[Bioc-devel] List of Deprecated Packages for Bioconductor 3.22
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://bioconductor.org/checkResults/3.22/bioc-LATEST/seqArchR/kjohnson3-checksrc.html 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 <
bioc-devel at r-project.org> 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 bioc-devel at r-project.org
mailing list
Do not un-deprecate a package yourself. You must request un-deprecation
from the Bioconductor core team at bioc-devel at r-project.org. 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
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