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GIT Logs

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

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Package: Aerith
Commit: fb5b4dcb8b4e61cda0d7be55261151f72d5a2504
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 11:52:24 -0600
Commit message:

 merge from upstream
Package: Aerith
Commit: 51cb983b07677508131293d614ff7da7438a01f9
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 11:45:50 -0600
Commit message:

 revise to 4 spaces for line indents, add citation
Package: Aerith
Commit: 0822bed2b3dce360a55c242064abca8b3c11bc78
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 10:36:18 -0600
Commit message:

 refine readme.md under windows, replace @ to slot(), add demo for precursor_peak_calculator_DIY_averagine
Package: Aerith
Commit: daab67b840523d8a06f010a53dc8876dce439064
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-28 11:35:29 -0500
Commit message:

 fix missing \value sections
Package: Aerith
Commit: 4b7c6e74383de7768a3a2f2cd3e25938d0fdaaa8
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-27 21:12:42 -0500
Commit message:

 fix missing \value sections
Package: Aerith
Commit: c76491be1ee5ac7da3903c40a8516476ca18f94b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-27 02:26:16 -0500
Commit message:

 fix .git files limit error, and Empty or missing \value sections warning
Package: Aerith
Commit: 14be7828634932aa9a271cd192a7481f0bebc07b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-23 13:41:31 -0500
Commit message:

 fix compile error on mac
Package: Aerith
Commit: 15b5517161a43614b682857b1ff2647bb730699c
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-10 03:34:58 -0500
Commit message:

 bump version
Package: Aerith
Commit: d423cb4368f82ca79da370b466315de178beab7a
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-10 00:10:27 -0500
Commit message:

 add demos to some rcpp function, optimize vignettes
Package: Aerith
Commit: 3cf2424b72aa823f399299f084e2db8a97a538bb
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-10 02:50:29 -0500
Commit message:

 bump version
Package: Aerith
Commit: 5cd74d768f19b7123a96ca38ffdd034925fdd11d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-10 02:14:18 -0500
Commit message:

 revise document of plot-AAspectra
Package: Aerith
Commit: f88e03c1f55fce6d86728f974860b15e739ae091
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 21:08:54 -0500
Commit message:

 Remove configure.sh from tracking
Package: Aerith
Commit: 5d38018e4d0c2d539fea7ed172edc62e0fe75c2e
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 20:56:59 -0500
Commit message:

 revise document of plotAAspectra.R and plotProteinSipPct.R
Package: Aerith
Commit: ead6f5aed064a60e0a165b69d4e57bd2e8f4acbb
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 03:08:12 -0500
Commit message:

 Stop tracking vignettes/.gitignore
Package: Aerith
Commit: a2b62a6647d90678fb25c9084a6aec27dfd81a3e
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 03:04:31 -0500
Commit message:

 Stop tracking .vscode
Package: Aerith
Commit: 51eefb946f5d474fa83125480eaf0cba865d53cf
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 02:59:11 -0500
Commit message:

 Stop tracking .gitignore .Rbuildignore
Package: Aerith
Commit: 20fbafecbc821c3ee382f329c3193d2645d3474b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-08 22:20:21 -0500
Commit message:

 change tests using built-in demo files
Package: Aerith
Commit: 2134f96cd01e73690666b3655dce216ba944a98b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-08 00:19:45 -0500
Commit message:

 update Score-function-test-of-PSM.Rmd, Theoretic-spectra-generation-of-SIP-labeled-compound.Rmd, Theoretic-spectra-generation-of-SIP-labeled-peptide.Rmd, Visualization-of-SIP-proteomic-result.Rmd. Remove eval=FALSE chunks
Package: Aerith
Commit: 2cbcafad6acad8465de0129619f9bd0b4434b6d0
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-04 22:41:57 -0500
Commit message:

 update Aerith.Rmd, Input-data-format.Rmd, PSM-annotation-and-visualization.Rmd. Remove eval=FALSE chunks
Package: Aerith
Commit: 1e1b25e9ced78d33a014b5ef6bcb7a757522b8d4
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-04 02:14:33 -0500
Commit message:

 add filterIsotopicPeaksTopN, set OMP_STACKSIZE = "16M" when init, add parameters for plotMolecularIsotopes
Package: Aerith
Commit: ee0440910e72ede5817e68504b8a8d403731ef8b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-16 20:26:39 -0500
Commit message:

 Merge branch 'main' into dev
Package: Aerith
Commit: 2e68fa7d7044a1d73ed2278b7082166e2b67a45d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-15 21:48:55 -0500
Commit message:

 bump version
Package: Aerith
Commit: 7b85b0f4af9e78fa5635930fef7cd78852a55d61
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-15 21:39:12 -0500
Commit message:

 fix cran warnings
Package: Aerith
Commit: 86278f024894870448803ddd12680db66635860f
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 02:19:30 -0500
Commit message:

 bump version
Package: Aerith
Commit: 0561ae7433f60fe118ea521a1cbf204a27d11942
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 02:13:21 -0500
Commit message:

 Merge updates for .gitignore, plotPSMs.R, readScans.cpp, and test_scorePSM.R from dev branch for fix R CMD check error
Package: Aerith
Commit: 3690ddba0ac326da4e96665ee75cfcfd1645c5cb
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 01:26:32 -0500
Commit message:

 fix R CMD check error
Package: Aerith
Commit: 5b7976ae8734baca35afcfd4a58d4ae9291e4f01
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 21:03:37 -0500
Commit message:

 Merge branch 'dev'
Package: Aerith
Commit: 3b76f8694408b2fbe8f83d24677cadf82dd5cc86
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 20:58:52 -0500
Commit message:

 revise vignettes
Package: Aerith
Commit: d0dc7dfd95dc4b576fc4b01004bcc7305334f098
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 19:37:52 -0500
Commit message:

 remove extdata
Package: Aerith
Commit: 505058eb0e3cab829a44a6729a244476cee677bc
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 19:30:19 -0500
Commit message:

 revise vignette from dependent on rmd folder to inst/extdata folder
Package: Aerith
Commit: c094239fa09465c12106fd7cfc23189389a1064d
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-27 00:12:48 -0500
Commit message:

 Update DESCRIPTION with GPL-3.0
Package: Aerith
Commit: 8085436a0b014f996cf5103aa4f73b224b04d9a8
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-27 00:08:39 -0500
Commit message:

 Update LICENSE.md to markdown style
Package: Aerith
Commit: ab690e89d786b1e0b839b81d91bc383068a832ad
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-26 23:58:23 -0500
Commit message:

 Create LICENSE.md
Package: Aerith
Commit: ade1b3c791e178d452a5fc2190286fa046468915
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-26 23:50:59 -0500
Commit message:

 version bump
Package: Aerith
Commit: b923c98738f0f51ffe0007e404f0db74a7ee3157
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-26 03:32:46 -0500
Commit message:

 fix file path error of plotPSMs function on windows
Package: Aerith
Commit: 3bf7064eeaca157b9e497209792da6e47ece644d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-26 01:22:35 -0500
Commit message:

 Add documentation for the exported functions recommended by Bioconductor.
Package: Aerith
Commit: 4e519962b75b9639076842a9cc166b8adef6fb23
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-21 12:34:01 -0500
Commit message:

 fix warning form BiocCheck::BiocCheck
Package: Aerith
Commit: d73eda880c2f51863845f5ccf614bde36d0aa1bc
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-21 03:48:21 -0500
Commit message:

 revise for bioconductor submitting
Package: Aerith
Commit: 9a9b4178f1d074bda505a1a3da97506f0b4ea491
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-05 00:54:50 -0500
Commit message:

 add link parameter for openmp on windows, add suggesting import of mzR and MSnbase
Package: Aerith
Commit: 11af7bb44219f58cb95ccafe83f305ac506fd4f8
Author: xyz1396 <1074082710@qq.com>
Date: 2025-04-16 12:18:51 -0500
Commit message:

 optimize readme
Package: Aerith
Commit: 348d6f2490bb8c62bcfbf4e8d2b0df3f230dce78
Author: xyz1396 <1074082710@qq.com>
Date: 2025-04-16 02:27:37 -0500
Commit message:

 add simplified calculation of WDPscore; revise spectral entropy to consider all peak intensity in real scan
Package: Aerith
Commit: 35f88206f57bfa61ceaa4220989611a9027a4653
Author: xyz1396 <1074082710@qq.com>
Date: 2025-03-11 02:23:32 -0500
Commit message:

 add vignettes for score function and PSMs results visual
Package: Aerith
Commit: 40d7d6cf3938f4f1c2871dc42623ec0ee96085a9
Author: xyz1396 <1074082710@qq.com>
Date: 2025-02-15 01:43:03 -0600
Commit message:

 vignette of PSM-annotation-and-visualization, add line_width and color setting of function plotAAsectra, add MVH score from myrimatch
Package: Aerith
Commit: 36b6fa1451fe43e25a473a764c54b4e27c0b2409
Author: xyz1396 <1074082710@qq.com>
Date: 2025-01-09 12:36:09 -0600
Commit message:

 add vignettes
Package: Aerith
Commit: 1c8b1468bfc1b4259d0212b227d5afc30cc0bde0
Author: xyz1396 <1074082710@qq.com>
Date: 2024-12-24 20:01:26 -0600
Commit message:

 add .vscode folder in track
Package: Aerith
Commit: 77d9974813dc4b7636ac5f83c3a9700586499411
Author: xyz1396 <1074082710@qq.com>
Date: 2024-12-20 02:13:00 -0600
Commit message:

 optimize PSM feature extract speed. add mentocarlo and fft isotope peak generate function
Package: Aerith
Commit: 61a33e8de49f3a42c637e7a733d0d0a434545f37
Author: xyz1396 <1074082710@qq.com>
Date: 2024-11-06 20:02:47 -0600
Commit message:

 refine spe2pepreader, featureextractor, addfunction for reading pepxml file
Package: Aerith
Commit: 516d2205c36ea75d04b08424a438e73e19af6319
Author: xyz1396 <1074082710@qq.com>
Date: 2024-08-13 11:42:42 -0500
Commit message:

 add function for PSM isotopic peaks annotation
Package: Aerith
Commit: 7799545dd5c5e9e2c24f5fb7638dfa3980c83eb4
Author: xyz1396 <1074082710@qq.com>
Date: 2024-06-10 23:37:31 -0500
Commit message:

 delet test.cpp
Package: Aerith
Commit: 02762d7004eeb6d2506bd179bbfcc190173847bf
Author: xyz1396 <1074082710@qq.com>
Date: 2024-06-10 23:24:46 -0500
Commit message:

 add  and 
 </pre>
    </div>
  
    

      Package: Aerith

      Commit: 00d0a3032569b3bd0757f407e655fa9ce0a975ff

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-06-10 23:16:27 -0500

      Commit message:


	  
		
 extract other features from MS1 level of sipros spe2pep file
 

    

  
    

      Package: Aerith

      Commit: 4858d7533a1009e5ac0e5a04b2f4ebbe29b9ab16

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-05-09 00:03:46 -0500

      Commit message:


	  
		
 add extract feature function and move to sipros5 spe2pep format with precursor scannumber
 

    

  
    

      Package: Aerith

      Commit: 09a7bd60e549d3eba0ec3caa41106fbb900dbed4

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-04-23 00:16:07 -0500

      Commit message:


	  
		
 extract isotopic abundance from MS1
 

    

  
    

      Package: Aerith

      Commit: 822cb1e48c98ece0400911943c075d23dd955852

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-04-04 00:19:13 -0500

      Commit message:


	  
		
 update to the FT2 file format of Raxport5 and spe2pep format of Sipros 5
 

    

  
    

      Package: Aerith

      Commit: 2cb46fe672ef2d93e44b774c9e3416c9e3fa91c2

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-01-25 19:19:27 -0600

      Commit message:


	  
		
 improve reading ft file performance
 

    

  
    

      Package: Aerith

      Commit: e5e663da91be042bdf02e328e9e626d8c0439b33

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-11-23 22:22:23 -0600

      Commit message:


	  
		
 for reading .Spe2PepFile
 

    

  
    

      Package: Aerith

      Commit: b17b05879cd28c35da1e6ea2ebc772f49a8e5610

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-04-13 23:25:36 -0500

      Commit message:


	  
		
 add denoise function, refine psm plot function
 

    

  
    

      Package: Aerith

      Commit: b57eb395c5da366d1eb049d05801e1ee758c25de

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-08 00:10:20 -0600

      Commit message:


	  
		
 revise read me again
 

    

  
    

      Package: Aerith

      Commit: 6fc28afa592a6a100a454875b3dfe90da519172c

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-08 00:09:03 -0600

      Commit message:


	  
		
 revise read me
 

    

  
    

      Package: Aerith

      Commit: effc5a937e8f008714c92cfc56afe19f49018a3a

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-06 23:44:59 -0600

      Commit message:


	  
		
 change read me
 

    

  
    

      Package: Aerith

      Commit: a5a7dffb87b6305c422054f0c7cdb1777700b07d

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-06 23:42:45 -0600

      Commit message:


	  
		
 upload files
 

    

  
    

      Package: Aerith

      Commit: f3ce4b1be5ea409856d8d1f30b125346f6708377

      Author:  Phase Technician XYZ <1074082710@qq.com> 

      Date: 2023-01-06 22:05:49 -0600

      Commit message:


	  
		
 Initial commit 

    

  
    

      Package: CNVMetrics

      Commit: d592e3d52adb257d07c712cfd387e60022f18ef5

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-04 12:21:51 -0500

      Commit message:


	  
		
 Version bump in devel
 

    

  
    

      Package: CNVMetrics

      Commit: 0595e73baa825f9e3e5e16c64bc2836336758d98

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-04 12:11:34 -0500

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel'
 

    

  
    

      Package: CNVMetrics

      Commit: aa3731adfc55b9761a4ac53d20a984c1383b794a

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 19:34:16 -0500

      Commit message:


	  
		
 Update check-bioc
 

    

  
    

      Package: CNVMetrics

      Commit: 4bff88e58071879863a45fd807784924422d5100

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 19:28:48 -0500

      Commit message:


	  
		
 Update check-bioc
 

    

  
    

      Package: CNVMetrics

      Commit: c3e9b5181e6158c6bde8dc3725ea563682867b26

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 19:23:00 -0500

      Commit message:


	  
		
 Update test-coverage
 

    

  
    

      Package: CNVMetrics

      Commit: 9b7161a7ce5a6dbf57f748ed22731632717f2756

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 19:13:59 -0500

      Commit message:


	  
		
 Update check-bioc
 

    

  
    

      Package: CNVMetrics

      Commit: 77ddafcf94f1a4448d12bc28d7a0e28edac947d7

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 19:10:58 -0500

      Commit message:


	  
		
 Update cehck-bioc
 

    

  
    

      Package: CNVMetrics

      Commit: 85e857eaddf09fb9790bf4ae89399164e95e0d13

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 18:33:09 -0500

      Commit message:


	  
		
 bug fix: Update itemize sections throughout all documentation
 

    

  
    

      Package: MSstatsBioNet

      Commit: afe0d21e354a4b6323030ed353fe3da15360508d

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2025-11-04 12:01:49 -0500

      Commit message:


	  
		
 version bump

1.3.0 to 1.3.1 

    

  
    

      Package: MSstatsBioNet

      Commit: 135cdea37c5eb40660f977b63f9cdeef9201d1b0

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2025-11-04 11:52:15 -0500

      Commit message:


	  
		
 refactor(getSubnetworkFromIndra): deprecate force_include_proteins parameter in favor of force_include_other (#60)

 

    

  
    

      Package: GSVAdata

      Commit: c11ec1562be901869009054028b935b400dbfb42

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

      Date: 2025-11-04 17:53:49 +0100

      Commit message:


	  
		
 Remove old microarray data from Armstrong et al. (2002) that is not used anymore in the vignette of GSVA and added a dependency on the microarray annotation package hgu95a.db
 

    

  
    

      Package: Pirat

      Commit: 91397bab5f079c18ffb755b8b7b808d3f203a6cf

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-04 17:42:22 +0100

      Commit message:


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

    

  
    

      Package: Pirat

      Commit: 57be4dff76c5f494e72d9fcb897c94a10eb107b6

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-04 12:03:21 +0100

      Commit message:


	  
		
 Adapt to new basilisk
 

    

  
    

      Package: Pirat

      Commit: 8f4540e51d7a44b282ba17c47e9bd5e6fd05520f

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-04 10:58:45 +0100

      Commit message:


	  
		
 Try other python
 

    

  
    

      Package: ChIPseeker

      Commit: be792409cc50ffba769e70aa64aea646f6fe9ffa

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-04 22:26:51 +0800

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: ChIPseeker

      Commit: 5535fab4ee7076f961a4b8eeb7980c63deaf3e9e

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-04 22:19:15 +0800

      Commit message:


	  
		
 Merge pull request #265 from MingLi-929/devel

update test for change of txdb version 

    

  
    

      Package: ChIPseeker

      Commit: 0b85d6dab65e03c8579ca0f37e05e75ef049e8bc

      Author:  liming <limiang929@gmail.com> 

      Date: 2025-11-04 16:24:21 +0800

      Commit message:


	  
		
 update test for change of txdb version
 

    

  
    

      Package: ChIPseeker

      Commit: a073bc5481f6d286be23f2ab696cfee4412cac6a

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-01 14:46:55 +0800

      Commit message:


	  
		
 update bioc version
 

    

  
    

      Package: hammers

      Commit: 2bbd134c65fe4e7808b53a026382239c56688d24

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

      Date: 2025-11-04 21:28:35 +0800

      Commit message:


	  
		
 Improved examples
 

    

  
    

      Package: CatsCradle

      Commit: 032f58b80ed864814a43e963399c5fb40db966e4

      Author:  AnnaLaddach <annaladdach@gmail.com> 

      Date: 2025-11-04 12:21:19 +0000

      Commit message:


	  
		
 version bump in devel
 

    

  
    

      Package: CatsCradle

      Commit: 5d1c036f63e9be4e1846b51e04337636f47e09f2

      Author:  AnnaLaddach <annaladdach@gmail.com> 

      Date: 2025-11-04 12:06:23 +0000

      Commit message:


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

    

  
    

      Package: CatsCradle

      Commit: 619e425ed75d274cd74f1b997a233744b950256c

      Author:  AnnaLaddach <annaladdach@gmail.com> 

      Date: 2025-11-04 12:04:54 +0000

      Commit message:


	  
		
 Change to exSeuratObj for compatibility with Seurat updates
 

    

  
    

      Package: Rarr

      Commit: 602dac2c347cb959e3df42dd57c32b20ccc7479a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-04 12:15:56 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: 13a174342cebb0a6d0128ecfbfc1f5ed294a58a5

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-04 12:15:42 +0100

      Commit message:


	  
		
 Document endian news
 

    

  
    

      Package: Rarr

      Commit: 96c804f6dae9a0995917b9dd65f3556dcb394b33

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-04 08:46:14 +0100

      Commit message:


	  
		
 Do not apply endian_codec when writing unicode
 

    

  
    

      Package: Rarr

      Commit: 81d1560505ce1e3977dd61c495642b3e1cd367aa

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 19:47:40 +0100

      Commit message:


	  
		
 Make unicode a special case for endian codec
 

    

  
    

      Package: Rarr

      Commit: f5732264a2c280114d9ae135e67a5c1168ed0ca1

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 19:47:17 +0100

      Commit message:


	  
		
 Force some readBin() for little endian
 

    

  
    

      Package: Rarr

      Commit: ee35fcbbc55c0d0baed32565d8e13cae5d2ccc62

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 12:01:24 +0100

      Commit message:


	  
		
 Move .readVlenUTF8() to read_utils.R
 

    

  
    

      Package: Rarr

      Commit: 686852441740005f560f957ec77a1d6727002c1c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-28 20:02:19 +0100

      Commit message:


	  
		
 Skip DelayedArray tests on big endian

There is some strange results that hint at compatibility limitations lower in the stack
 

    

  
    

      Package: Rarr

      Commit: bc8e092e91d9242759e490daa1f7088cc815efa0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-28 17:16:39 +0100

      Commit message:


	  
		
 Implement endian codec
 

    

  
    

      Package: Rarr

      Commit: 640b950507c617588e038b0e7de6567525428182

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-18 16:49:14 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: b59146b1abf4328db2ada524586e2f90008333bb

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-18 16:49:04 +0200

      Commit message:


	  
		
 Mention transpose codec in NEWS
 

    

  
    

      Package: Rarr

      Commit: a93ce346e9bbcb4a1bc35b60e1c43a0c6c347aea

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 09:44:44 +0100

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: Rarr

      Commit: 68b2dcbd7b1960307d991a2795cd1ea7c8c2f7ef

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-18 16:43:11 +0200

      Commit message:


	  
		
 Test C-ordering roundtrip in both 2D and 3D
 

    

  
    

      Package: Rarr

      Commit: 07574108781297d15e68d7a7f248380ea6adb7a0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-18 16:42:56 +0200

      Commit message:


	  
		
 Add codec_transpose_decode()
 

    

  
    

      Package: Rarr

      Commit: 4fca3a9e2182740d4eea194acd91b8863745efe8

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-18 16:40:25 +0200

      Commit message:


	  
		
 Add standalone test for codecs
 

    

  
    

      Package: Rarr

      Commit: 6e3a5a72fca981cd27275b320a1bd163ea680c9a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-17 15:43:35 +0200

      Commit message:


	  
		
 Make tranpose an explicit codec
 

    

  
    

      Package: Rarr

      Commit: c70b915eb15b1296c5dd9dbd3695e4ece0080d09

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-17 16:09:01 +0200

      Commit message:


	  
		
 Add test for fill order in update_zarr_array()
 

    

  
    

      Package: hammers

      Commit: d815d5b4108ab9f61e6e5ca5ae1605aa010b073b

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

      Date: 2025-11-04 16:35:53 +0800

      Commit message:


	  
		
 Fixed tests
 

    

  
    

      Package: densvis

      Commit: 6d9f4c7441e3e04ad2233dfef1df50a661d8808b

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-11-04 08:09:39 +0000

      Commit message:


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

    

  
    

      Package: densvis

      Commit: 0d873976e154d3ea5e3a553e5e8617e0fb8ec09c

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-11-04 08:09:11 +0000

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: densvis

      Commit: 2876d50ef0a1770b630bccc840cae460aa0f4eea

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-11-04 08:07:57 +0000

      Commit message:


	  
		
 Merge branch 'devel' of github.com:alanocallaghan/densvis into devel
 

    

  
    

      Package: densvis

      Commit: 37a6b9dfbe6b1be76affcaeb1a3b3b6fa8bba9e3

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 05:50:18 +0100

      Commit message:


	  
		
 Update llvmlite version to 0.45.0

See #10 and https://github.com/numba/llvmlite/issues/1290
 

    

  
    

      Package: densvis

      Commit: 39d05b8da177baf5e301e704ff9ec5fb072f4f09

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 06:34:15 +0100

      Commit message:


	  
		
 Update package versions in basilisk.R 

    

  
    

      Package: densvis

      Commit: 43f8c237ce75c183927ee6548c69032b42de7301

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 06:28:48 +0100

      Commit message:


	  
		
 Update numpy version to 2.3.4 

    

  
    

      Package: densvis

      Commit: 0d409e623dbca2610ee2fc742a3a3d9ed04e905f

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 06:05:34 +0100

      Commit message:


	  
		
 Update llvmlite version constraint in basilisk.R 

    

  
    

      Package: densvis

      Commit: 991445075e4f4e6fcca0aa9a0a1e7b509d4ab908

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 06:01:10 +0100

      Commit message:


	  
		
 Update package versions for numba and numpy 

    

  
    

      Package: densvis

      Commit: 4eff40ea72964a493003917d9d00088d2d3fa062

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 05:50:18 +0100

      Commit message:


	  
		
 Update llvmlite version to 0.45.0

See #10 and https://github.com/numba/llvmlite/issues/1290 

    

  
    

      Package: densvis

      Commit: aa3ee7e0b60b2a9ad6013c61bb61f6140fa1d50a

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-23 15:25:10 +0100

      Commit message:


	  
		
 Merge branch 'devel' of github.com:alanocallaghan/densvis into devel
 

    

  
    

      Package: densvis

      Commit: 61e77f4f7594d3244ebeca026a392b734453bedb

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-23 15:25:06 +0100

      Commit message:


	  
		
 dispatch
 

    

  
    

      Package: MsBackendMetaboLights

      Commit: d9f698a7006cae72f35ccfad830dcd01427967ae

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

      Date: 2025-11-04 08:35:39 +0100

      Commit message:


	  
		
 Merge pull request #12 from rformassspectrometry/jomain

refactor: increase download retries 

    

  
    

      Package: MsBackendMetaboLights

      Commit: 8c857b442c8398f8375c59eeab333880b0701110

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

      Date: 2025-11-04 07:58:21 +0100

      Commit message:


	  
		
 feat: export retry() function
 

    

  
    

      Package: MsBackendMetaboLights

      Commit: f9a170aae5690225e0f7e65592123685be84ae20

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

      Date: 2025-11-04 06:42:57 +0100

      Commit message:


	  
		
 fix: fix unit tests based on the changed defaults
 

    

  
    

      Package: MsBackendMetaboLights

      Commit: b12c90dc53b1ec4483c491773beed23bf2039694

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

      Date: 2025-11-03 16:26:01 +0100

      Commit message:


	  
		
 refactor: increase download retries
 

    

  
    

      Package: OSTA

      Commit: 7d91daa53f8ab1a787db24903fc8630e145ebd82

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-11-04 10:30:41 +0800

      Commit message:


	  
		
 version and date
 

    

  
    

      Package: OSTA

      Commit: b3cba146a32da973cc97280e6cb28507dabe0f2c

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-11-04 10:30:11 +0800

      Commit message:


	  
		
 Merge branch 'sandbox' into devel
 

    

  
    

      Package: OSTA

      Commit: 3974747d5d189b3bafda382c9e8dc0697b64be2e

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-11-04 10:20:09 +0800

      Commit message:


	  
		
 revert version number
 

    

  
    

      Package: OSTA

      Commit: 0e29fb90256df8dc77b2329af7e14c6fb913f4a1

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-11-03 22:23:38 +0800

      Commit message:


	  
		
 Merge pull request #243 from lmweber/timing

runtime recording 

    

  
    

      Package: OSTA

      Commit: b2ae3120b5c36c18fde594a97115b421ce2bbd32

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-03 15:04:08 +0100

      Commit message:


	  
		
 use helper-style variable name to stash runtimes
 

    

  
    

      Package: OSTA

      Commit: f8fafcbb5fb2d39f5a4ded75b90421389510fa73

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-03 15:01:47 +0100

      Commit message:


	  
		
 v1.0.1
 

    

  
    

      Package: OSTA

      Commit: bbb77163c18f25c277dcd84be1dcf74e798c1f1c

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-03 15:00:53 +0100

      Commit message:


	  
		
 uncomment code
 

    

  
    

      Package: OSTA

      Commit: afc9d55e736fd8871c32fc383e4cabe45187ba7e

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-03 14:59:48 +0100

      Commit message:


	  
		
 add chunk hooks to record runtimes & print out tabular summary in apx
 

    

  
    

      Package: OSTA

      Commit: 12d7032ca9044cba8039727da4c29a48548f2837

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-02 17:22:35 +0100

      Commit message:


	  
		
 omit loading tx files
 

    

  
    

      Package: OSTA

      Commit: 6b7d5af0ee5a16f49ae6f16eaf8843fb768e01dd

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-02 14:07:39 +0100

      Commit message:


	  
		
 + imports: scRNAseq
 

    

  
    

      Package: OSTA

      Commit: 6b7553b95983942e2320609509e6e76e164d0bfc

      Author:  Helena L. Crowell <helena@crowell.eu> 

      Date: 2025-11-02 09:14:32 +0100

      Commit message:


	  
		
 img-quality control updates; added img-workflow-cosmx

 

    

  
    

      Package: OSTA

      Commit: e4fa4fc16bf714b9c5a8cbc77fd7ea7b6dc75ebd

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-02 09:13:46 +0100

      Commit message:


	  
		
 Merge branch 'sandbox' into cosmx
 

    

  
    

      Package: OSTA

      Commit: 6105e9f9d74d276533b813a729c808449cbe60cc

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-02 09:12:21 +0100

      Commit message:


	  
		
 hlc revision
 

    

  
    

      Package: OSTA

      Commit: 653467ecb81606211a9f4a3a639d151dd5d4ff4e

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-01 09:14:01 +0100

      Commit message:


	  
		
 omit :::
 

    

  
    

      Package: OSTA

      Commit: 57016a00c10593ec3fda5b8aad67825c591741c0

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-31 17:36:34 +0100

      Commit message:


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

    

  
    

      Package: OSTA

      Commit: 6d5bd1310a24cab0fb29ef830814fb1a59069069

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-31 17:33:05 +0100

      Commit message:


	  
		
 Minor changes
 

    

  
    

      Package: OSTA

      Commit: 41b7b1f6cac46078bbc0f9f93aa325f6a06cda21

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-31 16:58:00 +0100

      Commit message:


	  
		
 Cosmx Workflow
 

    

  
    

      Package: OSTA

      Commit: 1c25ac2cd6c36de77cf4fb74cc3994b994425dac

      Author:  Helena L. Crowell <helena@crowell.eu> 

      Date: 2025-10-31 08:11:57 +0100

      Commit message:


	  
		
 +IF in ind-image-analysis

 

    

  
    

      Package: OSTA

      Commit: 7c62e8d1cbd1023dd069c8600a6f305e4c91f741

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-10-31 08:11:13 +0100

      Commit message:


	  
		
 aesthetic revision to ease readability
 

    

  
    

      Package: OSTA

      Commit: fdc9caecfaba47b50ad1bcbb7726e5b3a3e16f63

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-29 12:02:50 +0100

      Commit message:


	  
		
 Add details on SpaceTrooper
 

    

  
    

      Package: OSTA

      Commit: 086963fcce528cd2e86063eb8649bbd75fbb2a7e

      Author:  billila <ilaria.billato@studenti.unipd.it> 

      Date: 2025-10-28 16:39:27 +0100

      Commit message:


	  
		
 fix minor
 

    

  
    

      Package: OSTA

      Commit: d736b86642b57efa459bff2c9a01ba4268e9f9fd

      Author:  billila <ilaria.billato@studenti.unipd.it> 

      Date: 2025-10-28 16:36:48 +0100

      Commit message:


	  
		
 fix minor
 

    

  
    

      Package: OSTA

      Commit: 12e6641c8e989c4660b13a7471fb6f51682bf880

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-27 15:56:45 +0100

      Commit message:


	  
		
 Cosmx workflow
 

    

  
    

      Package: OSTA

      Commit: 26f5ff835571e347cb1f9d33717f6614444771f2

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-27 15:55:47 +0100

      Commit message:


	  
		
 Merge branch 'sandbox' of github.com:drisso/PrinciplesSTA into sandbox
 

    

  
    

      Package: OSTA

      Commit: cae44658e941b03c1a5dc0ceb55b2723190980d2

      Author:  billila <ilaria.billato@studenti.unipd.it> 

      Date: 2025-10-27 12:40:36 +0100

      Commit message:


	  
		
 add bibliography
 

    

  
    

      Package: OSTA

      Commit: 180cf539d82aa5602bbb6bed02157ad751a608d3

      Author:  Ilaria Billato <78036851+billila@users.noreply.github.com> 

      Date: 2025-10-27 12:03:35 +0100

      Commit message:


	  
		
 Merge branch 'lmweber:devel' into devel
 

    

  
    

      Package: OSTA

      Commit: d78458a5aa9c884c991e0590207abf3d3ca1b086

      Author:  billila <ilaria.billato@studenti.unipd.it> 

      Date: 2025-10-21 11:24:19 +0200

      Commit message:


	  
		
 add immunofluorescence part
 

    

  
    

      Package: OSTA

      Commit: 5e9d61769c3f284e7b17ed381b680ee8150037cf

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-20 11:04:01 +0200

      Commit message:


	  
		
 SpaceTrooper is now in Bioconductor
 

    

  
    

      Package: DOTSeq

      Commit: a88fe9e5ee8ef2a32a4a5e6b4028a25499b6d2d7

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-11-04 15:08:36 +1300

      Commit message:


	  
		
 add pasilla
 

    

  
    

      Package: DOTSeq

      Commit: 38e729b6498bd7ae548b62972df9b52b7fdeefd4

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-11-04 14:54:22 +1300

      Commit message:


	  
		
 add pasilla
 

    

  
    

      Package: DOTSeq

      Commit: 8dee2dc5314eb07e59ab35ab0f96a368c20c1170

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-11-04 14:25:37 +1300

      Commit message:


	  
		
 add pasilla
 

    

  
    

      Package: DOTSeq

      Commit: bac9a08dfda4e6aa10fd0c11d252ce5fc484fded

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-11-04 14:19:57 +1300

      Commit message:


	  
		
 add pasilla
 

    

  
    

      Package: PhyloProfile

      Commit: afcd9c43bfc4ac89f1a77c1643b2a23440a7ad37

      Author:  AnnamTran <trvinh@gmail.com> 

      Date: 2025-11-03 23:28:53 +0100

      Commit message:


	  
		
 fixed core gene ident with strain; fixed cus profile with 1000+ genes/taxa
 

    

  
    

      Package: BSgenome

      Commit: c2fc0dbd3c611e8863caa1644e2b38b468a3d230

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

      Date: 2025-11-03 14:15:06 -0800

      Commit message:


	  
		
 BSgenome 1.79.1: Post-release cleanup

Functions BSgenome::forgeMasksFile, BSgenome::forgeSeqFiles,
BSgenome::forgeSeqlengthsRdaFile, BSgenome::forgeSeqlengthsRdsFile,
BSgenome::forgeBSgenomeDataPkg, and BSgenome::forgeMaskedBSgenomeDataPkg
are now formally defunct in BioC 3.23 after being deprecated in BioC 3.22.
 

    

  
    

      Package: DOTSeq

      Commit: 0c199eed545490dbce32176959534c2e0c0c104b

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-11-04 10:09:31 +1300

      Commit message:


	  
		
 change email
 

    

  
    

      Package: mobileRNA

      Commit: b58cca24d0f89b5500b8778d1b92175892816fd6

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-11-03 11:51:23 -0600

      Commit message:


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

# Conflicts:
#	DESCRIPTION
 

    

  
    

      Package: mobileRNA

      Commit: d30185c3993ed131507a1b3f5cd7246f833d158b

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-11-03 11:45:01 -0600

      Commit message:


	  
		
 VERSION CONTROL
 

    

  
    

      Package: mobileRNA

      Commit: 0d692d29a2803fa31322a797161c77f96c92f205

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-11-03 11:36:01 -0600

      Commit message:


	  
		
 Seqinfo to namespace

Namespace dependency missing from DESCRIPTION Imports/Depends entries: ‘Seqinfo’
 

    

  
    

      Package: smoppix

      Commit: fe4ac0dcb7829d0fe77454f7509b211f49c984b9

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-11-03 18:32:49 +0100

      Commit message:


	  
		
 version chqnge

Merge branch 'devel' of git.bioconductor.org:packages/smoppix
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
 

    

  
    

      Package: smoppix

      Commit: 5733e3d48a37a5b664a0588e3532f7c7756560de

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-11-03 18:30:46 +0100

      Commit message:


	  
		
 R version bump
 

    

  
    

      Package: smoppix

      Commit: aa6894c2938bc1847d05eb6c820700f92a53490b

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-11-03 18:20:09 +0100

      Commit message:


	  
		
 Document plotCells
 

    

  
    

      Package: smoppix

      Commit: d724a7f76635d897b072cdd16150154b1b1005ef

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-11-03 17:25:51 +0100

      Commit message:


	  
		
 Remove weird feature number restriction
 

    

  
    

      Package: smoppix

      Commit: c09cb4412cb43e4121236e20e86fa33c69443e60

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-10-27 16:50:57 +0100

      Commit message:


	  
		
 More space for the scale bar
 

    

  
    

      Package: LACHESIS

      Commit: 0cbd1e498faa282f4ec2522ea06ff9a363bed98e

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

      Date: 2025-11-03 15:21:55 +0000

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: eisaR

      Commit: 7a06cdb610f7b6cd6065d1fc0e20c1abbefde352

      Author:  mbstadler <stadler.michael@gmail.com> 

      Date: 2025-11-03 15:29:00 +0100

      Commit message:


	  
		
 skip missing-library tests also on r-universe

Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
 

    

  
    

      Package: MetaProViz

      Commit: 5d2405206e5945f166149fee824d1798fccdd2b3

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-11-03 13:15:41 +0100

      Commit message:


	  
		
 nothing
 

    

  
    

      Package: MsBackendSql

      Commit: c6833d3d76cbec02dd3decba0abd43e8736da54b

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

      Date: 2025-11-03 12:57:03 +0100

      Commit message:


	  
		
 Merge pull request #33 from rformassspectrometry/jomain

Ensure peaks are ordered correctly with longForm() and duckdb 

    

  
    

      Package: MsBackendSql

      Commit: 2a72440121346993bf607cf9cd8d22bbcb7b9f4c

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

      Date: 2025-11-03 11:47:38 +0100

      Commit message:


	  
		
 update version
 

    

  
    

      Package: MsBackendSql

      Commit: 0d4a5ed1a19697b809f670eb594ee628d788140c

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

      Date: 2025-11-03 11:42:40 +0100

      Commit message:


	  
		
 ci: use devel versions of R
 

    

  
    

      Package: MsBackendSql

      Commit: d63ecc6eced96b231840dea241d4441197f196d1

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

      Date: 2025-11-03 11:39:40 +0100

      Commit message:


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

    

  
    

      Package: MsBackendSql

      Commit: 085ff671b208fde89c229026b4ffbe8d15399da3

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

      Date: 2025-11-03 11:37:47 +0100

      Commit message:


	  
		
 refactor: use ORDER BY with JOIN query for duckdb

- For `longForm()` and duckdb backend: include an ORDER BY statement to the
  JOIN query (issue #31).
 

    

  
    

      Package: MsBackendSql

      Commit: 69e8aa564680319b88d820958261179713798923

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

      Date: 2025-10-30 17:16:23 +0100

      Commit message:


	  
		
 refactor: prepare full duckdb support (issue #31)

- For storage of peaks data in long-form add a peak_id_ database table column
  depending on the database used (e.g. duckdb).
 

    

  
    

      Package: spatialFDA

      Commit: bd8c241aacd70eec883ad5cbea6d3cd804744c87

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-11-03 11:07:08 +0100

      Commit message:


	  
		
 removed scam option added news to all changes so far
 

    

  
    

      Package: spatialFDA

      Commit: a174d57bcb749c1c1c6fa111594d44793ae06ffd

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-11-03 09:28:55 +0100

      Commit message:


	  
		
 merge version Bump
 

    

  
    

      Package: spatialFDA

      Commit: 570ed9e8a3d1785bc6230848fcbcf895682f7e0f

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-31 11:31:06 +0100

      Commit message:


	  
		
 Merge branch 'devel' of github.com:mjemons/spatialFDA into devel
merge formula fix and prefit arg passing
 

    

  
    

      Package: spatialFDA

      Commit: e6916ca33e526adec47fc5767fd1c5da8a2b3acf

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-31 11:30:10 +0100

      Commit message:


	  
		
 pass arguments to prefit
 

    

  
    

      Package: spatialFDA

      Commit: 2a7217d5929e504f92d8fc41b0ceb4bd9e18e094

      Author:  Martin Emons <55688661+mjemons@users.noreply.github.com> 

      Date: 2025-10-28 16:14:14 +0100

      Commit message:


	  
		
 Merge pull request #21 from mjemons/FixEnvCall

fix environemnt problems 

    

  
    

      Package: spatialFDA

      Commit: f1f50098ac06dd3c50dc4f20804917f9d8bb677c

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-28 15:39:05 +0100

      Commit message:


	  
		
 fix environemnt problems
 

    

  
    

      Package: spatialFDA

      Commit: fb7e3bdff11d49a583166ce3b44239ff307b1369

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-26 13:44:04 +0100

      Commit message:


	  
		
 option to sqrt transform weights
 

    

  
    

      Package: spatialFDA

      Commit: d6a512ea7b313360080efa48705f64eea5999362

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-23 12:58:02 +0200

      Commit message:


	  
		
 changed cutoff calculation
 

    

  
    

      Package: spatialFDA

      Commit: 5789b3c953b4fdc346505c50ecd94c4f51ad2a7a

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-22 18:44:34 +0200

      Commit message:


	  
		
 implemented AR1.rho parameter
 

    

  
    

      Package: spatialFDA

      Commit: 59fa04d9d031d17a0cc1b4cdcb806a34d46d74a3

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-22 11:20:27 +0200

      Commit message:


	  
		
 implemented shape constraint with scam
 

    

  
    

      Package: spatialFDA

      Commit: 4fb29b64c13d12f4d2cce54fb0a81df683bbb79f

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-20 17:51:56 +0200

      Commit message:


	  
		
 remove message statement
 

    

  
    

      Package: spatialFDA

      Commit: 6c6aec9b08b523dbfb2d6aa27b5f7655389414c9

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-20 17:48:02 +0200

      Commit message:


	  
		
 fix ID
 

    

  
    

      Package: spatialFDA

      Commit: ad271eee4dc13b25dbea666c7fee7565ef20a945

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-20 17:42:57 +0200

      Commit message:


	  
		
 fix call of ID variable
 

    

  
    

      Package: spatialFDA

      Commit: 6f0ae0493bb2eb648ecb512e3f67402807fa1ff1

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-20 17:30:40 +0200

      Commit message:


	  
		
 fix Errors in UpperDeltaProb
 

    

  
    

      Package: spatialFDA

      Commit: 1d97e6b0ed5f8a8bcd2c9a0b8a93619340520a60

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-20 16:40:41 +0200

      Commit message:


	  
		
 for G functions, add a filtering of the constant 1 part
 

    

  
    

      Package: spatialFDA

      Commit: e107c9d2dae62346733c77149814a1dff4cbc5d3

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-16 10:36:27 +0200

      Commit message:


	  
		
 pass H explicitly to the gam
 

    

  
    

      Package: spatialFDA

      Commit: 004a9665455b37ee76bf5808155ebdc04c629001

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-16 08:06:41 +0200

      Commit message:


	  
		
 correct dimenions for H with prefit
 

    

  
    

      Package: spatialFDA

      Commit: 6ebc362cac881c98bd19207507045e53562dd8d9

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-15 20:52:24 +0200

      Commit message:


	  
		
 add option to define a ridge penalty
 

    

  
    

      Package: spatialFDA

      Commit: 95b67b4bda060fcac067988697129e5a37bed89f

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-13 11:30:08 +0200

      Commit message:


	  
		
 bug fix for GAM
 

    

  
    

      Package: alabaster.base

      Commit: 1d97e98f8966c6f7124c7c0114113c0cd584054f

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

      Date: 2025-11-02 23:55:31 -0800

      Commit message:


	  
		
 Set default bit64conversion= argument for updated rhdf5.
 

    

  
    

      Package: SVP

      Commit: e8643518b2e10dc19c90710c95218fd6f68d9320

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-11-03 15:03:04 +0800

      Commit message:


	  
		
 bump version and update news
 

    

  
    

      Package: SVP

      Commit: 1d4c0b14d805ea653f49c0bc12f6c68bcaa72f33

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-06-15 17:13:00 +0800

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: SVP

      Commit: 951bd752e1d1a7c50bcb26a2ab321d2a531f1778

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-06-15 17:11:04 +0800

      Commit message:


	  
		
 update the visualization of plot_lisa_feature
 

    

  
    

      Package: SVP

      Commit: a49b5bf82b1729eb506dbde9b4f8dedc3401ae50

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-06-15 16:28:54 +0800

      Commit message:


	  
		
 Merge branch 'main' into RELEASE_3_21
 

    

  
    

      Package: SVP

      Commit: 795043f6c238032353361c82d613e56245adb696

      Author:  xushuangbin <xshuangbin@163.com> 

      Date: 2025-06-13 19:02:22 +0800

      Commit message:


	  
		
 update knn.k.use arg
 

    

  
    

      Package: SVP

      Commit: 5bbb304924c679fef74e0e64e896f1fe0f7abfee

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

      Date: 2025-05-08 12:30:33 -0400

      Commit message:


	  
		
 Version bump to trigger rebuilding/propagation of Windows and Mac binaries
 

    

  
    

      Package: SVP

      Commit: ecd5f0785ccd0239a037b3a3ac90a335ca34a3e8

      Author:  xushuangbin <xshuangbin@163.com> 

      Date: 2025-04-17 17:06:19 +0800

      Commit message:


	  
		
 bioc3.21 release
 

    

  
    

      Package: sesameData

      Commit: 6ec5de603daa0c31a1eb02765b7f8bb7c3094219

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-02 20:50:11 -0500

      Commit message:


	  
		
 bump to 1.29.1, updated data using zenodo upload
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 9871264f23563e1a5d8850e4845cc8c6cd3b3ad7

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:43:39 +1100

      Commit message:


	  
		
 Version up
 

    

  
    

      Package: tidySpatialExperiment

      Commit: ab73876ae0767bae980c1e2832b4037816fa9ca3

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:43:16 +1100

      Commit message:


	  
		
 Merge BioConductor repository version bumps
 

    

  
    

      Package: tidySpatialExperiment

      Commit: fa6d5f3d0645b427c4aa7084db1ef2f577e4e9a8

      Author:  william-hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:37:00 +1100

      Commit message:


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

Remove conflicting functions 

    

  
    

      Package: tidySpatialExperiment

      Commit: 069aeb8771c088f7197ac183d05195600db8cc38

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:22:02 +1100

      Commit message:


	  
		
 Version up
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 77c2b87bc7d544f92c1398e40fb92c1dfc6cad5f

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:21:47 +1100

      Commit message:


	  
		
 Udpate 'bind_cols()' and 'bind_rows()' tests
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 1736874d0451cf19b93d42edbab18cfb7d8f6c25

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:15:29 +1100

      Commit message:


	  
		
 Udpate 'bind_cols()' and 'bind_rows()' examples
 

    

  
    

      Package: tidySpatialExperiment

      Commit: b5569de1409f691bb4388fb76a909049a05c81c5

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 17:11:18 +1100

      Commit message:


	  
		
 Version up
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 72509422a37c352fbc2ab33f46a21e9fd0828d6c

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 17:11:00 +1100

      Commit message:


	  
		
 Move ttservice to Depends field
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 540688a56bba7d7782e5d36eb29cddeda1ce4eb1

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:33:39 +1100

      Commit message:


	  
		
 Version up
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 66dfb4e59d883ad567ace4397db2eade0b389ac5

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:33:24 +1100

      Commit message:


	  
		
 Add missing function import
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 6dfa2a18da90b818b6b46fc2de03a78983e41148

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:21:26 +1100

      Commit message:


	  
		
 Remove redefinition of 'bind_cols()' and 'bind_rows()'
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 7261a13bd29b467269aa84fcc8e8a842c96739c8

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:09:13 +1100

      Commit message:


	  
		
 Add missing function import
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 83be70103f67dff8f12ce5c5d2fdc9d8181615d3

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:04:47 +1100

      Commit message:


	  
		
 Remove unused import
 

    

  
    

      Package: tidySpatialExperiment

      Commit: e0d8f0a68049b82aa752c2235efc3949e39cb381

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:00:03 +1100

      Commit message:


	  
		
 Remove redefinition of 'aggregate_cells()'
 

    

  
    

      Package: tidySpatialExperiment

      Commit: e8f82a3f56a33c3843ccb6b37acda1c1f6928b36

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 15:57:16 +1100

      Commit message:


	  
		
 Consolidate unnesting functions
 

    

  
    

      Package: SplicingGraphs

      Commit: 8abbef909f4c249fc62e4aa05c89b3a1fcaefb2d

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

      Date: 2025-11-02 09:50:45 -0800

      Commit message:


	  
		
 drop use of precomputed SplicingGraphs object 'sg_with_reads' in vignette
 

    

  
    

      Package: SplicingGraphs

      Commit: 0f477f251da074de5f54a7072a6f2cb54307089c

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

      Date: 2025-11-02 01:00:36 -0700

      Commit message:


	  
		
 SplicingGraphs 1.51.1: Repair vignette

The latest TxDb.Hsapiens.UCSC.hg19.knownGene (v 3.22.1, based on UCSC
track GENCODE V48lift37) is no longer suitable for the SplicingGraphs
vignette so we've switched to TxDb.Hsapiens.UCSC.hg19.refGene.
 

    

  
    

      Package: clusterProfiler

      Commit: c6e07d0e9c363a5102ca04de419b7d72bf739495

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-01 22:45:20 +0800

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: clusterProfiler

      Commit: 8669269d14d4f948d5975e56e6fb2d44367b885c

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-01 22:43:26 +0800

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: clusterProfiler

      Commit: f0243622a9d885dca2a44bd69383f2a3a76fe4ba

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-10-30 16:10:09 +0800

      Commit message:


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

    

  
    

      Package: clusterProfiler

      Commit: 3e5d5a4b2ae2a486cbf72b7c2f540e0fbf4f0315

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-10-30 16:08:35 +0800

      Commit message:


	  
		
 update enrich-pc
 

    

  
    

      Package: clusterProfiler

      Commit: 394892e4ff69fb14fc0d451adfca028fb72a69c3

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-10-23 21:05:53 +0800

      Commit message:


	  
		
 update
 

    

  
    

      Package: clusterProfiler

      Commit: 39395ce1f997da2f29a5a4b2d92d4d9e72923d53

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-04-17 09:51:00 +0800

      Commit message:


	  
		
 update bioc version
 

    

  
    

      Package: SwarnSeq

      Commit: 8f1ca0a58c8de9676dcdb81f4bcdc419f271bbc3

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:15:27 +0530

      Commit message:


	  
		
 SingleCellExperiment was used in modification.
 

    

  
    

      Package: splatter

      Commit: 646e458e9556ff2feaa712e60e8fa3d88a8ddd93

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:08:53 +0100

      Commit message:


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

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_22 branch
 

    

  
    

      Package: splatter

      Commit: 2e75db7706855754b14aeb33586007fe5adc0769

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:05:04 +0100

      Commit message:


	  
		
 Bioconductor 3.22 release
 

    

  
    

      Package: splatter

      Commit: 319c55c6d00007a78c8dd61ac8c815f9d4e68b4e

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:03:18 +0100

      Commit message:


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

* upstream/RELEASE_3_22:
  bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 

    

  
    

      Package: splatter

      Commit: 65286c7789f10c4ebc7f34b0e5a8fdc6616472a2

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2025-08-12 07:00:48 +0200

      Commit message:


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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 

    

  
    

      Package: splatter

      Commit: 5c03bcf28383ee4fbe9f4eee8e778984ef89bf86

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-07-10 17:47:12 +0200

      Commit message:


	  
		
 Add write permissions to pkgdown workflow
 

    

  
    

      Package: splatter

      Commit: 4e21ebc92774f23139d3ee8e85115141287817f5

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-07-09 21:24:38 +0200

      Commit message:


	  
		
 Update check GHA (#181)

* Update check GHA

* Fix missing biocversion_str in check GHA

* Fix typo in check GHA 

    

  
    

      Package: zellkonverter

      Commit: 38b921d8aa6cf264b9d8140f981cf1dd0f8e0b83

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:21:07 +0100

      Commit message:


	  
		
 Fix version in NEWS
 

    

  
    

      Package: zellkonverter

      Commit: 57b9d7a337d0cad27d4c9b9320425e8e37c73994

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:20:22 +0100

      Commit message:


	  
		
 Bioconductor 3.23 devel
 

    

  
    

      Package: zellkonverter

      Commit: e34e43c8e309fec966d3a46f13207944f6aed68e

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:19:23 +0100

      Commit message:


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

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_22 branch
 

    

  
    

      Package: zellkonverter

      Commit: 4a98e5cb1ce541d6182bd1700466b8c8cceca3dd

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:14:25 +0100

      Commit message:


	  
		
 Bioconductor 3.22 release
 

    

  
    

      Package: zellkonverter

      Commit: c357324e8ee9e81b72c88dacb41d90067ea1f785

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:13:20 +0100

      Commit message:


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

* upstream/RELEASE_3_22:
  bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 

    

  
    

      Package: Rsubread

      Commit: 8fedb934b06a7a72aa56a51d4ca0a6ef5f086036

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

      Date: 2025-11-01 17:11:35 +1100

      Commit message:


	  
		
 altered cellCounts for testing features
 

    

  
    

      Package: smoothclust

      Commit: 1246c80e932cd1a18dccfa1359c8490b461fa539

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-11-01 10:00:55 +0800

      Commit message:


	  
		
 update GHA
 

    

  
    

      Package: OrganismDbi

      Commit: a63751b6cc056aff02cfdedc1ef981d3317729a0

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

      Date: 2025-10-31 15:33:12 -0700

      Commit message:


	  
		
 OrganismDbi 1.53.2: Post-release cleanup

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

Also arguments 'url' and 'port' are now defunct after being
deprecated in BioC 3.22.
 

    

  
    

      Package: leapR

      Commit: 5e355f7e8d673a5f1cf5bb93909be726bba775d4

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

      Date: 2025-10-31 13:11:57 -0700

      Commit message:


	  
		
 updated documentation
 

    

  
    

      Package: leapR

      Commit: 4cdd6344f88838c68806c35f56bb8083c61b7eec

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

      Date: 2025-10-31 12:44:33 -0700

      Commit message:


	  
		
 made last bits of changes
 

    

  
    

      Package: leapR

      Commit: bd8d9ffeff39c4694c1bab7c8fa90245875a45bc

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

      Date: 2025-10-30 15:42:33 -0700

      Commit message:


	  
		
 updated to account for additional bioC issues

- figured out the seq_len vs seq_along issue
- shortened lines
- added input checking
- fixed typos
- added man page
 

    

  
    

      Package: scrapper

      Commit: 1a313d952522e945e6ef66e342a36d378e3a54a6

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

      Date: 2025-10-31 00:26:44 -0700

      Commit message:


	  
		
 Updated bindings for the latest version of scran_graph_cluster.

Also minor bug fix for creating unweighted graphs.
 

    

  
    

      Package: scrapper

      Commit: d6a9e9e51335abfc3794dd9e7413cc33120e912c

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

      Date: 2025-10-29 15:39:30 -0700

      Commit message:


	  
		
 Updated the ignore file, moved Rigraphlib to LinkingTo.
 

    

  
    

      Package: scrapper

      Commit: 875fd4c9f972eb7807ec54523585560afce7bcf8

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

      Date: 2025-10-29 15:18:17 -0700

      Commit message:


	  
		
 Stripped out the analyze() function from the vignette.

Now that it's been moved to scrapple::analyze.se().
 

    

  
    

      Package: assorthead

      Commit: 16d94c97a39c30c5e6768f44b765c9e40083062f

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

      Date: 2025-10-30 21:01:35 -0700

      Commit message:


	  
		
 Updated vendored copies of raiigraph, scran_graph_cluster.
 

    

  
    

      Package: Rigraphlib

      Commit: 445817dc273b67afbf41d48a0b9a150bc075dec8

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

      Date: 2025-10-30 20:59:58 -0700

      Commit message:


	  
		
 Updated vendored version of igraph to 1.0.0.

Also commit the source code directly instead of storing a tarball, to get
around the BioC Git server's file size limits.
 

    

  
    

      Package: ShortRead

      Commit: c488f2966454c7bd2cadccb96415f3ef97ac3134

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

      Date: 2025-10-31 09:50:57 -0700

      Commit message:


	  
		
 ShortRead 1.69.1: Import pattern() from pwalign instead of Biostrings
 

    

  
    

      Package: GXwasR

      Commit: a56e631c0f0f781be8645062656bd0e792f2fc65

      Author:  Banabithi Bose <banabithi.bose@gmail.com> 

      Date: 2025-10-31 10:03:32 -0500

      Commit message:


	  
		
 Version bumped.
 

    

  
    

      Package: GXwasR

      Commit: 20442b403ef8da8d09d1dd180604692f7511e36a

      Author:  D Mayer <32186106+the-mayer@users.noreply.github.com> 

      Date: 2025-10-31 06:19:33 -0600

      Commit message:


	  
		
 Merge pull request #60 from boseb/misc-bioc

Vignette and Style 

    

  
    

      Package: GXwasR

      Commit: d4fd65bd42b3c6b4b2fcac25a0b02d901524382d

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-30 08:45:20 -0400

      Commit message:


	  
		
 changes for BiocCheck
- F to FALSE in preimputationQC
- apply biocthis::bioc_style()
 

    

  
    

      Package: bsseq

      Commit: 46b4295329703d0bf694c707c816772bfbf4c037

      Author:  Kasper Daniel Hansen <kasperdanielhansen@gmail.com> 

      Date: 2025-10-31 11:03:21 -0400

      Commit message:


	  
		
 Making read.modkit and read.modbam2bed defunct
 

    

  
    

      Package: bsseq

      Commit: 13d941106f789484620bf16c62feff3d9f877c6c

      Author:  Kasper Daniel Hansen <kasperdanielhansen@gmail.com> 

      Date: 2025-10-31 09:58:40 -0400

      Commit message:


	  
		
 merging from release
 

    

  
    

      Package: bsseq

      Commit: a0f3ce3f5728d805476f0aad9e44a4748323a028

      Author:  Kasper Daniel Hansen <kasperdanielhansen@gmail.com> 

      Date: 2025-10-10 11:25:36 -0400

      Commit message:


	  
		
 getting rid of Travis since we have been using Github Actions for a while
 

    

  
    

      Package: MetaProViz

      Commit: 06811fcdb5a4cc52185613d4bdf5a2e380ed8f37

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 15:22:56 +0100

      Commit message:


	  
		
 code formatting: break long argument lists
 

    

  
    

      Package: MetaProViz

      Commit: 47cc5a9af900ada0782bc9d7e2a58f50facf9e88

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 11:55:36 +0100

      Commit message:


	  
		
 Bump version: 3.99.17 → 3.99.18
 

    

  
    

      Package: MetaProViz

      Commit: da03ed010c71f69526dfac528350166045b15623

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 11:55:33 +0100

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: db946fdfec3526daa164a215d2e4fec045f71529

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 11:54:50 +0100

      Commit message:


	  
		
 moved examples of ID translation functions into `\dontrun` due to 15 min BioC timeout for R CMD check
 

    

  
    

      Package: dmGsea

      Commit: 248aa7cd204a3a7eb4cb6aa0e3138ecc660b9aa3

      Author:  xuz1 <xuz@niehs.nih.gov> 

      Date: 2025-10-31 09:40:12 -0400

      Commit message:


	  
		
 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

    

  
    

      Package: DESpace

      Commit: 3dbd101c6483dc2e536fc8eced1da63fbdc94e69

      Author:  peicai <peiying.cai@gmail.com> 

      Date: 2025-10-31 13:13:38 +0100

      Commit message:


	  
		
 updated citation
 

    

  
    

      Package: rhdf5

      Commit: 8cd8dc6e82333e4baaa093d59d2f20f6f5586118

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 09:46:45 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: 97e6d85586c8d5a105b6786df227bc3ef0a2ec64

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 09:46:29 +0100

      Commit message:


	  
		
 Mention fix in NEWS
 

    

  
    

      Package: rhdf5

      Commit: ca84366af7955b3ae300c53b6b4444b7377cd8f8

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 20:15:03 +0200

      Commit message:


	  
		
 Fix orientation on native unsigned int
 

    

  
    

      Package: rhdf5

      Commit: 514f9f1f63d60ce9cc5d6787b07c443b175cf72c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 18:33:23 +0200

      Commit message:


	  
		
 Add regression test for #157
 

    

  
    

      Package: rhdf5

      Commit: 74937b0c7afb6f6dd1b63dda214cc8091a4082f0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 09:14:16 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: f81b9097ca9da16e43addfd3fdc7299b42153bca

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 09:12:57 +0100

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: rhdf5

      Commit: 31b7c2e9288835c3cddb386b7bdc4d25bc164070

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 15:08:11 +0200

      Commit message:


	  
		
 Use double quotes
 

    

  
    

      Package: rhdf5

      Commit: 7b422fbaf166df85fadb11180ac304d8a4606a5b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:33:59 +0200

      Commit message:


	  
		
 Use dedicated ...length() base function where appropriate
 

    

  
    

      Package: rhdf5

      Commit: 0ed9fb9673dd5b7c238241637b9b471022dd4c69

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:33:33 +0200

      Commit message:


	  
		
 Use dedicated nzchar() base function where appropriate
 

    

  
    

      Package: rhdf5

      Commit: 5ea680b34dbd6cba2bec7fe75e4789e6271c127e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:33:02 +0200

      Commit message:


	  
		
 Do not pass functions as characters
 

    

  
    

      Package: rhdf5

      Commit: a32b4a3096ef8d58e0cbaca5bee629e19c5ac53d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:06:10 +0200

      Commit message:


	  
		
 Make bit64conversion default explicit
 

    

  
    

      Package: rhdf5

      Commit: 7d7eb9e6ef6e9b706ed477db7f829715986fc67d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:05:54 +0200

      Commit message:


	  
		
 Remove unnecessary ifelse()
 

    

  
    

      Package: rhdf5

      Commit: 6040f892c6c9f43dcb85e64949ee5196050bf667

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:05:40 +0200

      Commit message:


	  
		
 document return
 

    

  
    

      Package: rhdf5

      Commit: 966e5c10ace603fc729d2878f2a0117529ff7e08

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:04:45 +0200

      Commit message:


	  
		
 Reduce nesting and remove unnecessary parentheses
 

    

  
    

      Package: rhdf5

      Commit: 460149fd55b36ca3637a166d8653d80397337069

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 12:46:36 +0200

      Commit message:


	  
		
 Fix some long lines
 

    

  
    

      Package: rhdf5

      Commit: 48148dfa9d4f0a0db2184cab120206c23857c9c3

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 12:31:19 +0200

      Commit message:


	  
		
 Fix package name in vignette
 

    

  
    

      Package: rhdf5

      Commit: 3133c72125d4ec5bed648cf507998a60ed288fbf

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:44:22 +0200

      Commit message:


	  
		
 Remove unused variables
 

    

  
    

      Package: rhdf5

      Commit: ee3e7eb49dcefcda154fa124399655a6e73092fc

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:35:47 +0200

      Commit message:


	  
		
 Use seq_along() where possible
 

    

  
    

      Package: rhdf5

      Commit: 4be344a10a2954d4482e18fd91ce0a3870a14ebc

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:32:17 +0200

      Commit message:


	  
		
 Simplify newnames definition
 

    

  
    

      Package: rhdf5

      Commit: 89ea65ea690a2bfc39461f3614c5ed94f9d79076

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:25:29 +0200

      Commit message:


	  
		
 Remove sapply() where possible
 

    

  
    

      Package: rhdf5

      Commit: 1454dddd24abc35212a589d7abaf42dfb7b362ab

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:13:06 +0200

      Commit message:


	  
		
 Use shortcircuit boolean operator where appropriate
 

    

  
    

      Package: rhdf5

      Commit: 04d998f8b476e45200c1d200af4f60b00556021c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:08:06 +0200

      Commit message:


	  
		
 Use anyNA() where appropriate
 

    

  
    

      Package: rhdf5

      Commit: 8a011597e6910e8f8c40f36a38c585e6712071d1

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 10:55:08 +0200

      Commit message:


	  
		
 Setup lintr
 

    

  
    

      Package: rhdf5

      Commit: 425e4616b4ef9d85b50d9e65a2651cb11ac81a36

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-15 15:25:39 +0200

      Commit message:


	  
		
 Fix R CMD check NOTE about method consistency
 

    

  
    

      Package: rhdf5

      Commit: 65a1611cd377311ee5ef150e58df101946d5fc8c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-15 15:00:48 +0200

      Commit message:


	  
		
 Add curl as a devel dependency

Since it is required for testthat::skip_if_offline()
 

    

  
    

      Package: rhdf5

      Commit: c80c3aebee0a32d0128953b4e529f201bd88edc7

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-30 19:32:59 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: b8eda3c92e355a8fcc0af994988c9e7bf8ce7a3e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:15:03 +0200

      Commit message:


	  
		
 Mark deNBI as funder
 

    

  
    

      Package: rhdf5

      Commit: afba574a116b85d0b5558b8c79b5fe31db12a2bd

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:12:44 +0200

      Commit message:


	  
		
 Update logo location in README
 

    

  
    

      Package: rhdf5

      Commit: 23c0bf600d50dafcee763f4b6ff11c416afeb45d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:12:05 +0200

      Commit message:


	  
		
 Update logo & favicon
 

    

  
    

      Package: rhdf5

      Commit: 8aa529c74586f07b7670fff5ab1117db540d3776

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:09:55 +0200

      Commit message:


	  
		
 Add pkgdown link to DESCRIPTION
 

    

  
    

      Package: rhdf5

      Commit: 9b6dc3554666736f50f4d91fa0e74246d4a43495

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:09:24 +0200

      Commit message:


	  
		
 Fix settings
 

    

  
    

      Package: rhdf5

      Commit: c585976b4cd518da14b61c71a9bd61e315744324

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:08:08 +0200

      Commit message:


	  
		
 Add pkgdown.yaml GHA workflow
 

    

  
    

      Package: rhdf5

      Commit: 8c3c468cb57475a02f9145b91cf3467a8dd9c417

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:07:45 +0200

      Commit message:


	  
		
 Fix _pkgdown.yml
 

    

  
    

      Package: rhdf5

      Commit: 17e09a5d824cfdcf45d41df79b6c639ee4ada64a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 16:03:04 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: b77315e2755bf0d1e2f99ecd85ff98880720ea10

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 16:00:25 +0200

      Commit message:


	  
		
 Run ignored test
 

    

  
    

      Package: rhdf5

      Commit: 93e1df44d5f5bc805147e1ad3e1044b0b628c0c4

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-30 19:05:05 +0100

      Commit message:


	  
		
 Fix ref to git blame ignore after force push
 

    

  
    

      Package: rhdf5

      Commit: 99c048f38908d7851a8017d42db76e0226e50a53

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 10:47:21 +0200

      Commit message:


	  
		
 Remove travis config file
 

    

  
    

      Package: rhdf5

      Commit: bf471b18935a0031eedd30868eb746a3b7a2d2c0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 10:46:48 +0200

      Commit message:


	  
		
 Gitignore venvs
 

    

  
    

      Package: rhdf5

      Commit: ffa8132a43223c1f41e22ce86e42709ab7aa8539

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-15 10:51:22 +0200

      Commit message:


	  
		
 Use simpler r-hub workflow for big endian platforms
 

    

  
    

      Package: rhdf5

      Commit: 72fc7c925e704b168873546cf1df1791f7ac9d85

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-15 10:50:51 +0200

      Commit message:


	  
		
 Ignore reformatting commits in git blame
 

    

  
    

      Package: rhdf5

      Commit: 77041f3d63e3dcb185e5a7a72fe70d0f4e239b7c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-14 20:17:43 +0200

      Commit message:


	  
		
 Reformat code via air & styler (#173)

 

    

  
    

      Package: UCell

      Commit: 1e041f76a552ea7821f8e1e4bc46c9e60505b007

      Author:  Massimo Andreatta <massimo.andreatta@unil.ch> 

      Date: 2025-10-31 09:53:43 +0100

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: UCell

      Commit: 14f793cfac4b90cc2f877befa98a7f60b5d730ee

      Author:  Massimo Andreatta <massimo.andreatta@unil.ch> 

      Date: 2025-10-31 09:32:23 +0100

      Commit message:


	  
		
 Merge branch 'devel'
 

    

  
    

      Package: UCell

      Commit: 4f824e3ec02839c250093d4e8bee9b3caafd1425

      Author:  Massimo Andreatta <massimo.andreatta@unil.ch> 

      Date: 2025-10-06 13:28:31 +0200

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: Rarr

      Commit: f1e408688a973613c15a6845501d30a19df76782

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 08:54:37 +0100

      Commit message:


	  
		
 Bump patch version
 

    

  
    

      Package: Rarr

      Commit: c0ae2d5d47a459486e4cceddd03bdae92a66438e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 08:54:30 +0100

      Commit message:


	  
		
 Mention new vignette in NEWS
 

    

  
    

      Package: Rarr

      Commit: a94170c2391bef6041c41fe5dfd404385c876cc5

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-28 16:03:49 +0100

      Commit message:


	  
		
 Move table of supported feature to a dedicated vignette

So that it's more easily findable on the Bioconductor landing page
 

    

  
    

      Package: Rarr

      Commit: fa55d187b360f855cc9a2360bbe601f576981d6d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-22 17:33:02 +0200

      Commit message:


	  
		
 Delint NEWS
 

    

  
    

      Package: FLAMES

      Commit: 78876583058a5fadca22c5172216afed07b7250e

      Author:  Changqing Wang <wang.ch@wehi.edu.au> 

      Date: 2025-10-31 17:11:54 +1100

      Commit message:


	  
		
 Merge branch 'RELEASE_3_22' into devel
 

    

  
    

      Package: FLAMES

      Commit: 41bbd55e1d26366696ff33d3a8055cdb6223aaf0

      Author:  Changqing Wang <wang.ch@wehi.edu.au> 

      Date: 2025-10-31 16:50:56 +1100

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: FLAMES

      Commit: a97a0058712a32856f6fd5dc1f8f9d6c8537eae2

      Author:  Ching Yin, WAN <126227662+chingyinwan@users.noreply.github.com> 

      Date: 2025-10-31 13:45:21 +1100

      Commit message:


	  
		
 Fix the expect_cell_number check 

    

  
    

      Package: FLAMES

      Commit: 57a56ff86aa8c74c41736df9fc72f223c545f111

      Author:  Changqing Wang <wang.ch@wehi.edu.au> 

      Date: 2025-10-31 16:47:51 +1100

      Commit message:


	  
		
 update citation and authors
 

    

  
    

      Package: MetaProViz

      Commit: 8f122b35da767ae92e14cd52d472d6f29908fabb

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 02:17:17 +0100

      Commit message:


	  
		
 Bump version: 3.99.16 → 3.99.17
 

    

  
    

      Package: MetaProViz

      Commit: a77dd16505394cb81eb7b6e7250038157650b8fa

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 02:17:10 +0100

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: 0d8601314178acaf1936e3b3430e0dd884fa2742

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 02:00:55 +0100

      Commit message:


	  
		
 Bump version: 3.99.15 → 3.99.16
 

    

  
    

      Package: MetaProViz

      Commit: 8d73415c33319f6002b46915f6203f8c642cb956

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 02:00:07 +0100

      Commit message:


	  
		
 cleaned up stray docstring lines, redundant file headers, consolidated messy formatting of "section title" comments in code
 

    

  
    

      Package: MetaProViz

      Commit: a502e7c700db4bc2136c0ad640840d89af0b01d4

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 01:06:45 +0100

      Commit message:


	  
		
 Bump version: 3.99.14 → 3.99.15
 

    

  
    

      Package: MetaProViz

      Commit: ee09bbf4dcbb93c4cb95a22d98f23d5199ea6c31

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 01:06:24 +0100

      Commit message:


	  
		
 `.Rbuildignore`: maybe this helps with the warning about `inst/scripts` empty directory on Bioc build servers
 

    

  
    

      Package: MetaProViz

      Commit: d690bbc9b1bda93f0982cf0f17e597ccedae3f9a

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 00:50:38 +0100

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: 046bb300d0274a9f7baf6369c9d74074abaaef21

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-31 00:11:12 +0100

      Commit message:


	  
		
 docstring examples code formatting & 80 char line length
 

    

  
    

      Package: MetaProViz

      Commit: 8819461fb58b1a04728c03981588e84db788bacd

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 23:01:36 +0100

      Commit message:


	  
		
 docstrings: title lengths, line lengths, indentation
 

    

  
    

      Package: MetaProViz

      Commit: b489f48e907d95f33d45308ce144fc04da0995fd

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 18:23:15 +0100

      Commit message:


	  
		
 Merge branch 'main' of github.com:saezlab/MetaProViz
 

    

  
    

      Package: MetaProViz

      Commit: 7a58e57a7693c4cd85335558215a1ff6798021a5

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 18:14:12 +0100

      Commit message:


	  
		
 `vignettes/prior-knowledge`: missing comma (syntax)
 

    

  
    

      Package: MetaProViz

      Commit: 21accc849f2bdfc53a36ec05f751599db0b9eb7e

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-30 17:46:18 +0100

      Commit message:


	  
		
 Merge pull request #120 from saezlab/devel

Devel 

    

  
    

      Package: MetaProViz

      Commit: a59fa56ebb3f3b84d6acb1193542afcfeb5b3838

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-30 17:20:18 +0100

      Commit message:


	  
		
 Merge pull request #119 from saezlab/devel

Merge Devel into main 

    

  
    

      Package: SparseArray

      Commit: 148eea94c07e455a7717479ebade706f7f3fb45f

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

      Date: 2025-10-30 21:21:39 -0700

      Commit message:


	  
		
 SparseArray 1.11.1: Small teak to unit tests
 

    

  
    

      Package: Biostrings

      Commit: 778d5f9589e114e13aa23c71c861ce1aa594a8f5

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

      Date: 2025-10-30 18:41:20 -0700

      Commit message:


	  
		
 Biostrings 2.79.1: Post-release cleanup

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

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

Additionally, the XStringPartialMatches class and following functions
are now gone after being defunct in BioC 3.22 or non-functional for
years: matchprobes(), subpatterns(), pmatchPattern(), lcsubstr().
 

    

  
    

      Package: txdbmaker

      Commit: 5069001b1b008174f6896ce604dd64cf1e4e479f

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

      Date: 2025-10-30 17:12:43 -0700

      Commit message:


	  
		
 txdbmaker 1.7.1

Utility function supportedMiRBaseBuildValues(), argument 'miRBaseBuild',
and argument 'port' are now gone after being defunct in BioC 3.22.
Note that 'miRBaseBuild' and 'port' were arguments of several functions
in the txdbmaker package.
 

    

  
    

      Package: HPO.db

      Commit: 5d27546bae6a1d2f2221f08400b533ca6c37d8eb

      Author:  huerqiang <13766876214@163.com> 

      Date: 2024-07-29 21:58:53 +0800

      Commit message:


	  
		
 update data
 

    

  
    

      Package: HPO.db

      Commit: e916f92e3017e3a280894d678259b914bfa418d2

      Author:  huerqiang <13766876214@163.com> 

      Date: 2024-07-25 20:34:28 +0800

      Commit message:


	  
		
 update metadata.R
 

    

  
    

      Package: OrganismDbi

      Commit: ba2e70db159bd71ebe4f62ccc115d3455f9d4603

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

      Date: 2025-10-30 10:58:09 -0700

      Commit message:


	  
		
 OrganismDbi 1.53.1: microRNAs() was removed from GenomicFeatures 1.63.1
 

    

  
    

      Package: MetaProViz

      Commit: 1cfb3b14d2ea2d061177eff8ded82be9cdb225a8

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 18:05:03 +0100

      Commit message:


	  
		
 Bump version: 3.99.13 → 3.99.14
 

    

  
    

      Package: MetaProViz

      Commit: 455926da7b219e47fc76f7b904c92f63ecd51b36

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 18:04:54 +0100

      Commit message:


	  
		
 quick-start vignette: indent also html by 4 spaces
 

    

  
    

      Package: MetaProViz

      Commit: 92d4a873b02104ff608925839443b38740fe2d3e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 18:01:43 +0100

      Commit message:


	  
		
 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
 

    

  
    

      Package: MetaProViz

      Commit: 365f10343ce7c7437020ea58dc89a555d3abcdda

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 18:01:36 +0100

      Commit message:


	  
		
 Bump version: 3.99.12 → 3.99.13
 

    

  
    

      Package: MetaProViz

      Commit: fd0153cf3ddb94255170feb24546c8c31116b517

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 18:01:28 +0100

      Commit message:


	  
		
 removed space(!) from file names; `vignettes/pkgdown` to `Rbuildignore`
 

    

  
    

      Package: MetaProViz

      Commit: 2787646eb0ead967946484e4513ca57a2db4e988

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 18:00:19 +0100

      Commit message:


	  
		
 `vignettes/pkgdown` to `Rbuildignore`
 

    

  
    

      Package: MetaProViz

      Commit: 45de17ea1bf38cd02334a989638a212216173715

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-30 17:45:03 +0100

      Commit message:


	  
		
 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
 

    

  
    

      Package: MetaProViz

      Commit: 959197be83ccbe7ac1306963629dfc1223fc8304

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-30 17:44:49 +0100

      Commit message:


	  
		
 added comma
 

    

  
    

      Package: MetaProViz

      Commit: 29d9371264be7b478da02ffe14150e5169f9014e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 17:44:34 +0100

      Commit message:


	  
		
 Bump version: 3.99.11 → 3.99.12
 

    

  
    

      Package: MetaProViz

      Commit: c85b35fdc2bd908859acd62bea7181516db9cf11

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 17:43:16 +0100

      Commit message:


	  
		
 4 spaces indentation of vignette code
 

    

  
    

      Package: MetaProViz

      Commit: ef203ef6d14cef8097a29cc2d244d811bc8e3f00

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-30 17:38:50 +0100

      Commit message:


	  
		
 4 spaces indentation of R code
 

    

  
    

      Package: MetaProViz

      Commit: 1d4345816db5a0f1e68c0f6976640d856f5df18a

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-30 16:29:15 +0100

      Commit message:


	  
		
 included svg file for vignettes
 

    

  
    

      Package: MetaProViz

      Commit: a1a8487e1ff331cb184bae62e8f60b84a731c030

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-30 16:29:03 +0100

      Commit message:


	  
		
 comapre_pk() issue fixed by using echo=FALSE
 

    

  
    

      Package: MetaProViz

      Commit: 9f366874261ae3f9f8a388879d5126bcc472b350

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-30 16:22:13 +0100

      Commit message:


	  
		
 Added second image for sample-metadata vignette
 

    

  
    

      Package: MetaProViz

      Commit: 68ee2662303ad93b1f58d4dff42e6be37699280a

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-30 16:03:51 +0100

      Commit message:


	  
		
 Create sample-metadata.Rmd_compare-pk chunk.svg
 

    

  
    

      Package: MetaProViz

      Commit: 5fc6a48c8eaaa7e4b4f9ac99287a06b59427d8d6

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-30 16:03:47 +0100

      Commit message:


	  
		
 Added eval=FALSE to sample-metadata.Rmd
 

    

  
    

      Package: MetaProViz

      Commit: a2d0eb1c59e68eb30e01f26d8d3d3aebc768cf82

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-30 10:11:01 +0100

      Commit message:


	  
		
 Added some more details for the se object
 

    

  
    

      Package: MetaProViz

      Commit: 81391cac2a34311cc97a078099eda9bc7e1093f0

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-29 18:53:01 +0100

      Commit message:


	  
		
 Bump version: 3.99.10 → 3.99.11
 

    

  
    

      Package: MetaProViz

      Commit: 78d2a72f48c9e9d88d08e0c111b285c63188fa5f

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-29 18:52:54 +0100

      Commit message:


	  
		
 a bunch of minor formatting
 

    

  
    

      Package: MetaProViz

      Commit: 740d2842688db2d2100fc88e5e304eddbd1ab228

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-29 18:00:46 +0100

      Commit message:


	  
		
 removed all `Suppress(Warnings|Messages)`
 

    

  
    

      Package: MetaProViz

      Commit: 4121bdd2dc29debe38510680d8b9ad72d0457f22

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-29 15:34:48 +0100

      Commit message:


	  
		
 `dma`: removed unused code
 

    

  
    

      Package: MetaProViz

      Commit: 472bf889dffd218607497428726ff20b8776d11d

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-29 15:16:43 +0100

      Commit message:


	  
		
 `DiffMetAn`: refactored messages to make them less ugly, and also to address NOTE `Avoid the use of "paste" in condition signals`
 

    

  
    

      Package: MetaProViz

      Commit: fbd9f964b302bc4ccef8fefe9e9ec0a6850dd232

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-29 14:34:14 +0100

      Commit message:


	  
		
 replaced newly introduced `1:...` with `seq_len(...)`
 

    

  
    

      Package: MetaProViz

      Commit: 8976ac946dadbcc989773db4afe0767d18d3bae1

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-29 14:13:14 +0100

      Commit message:


	  
		
 removed `<<-` leftover from some debugging works
 

    

  
    

      Package: MetaProViz

      Commit: 66c6674843301dcf1eda88a1c6e523b4685ffd72

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-29 13:51:08 +0100

      Commit message:


	  
		
 `NEWS`: filled past history based on GitHub Releases page
 

    

  
    

      Package: MetaProViz

      Commit: 4599afeb0b9f93ea26329f044c664d6311b19529

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 11:08:01 +0100

      Commit message:


	  
		
 updated documentation
 

    

  
    

      Package: MetaProViz

      Commit: 76b2380e09a7e8c0090a33afb9ded92f760e8db5

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 11:07:50 +0100

      Commit message:


	  
		
 added S4Vectors as dependency in description
 

    

  
    

      Package: MetaProViz

      Commit: 792c9f5fe257248e85bfb5f736583c1c84b04efb

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 11:07:35 +0100

      Commit message:


	  
		
 updated documentation of helper process_se
 

    

  
    

      Package: MetaProViz

      Commit: 25ab6e2b6fb5bc9c750b9bff41cd43c37a2620d0

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 11:07:12 +0100

      Commit message:


	  
		
 added importFrom updates in processing, replicate_sum, pool_estimation
 

    

  
    

      Package: MetaProViz

      Commit: 093e8b1d23f388f64da31d063a863eb31b791d41

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:54:33 +0100

      Commit message:


	  
		
 Update viz_superplot.Rd
 

    

  
    

      Package: MetaProViz

      Commit: de3da01e6e7411f21e9aeafe736f67178180e680

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:54:28 +0100

      Commit message:


	  
		
 enabled se object as input default for viz_superplot()
 

    

  
    

      Package: MetaProViz

      Commit: 7f5c5941eefc6d3d0d1ca1c02be3082f92d5fb4c

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:45:35 +0100

      Commit message:


	  
		
 updated documentation
 

    

  
    

      Package: MetaProViz

      Commit: e8b558287de381228be5fc7508e1827fb60b102e

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:45:10 +0100

      Commit message:


	  
		
 enabled se object input as default for viz_pca
 

    

  
    

      Package: MetaProViz

      Commit: 2e552461faaf532e8a2a11ab0f178bada7868641

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:38:59 +0100

      Commit message:


	  
		
 updated documentation
 

    

  
    

      Package: MetaProViz

      Commit: 7b4c2044a26ad22d3e7e8ad56c497a89eeff0767

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:38:49 +0100

      Commit message:


	  
		
 typo in parameter description of dma
 

    

  
    

      Package: MetaProViz

      Commit: dd48a4aa6d714c414dc585edf302550327b44b3c

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:38:37 +0100

      Commit message:


	  
		
 enabled se object input as default for viz_heatmap
 

    

  
    

      Package: MetaProViz

      Commit: 4b4ac08283d584232c4355e0777d50d5b9bd4b1d

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:26:14 +0100

      Commit message:


	  
		
 updated documentation
 

    

  
    

      Package: MetaProViz

      Commit: 5aef425a5774b01fddbc2dbe8f3626af44ff598f

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:26:05 +0100

      Commit message:


	  
		
 changed typo in parameter description
 

    

  
    

      Package: MetaProViz

      Commit: 86006fdf01a23be1915e6d53ceb8c8637c65c401

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:25:50 +0100

      Commit message:


	  
		
 added se object input as default
 

    

  
    

      Package: MetaProViz

      Commit: 7fedbfed17798e8bcfedfc22163b1609322e36b8

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:13:29 +0100

      Commit message:


	  
		
 updates documentation
 

    

  
    

      Package: MetaProViz

      Commit: 18f3b65d5962a458bc4d1ba812c935855033cae2

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:13:01 +0100

      Commit message:


	  
		
 enables se object input as default for metadata analysis
 

    

  
    

      Package: MetaProViz

      Commit: e5b4a8a00893f7e33dd6e92cfebf2a181fc0a34b

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:07:55 +0100

      Commit message:


	  
		
 aded tissue_norm_se to ToyData description
 

    

  
    

      Package: MetaProViz

      Commit: 454b459c79981fed016466396e3f8ef5ca120679

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 10:07:38 +0100

      Commit message:


	  
		
 Create tissue_norm_se.rda
 

    

  
    

      Package: MetaProViz

      Commit: b56ce2b43b798e32c1879fe3f44d2fcd394e3b64

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 09:27:09 +0100

      Commit message:


	  
		
 Update dma.Rd
 

    

  
    

      Package: MetaProViz

      Commit: 586532d9487990fb64dc7391ec1e3e030b43df29

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 09:27:02 +0100

      Commit message:


	  
		
 Aded se object input to dma()
 

    

  
    

      Package: MetaProViz

      Commit: a98a4fa151d73ec291eaebbf96f356265bd52714

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 08:59:12 +0100

      Commit message:


	  
		
 updated documentation for replicate_sum()
 

    

  
    

      Package: MetaProViz

      Commit: ee46b3faec76b48a4837da37f35c92f4fb1da13f

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 08:56:40 +0100

      Commit message:


	  
		
 Finished the export of the SE in pool_estimation
 

    

  
    

      Package: MetaProViz

      Commit: 6abbeb3d06b73175b6826b449c38d18171b9032f

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 08:56:12 +0100

      Commit message:


	  
		
 Extended Se helper to set DFs to NULL if they are empty.
 

    

  
    

      Package: MetaProViz

      Commit: f5fc33b72c727644eac94485820fa7c3f5b3a3fd

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-29 08:20:20 +0100

      Commit message:


	  
		
 Added rownames to se output of replicate_sum() and shortened example
 

    

  
    

      Package: MetaProViz

      Commit: f3bca9757246ea3a9ba9560eb9a242aa3bf8ad7d

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 17:03:08 +0100

      Commit message:


	  
		
 updated documentation
 

    

  
    

      Package: MetaProViz

      Commit: dc2fef77ccadb18510306edc4028f428d7532d65

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 17:02:34 +0100

      Commit message:


	  
		
 Added se object to pool_estimation()
 

    

  
    

      Package: MetaProViz

      Commit: 6ece920ca3ff923d984f331804ae9f766f844856

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 17:02:13 +0100

      Commit message:


	  
		
 updated example data for intracell_raw_se
 

    

  
    

      Package: MetaProViz

      Commit: de2cb903d1d66c0554b10b247833f7a9c422bbf0

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 16:19:36 +0100

      Commit message:


	  
		
 Allowed se onject input/output for replicate_sum()
 

    

  
    

      Package: MetaProViz

      Commit: 2dde802b05630829ca142da06b986b919dcaafbd

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 16:00:43 +0100

      Commit message:


	  
		
 Updated documentation
 

    

  
    

      Package: MetaProViz

      Commit: c110f3949388aa7f1f9756d156d5f41dc30d3a07

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 15:59:45 +0100

      Commit message:


	  
		
 Used the helper function in processing
 

    

  
    

      Package: MetaProViz

      Commit: 6ce85c629b73dac6d07c467d92be5a364fbc5260

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 15:59:35 +0100

      Commit message:


	  
		
 Created helper function to unpack se experiments for our functions
 

    

  
    

      Package: MetaProViz

      Commit: df73c9976b451982eb77c8f2b57402122d231e66

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 15:59:05 +0100

      Commit message:


	  
		
 Update intracell_raw_se.rda
 

    

  
    

      Package: MetaProViz

      Commit: bb174d6224bc649b91069f6e29b3cbfa6eb87570

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 15:26:37 +0100

      Commit message:


	  
		
 updated processing parameters documentation
 

    

  
    

      Package: MetaProViz

      Commit: d3dab295d2e2d2a8294136f5ec4bcdc87cf2d365

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 15:26:06 +0100

      Commit message:


	  
		
 Updated parameter default
 

    

  
    

      Package: MetaProViz

      Commit: a25863c60e7e7a6835fd4a983ff257739c9f0c38

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 15:09:54 +0100

      Commit message:


	  
		
 updated man
 

    

  
    

      Package: MetaProViz

      Commit: 6e5e009cf60c8cedbd3996183d0ccee92ee6c6d7

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 14:59:40 +0100

      Commit message:


	  
		
 load using data()
 

    

  
    

      Package: MetaProViz

      Commit: c8d04c01173fdde21377b24e57caecf92cfb04a7

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 14:51:50 +0100

      Commit message:


	  
		
 added an se file toydata for @example
 

    

  
    

      Package: MetaProViz

      Commit: 39560ad843cd61f3b0946c20f467f0f7433a807a

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 14:51:34 +0100

      Commit message:


	  
		
 Added example, and code to allow summarizedExperiment input
 

    

  
    

      Package: MetaProViz

      Commit: 1950bea2295245d89717897e274cc058ddf10d36

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-10-28 14:51:13 +0100

      Commit message:


	  
		
 Added SummarizedExperiment as dependency
 

    

  
    

      Package: MetaProViz

      Commit: 48def15677fb08c0737a64e02e5eb0cbf75b4188

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-28 04:49:25 +0100

      Commit message:


	  
		
 Bump version: 3.99.9 → 3.99.10
 

    

  
    

      Package: MetaProViz

      Commit: 341612d5445c1def1813c7eae73b75de181d023c

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-28 04:49:21 +0100

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: 81fb78a0d1bd87fc120e4f8b8ba5e7a70ae0abba

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-28 04:49:11 +0100

      Commit message:


	  
		
 some more formatting issues fixed
 

    

  
    

      Package: MetaProViz

      Commit: 645924151d4ec744896ca9f8d211a5486b356834

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-28 03:40:16 +0100

      Commit message:


	  
		
 `mpv_shapiro`: return `NA` where `shapiro.test` fails due to no variance in one of the variables
 

    

  
    

      Package: MetaProViz

      Commit: cc91700cf723a87f6f6abed4d8a285daacf56aea

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-28 02:49:13 +0100

      Commit message:


	  
		
 Bump version: 3.99.8 → 3.99.9
 

    

  
    

      Package: MetaProViz

      Commit: 97c7dae3fdebb61a2b3c160f29a3f15887360e0c

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-28 02:47:45 +0100

      Commit message:


	  
		
 chunk names for `quick-start` vignette + removed duplicate eval/echo chunks
 

    

  
    

      Package: MetaProViz

      Commit: 0dbbaea3d6236f41a37b952f9cac1eec945e7b5f

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-28 02:31:53 +0100

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: 4a70dab0af4ada74f05f6dae77313bee2b4d7189

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-28 02:31:26 +0100

      Commit message:


	  
		
 formatting changes to address BiocCheck notes and for readability
 

    

  
    

      Package: MetaProViz

      Commit: 64587fcde421a2d67f71a01a0a3c3166698d9b87

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-27 16:44:31 +0100

      Commit message:


	  
		
 normalized indentation (4 spaces)
 

    

  
    

      Package: MetaProViz

      Commit: 5a9f86a73b8c7cdc7263412da5f6f47da6ee02e2

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-27 16:22:48 +0100

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: 3bf465c66fe0dec5600a7fb6d335b9cab269f6ae

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-27 16:22:38 +0100

      Commit message:


	  
		
 `R code`: address `1:...` → `seq_len(...)`, `suppressMessages/Warnings`, `paste` in condition messages and other `BiocCheck` notes
 

    

  
    

      Package: MetaProViz

      Commit: a9ce991849a8de8d608a01baf477ae3786951714

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-27 16:21:14 +0100

      Commit message:


	  
		
 `vignettes`: chunk names
 

    

  
    

      Package: MetaProViz

      Commit: 4a97fd9db590f51d1c40e668e2b1434739484d7c

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-27 16:20:31 +0100

      Commit message:


	  
		
 `DESCRIPTION`: added `Clustering` and `Pathways` to `BiocViews`
 

    

  
    

      Package: MetaProViz

      Commit: a9cde62a824d76d11683c6e39d8c2d4fcc2beb4f

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 22:19:18 +0100

      Commit message:


	  
		
 `DESCRIPTION`: added `fnd` role to Christina
 

    

  
    

      Package: MetaProViz

      Commit: 39ef5436a492cae7c73658d79086dc541fe99f90

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 22:07:18 +0100

      Commit message:


	  
		
 removed some `MetaProViz:::` and removed stray line with `equivalent_features`
 

    

  
    

      Package: MetaProViz

      Commit: e9852e07b287ebe5c17e882b6a9fc91d2fda6962

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 21:55:51 +0100

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: b71f4f13120a84979b7d7df7901767f3820d6291

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 21:55:32 +0100

      Commit message:


	  
		
 addressed remaining undeclared NSE variables and missing imports
 

    

  
    

      Package: MetaProViz

      Commit: fa8ba31f979f8e5146c699918347190ab55837e6

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 21:23:23 +0100

      Commit message:


	  
		
 `viz_superplot`: updated internal func name `aov` → `mpv_aov`
 

    

  
    

      Package: MetaProViz

      Commit: 7c6f038aaddd5f71141fdddb6c8eb30c3a2825fb

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 21:21:02 +0100

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: 257dfc3d54063cee77caf36e1d800a32ebfbbcb5

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 21:18:20 +0100

      Commit message:


	  
		
 addressed remaining undeclared NSE variables and missing imports
 

    

  
    

      Package: MetaProViz

      Commit: e61d45635db3973bc1d53135ef3e54a56e3ce079

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 20:42:46 +0100

      Commit message:


	  
		
 `viz_superplot`: do not override `sd`, it is from `stats`
 

    

  
    

      Package: MetaProViz

      Commit: ff58f5d51c1f83110c2202620a9698b5506a75e9

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 19:38:06 +0100

      Commit message:


	  
		
 Bump version: 3.99.7 → 3.99.8
 

    

  
    

      Package: MetaProViz

      Commit: d0270aa5f3fc553152e8667e31d9a2d526905a15

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 19:37:50 +0100

      Commit message:


	  
		
 addressed partial argument match cases
 

    

  
    

      Package: MetaProViz

      Commit: d11da8423e56da7bd57f6ddb8233a6f998aee8cc

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 19:35:07 +0100

      Commit message:


	  
		
 addressed function and variable name chaos in `DMA.R`
 

    

  
    

      Package: MetaProViz

      Commit: 401ec38b8390cefead0a3d4e8a711ecfcaa5d2db

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 19:27:42 +0100

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: 73f53506c8ba5b7993562b2331a3f7dcc0c83c6f

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 19:27:31 +0100

      Commit message:


	  
		
 added NSE vs R CMD check variable declarations + missing imports to address "no visible binding/func def" notes
 

    

  
    

      Package: MetaProViz

      Commit: 487a8c4fa810cf26338fab91c4814d151dc38713

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 18:26:20 +0100

      Commit message:


	  
		
 `vignettes`: removed duplicate chunks with displayed code + scrollable plots
 

    

  
    

      Package: MetaProViz

      Commit: 4d2e01b55e787945c8da6e1ea1eb00e1e29f620e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 17:58:40 +0100

      Commit message:


	  
		
 static figure used in `readme`
 

    

  
    

      Package: MetaProViz

      Commit: 7bba24cac74ece73b600e589b6ab59750ed42723

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 17:57:37 +0100

      Commit message:


	  
		
 removed old `README.Rmd`
 

    

  
    

      Package: MetaProViz

      Commit: df4f5e576fc14ce5765110c94b0c0eaa47a8431b

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 17:57:27 +0100

      Commit message:


	  
		
 `readme`: use a simple `md` file, do not generate from `Rmd`
 

    

  
    

      Package: MetaProViz

      Commit: 7d0c78ddb6d45a91c1c0eaf5d3d7adb4117266aa

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 17:56:41 +0100

      Commit message:


	  
		
 `rbuildignore`: readme file backups
 

    

  
    

      Package: MetaProViz

      Commit: 03411ad72ed001a64dc904d1f2b01a72ddbee68e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 17:56:22 +0100

      Commit message:


	  
		
 fixed figure generating for the readme
 

    

  
    

      Package: MetaProViz

      Commit: 7313a25e3734c59fa9917d76258ca780208c07ad

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 17:39:11 +0100

      Commit message:


	  
		
 removed unused imports `SummarizedExepriment` and `cosmosR`
 

    

  
    

      Package: MetaProViz

      Commit: 81968f4cb37911f136457e7dc53faf51efe93085

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 17:31:58 +0100

      Commit message:


	  
		
 `viz_upset`: emmit message when rendering fails instead of crashing
 

    

  
    

      Package: MetaProViz

      Commit: 4399bc919511b24da03ca0f9ca48562c80d031cc

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-26 17:30:55 +0100

      Commit message:


	  
		
 bypass `ggsave` with `ComplexUpset` plots
 

    

  
    

      Package: MetaProViz

      Commit: 48a24a6e61bdc2578e0f91ed9e7fbd52a9738f65

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 22:29:55 +0200

      Commit message:


	  
		
 `viz_upset`: removed `axis.text.y` from set sizes plot
 

    

  
    

      Package: MetaProViz

      Commit: 2f5d6416305dfb656aa665c2aa18e53df8d48475

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 22:03:42 +0200

      Commit message:


	  
		
 `viz_upset`: removed `axis.text.x` from intersection size plot
 

    

  
    

      Package: MetaProViz

      Commit: 23ee79814e411ad6b76834c9ad83b87e9a420cc2

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 20:30:09 +0200

      Commit message:


	  
		
 `vignettes`: removed leading colon in front of some `viz_*` function calls
 

    

  
    

      Package: MetaProViz

      Commit: e1c27796d16baf94680cc14a84907c06dbcacce2

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 19:52:41 +0200

      Commit message:


	  
		
 Merge branch 'devel'
 

    

  
    

      Package: MetaProViz

      Commit: fa296c50edfffbb45c74db75e14fbc8046056c23

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 19:52:31 +0200

      Commit message:


	  
		
 `vignettes`: fixed calls to internal functions `plot_grob_*` (not sure why we have those in vignettes)
 

    

  
    

      Package: MetaProViz

      Commit: 0b9ba11451c876c7dc7e3a3d120e535d492dfe30

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 19:23:55 +0200

      Commit message:


	  
		
 Merge branch 'devel'
 

    

  
    

      Package: MetaProViz

      Commit: 9185ba6f15a010f47a16b7128d32499b72b524ba

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 19:23:48 +0200

      Commit message:


	  
		
 Bump version: 3.99.6 → 3.99.7
 

    

  
    

      Package: MetaProViz

      Commit: 3ad9fdac24ab3e1f5285c52d48f89054cd8c088f

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 19:12:35 +0200

      Commit message:


	  
		
 `vignettes`: set output to `BiocStyle::html_document`
 

    

  
    

      Package: MetaProViz

      Commit: cbada7f6aab4f25a7efc00fa5db4403d65f45785

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 19:01:58 +0200

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: 45e31d0c9f9f226a279b59214a1600df21efcf86

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 19:01:40 +0200

      Commit message:


	  
		
 `mca_core`: `data` call in docstring example
 

    

  
    

      Package: MetaProViz

      Commit: 61c82570e3c3e92fd1aab5ca9593058bb3bebc34

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 18:49:46 +0200

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: 9d014354d4d76b8a6af9891871f2d9791d65f857

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 18:49:35 +0200

      Commit message:


	  
		
 `data` call in doc example of `checkmatch_pk_to_data`
 

    

  
    

      Package: MetaProViz

      Commit: 596900ba974d33975e79f4921b0ae5c280fb1f27

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 18:24:43 +0200

      Commit message:


	  
		
 Bump version: 3.99.5 → 3.99.6
 

    

  
    

      Package: MetaProViz

      Commit: 7cef3a4a84a44bc5c9a50c148aa21b9d7777ff26

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 18:24:26 +0200

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: 7f24bea9c436253cfed1734b9bcd5764c9404704

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 18:24:04 +0200

      Commit message:


	  
		
 `data()` calls in docstring examples and R code since we have to disable `LazyData`
 

    

  
    

      Package: MetaProViz

      Commit: f3132c4cfbcc3cc2d4ef77e6b79f57f58281d559

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-25 18:08:53 +0200

      Commit message:


	  
		
 `test-check_param`: `data()` call since `LazyData` is disabled
 

    

  
    

      Package: MetaProViz

      Commit: c7fecc8e2d5c9541e7741ae25abb156f0e700525

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-24 22:07:21 +0200

      Commit message:


	  
		
 added `data()` calls to vignettes since we had to disable `LazyData`
 

    

  
    

      Package: MetaProViz

      Commit: 397732e4d3636ee88b5c5a0a624049622d2dea83

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-24 21:45:49 +0200

      Commit message:


	  
		
 Bump version: 3.99.4 → 3.99.5
 

    

  
    

      Package: MetaProViz

      Commit: 8ff1f1bf9a2363c1d0483eeb1d7704bb43346858

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-24 21:45:23 +0200

      Commit message:


	  
		
 moved figure code from `README.Rmd` to `inst/scripts/readme-figure.R`
 

    

  
    

      Package: MetaProViz

      Commit: 0e6249532c77b31a5a6f5478a29c5f37a942b77b

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-24 21:06:38 +0200

      Commit message:


	  
		
 removed `MetaProViz::` from vignette code
 

    

  
    

      Package: MetaProViz

      Commit: 9a1343a235879a4aba36cd683ec774394d757765

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-24 21:02:55 +0200

      Commit message:


	  
		
 fixed `.bumpversion.cfg` and `omnipathr-log` in `.Rbuildignore`
 

    

  
    

      Package: MetaProViz

      Commit: d11fa5da6e0832ea281feb02bb3bcdebab97ba1b

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-24 21:00:09 +0200

      Commit message:


	  
		
 created `NEWS.md`
 

    

  
    

      Package: MetaProViz

      Commit: 58436c4f3d5041e172bc74bf55568eaf74fd3413

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-24 20:58:04 +0200

      Commit message:


	  
		
 `DESCRIPTION`: set `LazyData` to `false`; added `Software` to `BiocViews`
 

    

  
    

      Package: MetaProViz

      Commit: 021af0c728cfe594b230fc499938a4d72a89020d

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-24 20:56:58 +0200

      Commit message:


	  
		
 removed `eval=FALSE` chunk from `README.Rmd`
 

    

  
    

      Package: MetaProViz

      Commit: da67a0e4aacf63082e1f4b17574f25bee92a8cce

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-24 20:46:19 +0200

      Commit message:


	  
		
 moved `_pkgdown.yml` under `pkgdown/`
 

    

  
    

      Package: MetaProViz

      Commit: 2f3d7d6dde539bb26cb79df7372c74b0a89a8bfc

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-24 19:46:21 +0200

      Commit message:


	  
		
 `github ci`: install `EnhancedVolcano` in build & check workflow: it is not yet BioC 3.22, will see if it gets removed
 

    

  
    

      Package: MetaProViz

      Commit: 6bf081a116154387739ee2de2609672758d3585b

      Author:  jannikfranken <jannik8513@gmail.com> 

      Date: 2025-10-24 13:03:59 +0100

      Commit message:


	  
		
 reverting last commit
 

    

  
    

      Package: MetaProViz

      Commit: ce82bac24f538faac99b81994d2774f8ab70cfb3

      Author:  jannikfranken <jannik8513@gmail.com> 

      Date: 2025-10-24 12:48:19 +0100

      Commit message:


	  
		
 test explicit installation of EnhancedVolcano
 

    

  
    

      Package: MetaProViz

      Commit: dfedddc3a18059a1125fb3e47673b4791ae5dec4

      Author:  jannikfranken <jannik8513@gmail.com> 

      Date: 2025-10-24 11:31:24 +0100

      Commit message:


	  
		
 formatting
 

    

  
    

      Package: MetaProViz

      Commit: 5403e5e4981b3366025d6f0057bd977337b4900a

      Author:  jannikfranken <jannik8513@gmail.com> 

      Date: 2025-10-23 17:44:08 +0100

      Commit message:


	  
		
 code refactoring of count_id function
 

    

  
    

      Package: MetaProViz

      Commit: 8b6b3bb03a33e69fd57750ff789b136b1082bdc5

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-09 23:04:08 +0200

      Commit message:


	  
		
 `pkgdown`: copied over bibliography to `vignettes/pkgdown`
 

    

  
    

      Package: MetaProViz

      Commit: 75125aabfe630c75fd3eee1c0514461ace735534

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-09 22:09:25 +0200

      Commit message:


	  
		
 `pkgdown`: attempt to fix articles menu item definitions
 

    

  
    

      Package: MetaProViz

      Commit: 242f0ce81b5b0091ff6bed7ffd028cbe7fadcf50

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-09 21:38:08 +0200

      Commit message:


	  
		
 `pkgdown`: fixed yaml formatting issue
 

    

  
    

      Package: BiocVersion

      Commit: 252d7c8f03a39a9b83f6de7e9dbf9a5ee6584365

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

      Date: 2025-10-30 11:29:14 -0400

      Commit message:


	  
		
 version bump 3.23.1
 

    

  
    

      Package: BiocVersion

      Commit: d18b787362277e2aee51497e93641fcbdb6a0b7f

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

      Date: 2025-10-30 11:29:12 -0400

      Commit message:


	  
		
 bump R version requirement
 

    

  
    

      Package: ggtree

      Commit: af2f26ce0d73af29ee6bd627b032af4c87c5760e

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-10-30 22:26:19 +0800

      Commit message:


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

    

  
    

      Package: ggtree

      Commit: 848117f4035fb4ba3d70d3c903fd03c3c624e6de

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-10-30 22:18:04 +0800

      Commit message:


	  
		
 Merge pull request #677 from xiangpin/geom_strip_update

Geom strip update 

    

  
    

      Package: ggtree

      Commit: 08392bcac5ed9c34215fec4cfeeb39e1f26faba1

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-10-29 20:58:18 +0800

      Commit message:


	  
		
 update for striplabel object
 

    

  
    

      Package: ggtree

      Commit: 6e8cdebebd7ff0c43a69336897168f018b15e695

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-10-29 20:51:27 +0800

      Commit message:


	  
		
 typo
 

    

  
    

      Package: ggtree

      Commit: 3c718256c39a0481a683b88636bb2b339c300d68

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-10-29 11:51:10 +0800

      Commit message:


	  
		
 update geom_strip
 

    

  
    

      Package: ggtree

      Commit: 7389dfac6c4c63237d9357561e0fe5076cf70cdb

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-10-30 22:22:26 +0800

      Commit message:


	  
		
 bug fixed
 

    

  
    

      Package: DMRcaller

      Commit: 9bc02194dd099645f2de36a85166e9708f2a7993

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

      Date: 2025-10-30 09:44:07 -0400

      Commit message:


	  
		
 Update NEWS

 - please format news correctly
 

    

  
    

      Package: plaid

      Commit: 4214e5c2e9701abf46e7409217c7ae8c1593e427

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-10-30 11:08:49 +0100

      Commit message:


	  
		
 add test coverage
 

    

  
    

      Package: gDRstyle

      Commit: 25af3a58eb47fdef2de53673957aeaccf4825177

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

      Date: 2025-10-30 10:33:37 +0100

      Commit message:


	  
		
 Merge pull request #94 from gdrplatform/GDR-3164

Gdr 3164 

    

  
    

      Package: gDRstyle

      Commit: 7c5e90196c4a6d56dc313c77bf1361c7aece6de0

      Author:  Arek Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2025-10-30 07:15:15 +0100

      Commit message:


	  
		
 chore: bump v+c
 

    

  
    

      Package: gDRutils

      Commit: 4a412dcdde9445bfc22df02ad8bae48ec7ffbb09

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

      Date: 2025-10-30 10:33:15 +0100

      Commit message:


	  
		
 Merge pull request #175 from gdrplatform/GDR-3164

Gdr 3164 

    

  
    

      Package: gDRutils

      Commit: 78a0036a2af5dff3425091c9ec4a0212b30b2a20

      Author:  Arek Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2025-10-30 07:17:14 +0100

      Commit message:


	  
		
 chore: bump v+c
 

    

  
    

      Package: gDRimport

      Commit: 16632cf8742f5d0dae1d8300ab730d679b41a9ec

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

      Date: 2025-10-30 10:32:55 +0100

      Commit message:


	  
		
 Merge pull request #109 from gdrplatform/GDR-3164

Gdr 3164 

    

  
    

      Package: gDRimport

      Commit: 8b2f59e960b10bc8c024e6888a69970081e87ee0

      Author:  Arek Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2025-10-30 07:21:49 +0100

      Commit message:


	  
		
 chore: bump v+c
 

    

  
    

      Package: gDRtestData

      Commit: dde35d0a211555c178577accb2b0777ad9164f26

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

      Date: 2025-10-30 10:32:19 +0100

      Commit message:


	  
		
 Merge pull request #73 from gdrplatform/GDR-3164

Gdr 3164 

    

  
    

      Package: gDRtestData

      Commit: 51c3696af4f673e0592370e4eb00305277e2e946

      Author:  Arek Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2025-10-30 07:24:27 +0100

      Commit message:


	  
		
 chore: bump v+c
 

    

  
    

      Package: gDRcore

      Commit: 6b41ab3c89949301491e93c4850bd9da5247e123

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

      Date: 2025-10-30 10:31:59 +0100

      Commit message:


	  
		
 Merge pull request #186 from gdrplatform/GDR-3164

Gdr 3164 

    

  
    

      Package: gDRcore

      Commit: 608a3195b220cfdf3d1adb3d87278b4713e4dc0a

      Author:  Arek Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2025-10-30 07:19:54 +0100

      Commit message:


	  
		
 chore: bump v+c
 

    

  
    

      Package: gDR

      Commit: 9871bb8b277020860c967a6cfbed5075acaaafd3

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

      Date: 2025-10-30 10:31:39 +0100

      Commit message:


	  
		
 Merge pull request #57 from gdrplatform/GDR-3164

Gdr 3164 

    

  
    

      Package: gDR

      Commit: a62acd6e7fa3e2a76e0f2575c2f9e2df1174bf1c

      Author:  Arek Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2025-10-30 08:18:11 +0100

      Commit message:


	  
		
 build: trigger build
 

    

  
    

      Package: gDR

      Commit: dd8b0d85ca408668fb55ef84267f5345ad48c83f

      Author:  Arek Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2025-10-30 07:26:21 +0100

      Commit message:


	  
		
 chore: bump v+c
 

    

  
    

      Package: GenomicFeatures

      Commit: d92f2d08fddfda772940a4ec1e4d50449f05910e

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

      Date: 2025-10-29 23:00:29 -0700

      Commit message:


	  
		
 GenomicFeatures 1.63.1: Remove all defunct functions

After they got formally deprecated in GenomicFeatures in BioC 3.21 and
defunct in BioC 3.22, all the functions that went to txdbmaker in BioC 3.19
are now gone for good.
 

    

  
    

      Package: igblastr

      Commit: 2880899d1422b9b7c26bf7ec10ba7e9c21b9e37c

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

      Date: 2025-10-29 20:02:06 -0700

      Commit message:


	  
		
 update TODO
 

    

  
    

      Package: CBN2Path

      Commit: d38f8865b00b14d27cc272ce2f3821e01506e14a

      Author:  William Choi-Kim <will.choi.kim@gmail.com> 

      Date: 2025-10-29 21:14:05 -0500

      Commit message:


	  
		
 fix maintainers
 

    

  
    

      Package: CBN2Path

      Commit: 6c77e1c71d41cf8bacf986af3c7ed6003d00b591

      Author:  William Choi-Kim <will.choi.kim@gmail.com> 

      Date: 2025-10-29 20:16:43 -0500

      Commit message:


	  
		
 bump
 

    

  
    

      Package: CBN2Path

      Commit: dcca0871fb2ea5f8de27dcdc1e75b5c07ae4746a

      Author:  William Choi-Kim <will.choi.kim@gmail.com> 

      Date: 2025-10-29 20:16:25 -0500

      Commit message:


	  
		
 fix output in vignette
 

    

  
    

      Package: CBN2Path

      Commit: 008ec1140a3f44ae2442698b2b1e625431f37e0c

      Author:  William Choi-Kim <will.choi.kim@gmail.com> 

      Date: 2025-10-29 20:02:41 -0500

      Commit message:


	  
		
 bump
 

    

  
    

      Package: CBN2Path

      Commit: 363638bde89ddd251be8ef15a792f23ba5abf69c

      Author:  William Choi-Kim <will.choi.kim@gmail.com> 

      Date: 2025-10-29 20:02:36 -0500

      Commit message:


	  
		
 fix title
 

    

  
    

      Package: ontoProc

      Commit: a09f239272f1f0b6432299902a6b7d3cb610569d

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-10-29 19:20:08 -0400

      Commit message:


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

    

  
    

      Package: ontoProc

      Commit: f2c1b3f170ce3e23ed97712695fb8309b0888c6d

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-10-29 19:20:08 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 

    

  
    

      Package: ontoProc

      Commit: 8aa7338665702565e010f1d02be2fa37c7ac2d39

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

      Date: 2025-10-08 11:44:19 -0400

      Commit message:


	  
		
 introducing calls to .Defunct, fix vignette
 

    

  
    

      Package: ontoProc

      Commit: 869e2926838d1fc6a1cbda399c406577a31bd2b1

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

      Date: 2025-09-01 14:39:18 +0000

      Commit message:


	  
		
 Replace .Deprecated with .Defunct for specified functions

Co-authored-by: vjcitn <4624066+vjcitn@users.noreply.github.com>
 

    

  
    

      Package: ontoProc

      Commit: 991f8631f7024a7a8c59296926a579a388aa8c3f

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

      Date: 2025-09-01 14:29:52 +0000

      Commit message:


	  
		
 Initial plan 

    

  
    

      Package: BiocCheck

      Commit: 09886edfc32ebe81d0ccf979be47d29d7a014df5

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-10-29 19:20:08 -0400

      Commit message:


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

    

  
    

      Package: BiocCheck

      Commit: 79a36192a2e7be561fed684325f5a7474297f601

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-10-29 19:20:08 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 

    

  
    

      Package: BiocCheck

      Commit: 9a9c0c117c7f4689bab50ccf4f9c498be4f3b265

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

      Date: 2025-10-14 12:27:27 -0400

      Commit message:


	  
		
 version bump 1.45.20
 

    

  
    

      Package: BiocCheck

      Commit: 2ae2a644bcf8306d1272558160fa5415bb7e73fd

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

      Date: 2025-10-14 12:27:25 -0400

      Commit message:


	  
		
 add chunk labels
 

    

  
    

      Package: BiocCheck

      Commit: 6c045d7ec60703e81c1d706663ece0d748ff8ff4

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

      Date: 2025-10-14 12:19:29 -0400

      Commit message:


	  
		
 version bump 1.45.19
 

    

  
    

      Package: BiocCheck

      Commit: e08267bf500a457632e52946c1a58c452d951250

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

      Date: 2025-10-14 12:19:26 -0400

      Commit message:


	  
		
 update checkFormatting recommendation
 

    

  
    

      Package: BiocCheck

      Commit: 9f7d48187c16e795c3370ced9dcf9c5186db9e3b

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

      Date: 2025-08-26 17:26:27 -0400

      Commit message:


	  
		
 version bump 1.45.18
 

    

  
    

      Package: BiocCheck

      Commit: f29991f0e5493988c17c142a6b929ac72ebb9f5d

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

      Date: 2025-08-26 17:25:32 -0400

      Commit message:


	  
		
 use .RdTags from tools internally
 

    

  
    

      Package: BiocCheck

      Commit: 51f668194d788ef88dbcdde6326133196bc617b2

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

      Date: 2025-08-26 17:04:59 -0400

      Commit message:


	  
		
 minor formatting
 

    

  
    

      Package: BiocCheck

      Commit: bf08c5162814a5ab85f025bc69619c292063f42f

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

      Date: 2025-08-26 15:24:03 -0400

      Commit message:


	  
		
 simplify checkUsageOfDont
 

    

  
    

      Package: BiocCheck

      Commit: 0c2774a92cb0503016d574654b9e1b8dcc258a0c

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

      Date: 2025-08-26 14:36:26 -0400

      Commit message:


	  
		
 simplify operation in checkExportsAreDocumented
 

    

  
    

      Package: BiocCheck

      Commit: 76717748d312728f469172f217a9431fae6fe480

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

      Date: 2025-08-26 11:40:41 -0400

      Commit message:


	  
		
 version bump 1.45.17
 

    

  
    

      Package: BiocCheck

      Commit: e5c74a53806f1e8c3736c683b91ee81902f31f92

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

      Date: 2025-08-26 11:40:34 -0400

      Commit message:


	  
		
 update docs re --no-check-namespace
 

    

  
    

      Package: BiocCheck

      Commit: 899a2f59e17a71c9bc78aa81385caeba6c9310cc

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

      Date: 2025-08-25 15:35:00 -0400

      Commit message:


	  
		
 version bump 1.45.16
 

    

  
    

      Package: BiocCheck

      Commit: e3fca390e1251206dd58c560243b80d382adf94c

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

      Date: 2025-08-25 15:34:32 -0400

      Commit message:


	  
		
 add note about using BiocCheckGitClone
 

    

  
    

      Package: BiocCheck

      Commit: c60b365351c4ac7bbf4f11211df9fafc8f49828d

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

      Date: 2025-08-25 15:19:58 -0400

      Commit message:


	  
		
 add checkNAMESPACE to BiocCheckGitClone
 

    

  
    

      Package: BiocCheck

      Commit: d30e2e5ef546d8c0a5718647970c9f008d8a24a4

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

      Date: 2025-08-25 14:36:28 -0400

      Commit message:


	  
		
 version bump 1.45.15
 

    

  
    

      Package: BiocCheck

      Commit: 88a7b96e8d28dbbfa2da884cfcfdec3139e26a4f

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

      Date: 2025-08-25 14:36:22 -0400

      Commit message:


	  
		
 add GPL (>= 3) test for checkLicenseForRestrictiveUse
 

    

  
    

      Package: BiocCheck

      Commit: 6d7d744120cbc2ebcf6bb1dbfb62410265b34f78

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

      Date: 2025-08-25 14:20:21 -0400

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: BiocCheck

      Commit: 26999008abedbf15d9bbdf27b077202727c1800e

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

      Date: 2025-08-25 14:04:41 -0400

      Commit message:


	  
		
 version bump 1.45.14
 

    

  
    

      Package: BiocCheck

      Commit: 972b24f7f8b70a13b5ebfd6c50a5524d7e743bec

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

      Date: 2025-08-25 13:53:41 -0400

      Commit message:


	  
		
 add checkNAMESPACE for catch all exportPattern
 

    

  
    

      Package: BiocCheck

      Commit: 304cf4ea27500a7c708329fe134d999af8aab845

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

      Date: 2025-08-25 13:53:15 -0400

      Commit message:


	  
		
 version bump 1.45.13
 

    

  
    

      Package: BiocCheck

      Commit: dc640717763e962fe2cc6aa395ba35a284aa62fb

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-25 19:51:10 +0200

      Commit message:


	  
		
 Sort BiocCheck() options alphabetically in documentation (#229)

 

    

  
    

      Package: AnVIL

      Commit: b498d04e6660e4ce7ea1d504dda5b312c58035f8

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-10-29 19:20:07 -0400

      Commit message:


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

    

  
    

      Package: AnVIL

      Commit: d87ee9cc4182ea9e9d3179939e1037bcfd5e78e5

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-10-29 19:20:07 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 

    

  
    

      Package: AnVIL

      Commit: 1e39a3fe05596973e2552f2408ec7cfe988f5407

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

      Date: 2025-09-22 10:20:32 -0400

      Commit message:


	  
		
 version bump 1.21.10
 

    

  
    

      Package: AnVIL

      Commit: e783cd8e22507678d98f82ee95c571f8aab6762e

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

      Date: 2025-09-22 10:20:30 -0400

      Commit message:


	  
		
 update Dockstore API
 

    

  
    

      Package: AnVIL

      Commit: 62ae1fecc26c92011b1e47c7eea87a3750194256

      Author:  nektos/act <nektos/act@users.noreply.github.com> 

      Date: 2025-09-22 14:07:06 +0000

      Commit message:


	  
		
 Update API
 

    

  
    

      Package: AnVIL

      Commit: 5a3c6094936de699856f9801010ce21a3289fd24

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

      Date: 2025-08-11 11:36:03 -0400

      Commit message:


	  
		
 action uses workflow_dispatch branch
 

    

  
    

      Package: SpiecEasi

      Commit: 18c9537d1f632c34aa4e9e571d8e67503c0c9d75

      Author:  Zachary Kurtz <zdkurtz@gmail.com> 

      Date: 2025-10-29 15:53:57 -0400

      Commit message:


	  
		
 Bump version: 1.99.2 → 1.99.3
 

    

  
    

      Package: SpiecEasi

      Commit: c0c492954e78508cd98a36d206a11ac42e975c63

      Author:  Zachary Kurtz <zdkurtz@gmail.com> 

      Date: 2025-10-29 15:10:30 -0400

      Commit message:


	  
		
 remove unecessary Rbuildignore entries 2
 

    

  
    

      Package: SpiecEasi

      Commit: 39a1340d789cf4f314c27aaf01a4ef7ce8c2ef22

      Author:  Zachary Kurtz <zdkurtz@gmail.com> 

      Date: 2025-10-29 15:10:03 -0400

      Commit message:


	  
		
 remove unecessary Rbuildignore entries
 

    

  
    

      Package: SpiecEasi

      Commit: 933aac0d51bbc9afe6468d3961acd2308bef3f5f

      Author:  Zachary Kurtz <zdkurtz@gmail.com> 

      Date: 2025-10-29 13:48:57 -0400

      Commit message:


	  
		
 fixes and update NEWS
 

    

  
    

      Package: SpiecEasi

      Commit: 14d53ac238972b2e14d34acda7cc9a26a8090ab1

      Author:  Zachary Kurtz <zdkurtz@gmail.com> 

      Date: 2025-10-29 13:42:28 -0400

      Commit message:


	  
		
 address reviewer comments
 

    

  
    

      Package: GXwasR

      Commit: 52839c3e53179d813dc1a3f009c2666062ade386

      Author:  Banabithi Bose <banabithi.bose@gmail.com> 

      Date: 2025-10-29 14:07:14 -0500

      Commit message:


	  
		
 Version bumped.
 

    

  
    

      Package: GXwasR

      Commit: 6b8e873c5b5423e96b213893e4257a401e2dc1c4

      Author:  D Mayer <32186106+the-mayer@users.noreply.github.com> 

      Date: 2025-10-29 13:02:22 -0600

      Commit message:


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

QCsample() Fix

fixes #55 

    

  
    

      Package: GXwasR

      Commit: c5c1bd6a7ec242afb051be9f3d3ff625b02a0f1c

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-28 17:19:52 -0400

      Commit message:


	  
		
 Merge commit 'a3a4d3d648646f7f95a9fc0509ac419ff90e820d'
 

    

  
    

      Package: GXwasR

      Commit: 56c18a698e9fbb609420cd2433b503b058571348

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-28 17:03:05 -0400

      Commit message:


	  
		
 cleanup pathing
 

    

  
    

      Package: GXwasR

      Commit: eadf866f9a02e3d0898090b28459c6606dde4dc9

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-28 17:00:52 -0400

      Commit message:


	  
		
 add test for `het <- NULL`
 

    

  
    

      Package: GXwasR

      Commit: daf8d9ecef705bbd4c56bd3ee2e053c0c63d04d3

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-28 16:30:53 -0400

      Commit message:


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

Co-authored-by: Jacklyn Ashmus <jacklyn-ashmus@users.noreply.github.com>
 

    

  
    

      Package: GXwasR

      Commit: a3a4d3d648646f7f95a9fc0509ac419ff90e820d

      Author:  D Mayer <32186106+the-mayer@users.noreply.github.com> 

      Date: 2025-10-28 11:48:01 -0600

      Commit message:


	  
		
 Merge pull request #58 from boseb/misc-fixes

Fix LaTeX Unicode errors in .Rd documentation 

    

  
    

      Package: GXwasR

      Commit: 90ec31b9244e210cd90f626c0579ffd66a31e679

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-27 17:10:25 -0400

      Commit message:


	  
		
 apply bioc styling
 

    

  
    

      Package: GXwasR

      Commit: f48b470f4b7d2046f6e4175b88842d16ae188748

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-27 17:06:35 -0400

      Commit message:


	  
		
 bioc convention, use FALSE instead of F
 

    

  
    

      Package: GXwasR

      Commit: 9f418165160fd9366d393a05bb09b6c894eded89

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-27 17:04:31 -0400

      Commit message:


	  
		
 remaining rd fixes for pdf manual
 

    

  
    

      Package: GXwasR

      Commit: 90a07c5ca159408a6c70f3a7ebc7277151d10f93

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-27 15:28:36 -0400

      Commit message:


	  
		
 fix equations in PvalComb documentation
 

    

  
    

      Package: GXwasR

      Commit: e1a123b28acfbbb9c8ca7b4e5e507aad5b78290d

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-27 15:10:52 -0400

      Commit message:


	  
		
 GXwas() documentation fixes:
- address LaTeX in equations
 

    

  
    

      Package: GXwasR

      Commit: 3121d14094da480077ba7bcf90ed1089eb9cba56

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-27 14:29:40 -0400

      Commit message:


	  
		
 fix: You can't use `macro parameter character #' in math mode.
 

    

  
    

      Package: GXwasR

      Commit: 258ee070d61af8284cc40b2b357c852c6fef4f00

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-27 14:09:12 -0400

      Commit message:


	  
		
 fix CITATION warning
- replace curly apostrophe with straight (UTF8 compliant)
 

    

  
    

      Package: iscream

      Commit: b1bda1ce7d0ecfd506170a0d8e3c510a72fbb323

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2025-10-29 14:17:07 -0400

      Commit message:


	  
		
 chore(DESCRIPTION): bump version
 

    

  
    

      Package: iscream

      Commit: e860cdce34b791c581649e4bf8d6d39e8572eddd

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2025-10-29 14:07:40 -0400

      Commit message:


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

checking of pkg-config existence makes the whole condition false when
its available and falls into error when using rhtslib with non-empty
$RHTSLIB_CFLAGS
 

    

  
    

      Package: Rhtslib

      Commit: 0dcad2a3b6e818dcc5d763d896c8e8fd88f50d8b

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

      Date: 2025-10-29 11:52:40 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: Seqinfo

      Commit: 17fc74a1922470a86ae999ad33314f34ad7c9abb

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

      Date: 2025-10-29 11:52:20 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: GenomeInfoDb

      Commit: f31cf8b472e426f00a9425752e3c3258fe30c40c

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

      Date: 2025-10-29 11:52:07 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: S4Arrays

      Commit: 6660826fc80007a1f3cbc2e75a5f3c3eee606c3c

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

      Date: 2025-10-29 11:51:51 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: IRanges

      Commit: 167f22b933c30e37902a32b8f632434a3936ec43

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

      Date: 2025-10-29 11:51:39 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: GenomicRanges

      Commit: 1dfb82d3ddf83e1d751be4b42576f0e491611c27

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

      Date: 2025-10-29 11:50:52 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: Biostrings

      Commit: fb3d33011c84a442efde15436b93aca4b7e7c8db

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

      Date: 2025-10-29 11:50:40 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: GenomicAlignments

      Commit: 085e9df7b3aa4f13c5cd31bca06e767fad680b6b

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

      Date: 2025-10-29 11:50:25 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: h5mread

      Commit: 376f55fb8d8e1548e6e48bb89784a820fad662c3

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

      Date: 2025-10-29 11:49:58 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: txdbmaker

      Commit: 9bfc03435c75132d1da54a2a3e6a94a09d824b12

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

      Date: 2025-10-29 11:49:40 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: SummarizedExperiment

      Commit: 7a9787ce769f9e22d5791e6b01a776846eca0ce9

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

      Date: 2025-10-29 11:49:30 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: DelayedArray

      Commit: a1ebb83a81013d3eb14c18d2a516393013c1bfe9

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

      Date: 2025-10-29 11:49:13 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: S4Vectors

      Commit: cead68c81c2e52b2afb148d2e065af70b81108f3

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

      Date: 2025-10-29 11:48:28 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: BiocGenerics

      Commit: 5fcc999682961471c83a0c17e38b8a7f4d42d570

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

      Date: 2025-10-29 11:48:01 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: GenomicFeatures

      Commit: 39d50f6f7b2707e78e0e6170c8859891ad1bab9d

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

      Date: 2025-10-29 11:47:40 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: BSgenome

      Commit: ed2fb5832bf91f7ecea2f79c4daaf39c898eb47f

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

      Date: 2025-10-29 11:47:19 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: BSgenomeForge

      Commit: c7d1729bac87cf0ec7497d769d57d39f1a742dbe

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

      Date: 2025-10-29 11:46:49 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: pwalign

      Commit: a8e536a6decdb3c2aa9ee00301ff3296c57a375d

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

      Date: 2025-10-29 11:46:16 -0700

      Commit message:


	  
		
 update NEWS
 

    

  
  


</div>

</div>