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, Herv� Pag�s <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 > > > -- > Herv� Pag�s > > 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= [[alternative HTML version deleted]]
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