[Bioc-devel] Increase version of system dependency?

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Wed Oct 19 03:36:05 CEST 2022

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.



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

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