Hi Sarvesh, Regarding seqArchR, I recommend using reticulate to manage the Python dependency since seqArchR already depends on it and is using it to source a Python file, but it currently requires a system-wide install. This will give you more control over its configuration as the maintainer and reduce user's burden to set up the package. Have a look at https://rstudio.github.io/reticulate/reference/py_require.html.
Andres Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team ________________________________ From: Bioc-devel <[email protected]> on behalf of Sarvesh Nikumbh <[email protected]> Sent: Monday, October 13, 2025 12:22 PM To: Bioc-devel <[email protected]> Subject: Re: [Bioc-devel] List of Deprecated Packages for Bioconductor 3.22 * This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * Hi Bioc team, Understand that problems in seqArchR and seqArchRplus weren't addressed in time so they are facing deprecation. I had lost access to my github account, but now I have regained it. I am looking at the build report for seqArchR: https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.22/bioc-LATEST/seqArchR/kjohnson3-checksrc.html__;!!LRXxDv2l!QAA92Cyqu8OY0SOOTck3o89jQ5V_NcAo7SUQBZ0o44qgD7EfHcE_g-mG_nsjA1Hnu3g1ZKlM1hcLcoCtJFQsPZW9pDGM3pwkZW_5$ This again shows 'Module sklearn not found'. Installing scikit-learn should make it work. Is there anything I can do to help with this? With regards to seqArchRplus, it is the issue with slickR being unavailable on CRAN. I will implement a workaround (include relevant code with attribution or deprecate the function). Please let me know if hastily implementing fixes will work for the current release deadline -- branch may be frozen by now. Thanks and best wishes, Sarvesh On Fri, 10 Oct 2025 at 17:56, Kern, Lori via Bioc-devel < [email protected]> wrote: > The Bioconductor Team is continuing to identify packages that will be > deprecated in the next release to allow for the Bioconductor community to > respond accordingly. This is the current list of deprecated packages for > Bioc 3.22. > > It should be noted, we did try to reach out to these package maintainers > multiple times and they were either unresponsive or had emails bounce. We > encourage anyone that is familiar with a package maintainer on this list to > reach out to them and notify them directly. Packages can be un-deprecated > if a maintainer fixes the package to build/check cleanly before the next > release and requests un-deprecation on the [email protected] > mailing list > > Do not un-deprecate a package yourself. You must request un-deprecation > from the Bioconductor core team at [email protected]. We will not > recognize a self un-deprecation > > Software User Requested: > DEP > gpuMagic > hiAnnotator > hiReadsProcessor > interactiveDisplay > interactiveDisplayBase > Repitools > rRDP > Streamer > > Software Unresponsive: > bgx > BiGGR > biodbHmdb > biodbNci > biodbNcbi > biodbUniprot > ccmap > CellScore > CINdex > cisPath > Harshlight > hypeR > lapmix > LinTInd > lute > MADSEQ > MAST > oppti > PhenStat > qckitfastq > ReactomeGraph4R > Rfastp > rGADEM > SARC > seqArchR > seqArchRplus > seqTools > TitanCNA > TransView > traviz > XNAString > > Experiment Data Requested: > rRDPData > > Experiment Data Unresponsive: > curatedCRCData > > Workflows Requested: > spicyWorkflow > > There may be a few others added to the list prior to the release. We will > announce any further changes or additions. > > > > Lori Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!QAA92Cyqu8OY0SOOTck3o89jQ5V_NcAo7SUQBZ0o44qgD7EfHcE_g-mG_nsjA1Hnu3g1ZKlM1hcLcoCtJFQsPZW9pDGM3q3qIw3D$ > -- thanks! -Sarvesh -------------------------------------------- Q: Why is this email five sentences or less? A: https://urldefense.com/v3/__http://five.sentenc.es__;!!LRXxDv2l!QAA92Cyqu8OY0SOOTck3o89jQ5V_NcAo7SUQBZ0o44qgD7EfHcE_g-mG_nsjA1Hnu3g1ZKlM1hcLcoCtJFQsPZW9pDGM3iyry7Yg$ [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!QAA92Cyqu8OY0SOOTck3o89jQ5V_NcAo7SUQBZ0o44qgD7EfHcE_g-mG_nsjA1Hnu3g1ZKlM1hcLcoCtJFQsPZW9pDGM3q3qIw3D$ [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
