[Bioc-devel] Omada package failing due to removed dependency

2023-06-28 Thread Sokratis Kariotis
Dear Bioconductor team, I received an email that my package "Omada" is failing in release and devel. I had a look and the problem seems to be: *ERROR: dependency ‘clusterCrit’ is not available for package ‘omada’*. So the package clusterCrit was removed. Is there a way I can use a archived version

Re: [Bioc-devel] package failing

2023-06-28 Thread Vincent Carey
Please provide more details in the future. What is the name of the package, which branch of Bioconductor? The packages I can see seem to be in a warning state. * checking Rd \usage sections ... WARNING Documented arguments not in \usage in documentation object 'show,SampleSet-method': ‘...’ F

[Bioc-devel] package failing

2023-06-28 Thread Kathleen Oros Klein
My package is failing, install and build are OK but under check I have timeout. Anyone can help me how to fix this? kathleen [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bio

Re: [Bioc-devel] DNAcopy git push issue

2023-06-28 Thread Venkat Seshan
I saw an error message close to mine mentioned here https://github.com/Bioconductor/bioc_git_transition/issues/30 I cloned the package using ssh and so could not be the cause. On Wed, Jun 28, 2023 at 3:53 PM Venkat Seshan wrote: > I noticed that my prior message was mangled by outlook and so

Re: [Bioc-devel] DNAcopy git push issue

2023-06-28 Thread Venkat Seshan
I noticed that my prior message was mangled by outlook and so resending from gmail. Thanks. I cloned the repo afresh and set up the remote. seshanv@omega0:~/GitRepos/Bioc/DNAcopy$ git remote -v origin g...@github.com:veseshan/DNAcopy.git (fetch) origin g...@github.com:veseshan/DNAcopy.git

Re: [Bioc-devel] List of Deprecated Packages for Bioc3.18

2023-06-28 Thread Kern, Lori
The motifbreakR maintainers have reached out and it will not be deprecated. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From:

[Bioc-devel] RSS feeds not updating for some packages

2023-06-28 Thread Stephanie Gogarten
Hi, One of my packages currently has an error in devel: https://bioconductor.org/checkResults/devel/bioc-LATEST/GWASTools/ However, the RSS feed does not show this error and was last updated in April 2022: http://bioconductor.org/rss/build/packages/GWASTools.rss I spot-checked a few other packag

Re: [Bioc-devel] DNAcopy git push issue

2023-06-28 Thread Kern, Lori
I'm not sure why the upstream has a mailto:​ at the start but perhaps try resetting upstream to `g...@git.bioconductor.org:packages/DNAcopy.git` The credentials are set up correctly. Perhaps also adding a new ssh key to the BiocCredentials

Re: [Bioc-devel] Request for undeprecation of motifbreakR

2023-06-28 Thread Kern, Lori
Please also make sure that an active email is in the maintainer field of the DESCRIPTION; this is the email we use for communication. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffa

Re: [Bioc-devel] Request for undeprecation of motifbreakR

2023-06-28 Thread Kern, Lori
Thank you. Yes we can undeprecate the package. Please remember to also push your changes to RELEASE_3_17 branch as the package is also failing there. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlt

[Bioc-devel] DNAcopy git push issue

2023-06-28 Thread Seshan, Venkatraman
After a long time of not needing any change to the package I tried to push changes upstream and got the following error: seshanv@omega0:~/GitRepos/DNAcopy$ git push upstream devel FATAL: W any packages/DNAcopy mailto:venka...@mskcc.org DENIED by fallthru (or you mis-spelled the reponame) fatal: C