils from github
 

    

  
    

      Package: Spectra

      Commit: ee3e6365e0e065b174119648cdfdb5c68a72cb61

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

      Date: 2026-03-16 10:45:51 +0100

      Commit message:


	  
		
 feat: add rbindlistWithRownames function

- Add `rbindlistWithRownames()` function that uses `data.table::rbindlist()` for
  row binding `data.frame`s and conserves eventually present row names.
- Fix of unit tests based on latest updates in *MsCoreUtils*.
 

    

  
    

      Package: CCPlotR

      Commit: 6e010b74cd76adefa994a1f2cc873e240009ce4b

      Author:  Sarah145 <sarah@boughbio.com> 

      Date: 2026-03-16 10:30:34 -0400

      Commit message:


	  
		
 bump pakage version
 

    

  
    

      Package: CCPlotR

      Commit: d668df5ebf701a50a88fe0004e6b28b100dc7506

      Author:  Sarah145 <sarah@boughbio.com> 

      Date: 2026-03-13 17:52:51 -0400

      Commit message:


	  
		
 fix regex issue and remove ggbump dependency
 

    

  
    

      Package: CCPlotR

      Commit: efc6afc87d1a3b351df3b234e131e3c16c548bd0

      Author:  Sarah <sarah@boughbio.com> 

      Date: 2024-07-23 16:10:05 -0400

      Commit message:


	  
		
 fix legend in cc_dotplot
 

    

  
    

      Package: flowSpecs

      Commit: fa6e2b255b1dc7812257113b3221aef25208f380

      Author:  Jakob Theorell <jakob.theorell@ki.se> 

      Date: 2026-03-16 15:22:30 +0100

      Commit message:


	  
		
 Updates for wider compatibility with spectral sorters, including the BD S8.
 

    

  
    

      Package: tripr

      Commit: df42ef6a687e2668891a03e82a4b0731a19c084b

      Author:  KonstantinosKardamiliotis <k.kardamiliotis@gmail.com> 

      Date: 2026-03-16 16:14:40 +0200

      Commit message:


	  
		
 Bioc 3.23 push
 

    

  
    

      Package: Rhdf5lib

      Commit: c0f2cf6798e5e051ddaf868fd369d40b6e678606

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 13:05:07 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rhdf5lib

      Commit: 5a3c75c60e3215a0af99d6f83ac1f5bda9411d1c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 11:45:10 +0100

      Commit message:


	  
		
 Tweak download script to remove examples folder
 

    

  
    

      Package: Rhdf5lib

      Commit: 9489254505025497ce4ffe44b05cbe801018b473

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 11:44:26 +0100

      Commit message:


	  
		
 Remove HDF5Examples
 

    

  
    

      Package: COTAN

      Commit: f5f5c7c1d79709593a340727d948cab05a1db755

      Author:  trinetra75 <marco.fantozzi@gmail.com> 

      Date: 2026-03-15 11:50:54 +0100

      Commit message:


	  
		
 Bumped-up version and updated NEWS.md
 

    

  
    

      Package: COTAN

      Commit: 9f21eae6e841834fa8a60426b31a7750adc46872

      Author:  Marco Fantozzi <57561972+trinetra75@users.noreply.github.com> 

      Date: 2026-03-15 11:24:22 +0100

      Commit message:


	  
		
 Add DEA vignette (#136)

* Added new vignette with basic scaffolding

* Updated the NEWS.md and README.md to new vignette situation

Updated links to `bioc.r-universe.dev` instead of BioConductor
main site

* Updated tests for `calculatePValue()` about multi-cores

* Fixed issues with vignettes

* Fixed minor issues with vignettes

Added explanation about DEA

* Finished the DEA vignette

Fixed bug in `clustersMarkersHeatmapPlot()` to support repetitions
of genes in the markers' list

Speed up of the above function in cases when no `groupMarkers`
are passed in

Added minimal `COEX` explanation in UT vignette

Upated spell-checker 

    

  
    

      Package: COTAN

      Commit: dbec605aafcbd8e74d9ca1b716c9c0fbd019e0de

      Author:  Marco Fantozzi <57561972+trinetra75@users.noreply.github.com> 

      Date: 2026-03-11 09:24:02 +0100

      Commit message:


	  
		
 Refactor vignettes spltting the guides into four separate files (#135)

* Added New vignette about dataset cleaning

* Fixed minor issues

* Minor fixes

* Updated git/R ignores

* Fixed  options and a few spelling mistakes

* Further fixing of  options

* Avoid deleting the downloaded datatsets

Reduced html size by lowering dpi

* Restored figures size

* Added origin data file for vignettes

Added new vignette about genes' clustering

* Stored the vignette.split.clusters factor

Needed to decide which cells were dropped duting cleaning

* Continued praparation of Genes' Clusters vignette

Added `COEX` and `GDI` calculations
Added contingency tables look-up
Dropped spurious code from original copy

* Completed Genes' Clustering vignette

* Finished the Genes' clustering vignette

Added preparatory copy of UT vignette

* Added `vignette.merge.clusters` to data folder

Improved Uniform Clustering vignette

* Minor bugfixes

Added parameter `minimumUTClusterSize` to `cellsUniformClustering()`
function

Solved issue with `sets` parameter in `heatmapPlot()` not accepting
integer floats

Cleaned `calculateGDI()` function code

* Updated test comparison file for GDI

* Check the dataset was downloaded before using it

* Linted chunk labels

Added `Cairo` and `ragg` to suggested packages

* Faster p-value calculations

Allowed the function `calculatePValue()` to run un multiple cores

Propagated number of cores parameter to heatmap plot functions

* Added tests for plot functions

* Dropped old vignette

* Finished Uniform Clustering vignette 

    

  
    

      Package: COTAN

      Commit: 5d28745ff696d4e57bf73b7dbdc559ebcc708b55

      Author:  Marco Fantozzi <57561972+trinetra75@users.noreply.github.com> 

      Date: 2026-03-11 09:21:00 +0100

      Commit message:


	  
		
 Minor bugfixes (#134)

* Minor bugfixes

Added parameter `minimumUTClusterSize` to `cellsUniformClustering()`
function

Solved issue with `sets` parameter in `heatmapPlot()` not accepting
integer floats

Cleaned `calculateGDI()` function code

* Updated test comparison file for GDI 

    

  
    

      Package: DELocal

      Commit: eb7eed98e17562086f9edb042e2b44932402bcae

      Author:  vondorishi <rishi.dasroy@gmail.com> 

      Date: 2026-03-16 12:12:44 +0200

      Commit message:


	  
		
 version bump in devel
 

    

  
    

      Package: DELocal

      Commit: a9532bc563a7b55dfae688ea95fe9e0cb147199d

      Author:  vondorishi <rishi.dasroy@gmail.com> 

      Date: 2026-03-16 12:11:33 +0200

      Commit message:


	  
		
 bug fix: base::message
 

    

  
    

      Package: Rhdf5lib

      Commit: 20063c758da163b2cf8e84bce0bc67e9b05d884d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 11:10:47 +0100

      Commit message:


	  
		
 Remove outdated info about CPP_FLAGS

Since we didn't include the option to use a custom HDF5 library yet
 

    

  
    

      Package: MsCoreUtils

      Commit: a49ad2334b43a11b43dda647fd1fea53dd0d8757

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

      Date: 2026-03-16 10:24:24 +0100

      Commit message:


	  
		
 Merge pull request #144 from rformassspectrometry/jomain

docs: fix unsupported Unicode characters 

    

  
    

      Package: MsCoreUtils

      Commit: 3b62078f256c951585e5ddc40bb6fc3feb947cbf

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

      Date: 2026-03-16 10:18:26 +0100

      Commit message:


	  
		
 fix: join_gnps to support paramter type again
 

    

  
    

      Package: MsCoreUtils

      Commit: 1548cd5b908b67878982830a0f34d851d46cd1ba

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

      Date: 2026-03-16 09:59:27 +0100

      Commit message:


	  
		
 docs: fix unsupported Unicode characters
 

    

  
    

      Package: RnBeads

      Commit: 3ca828245b245993df1499b3c82314166759c0d2

      Author:  Michael Scherer <michael.scherer@dkfz.de> 

      Date: 2026-03-16 11:13:35 +0100

      Commit message:


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

    

  
    

      Package: RnBeads

      Commit: 6ecaedfc44fd65a790458d95d56e7f2190e5a5ff

      Author:  Scherer <m261r@b370-worker01.dkfz-heidelberg.de> 

      Date: 2026-03-09 13:55:23 +0100

      Commit message:


	  
		
 Fixed R CMD check issues
 

    

  
    

      Package: RnBeads

      Commit: 841c93a452d781d0821107cea04f45f203a2f3b4

      Author:  Scherer <m261r@b370-worker01.dkfz-heidelberg.de> 

      Date: 2026-02-17 16:46:11 +0100

      Commit message:


	  
		
 Implemented the first version of XenoMix
 

    

  
    

      Package: DOTSeq

      Commit: cb85681022775100443426442a338c3f2ab85096

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-16 14:52:52 +0800

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: DOTSeq

      Commit: 4e6736bc61cd59fc785a15754db2e132c466406c

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-16 14:25:02 +0800

      Commit message:


	  
		
 set id_mapping to FALSE
 

    

  
    

      Package: DOTSeq

      Commit: 708016c4970ceb730c01b8ac7af1e6d6261b4d53

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-16 13:49:35 +0800

      Commit message:


	  
		
 add unit test
 

    

  
    

      Package: DOTSeq

      Commit: 3df84910720c313d687c6c3611e8a0d6c6d44708

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-16 12:16:09 +0800

      Commit message:


	  
		
 add example
 

    

  
    

      Package: DOTSeq

      Commit: 7e2c13f5a3066081aaed200b9832407c2c38ffab

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-02-01 20:49:03 +1300

      Commit message:


	  
		
 add countReadsSingleCell and helpers
 

    

  
    

      Package: DOTSeq

      Commit: fd17f345fd7cc5e119f3cae0e47854a68eacb052

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-12-01 12:42:55 +1300

      Commit message:


	  
		
 update installation instructions
 

    

  
    

      Package: DOTSeq

      Commit: 82540c67abd148761ac44b7011457ab8cb2d3afb

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-12-01 12:37:54 +1300

      Commit message:


	  
		
 update installation instructions
 

    

  
    

      Package: DOTSeq

      Commit: e49e0fe2dcfe35d63530c5ca2a6bded284c0c161

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-12-01 12:11:27 +1300

      Commit message:


	  
		
 update installation instructions
 

    

  
    

      Package: DOTSeq

      Commit: 7ae3156e9c29edb60f19330bb627856a0d616ba7

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-12-01 12:10:52 +1300

      Commit message:


	  
		
 update installation instructions
 

    

  
    

      Package: DOTSeq

      Commit: b9826598b957953c57b5b7153a1ca5ffe5891ec1

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-12-01 12:10:05 +1300

      Commit message:


	  
		
 update installation instructions
 

    

  
    

      Package: scoup

      Commit: f0f8a89d8d6ef4155c5afb28098893618b77e7cc

      Author:  thsadiq <hassan.t.sadiq@gmail.com> 

      Date: 2026-03-16 07:33:09 +0200

      Commit message:


	  
		
 Edited American English out of paper
 

    

  
    

      Package: scoup

      Commit: 58f24d5bbdd8f915a01bebcbbc07dad21fd41a22

      Author:  thsadiq <hassan.t.sadiq@gmail.com> 

      Date: 2026-03-16 06:47:37 +0200

      Commit message:


	  
		
 Edited American English out of paper
 

    

  
    

      Package: scoup

      Commit: 102104b309e1cfd71632c78aa026c02256c8d6f0

      Author:  Hassan Sadiq <hassan.t.sadiq@gmail.com> 

      Date: 2026-03-05 11:23:18 +0200

      Commit message:


	  
		
 Corrected doi typo in paper.bib 

    

  
    

      Package: SpNeigh

      Commit: 5dcdd14b5dc1013f6d9350fd9bf6e6baf70dd515

      Author:  jinming-cheng <jinming.cheng2018@gmail.com> 

      Date: 2026-03-16 11:22:29 +0800

      Commit message:


	  
		
 update extractCoords.data.frame
 

    

  
    

      Package: tidyprint

      Commit: 704be89304cb71044de200cb4a845460328ae55a

      Author:  Chen Zhan <8347019+zhanchen@users.noreply.github.com> 

      Date: 2026-03-16 11:31:15 +1030

      Commit message:


	  
		
 Merge pull request #31 from tidyomics/fix-pasilla-show

Fix pasilla show 

    

  
    

      Package: tidyprint

      Commit: c15fa33493786bc7a2ce031b6be83b626956c24f

      Author:  Chen Zhan <chen.zhan@adelaide.edu.au> 

      Date: 2026-03-16 11:13:21 +1030

      Commit message:


	  
		
 Set version to 0.99.10
 

    

  
    

      Package: tidyprint

      Commit: 1254b8ff99132d3f053a6713e63179129d31c878

      Author:  Chen Zhan <chen.zhan@adelaide.edu.au> 

      Date: 2026-03-16 11:12:21 +1030

      Commit message:


	  
		
 Remove skip_if_not_installed for pasilla test, keep version 1.0.1
 

    

  
    

      Package: tidyprint

      Commit: 0cd1fd599719819165494c69cd57ff02a09b46a2

      Author:  Chen Zhan <chen.zhan@adelaide.edu.au> 

      Date: 2026-03-16 10:30:11 +1030

      Commit message:


	  
		
 Bump version to 1.0.1
 

    

  
    

      Package: tidyprint

      Commit: 5078eb3ee8520c541c81ea8ebd3494f2326b6337

      Author:  Chen Zhan <chen.zhan@adelaide.edu.au> 

      Date: 2026-03-16 10:02:32 +1030

      Commit message:


	  
		
 Bump version to 0.99.10, skip pasilla test when pasilla not installed
 

    

  
    

      Package: tidyprint

      Commit: e3c42c2a2089b3392d9ac97276a57d4e4d68498a

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-12 17:55:32 +1030

      Commit message:


	  
		
 Add pasilla as a suggested package and enhance pasilla printing test

- Included 'pasilla' in the DESCRIPTION file under suggests.
- Updated the test for pasilla printing to create a SummarizedExperiment object and ensure it prints without errors, improving robustness of the test suite.

to reproduce the error comment

  if (is.data.frame(x)) {
    x <- as.matrix(x)
  }

  in plyxp_utils.R
 

    

  
    

      Package: tidyprint

      Commit: 765416dc08e6567620a520cb116f3a01c79436cf

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-12 17:52:44 +1030

      Commit message:


	  
		
 solved the data.frame bug
 

    

  
    

      Package: tidyprint

      Commit: 5a1a1af1eb8b76d5dba74c9adcfb43c4e58665ec

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-12 17:49:06 +1030

      Commit message:


	  
		
 Add regression test for pasilla printing without subsetting error

- Introduced a test to ensure that the pasilla dataset prints correctly without triggering subsetting errors.
- This regression test addresses a previously encountered issue with 7-sample data that caused errors when subsetting elements beyond the available range.
 

    

  
    

      Package: rtracklayer

      Commit: d9b23f963c621e4aa8e5e52c6e4da50d5d213e1a

      Author:  Michael Lawrence <lawremi@gmail.com> 

      Date: 2026-03-15 16:55:15 -0700

      Commit message:


	  
		
 nrow(schema) returns NA when itemCount information is not present
 

    

  
    

      Package: rtracklayer

      Commit: 86bccb7b0ddc4725448371ff0c4fc0d1b8e4ff88

      Author:  Michael Lawrence <lawremi@gmail.com> 

      Date: 2026-03-15 16:48:15 -0700

      Commit message:


	  
		
 change table existence check to allow for tables not attached to a data track. Fixes #147
 

    

  
    

      Package: snpStats

      Commit: 0ad6fb0589c1ccc357d0d88da6f4cb7c8e513dc3

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-15 19:00:05 -0400

      Commit message:


	  
		
 adding backport, to devel... probably not needed
 

    

  
    

      Package: VariantTools

      Commit: 0995c69949a5173c233742ec32a2cb96bbfb9a6c

      Author:  Michael Lawrence <lawremi@gmail.com> 

      Date: 2026-03-15 15:56:34 -0700

      Commit message:


	  
		
 update cached vignette data
 

    

  
    

      Package: VariantTools

      Commit: 176ab7c45f73de1ab1fcafa15ad009182f12e272

      Author:  Michael Lawrence <lawremi@gmail.com> 

      Date: 2026-03-15 15:48:02 -0700

      Commit message:


	  
		
 remove redundant arg
 

    

  
    

      Package: VariantTools

      Commit: 867d5a5322c00fae274521e0befdfe494f39fdbd

      Author:  Michael Lawrence <lawremi@gmail.com> 

      Date: 2026-03-15 15:46:52 -0700

      Commit message:


	  
		
 genome() was moved to GenomeInfoDb
 

    

  
    

      Package: VariantTools

      Commit: 33de3fd2a9defe0cc038e7a5b5d4dc6a163b0586

      Author:  Michael Lawrence <lawremi@gmail.com> 

      Date: 2026-03-15 15:43:43 -0700

      Commit message:


	  
		
 fix Rd syntax error
 

    

  
    

      Package: VariantTools

      Commit: ac0805b9e55f461f947ee5d8bf0e2c268bce16dc

      Author:  Michael Lawrence <lawremi@gmail.com> 

      Date: 2026-03-15 15:17:06 -0700

      Commit message:


	  
		
 some latex cleanup
 

    

  
    

      Package: biomformat

      Commit: 68ba178b54fba5371ae043187b2cc1796f4c26ec

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-15 12:21:42 -0700

      Commit message:


	  
		
 Update .gitignore
 

    

  
    

      Package: biomformat

      Commit: bde886213e423a95fb4a1e16903f825fdd1e27c5

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-15 12:13:02 -0700

      Commit message:


	  
		
 Update Joseph Paulson email to joseph.paulson@yale.edu (v1.39.16)

Updated Authors@R person() entry for Joseph N. Paulson from
jpaulson@jimmy.harvard.edu to joseph.paulson@yale.edu.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

    

  
    

      Package: biomformat

      Commit: c2c99e1ba32a9408969cb3198b6ea770133b3619

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-15 12:04:00 -0700

      Commit message:


	  
		
 Fix Authors@R: replace deprecated Author/Maintainer fields (v1.39.15)

BiocCheck >= 1.46 ERRORs on the presence of the old Author: and
Maintainer: fields — they must be replaced with Authors@R: using
person() with role=c('aut','cre') for the maintainer. This was the
root cause of the Bioconductor team's 'invalid email' complaint: the
field format itself was structurally invalid per current BiocCheck
rules, independent of the address string.

Also:
- Update maintainer email to joey711@gmail.com (reachable address).
- Add .BiocCheck to .Rbuildignore so BiocCheck output folders are
  never included in the built tarball.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
BiocCheck: 1 ERROR (Watched Tags on support.bioconductor.org —
  requires manual web action, cannot be fixed in code).
 

    

  
    

      Package: biomformat

      Commit: 27866a7253bf198020cadc94dd447d99ec1561b1

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-15 11:38:23 -0700

      Commit message:


	  
		
 Fix email address in DESCRIPTION (v1.39.15)

Updated Maintainer and Author email from mcmurdie@alumni.stanford.edu
to joey711@gmail.com as requested by the Bioconductor team. The alumni
Stanford address was flagged as potentially unreachable.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

    

  
    

      Package: plyranges

      Commit: 9bfc93addec3c7f58b66770d850baefffe513feb

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

      Date: 2026-03-15 15:04:49 -0400

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: plyranges

      Commit: 1f434baf6a045fd7fc9a217f1d4675a1935473dd

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

      Date: 2026-03-15 14:52:39 -0400

      Commit message:


	  
		
 moving README content to a more-examples vignette
 

    

  
    

      Package: biomformat

      Commit: a5a1f6c171ae939a731e60185fd4d0f4e5e09087

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-15 10:48:42 -0700

      Commit message:


	  
		
 Add vignette sections: make_biom workflow + named subsetting (v1.39.14)

Added two new sections to vignettes/biomformat.Rmd:

1. 'Constructing a BIOM from R data' (addresses Issues #4, #6, #9):
   End-to-end make_biom() workflow with an ASV count matrix and a
   list-valued taxonomy column (the dada2/amplicon pattern). Shows
   write_biom()/read_biom() round-trip, and includes a callout
   directing large-dataset users to write_hdf5_biom() (Issue #8).
   The HDF5 code chunk is guarded by eval=requireNamespace('rhdf5').

2. 'Subsetting biom_data() by name': demonstrates the previously
   undocumented character-vector row/col subsetting interface.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

    

  
    

      Package: biomformat

      Commit: 5d8dcdcfdef8cb5adbf424cef3d51431e19ef56d

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-15 10:48:26 -0700

      Commit message:


	  
		
 Fix #8: document write_biom() 2^31-1 byte size limit (v1.39.13)

Added @details to write_biom() documentation explaining that jsonlite
serialises the entire BIOM object to a single R character string, which
is subject to R's 2^31-1 byte limit on character scalars. Users with
very large datasets are now explicitly directed to write_hdf5_biom()
which streams to HDF5 and has no such limitation.

Regenerated man/write_biom.Rd via roxygen2::roxygenise().

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

    

  
    

      Package: biomformat

      Commit: 948e1885fe722418c0669d15284f2f82fedf4821

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-15 10:48:10 -0700

      Commit message:


	  
		
 Fix #7: add zero-column HDF5 fixture and regression tests (v1.39.12)

Added inst/extdata/zero_col_hdf5.biom — a minimal 3×3 HDF5 BIOM where
sample 'ZeroSamp' (column 2) has all-zero counts. The CCS indptr for
the sample-major storage is [0,3,3,6]: indptr[1]==indptr[2] means
ZeroSamp has zero non-zero entries, directly exercising the edge case
reported in Issue #7.

Added inst/extdata/create_zero_col_hdf5.R: reproducible generation
script using rhdf5 directly.

Added two tests in test-hdf5-write.R (both guarded by
skip_if_not_installed('rhdf5')):
  - Read fixture, verify ZeroSamp column is all zeros, Samp1=[1,3,5],
    Samp3=[2,4,6], and dimensions/names are correct.
  - Round-trip through write_hdf5_biom() + read_biom(): ZeroSamp
    remains all-zero, full matrix equality preserved.

These tests confirm that generate_matrix() (rewritten in v1.39.8 to
use sparseMatrix directly from CCS triplets) correctly handles the
case where diff(indptr) is 0 for a sample column.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

    

  
    

      Package: biomformat

      Commit: 16c3e53085fbc1e47c2d6faf6018135de89b8c22

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-15 10:37:07 -0700

      Commit message:


	  
		
 Fix #4 #6: make_biom() NULL id as {}, taxonomy as bare array (v1.39.11)

Issue #4: NULL id was serialised as {} (empty JSON object) by jsonlite
because toJSON(list(id=NULL,...), auto_unbox=TRUE) maps NULL to {}.
Fix: make_biom() substitutes 'No Table ID' when id is NULL, matching
the BIOM spec default and ensuring write_biom() -> read_biom() is a
lossless round-trip. validObject() now succeeds on the round-tripped
object.

Issue #6: when observation_metadata (or sample_metadata) is a
data.frame with list columns (e.g. a 'taxonomy' column holding
character vectors of rank assignments, as produced by dada2),
the metadata was serialised as a bare JSON array ([[...]]) instead
of a named JSON object ({taxonomy:[...]}). The BIOM spec and
downstream tools (phyloseq import_biom(), the Python biom library)
require the named-object form. Root cause: as.matrix() on a
list-column data.frame produces a list-matrix; as.list(row) then
strips field names. Fix: detect list-column data.frames and build
per-row metadata directly as named lists, bypassing as.matrix().
Closes #6. Also resolves user-support Issue #9 (dada2 -> biom ->
write_biom workflow now works correctly).

Adds 4 regression tests in test-IO.R.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

    

  
    

      Package: biomformat

      Commit: b8cf9046896ee782e04ebec59aa08d88353056ea

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-15 10:23:32 -0700

      Commit message:


	  
		
 Remove HANDOFF.md (agent handoff artefact, not part of package)
 

    

  
    

      Package: biomformat

      Commit: 86db19410c4687c3ec4abc3c442b1b7ddc1b78ff

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-15 10:17:06 -0700

      Commit message:


	  
		
 Add HANDOFF.md: GitHub issues + test gaps + vignette gaps for next agent
 

    

  
    

      Package: HiSpaR

      Commit: 11f59c87eef0d845bde84124c63aa6b546a5f437

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-16 00:30:18 +0800

      Commit message:


	  
		
 bump version to 0.99.5
 

    

  
    

      Package: HiSpaR

      Commit: 9066a098eae9afea791debc709ad56318036468d

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-16 00:28:47 +0800

      Commit message:


	  
		
 add tests for HiCExperiment input, safe_mode=TRUE, and output_dir auto-creation
 

    

  
    

      Package: HiSpaR

      Commit: c954cc2c5d61519be5341549389bfccd5812fa2a

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-16 00:12:04 +0800

      Commit message:


	  
		
 bump version to 0.99.4
 

    

  
    

      Package: HiSpaR

      Commit: d6c954735c151c8b13495b0a469b872434f97b6b

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-16 00:10:42 +0800

      Commit message:


	  
		
 convert key parameters from section to paragraph
 

    

  
    

      Package: HiSpaR

      Commit: ee3fba82b93325cdb55a01ed05f7009bcd319559

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 23:42:53 +0800

      Commit message:


	  
		
 bump version to 0.99.3
 

    

  
    

      Package: HiSpaR

      Commit: ad484e50f990bc573e56cce2c2f356a03d2b210d

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 23:42:07 +0800

      Commit message:


	  
		
 remove post_scale_positions.txt, update vignette accordingly
 

    

  
    

      Package: HiSpaR

      Commit: adb86bce5ae0fc07e33f529df19a835251cf75f0

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 23:40:28 +0800

      Commit message:


	  
		
 refined RMD
 

    

  
    

      Package: HiSpaR

      Commit: 8087fea834ef1627cd9a2dc4fb698d4cc344dfab

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 23:33:48 +0800

      Commit message:


	  
		
 update vignette: add pre-code summary, fix mcmc progress and saved files descriptions
 

    

  
    

      Package: HiSpaR

      Commit: 72154ecb1c0d065457e90611135e0c87ed823fa7

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 23:30:24 +0800

      Commit message:


	  
		
 refined rmd
 

    

  
    

      Package: HiSpaR

      Commit: 8977d3efc3ec4dbc08326bd7a8ca11169a0eec07

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 23:28:34 +0800

      Commit message:


	  
		
 remove 'contact matrix set successfully' from output
 

    

  
    

      Package: HiSpaR

      Commit: 1685b803a92a0259ed282705511edbb45aec2b57

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 23:27:05 +0800

      Commit message:


	  
		
 fix saved files list to match what is actually written to disk
 

    

  
    

      Package: HiSpaR

      Commit: 27b97ef0f2b7e718d9dd56e22dd099fb4c16dc2f

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 23:16:04 +0800

      Commit message:


	  
		
 simplify verbose output: remove redundant lines, condense phases to [Phase] Completed
 

    

  
    

      Package: HiSpaR

      Commit: 213069efe0bb4c8200dc364c330693c2b58e202f

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 23:07:05 +0800

      Commit message:


	  
		
 refined rmd
 

    

  
    

      Package: lcmsPlot

      Commit: 9875875fb402704ecb425f3455044e093c249b8d

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-03-15 15:07:34 +0000

      Commit message:


	  
		
 chore: migrate data.frame usage to tibble throughout (#28)

Replace data.frame(), as.data.frame(), and is.data.frame() with their
tibble equivalents (tibble(), as_tibble(), is_tibble()) across all R
source files. Add tibble to Imports in DESCRIPTION and NAMESPACE.

Also fix three related issues found during the migration:
- Correct all_of() call in creators-chromatograms.R to pass a single
  character vector instead of multiple arguments
- Qualify bare tibble() calls in @examples as tibble::tibble() so
  examples run without the package namespace attached
- Expand get_metadata() docs with @section entries covering all nine
  dispatch methods (MChromatograms, XChromatograms, XChromatogram,
  XcmsRawList, ExternalDataSource, DBIConnection) 

    

  
    

      Package: CDI

      Commit: 7c325d28d3e6f666a9d2ea6bf59bfd99fddab127

      Author:  Jiyuan Fang <jf243@duke.edu> 

      Date: 2026-03-15 23:02:33 +0800

      Commit message:


	  
		
 Sync bug fix from RELEASE_3_22
 

    

  
    

      Package: CDI

      Commit: e097896317ec54ed7a20dcd7065e3b0f9b67c849

      Author:  Jiyuan Fang <jf243@duke.edu> 

      Date: 2026-03-15 22:58:01 +0800

      Commit message:


	  
		
 Remove built package tarball
 

    

  
    

      Package: CDI

      Commit: b181918034df2aac709196e9710d0aabfd93b745

      Author:  Jiyuan Fang <jf243@duke.edu> 

      Date: 2026-03-15 22:42:42 +0800

      Commit message:


	  
		
 fix bugs caused by Seurat update
 

    

  
    

      Package: postNet

      Commit: 81dfe2f247bbb857f21dc5db7854c706a66d3c64

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-03-15 14:57:35 +0000

      Commit message:


	  
		
 KS
 

    

  
    

      Package: HiSpaR

      Commit: ac1cbdd90cb75fbc637db1eeec17fbd69c3e3547

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 22:44:53 +0800

      Commit message:


	  
		
 bump version to 0.99.2
 

    

  
    

      Package: HiSpaR

      Commit: 2e2ead6fe36c9b868ba0859902bc49573c7cc9a3

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 22:40:33 +0800

      Commit message:


	  
		
 address bioconductor reviewer feedback (almeidasilvaf)

- fix url/bugreports typo in description (hispar not hispa)
- expand unit tests to cover non-square input, invalid output_dir, filter_quantile with/without loci removed, safe_mode=false, verbose=false
- add su1_contact_mat and hicexperiment class descriptions to vignette
- move key parameters section before the example code chunk
- add output description section after example chunk (verbose output, return value, model interpretation)
- replace devtools/r cmd install instructions with biocmanager::install in readme
 

    

  
    

      Package: HiSpaR

      Commit: d7349291582fc7603f6f12d6098a74f37e0f5cbc

      Author:  masterstormtrooper <lyc22@mails.tsinghua.edu.cn> 

      Date: 2026-03-15 21:46:17 +0800

      Commit message:


	  
		
 modified gitignore
 

    

  
    

      Package: postNet

      Commit: f4df36db2081db3632bdf917b563088efbdb8fdc

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-03-15 14:22:45 +0000

      Commit message:


	  
		
 KS
 

    

  
    

      Package: postNet

      Commit: c0f68ad5fa84af1c2c7843c64d75845365b7fac7

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-03-15 11:18:21 +0000

      Commit message:


	  
		
 KS
 

    

  
    

      Package: postNet

      Commit: 79648791da86548d29a994a1eb858813ffa68ac7

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-03-15 11:16:13 +0000

      Commit message:


	  
		
 KS
 

    

  
    

      Package: postNet

      Commit: ea1d7489f81d7b25620a8668235c911166ede07e

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-03-15 10:32:20 +0000

      Commit message:


	  
		
 KS
 

    

  
    

      Package: postNet

      Commit: 558556555bb361649f7fe216135c1fde8e6ab265

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-03-15 10:03:23 +0000

      Commit message:


	  
		
 KS
 

    

  
    

      Package: postNet

      Commit: 69456dafa291a6927dc6c150136d2b08f956abef

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-03-15 09:51:19 +0000

      Commit message:


	  
		
 KS
 

    

  
    

      Package: postNet

      Commit: db28d36f7a06ce714ad6725877bfdb4537bf9312

      Author:  Krzysztof Szkop <krzysztof.szkop@gmail.com> 

      Date: 2026-03-15 09:46:50 +0000

      Commit message:


	  
		
 KS
 

    

  
    

      Package: Rhdf5lib

      Commit: f6fdc2f75af560603bde25dc179234a0b8a97758

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-14 15:05:01 +0100

      Commit message:


	  
		
 Ignore warnings on Fedora
 

    

  
    

      Package: Rhdf5lib

      Commit: 1688b858d53f14a053f64ab72ef1f3a618b978a1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-14 14:40:23 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rhdf5lib

      Commit: d36d1bf7b7598c375f7b974d090b010f2ef01eee

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-14 14:39:42 +0100

      Commit message:


	  
		
 Fix linking on Fedora
 

    

  
    

      Package: Rhdf5lib

      Commit: 4553424542b32046241277bfa8cffce883b4ab13

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-13 17:35:37 +0100

      Commit message:


	  
		
 Remove private headers
 

    

  
    

      Package: Rhdf5lib

      Commit: e413f970e65471cdeed41e149d4bc55b19fbc014

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-13 15:11:51 +0100

      Commit message:


	  
		
 Remove now unnecessary patching script
 

    

  
    

      Package: Rhdf5lib

      Commit: ba1ab0513a072a941ae888251b06857471b0fe6a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-13 15:09:24 +0100

      Commit message:


	  
		
 Remove outdated README
 

    

  
    

      Package: Rhdf5lib

      Commit: 970e0e0a665ab649603ba6f8cc45b3289bf697e3

      Author:  Jeroen Ooms <jeroenooms@gmail.com> 

      Date: 2026-03-13 16:22:44 +0100

      Commit message:


	  
		
 Change universe parameter to 'bioc' in workflow 

    

  
    

      Package: biomformat

      Commit: 4652383dd94fcb38e1543d41d2fc4d79d615c801

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 18:21:09 -0700

      Commit message:


	  
		
 Milestone 6: updated vignette with HDF5, tidy, SE, purrr sections (v1.39.10)

Extended the package vignette with four new sections, all guarded with
requireNamespace() so the vignette builds cleanly when optional Suggests
packages are absent:

* HDF5 (BIOM v2) I/O: read_biom() magic-byte routing, write_hdf5_biom()
  round-trip, and JSON->HDF5 conversion example.
* Tidy long-format: as.data.frame(biom) producing one row per
  (feature x sample) pair with metadata joined; as_tibble.biom().
* purrr-style workflows: per-sample total counts and Shannon diversity
  using purrr::map_dbl + dplyr, with base-R tapply fallback.
* SummarizedExperiment interop: biom_to_SummarizedExperiment() and
  as(x, 'SummarizedExperiment'), showing assay/colData/rowData access.
* Session info section.

Vignette renders cleanly (50 chunks, 0 errors) with all Suggests
packages present. R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing
vignette WARNINGs (inst/doc absent; built by Bioconductor BBS).
 

    

  
    

      Package: biomformat

      Commit: a69d671a2ca59c96d41854a9775c171c0841229a

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 18:10:02 -0700

      Commit message:


	  
		
 Milestone 5: write_hdf5_biom() + rhdf5 -> Suggests (v1.39.9)

NEW FEATURES
- write_hdf5_biom(x, biom_file): serialises a biom object to BIOM v2 HDF5.
  Writes both the sample-major CCS and observation-major CSR sparse matrices
  required by the spec, plus all sample and observation metadata (scalar and
  vector-valued, e.g. taxonomy). A lossless round-trip through
  read_biom() -> write_hdf5_biom() -> read_biom() is verified by 7 new
  tests in tests/testthat/test-hdf5-write.R.

BUG FIXES
- Move rhdf5 from Imports to Suggests. The package and all JSON-BIOM
  functionality loads without rhdf5 installed; HDF5 read/write functions
  (read_hdf5_biom, write_hdf5_biom) stop with a clear message when the
  package is absent.
- Fix roxygen block placement: read_hdf5_biom's @export block was separated
  from its function body by the new write_hdf5_biom body, causing roxygen2
  to drop read_hdf5_biom from the NAMESPACE. Block now immediately precedes
  its function definition.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

    

  
    

      Package: biomformat

      Commit: ba2e8d9b1b2d58fbc9ff60f5d6a9791d4a045eaa

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 18:03:14 -0700

      Commit message:


	  
		
 Milestone 4: sparse-direct generate_matrix() for HDF5/BIOM-v2 (v1.39.8)

Rewrote generate_matrix() (internal, called by read_hdf5_biom()) to build
the count matrix directly as a sparse Matrix from the CCS triplets stored
in the HDF5 file, instead of first constructing a dense base::matrix via
sapply() and then wrapping rows in lapply().

Key changes:
- Coerce rhdf5::h5read() 'array' objects to plain atomic vectors with
  as.integer() / as.numeric() before passing to sparseMatrix(); the
  'array' class is not accepted by sparseMatrix()'s x= argument.
- Build j_vec from rep(seq_len(n_samp), diff(indptr)) and i_vec from
  indices + 1L, then call sparseMatrix(i, j, x, dims) directly.
- Handle the all-zero edge case (length(vals) == 0L) explicitly.
- Return value is unchanged: list of named numeric vectors, one per
  observation row, as expected by the biom() constructor.

R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.
 

    

  
    

      Package: biomformat

      Commit: 8b9d0db809defec098899943198df0a3dc2e24f3

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 17:58:00 -0700

      Commit message:


	  
		
 Post-M3 cleanup: full roxygen2 7.x refresh (v1.39.7)

- Add @importFrom tags for methods::{as,is,new,setClass,setGeneric,
  setMethod,setValidity,show,validObject}, stats::setNames,
  utils::packageVersion throughout R/ sources so roxygenise() generates
  a complete NAMESPACE with no 'no visible global function' NOTEs.
- Drop hand-written @importFrom(rhdf5,h5read) - rhdf5 is Suggests and
  called via rhdf5::h5read() (fully-qualified), so no importFrom needed.
- Update R/allPackage.R: replace deprecated @docType package / NA
  sentinel with '_PACKAGE' string and @aliases biomformat.
- Add Encoding: UTF-8 and RoxygenNote: 7.3.3 to DESCRIPTION.
- Regenerate all man/*.Rd via roxygenise(); rename biom-package.Rd to
  biomformat-package.Rd per roxygen2 7.x convention.
- R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs
  (inst/doc absent; built by Bioconductor BBS, not locally).
 

    

  
    

      Package: biomformat

      Commit: 241bd2c38f9b0df49414b797d0280c994ee5c82f

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 17:30:37 -0700

      Commit message:


	  
		
 Merge modernise/03-tidy-interop into devel (v1.39.7)
 

    

  
    

      Package: biomformat

      Commit: f41a6f8477456bf365fcb56f6ca6c1cba2fc717c

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 17:30:37 -0700

      Commit message:


	  
		
 Milestone 3: tidy long-format interoperability (v1.39.7)

R/tidy-methods.R (new):
  - as.data.frame.biom(): long-format (feature_id, sample_id, count) tidy
    table with optional left-joined sample and observation metadata columns;
    pure base R, no tidyverse dependency
  - as_tibble.biom(): wraps as.data.frame.biom() via tibble (Suggests only)

DESCRIPTION:
  - Bump version to 1.39.7
  - Add tibble to Suggests
  - Add tidy-methods.R to Collate

NAMESPACE:
  - S3method(as.data.frame, biom)
  - export(as_tibble.biom)

man/:
  - as.data.frame.biom.Rd (new, hand-written; regenerated in M5)
  - as_tibble.biom.Rd (new, hand-written; regenerated in M5)

tests/testthat/test-tidy.R (new): 8 tests
 

    

  
    

      Package: Seqtometry

      Commit: b37b0f47bfb669df3cda8bfc59e183fbaa51d518

      Author:  Robert Kousnetsov <robert.kousnetsov@health.slu.edu> 

      Date: 2026-03-14 19:59:34 -0500

      Commit message:


	  
		
 Update to v0.99.2
 

    

  
    

      Package: biomformat

      Commit: 6052355ec58999e1ead21a0a0379153ea1a14d40

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 17:16:41 -0700

      Commit message:


	  
		
 Merge modernise/02-summarized-experiment into devel (v1.39.6)
 

    

  
    

      Package: biomformat

      Commit: 580345000d8a1e14eb88dbd11a580e0276295441

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 17:16:41 -0700

      Commit message:


	  
		
 Milestone 2: SummarizedExperiment interoperability (v1.39.6)

R/SE-methods.R (new):
  - biom_to_SummarizedExperiment(): converts biom object to SE, placing
    count matrix in assay('counts'), sample metadata in colData(),
    feature metadata in rowData(); NULL metadata -> empty DataFrame
  - as(biom, 'SummarizedExperiment') S4 coercion registered when SE available

man/biom_to_SummarizedExperiment.Rd (new):
  - Hand-written Rd (will be regenerated by roxygenise() in Milestone 5)

DESCRIPTION:
  - Bump version 1.39.5 -> 1.39.6
  - Add SummarizedExperiment, S4Vectors to Suggests
  - Add SE-methods.R to Collate

tests/testthat/test-SE.R (new):
  - 6 tests: class, assay values, colData, rowData, as() coercion,
    NULL metadata; all skipped gracefully without SE installed
 

    

  
    

      Package: biomformat

      Commit: 8909a2ab86e6c1f4f4c993ba9dfde5fedbc939b4

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 15:44:21 -0700

      Commit message:


	  
		
 Merge modernise/01-drop-plyr into devel (v1.39.5)
 

    

  
    

      Package: biomformat

      Commit: 0900a452048c72bca5400d5ccecd1c2a719065e4

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 15:43:59 -0700

      Commit message:


	  
		
 Milestone 1: drop plyr dependency, tighten Matrix imports (v1.39.5)

DESCRIPTION:
  - Remove plyr (>= 1.8) from Imports entirely
  - Bump R dependency to >= 4.1

R/BIOM-class.R:
  - make_biom(): replace alply() with lapply(seq_len(nrow(...)), ...)
    using obs_mat[i,] (not drop=FALSE) to preserve column names
  - make_biom(): use as.matrix(data) before t() so dispatch works for
    both base matrix and Matrix (dgeMatrix/dgCMatrix) objects
  - biom_data() dense path: replace laply() with do.call(rbind, lapply(...))
  - biom_data() sparse numeric path: replace ldply(x) with
    as.data.frame(do.call(rbind, x))
  - biom_data() sparse unicode path: replace ldply(x, function(x){...})
    with do.call(rbind, lapply(x, function(e) ...))
  - extract_metadata(): replace llply()/ldply() with lapply()/do.call()
  - parallel= argument: now no-op with deprecation warning in biom_data(),
    sample_metadata(), observation_metadata()

NAMESPACE:
  - Remove all importFrom(plyr, ...) entries
  - Replace import(Matrix) with importFrom(Matrix, Matrix, sparseMatrix, drop0)
  - Replace import(methods) with selective importFrom(methods, ...)

man/*.Rd:
  - biom_data-methods.Rd: update @param parallel (remove plyr/foreach links)
  - observation_metadata-methods.Rd: same
  - sample_metadata-methods.Rd: same

tests/testthat/test-accessors.R:
  - Add test that parallel=TRUE emits deprecation warning in biom_data(),
    sample_metadata(), observation_metadata()

R CMD check --as-cran: 0 ERRORs, 0 WARNINGs, 4 pre-existing NOTEs
 

    

  
    

      Package: ANCOMBC

      Commit: 318b1f02c651bcba6b75c2b7eb9954d44c86d36a

      Author:  FrederickHuangLin <huanglinfrederick@gmail.com> 

      Date: 2026-03-14 19:15:11 -0400

      Commit message:


	  
		
 Fix CVXR compatibility and add support for mia::agglomerateByRank()
 

    

  
    

      Package: lcmsPlot

      Commit: 5fac69d6f1c85fcee3a4508b1c8af396111cc932

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-03-14 22:51:32 +0000

      Commit message:


	  
		
 feat: add support for xcmsRaw, XChromatogram(s), and MChromatograms (#26)

Introduce XcmsRawList, a new S4 class wrapping one or more xcmsRaw
objects, and XcmsRawReader, a MsRawReader subclass that reads scan
headers and peaks directly from in-memory xcmsRaw slots without
opening a file connection. xcmsraw_to_readers() converts an
XcmsRawList to the named-list-of-readers expected by the rest of the
pipeline.

Add get_metadata() adapters for MChromatograms and improve the
sample_id_column fallback for XCMSnExp and MsExperiment so that
sample IDs are derived from file basenames when no explicit column is
provided.

Refactor the chromatogram creator into a unified create_chromatograms()
generic that dispatches on data object type, replacing the four
previous specialised generics (create_chromatograms_from_feature_ids,
create_chromatograms_from_features, etc.). This simplifies the public
API and makes it straightforward to add further input types. 

    

  
    

      Package: biomformat

      Commit: d8231beddc723dc865f9e9678d6b5d38596538cf

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 15:16:13 -0700

      Commit message:


	  
		
 Revert "Add HANDOFF.md: modernisation roadmap and agent handoff prompt"

This reverts commit 3476b33aed131911681f582b0d80d7be599c0128.
 

    

  
    

      Package: biomformat

      Commit: 3476b33aed131911681f582b0d80d7be599c0128

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 15:13:53 -0700

      Commit message:


	  
		
 Add HANDOFF.md: modernisation roadmap and agent handoff prompt

Documents the 8-milestone modernisation plan (v1.39.5 through v1.39.12):
  M1  modernise/01-drop-plyr            - drop plyr, tighten imports
  M2  modernise/02-summarized-experiment - SE interoperability
  M3  modernise/03-tidy-interop          - as.data.frame/tibble
  M4  modernise/04-sparse-matrix-fix     - generate_matrix() sparseMatrix
  M5  modernise/05-roxygen2-refresh      - regenerate NAMESPACE/man
  M6  modernise/06-write-hdf5            - write_hdf5_biom()
  M7  modernise/07-rhdf5-suggests        - rhdf5 -> Suggests
  M8  modernise/08-vignette              - updated vignette examples

HANDOFF.md added to .Rbuildignore so it is excluded from the built tarball.
 

    

  
    

      Package: biomformat

      Commit: ff979da0bce37a551a51af60d507e6fe107a77db

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 14:17:51 -0700

      Commit message:


	  
		
 Merge criticalfixes: BBS rescue milestones 1-3 (v1.39.2-v1.39.4)

Brings in all work from the criticalfixes topic branch:
  a388c18 Resolve NEWS merge conflict: take HEAD (ca0a956) content verbatim
  ca0a956 Milestone 3: Matrix drop=FALSE + HDF5 magic-byte routing (v1.39.4)
  c069dba Milestone 3: Matrix drop=FALSE + HDF5 magic-byte routing (v1.39.4)
  a7f9876 Milestone 2: Matrix ABI + rhdf5 dependency stabilisation (v1.39.3)
  7841f44 Merge master into devel; resolve DESCRIPTION conflict (v1.39.2)
  effbd0e 1.29.2 testthat and namespace fixes

Closes https://github.com/joey711/biomformat/issues/17
Closes https://github.com/joey711/biomformat/issues/14
Supersedes https://github.com/joey711/biomformat/pull/16
Closes https://github.com/joey711/biomformat/pull/12
Supersedes https://github.com/joey711/biomformat/pull/11
Partially addresses https://github.com/joey711/biomformat/issues/5
Partially addresses https://github.com/joey711/biomformat/issues/3
 

    

  
    

      Package: biomformat

      Commit: a388c181dd608c66816098ca1e407711a62a187a

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 10:46:53 -0700

      Commit message:


	  
		
 Resolve NEWS merge conflict: take HEAD (ca0a956) content verbatim

The conflict was between:
  HEAD (ca0a956): full cross-referenced NEWS entries for v1.39.2-v1.39.4
    with GitHub issue/PR URLs (Issues #3, #5, #14, #17; PRs #11, #12, #16)
  c069dba: earlier, less detailed milestone entries without cross-references

Resolution: take HEAD in full for all three 1.39.x entries. The upstream
commit (c069dba) is an older intermediate state of the same content;
HEAD is strictly a superset with all the same facts plus issue/PR links.
 

    

  
    

      Package: biomformat

      Commit: ca0a95614bcb58991cbcad1e102152b891fba85c

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 10:30:52 -0700

      Commit message:


	  
		
 Milestone 3: Matrix drop=FALSE + HDF5 magic-byte routing (v1.39.4)

R/BIOM-class.R - biom_data() drop=FALSE fix:
  Closes  https://github.com/joey711/biomformat/pull/12
    (Fix biom_data() when dealing with 1-taxon and 1-sample BIOM data)
  Supersedes https://github.com/joey711/biomformat/pull/11
    (Fix unidentical biom output by make_biom())
  - Dense path: wrap laply() result with matrix(m, nrow, ncol) to force
    2-D shape before Matrix() coercion, eliminating dimension collapse
    when rows or columns has length 1
  - Dense path: apply Matrix() coercion for all sizes (not just >1x1)
  - Sparse path: add drop=FALSE to m[rows, columns] subsetting so a
    single-row or single-column selection retains its matrix dimensions
  - Naming block: rownames()/colnames() applied unconditionally on all
    paths (both paths now always produce a 2-D object)

NEWS:
  - Rewrote all three milestone entries (v1.39.2, v1.39.3, v1.39.4) with
    precise GitHub issue and PR cross-references:
      Issue #17 https://github.com/joey711/biomformat/issues/17
      Issue #14 https://github.com/joey711/biomformat/issues/14
      Issue  #5 https://github.com/joey711/biomformat/issues/5
      Issue  #3 https://github.com/joey711/biomformat/issues/3
      PR    #16 https://github.com/joey711/biomformat/pull/16
      PR    #12 https://github.com/joey711/biomformat/pull/12
      PR    #11 https://github.com/joey711/biomformat/pull/11

README.md:
  - Replaced stale Travis-CI badge and outdated install instructions
    with current Bioconductor release/devel badges
  - Added Quick start code block
  - Added Recent changes summary table (v1.39.2-v1.39.4) with links to
    the specific GitHub issues/PRs resolved in each version
  - Updated Support section with current mailing list and support links
  - Removed outdated references to CRAN 'biom' package

tests/testthat/test-IO.R:
  - Added regression tests covering the drop=FALSE and magic-bytes fixes

tests/testthat/test-accessors.R:
  - Updated single-row/col/cell subsetting expectations to match the
    new matrix-returning contract of biom_data()

All 158 tests pass: FAIL 0 | WARN 0 | SKIP 0 | PASS 158
R CMD check --as-cran: 0 ERRORs, 0 WARNINGs (pre-existing vignette
  build WARNINGs unaffected), 4-5 pre-existing NOTEs
 

    

  
    

      Package: biomformat

      Commit: c069dbae7dcbe862e76ee9e126022ef0e37ea0e5

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 10:30:52 -0700

      Commit message:


	  
		
 Milestone 3: Matrix drop=FALSE + HDF5 magic-byte routing (v1.39.4)

R/BIOM-class.R - biom_data() drop=FALSE fix (PR #11 / PR #12):
  - Dense path: wrap laply() result with matrix(m, nrow, ncol) to force
    2-D shape before Matrix() coercion, eliminating dimension collapse
    when rows or columns has length 1
  - Dense path: apply Matrix() coercion for all sizes (not just >1 x >1),
    making single-row/col behaviour consistent with the full-matrix case
  - Sparse path: add drop=FALSE to m[rows, columns] subsetting so a
    single-row or single-column selection retains its matrix dimensions
    instead of collapsing to a dimensionless vector
  - Naming block: remove the is.null(dim(m)) branch; both paths now
    always produce a 2-D object so rownames()/colnames() apply
    unconditionally on every code path

DESCRIPTION:
  - Bump version 1.39.3 -> 1.39.4

NEWS:
  - Prepend CHANGES IN VERSION 1.39.4 with full description of both
    the drop=FALSE fix and the HDF5 magic-byte routing confirmation

tests/testthat/test-IO.R:
  - Add regression tests: sparse single-row, single-col, single-cell,
    and full-matrix dim() retention after drop=FALSE fix
  - Add regression tests: HDF5 magic-byte routing (no jsonlite error),
    correct JSON vs HDF5 fixture classification
  - Use literal 5L/6L in dim comparisons (avoids named-integer mismatch
    from biom_shape())
  - Add hdf5_file fixture path

tests/testthat/test-accessors.R:
  - Single-value block: use as.numeric()/as.vector()[1] to compare scalar
    values without S4 vs atomic type conflict
  - Single-row block: use as.matrix() on both sides for class-agnostic
    comparison (dgeMatrix vs dgCMatrix differ only in storage, not values)
  - Single-col block: same as.matrix() treatment

All 158 tests pass: FAIL 0 | WARN 0 | SKIP 0 | PASS 158
R CMD check --as-cran: 0 ERRORs, 0 WARNINGs, 4 pre-existing NOTEs
 

    

  
    

      Package: biomformat

      Commit: a7f9876c4a8f54f0a1c57e16a1428b7ecfb8948c

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 10:17:34 -0700

      Commit message:


	  
		
 Milestone 2: Matrix ABI + rhdf5 dependency stabilisation (v1.39.3)

DESCRIPTION:
  - Bump Matrix dependency (>= 1.2) -> (>= 1.7-0) to guard against
    SuiteSparse ABI breakage in R 4.4+ BBS environments

R/IO-methods.R:
  - read_biom(): replace JSON-first/HDF5-fallback heuristic with
    deterministic magic-bytes detection (reads first 4 bytes; routes
    to HDF5 parser iff \x89HDF signature detected, eliminating the
    'lexical error' when HDF5 files hit the JSON parser)
  - read_hdf5_biom(): add requireNamespace('rhdf5', quietly=TRUE) guard
    so missing rhdf5 or absent HDF5 system libs emit a graceful R-level
    warning instead of a fatal C-level abort
  - read_hdf5_biom(): wrap h5read() in tryCatch() to catch any
    C-level/system-library errors and re-emit as R warnings
  - Use rhdf5::h5read() namespace-qualified call throughout
  - Replace non-ASCII box-drawing chars in comments with ASCII '--'

NEWS:
  - Prepend CHANGES IN VERSION 1.39.3 entry documenting all changes
 

    

  
    

      Package: biomformat

      Commit: 7841f4441e1538bec2b177476c454ff1ec4a399f

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 10:12:04 -0700

      Commit message:


	  
		
 Merge master into devel; resolve DESCRIPTION conflict (v1.39.2)

- Take Version base from devel branch (1.39.x series, Bioconductor devel)
- Bump z-component to 1.39.2 to capture Milestone 1 work from master
- Take updated Date (2026-03-14) from master branch
- Carry forward all Milestone 1 changes already staged:
    * NAMESPACE: add importFrom(stats,setNames), importFrom(utils,packageVersion)
    * NEWS: prepend CHANGES IN VERSION 1.39.2 entry
    * tests/testthat/test-IO.R: replace deprecated expect_that() with
      modern testthat 3.x equivalents (expect_true, expect_identical, etc.)
 

    

  
    

      Package: biomformat

      Commit: effbd0ec25ad83e5b3fe03b63d6962c4f9db4df4

      Author:  Paul J. McMurdie <joey711@gmail.com> 

      Date: 2026-03-14 10:08:54 -0700

      Commit message:


	  
		
 1.29.2 testthat and namespace fixes
 

    

  
    

      Package: plyranges

      Commit: 7872af38620ef774e65b98a481ee39a563e5e985

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

      Date: 2026-03-14 10:02:46 -0400

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: plyranges

      Commit: 61cd7f8cc02b44076ad5f1c9bee664e1b4991f59

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

      Date: 2026-03-14 09:42:31 -0400

      Commit message:


	  
		
 fixing check issues
 

    

  
    

      Package: plyranges

      Commit: 180a0c55c2ee1bcd869cb9f9a891c2fb2bfcc908

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

      Date: 2026-03-13 14:10:46 -0400

      Commit message:


	  
		
 fixing function links in man page
 

    

  
    

      Package: plyranges

      Commit: 536e322fc8db1a7db60cfe86635d8ab37f1839db

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

      Date: 2026-03-13 14:07:40 -0400

      Commit message:


	  
		
 Merge pull request #122 from tidyomics/join_with_dist

Join with dist 

    

  
    

      Package: plyranges

      Commit: a3db5d7175d7e5abb3ffb2eecff3f3c8ca3ea25b

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

      Date: 2026-03-13 14:06:39 -0400

      Commit message:


	  
		
 adding distance for left overlap joins
 

    

  
    

      Package: plyranges

      Commit: c9693e4c3d65ec3636907beb7b996e04cfc1eafb

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

      Date: 2026-03-13 10:47:47 -0400

      Commit message:


	  
		
 Merge pull request #121 from tidyomics/join_mcols

Join mcols 

    

  
    

      Package: plyranges

      Commit: aa7154cdfef3e48f614b612a42ae847ab00b256d

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

      Date: 2026-03-11 14:55:36 -0400

      Commit message:


	  
		
 a workable version of mcols joins
 

    

  
    

      Package: plyranges

      Commit: 09289df2950374d3eada54712f20e9c624079634

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

      Date: 2026-02-24 13:48:32 -0500

      Commit message:


	  
		
 importing causes issues, backtracking
 

    

  
    

      Package: plyranges

      Commit: b600638ab1d77834e551ab7dab827792bc8e28dd

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

      Date: 2026-02-23 19:30:48 -0500

      Commit message:


	  
		
 import DFplyr in NAMESPACE also
 

    

  
    

      Package: plyranges

      Commit: 86da4a7835505d794161c469e406a8c4c868c723

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

      Date: 2026-02-19 13:04:00 -0500

      Commit message:


	  
		
 adding distance using ppaxisa approach
 

    

  
    

      Package: plyranges

      Commit: 5e25e7efe00f2ec1df1c4ed9f7fa114107cc38d1

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

      Date: 2026-02-16 15:04:19 -0500

      Commit message:


	  
		
 missing files
 

    

  
    

      Package: plyranges

      Commit: 1fdecc9dfacd748716c79d06c352ee6d0c766d14

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

      Date: 2026-02-16 14:57:33 -0500

      Commit message:


	  
		
 an mcols join using DFplyr
 

    

  
    

      Package: plyranges

      Commit: 76e5b0ccc5566dc254265db51ee8aefb8c03bde9

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

      Date: 2025-11-20 09:34:56 -0500

      Commit message:


	  
		
 Merge branch 'devel' of github.com:tidyomics/plyranges into devel
 

    

  
    

      Package: plyranges

      Commit: 37c2d9d44b2e1a456b7fd767bdbd703b21d704ae

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

      Date: 2025-11-20 09:34:52 -0500

      Commit message:


	  
		
 update to latest bioc for gha
 

    

  
    

      Package: plyranges

      Commit: 7114f0b1e8e908336c7e7fa2ca95a7ba7577a611

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

      Date: 2024-11-26 10:45:23 -0500

      Commit message:


	  
		
 start trying out a distance addition
 

    

  
    

      Package: PolySTest

      Commit: 0384429189266cae821f0ae75eef3f33b96777c6

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2026-03-14 11:43:58 +0100

      Commit message:


	  
		
 bioconductor version
 

    

  
    

      Package: PolySTest

      Commit: 4cf9fb07212e6650a68443f3f665d83454efd31f

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2026-03-14 11:37:55 +0100

      Commit message:


	  
		
 fallback to BH for all tests
 

    

  
    

      Package: PolySTest

      Commit: 8817a1fbeced24ab43ba12bf1e08365ad724cf39

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2025-11-22 16:45:22 +0100

      Commit message:


	  
		
 reduced upset plot for large data sts
 

    

  
    

      Package: BiocPkgTools

      Commit: 84c17b51649bb715406fdd6b9fbeb653970044db

      Author:  Sean Davis <seandavi@gmail.com> 

      Date: 2026-03-13 16:48:40 -0600

      Commit message:


	  
		
 Merge pull request #80 from vjcitn/devel

biocPkgList: add handling of fnd field when present in Authors@R 

    

  
    

      Package: BiocPkgTools

      Commit: 8cffb9679f3d212fce1ba7fa6d793982d60bf7d6

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-13 15:13:01 -0400

      Commit message:


	  
		
 fixing tests to respect [fnd] tag extraction
 

    

  
    

      Package: BiocPkgTools

      Commit: 1449eb98e04f9f7ecee587411d2c2a0533fde271

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-13 11:11:12 -0400

      Commit message:


	  
		
 Merge branch 'copilot/retrieve-fnd-field-value' of https://github.com/vjcitn/BiocPkgTools into copilot/retrieve-fnd-field-value
 

    

  
    

      Package: BiocPkgTools

      Commit: c68c428cf3d4ae47db71ba12ce34f9ed50314dec

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-13 11:10:09 -0400

      Commit message:


	  
		
 before new fnd work
 

    

  
    

      Package: BiocPkgTools

      Commit: ffb36be2e6907856e0e73003615167808406f5a1

      Author:  copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> 

      Date: 2026-03-13 12:55:42 +0000

      Commit message:


	  
		
 Fix .extract_fnd() to parse formatted Author field instead of eval(parse()) on Authors@R

Co-authored-by: vjcitn <4624066+vjcitn@users.noreply.github.com>
 

    

  
    

      Package: BiocPkgTools

      Commit: 0e0e3cbcab12fac9925a3d4dc83379db99d4423f

      Author:  copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> 

      Date: 2026-03-13 11:44:25 +0000

      Commit message:


	  
		
 Add fnd (funder) list-column to biocPkgList() output

Co-authored-by: vjcitn <4624066+vjcitn@users.noreply.github.com>
 

    

  
    

      Package: BiocPkgTools

      Commit: c9eb0061f6a6df2628b3555bbb931e62b41c8cc7

      Author:  copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> 

      Date: 2026-03-13 11:37:44 +0000

      Commit message:


	  
		
 Initial plan
 

    

  
    

      Package: signatureSearch

      Commit: d7bfb7f5231067a24fe6d6a5af06045339d57f78

      Author:  brendangongol <bgong001@ucr.edu> 

      Date: 2026-03-12 14:33:44 -0700

      Commit message:


	  
		
 addressing warning messages
 

    

  
    

      Package: leapR

      Commit: 00060024ed7ca08c877d3151a35d94b0728f2aad

      Author:  Sara JC Gosline <sara.gosline@pnnl.gov> 

      Date: 2026-03-13 09:37:29 -0700

      Commit message:


	  
		
 added doc changes
 

    

  
    

      Package: vsn

      Commit: 42738c4e1fca9bf162612c20b3cb6a1b6d990909

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-13 16:41:52 +0100

      Commit message:


	  
		
 Use BiocStyle::html_document for vignette
 

    

  
    

      Package: vsn

      Commit: b228fd87c14bd2cf93b1d0fcdeddb0f2e4c19b0d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-13 16:37:59 +0100

      Commit message:


	  
		
 Convert one vignette to Rmd
 

    

  
    

      Package: atacInferCnv

      Commit: 62862668ea89c04ef628346131e1eef4d56165e7

      Author:  Konstantin Okonechnikov <k.okonechnikov@gmail.com> 

      Date: 2026-03-13 16:20:18 +0100

      Commit message:


	  
		
 Bioconductor udpates
 

    

  
    

      Package: atacInferCnv

      Commit: 4601cb3a886fc6f48a1c9ed77af41e7112369024

      Author:  Konstantin Okonechnikov <k.okonechnikov@gmail.com> 

      Date: 2026-03-13 14:57:54 +0100

      Commit message:


	  
		
 Add options for infercnv object output  and improve testing
 

    

  
    

      Package: atacInferCnv

      Commit: d2083dc448f259b70bfb42de9ddf5b07547c6fbb

      Author:  Konstantin Okonechnikov <k.okonechnikov@gmail.com> 

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

      Commit message:


	  
		
 Add control verbose output option
 

    

  
    

      Package: atacInferCnv

      Commit: 74c5ac8884cfb8eca86943c62caf2bbebdce8276

      Author:  Konstantin Okonechnikov <k.okonechnikov@gmail.com> 

      Date: 2026-03-11 17:19:44 +0100

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: atacInferCnv

      Commit: c67ede4a0fcefb7ac0423c6aaaf08201c8bf4cf1

      Author:  Konstantin Okonechnikov <k.okonechnikov@gmail.com> 

      Date: 2026-03-11 17:19:15 +0100

      Commit message:


	  
		
 Update documentation, minor fixes
 

    

  
    

      Package: atacInferCnv

      Commit: 2c104830d0d331bd81785acd62219b48e9b69f47

      Author:  Konstantin Okonechnikov <k.okonechnikov@gmail.com> 

      Date: 2026-03-11 14:14:16 +0100

      Commit message:


	  
		
 Fix issues for bioconductor: plot save to file + add to documentation,  edit DESCRIPTION
 

    

  
    

      Package: OmicsMLRepoR

      Commit: f47a350da3208f48c644a2b53fe5b872cac7ec29

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-03-13 11:24:08 -0400

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: OmicsMLRepoR

      Commit: 5b35684313d0098ab08d6618e96ae8467c541d4a

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-03-13 11:13:21 -0400

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: OmicsMLRepoR

      Commit: b0cdc4a49c70404ff7c46be4cd295d2e6d4f6a9a

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-03-13 11:13:11 -0400

      Commit message:


	  
		
 update rols API endpoint
 

    

  
    

      Package: OmicsMLRepoR

      Commit: b7852e228d3414cc011cff33b26f526e5cef53a5

      Author:  Sehyun Oh <shbrief@gmail.com> 

      Date: 2026-03-04 09:15:38 -0500

      Commit message:


	  
		
 Fix bfcdownload() parameter name and version bump

Use 'rid' instead of 'rids' in bfcdownload() call to fix
vignette build error: "!missing(rid) is not TRUE"

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

    

  
    

      Package: SQLDataFrame

      Commit: 9a6235432dd7c8ad73e5e84ad97f4242ec851517

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:35:24 -0400

      Commit message:


	  
		
 Deprecated
 unresponsive
 

    

  
    

      Package: soGGi

      Commit: 4cd483eea316b6ed258c7fa29c57caedbe11243c

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:32:16 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: shiny.gosling

      Commit: 73003bf48bc0c4919fd0877d0086d771569f5a07

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:30:19 -0400

      Commit message:


	  
		
 Deprecation
unresponsive
 

    

  
    

      Package: receptLoss

      Commit: db9913346e7941421f683da2c58157e4c84d50d1

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:28:40 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: normr

      Commit: 94c4dd434f71b4987568eb0676b79a2092b95e8f

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:25:31 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: nearBynding

      Commit: aae0acfe6dc361b5d70af8d430e5de7380fdbaee

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:24:00 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: broadSeq

      Commit: 62139c2dd54d5abf47c7bba73ed529d9c6c63239

      Author:  vondorishi <rishi.dasroy@gmail.com> 

      Date: 2026-03-13 16:17:11 +0200

      Commit message:


	  
		
 version bump in devel
 

    

  
    

      Package: broadSeq

      Commit: f07ad6fcfcf8a5012d847dce203528523788106d

      Author:  vondorishi <rishi.dasroy@gmail.com> 

      Date: 2026-03-13 16:16:42 +0200

      Commit message:


	  
		
 bug fix: noiseq
 

    

  
    

      Package: microSTASIS

      Commit: 3e83a5853d7a6d77ff15a10b2af8cfa11e5d3884

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:20:36 -0400

      Commit message:


	  
		
 Deprecated

 - responded on github but not ready to make changes
 

    

  
    

      Package: mfa

      Commit: 0081c250b3d5cf7a99572263990d159a4a4112bd

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:19:07 -0400

      Commit message:


	  
		
 Deprecate
unresponsive
 

    

  
    

      Package: hca

      Commit: 0d9a910105409e946afc34747177996d3738a080

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:15:02 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: granulator

      Commit: 3196de12db57ae22aee0602691add074cd7ece1f

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:11:09 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: debCAM

      Commit: 82822845478afa32b7e8c22576b9b1d978336c9d

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:04:25 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: cummeRbund

      Commit: de9d0e0efa3cdc332742e33eb6a98dce253bd987

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 10:02:02 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: ccrepe

      Commit: 6507a100f77b63a9f846de826eb6af58373ee945

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 09:58:35 -0400

      Commit message:


	  
		
 Deprecate
unresponsive
 

    

  
    

      Package: beadarray

      Commit: 24de7980fd25a2ca76bc34c03b1e8cb81fc7b781

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 09:31:09 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: basecallQC

      Commit: 5f12426b250a2e3620a94eef4f95125eb4b3fe82

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 09:29:32 -0400

      Commit message:


	  
		
 Deprecate
unresponsive
 

    

  
    

      Package: barcodetrackR

      Commit: 1c0d03e0b37f30f81bfb1901cb9fab5ce766b4ec

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 09:26:58 -0400

      Commit message:


	  
		
 Deprecate
unresponsive
 

    

  
    

      Package: bamsignals

      Commit: 0211dc480417394d6699dd1cf0b813bf9f75b178

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 09:25:03 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: ballgown

      Commit: ef351b958b9fd9309f9af46d79c966b6afe524ea

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 09:19:57 -0400

      Commit message:


	  
		
 Deprecate
unresponsive
 

    

  
    

      Package: VariantToolsData

      Commit: 5b48cc76273ae0b56d9ca7723930910b2f4ca9b4

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 09:17:10 -0400

      Commit message:


	  
		
 Deprecate
unresponsive
 

    

  
    

      Package: VariantTools

      Commit: 76f582c8d0c8750e8a86baf0fbfad68d33e29a12

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 09:14:48 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: SigFuge

      Commit: 0ef5e6a26cb8e74da3948c7521a8fbaace12b0e6

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 09:12:47 -0400

      Commit message:


	  
		
 Deprecated
unresponsive
 

    

  
    

      Package: RiboProfiling

      Commit: 999158fb12d1e2400df5d80d3b493f8002f974c5

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-13 09:07:45 -0400

      Commit message:


	  
		
 Deprecate
unresponsive
 

    

  
  


</div>

</div>