Message-ID: <IA0PR14MB6416624C94EC74E9A3AC7E1DDAE4A@IA0PR14MB6416.namprd14.prod.outlook.com>
Date: 2025-10-03T16:17:56Z
From: Andres Wokaty
Subject: [Bioc-devel] BSgenome.* packages on taishan
In-Reply-To: <aef7eded-0886-4cfd-8de9-2e0a6da190c8@upf.edu>
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
* 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
>
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--
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
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