[Bioc-devel] Increase version of system dependency?

[Sarvesh Nikumbh]

Issue resolved. Thanks, Jennifer!

-Sarvesh

On Thu, 20 Oct 2022 at 20:18, Jennifer Wokaty <Jennifer.Wokaty using 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-bounces using r-project.org> on behalf of
> Sarvesh Nikumbh <sarvesh.nikumbh using gmail.com>
> *Sent:* Thursday, October 20, 2022 12:08 PM
> *To:* bioc-devel using r-project.org <bioc-devel using 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.github using 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.github using 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 using 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]]