[Bioc-devel] Increase version of system dependency?
@@rve@h@n|kumbh @end|ng |rom gm@||@com
Thu Oct 20 18:08:07 CEST 2022
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
Thanks in advance.
On Wed, 19 Oct 2022 at 02:36, Hervé Pagès <hpages.on.github using gmail.com>
> 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
> > the output to the extent that it is unreadable. The cause for this is the
> > deprecation/future version warning in NMF/scikitlearn
> > <
> > 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
> > call. But this gives an error on the Windows build machine, and is fine
> > Linux/macOS.
> > See
> > 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
Q: Why is this email five sentences or less?
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