My suggestion is that your interfaces to python be mediated with the
basilisk package. Please
contact me off line if you need assistance; see BiocSklearn for an
example; I am sure there are
others.
On Tue, Oct 18, 2022 at 12:31 PM Sarvesh Nikumbh <
sarvesh.nikumbh at gmail.com> 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
--
thanks!
-Sarvesh
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