Thanks for the reply, Hervé. In the interest of available time for this release, I will include 'packaging' in the SystemRequirements, and look to using basilisk for the next release.
Best, Sarvesh On Wed, 19 Oct 2022 at 02:36, Hervé Pagès <hpages.on.git...@gmail.com> wrote: > Hi Sarvesh, > > All I see is that seqArchR fails on palomino4 because Python module > 'packaging' is not available on that machine. > > The module seems to be available on the other builders though so no > problem there. > > Anyways if your package depends on that module (and it seems that it > does, via the inst/python/perform_nmf.py script), then you need to list > the module in your SystemRequirements. > > Then we'll make sure to install the module on all the builders. > > Thanks, > > H. > > > On 18/10/2022 09:31, Sarvesh Nikumbh 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 > > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > > -- thanks! -Sarvesh -------------------------------------------- Q: Why is this email five sentences or less? A: http://five.sentenc.es [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
