[Bioc-devel] Increase version of system dependency?

[Sarvesh Nikumbh]

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

-- 

thanks!
-Sarvesh

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