Issue resolved. Thanks, Jennifer! -Sarvesh
On Thu, 20 Oct 2022 at 20:18, Jennifer Wokaty <jennifer.wok...@sph.cuny.edu> wrote: > Hi Sarvesh, > > I've installed packaging on our devel Windows builder. We should see the > issue resolved in the next build report. > > Jen > ------------------------------ > *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of > Sarvesh Nikumbh <sarvesh.niku...@gmail.com> > *Sent:* Thursday, October 20, 2022 12:08 PM > *To:* bioc-devel@r-project.org <bioc-devel@r-project.org> > *Subject:* Re: [Bioc-devel] Increase version of system dependency? > > ***ATTENTION: This email came from an external source. Do not open > attachments or click on links from unknown senders or unexpected emails.*** > > Hi bioc team, > > Could you please install the Python module 'packaging' on palomino4? I have > pushed the updated SystemRequirements yesterday. Linux and macOS seem to > be fine. > Thanks in advance. > > Best wishes, > 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://urldefense.proofpoint.com/v2/url?u=https-3A__scikit-2Dlearn.org_stable_modules_generated_sklearn.decomposition.NMF.html&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz&s=DzxNJLg1ADaS3XDof9AnhKWeOBenp1DvnG6qt37swGk&e= > > > > > > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.16_bioc-2DLATEST_seqArchR_palomino4-2Dchecksrc.html&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz&s=yJdY-LnSsA0-Xfh47DYFXIxLFxWOy8gQEQu4BiIwBA0&e= > > > > > > > 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: > https://urldefense.proofpoint.com/v2/url?u=http-3A__five.sentenc.es&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz&s=tINaCsEcKRF4gJ2k-iW6J1n_Rsucc632G8xtz784wnI&e= > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz&s=CNOml7Ibm5f1NLsQePoNZeV9smJCxNRI5nNd8D2JVp0&e= > > -- 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