[Bioc-devel] Increase version of system dependency?

Sarvesh Nikumbh @@rve@h@n|kumbh @end|ng |rom gm@||@com
Tue Oct 18 22:20:37 CEST 2022

Hi Vince,

I did attempt to use basilisk for seqArchR, but met with some errors then.
See https://github.com/LTLA/basilisk/issues/13

If anyone has tried basilisk with BiocParallel, I will be happy to reach
out and find a way to mediate via basilisk.

I will write to you separately with more details if it is ok. I will be
glad to make basilisk+biocParallel work for seqArchR.


On Tue, 18 Oct 2022 at 17:51, Vincent Carey <stvjc using channing.harvard.edu>

> 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 using 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
>>         [[alternative HTML version deleted]]
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