[Bioc-devel] Increase version of system dependency?

[Sarvesh Nikumbh]

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://scikit-learn.org/stable/modules/generated/sklearn.decomposition.NMF.html
> >
> > 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://bioconductor.org/checkResults/3.16/bioc-LATEST/seqArchR/palomino4-checksrc.html
> >
> > 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

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