Hi Vince, I did attempt to use basilisk for seqArchR, but met with some errors then. See https://github.com/LTLA/basilisk/issues/13
If anyone has tried basilisk with BiocParallel, I will be happy to reach out and find a way to mediate via basilisk. I will write to you separately with more details if it is ok. I will be glad to make basilisk+biocParallel work for seqArchR. Best, Sarvesh On Tue, 18 Oct 2022 at 17:51, Vincent Carey <st...@channing.harvard.edu> wrote: > My suggestion is that your interfaces to python be mediated with the > basilisk package. Please > contact me off line if you need assistance; see BiocSklearn for an > example; I am sure there are > others. > > On Tue, Oct 18, 2022 at 12:31 PM Sarvesh Nikumbh < > sarvesh.niku...@gmail.com> wrote: > >> Hi bioc team, >> >> My package seqArchR though does not error in any way, but can spit out >> numerous warnings (originally from Python/scikit-learn which is a >> dependency) depending on the version of scikit-learn available. This >> fills >> the output to the extent that it is unreadable. The cause for this is the >> deprecation/future version warning in NMF/scikitlearn >> < >> https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.NMF.html >> > >> which is forced, so I cannot suppress it. >> >> I pushed a fix for this in the devel version -- where, instead of >> increasing the dependency version, I check the module version using >> packaging module from setuptools and appropriately make the python >> function >> call. But this gives an error on the Windows build machine, and is fine on >> Linux/macOS. >> See >> >> https://bioconductor.org/checkResults/3.16/bioc-LATEST/seqArchR/palomino4-checksrc.html >> >> I expected that setuptools will be available on all machines, because the >> previous alternative, distutils, is available with vanilla python, but is >> not recommended. >> >> Would you suggest having setuptools in the SystemRequirements or using >> distutils? >> Or simply depending on higher version of scikit-learn (the latest 1.2) -- >> which is the root cause of this issue anyway. >> >> Thanks and best, >> Sarvesh >> >> -- >> >> thanks! >> -Sarvesh >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > The information in this e-mail is intended only for th...{{dropped:26}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
