[Bioc-devel] Increase version of system dependency?

[Jennifer Wokaty]

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, Herv� Pag�s <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
> >
> --
> Herv� Pag�s
>
> 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=

	[[alternative HTML version deleted]]