[Bioc-devel] Increase version of system dependency?

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Tue Oct 18 18:51:12 CEST 2022

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

On Tue, Oct 18, 2022 at 12:31 PM Sarvesh Nikumbh <sarvesh.nikumbh using gmail.com>

> 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
>         [[alternative HTML version deleted]]
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