[Bioc-devel] Increase version of system dependency?

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 at r-project.org> on behalf of
Sarvesh Nikumbh <sarvesh.nikumbh at gmail.com>
*Sent:* Thursday, October 20, 2022 12:08 PM
*To:* bioc-devel at r-project.org <bioc-devel at r-project.org>
*Subject:* Re: [Bioc-devel] Increase version of system dependency?

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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 at 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 at gmail.com

--

thanks!
-Sarvesh

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