Dear colleagues, Since the release of Bioconductor 3.22 is coming closer (less than four weeks from now), I wanted to ask the following question: My package ?podkat? has been failing on ?taishan? for quite some time already. The reason is that the 'BSgenome.Mmusculus.UCSC.mm10.masked? package is not available on this server. The same is true for many (if not all) BSgenome-derived packages. That is also why some other packages fail, too. Can I expect that this will be fixed before the release or should I simply ignore this error? (I am reluctant to remove the ?Suggests? dependency in my package, since I would have to remove a valuable piece of documentation from the package vignette) Remarks and suggestions are cordially welcome! Thanks and best regards, Ulrich Bodenhofer
[Bioc-devel] BSgenome.* packages on taishan
3 messages · Ulrich Bodenhofer, Robert Castelo, Andres Wokaty
Hi, same experience here with VariantFiltering and BSgenome.Hsapiens.1000genomes.hs37d5: https://bioconductor.org/checkResults/3.22/bioc-LATEST/VariantFiltering/taishan-buildsrc.html robert.
On 3/10/25 09:56, Ulrich Bodenhofer wrote:
Dear colleagues, Since the release of Bioconductor 3.22 is coming closer (less than four weeks from now), I wanted to ask the following question: My package ?podkat? has been failing on ?taishan? for quite some time already. The reason is that the 'BSgenome.Mmusculus.UCSC.mm10.masked? package is not available on this server. The same is true for many (if not all) BSgenome-derived packages. That is also why some other packages fail, too. Can I expect that this will be fixed before the release or should I simply ignore this error? (I am reluctant to remove the ?Suggests? dependency in my package, since I would have to remove a valuable piece of documentation from the package vignette) Remarks and suggestions are cordially welcome! Thanks and best regards, Ulrich Bodenhofer
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Robert Castelo, PhD Associate Professor Dept. of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514
Thanks for raising this issue. I'll reach out to the new maintainer of taishan on the #arm-linux channel. You're welcome to follow the conversation there. Andres Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Robert Castelo via Bioc-devel <bioc-devel at r-project.org>
Sent: Friday, October 3, 2025 8:04 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Cc: Ulrich Bodenhofer <ulrich.bodenhofer at gmail.com>
Subject: Re: [Bioc-devel] BSgenome.* packages on taishan
Sent: Friday, October 3, 2025 8:04 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Cc: Ulrich Bodenhofer <ulrich.bodenhofer at gmail.com>
Subject: Re: [Bioc-devel] BSgenome.* packages on taishan
* This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hi, same experience here with VariantFiltering and BSgenome.Hsapiens.1000genomes.hs37d5: https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.22/bioc-LATEST/VariantFiltering/taishan-buildsrc.html__;!!LRXxDv2l!QNR9irjvQPL4vPz3h0F7F3nUT8b0GlY4vE3UBEH_5vpSdHIz2wg8jvN6OriFKFAeQNtcjcJHDZRGGZIBMcLmxnP0a6wUhNRokQ$ robert. On 3/10/25 09:56, Ulrich Bodenhofer wrote: > Dear colleagues, > > Since the release of Bioconductor 3.22 is coming closer (less than > four weeks from now), I wanted to ask the following question: My > package ?podkat? has been failing on ?taishan? for quite some time > already. The reason is that the 'BSgenome.Mmusculus.UCSC.mm10.masked? > package is not available on this server. The same is true for many (if > not all) BSgenome-derived packages. That is also why some other > packages fail, too. Can I expect that this will be fixed before the > release or should I simply ignore this error? (I am reluctant to > remove the ?Suggests? dependency in my package, since I would have to > remove a valuable piece of documentation from the package vignette) > Remarks and suggestions are cordially welcome! > > Thanks and best regards, > Ulrich Bodenhofer > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!QNR9irjvQPL4vPz3h0F7F3nUT8b0GlY4vE3UBEH_5vpSdHIz2wg8jvN6OriFKFAeQNtcjcJHDZRGGZIBMcLmxnP0a6xiVKJTKg$ -- Robert Castelo, PhD Associate Professor Dept. of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 _______________________________________________ Bioc-devel at r-project.org mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!QNR9irjvQPL4vPz3h0F7F3nUT8b0GlY4vE3UBEH_5vpSdHIz2wg8jvN6OriFKFAeQNtcjcJHDZRGGZIBMcLmxnP0a6xiVKJTKg$