Re: [Bioc-devel] Increase version of system dependency?

[Sarvesh Nikumbh]

Issue resolved. Thanks, Jennifer!

-Sarvesh

On Thu, 20 Oct 2022 at 20:18, Jennifer Wokaty 
wrote:

> Hi Sarvesh,
>
> I've installed packaging on our devel Windows builder. We should see the
> issue resolved in the next build report.
>
> Jen
> --
> *From:* Bioc-devel  on behalf of
> Sarvesh Nikumbh 
> *Sent:* Thursday, October 20, 2022 12:08 PM
> *To:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] Increase version of system dependency?
>
> ***ATTENTION: This email came from an external source. Do not open
> attachments or click on links from unknown senders or unexpected emails.***
>
> 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
> be fine.
> Thanks in advance.
>
> Best wishes,
>   Sarvesh
>
> On Wed, 19 Oct 2022 at 02:36, Hervé Pagès 
> wrote:
>
> > 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.
> >
> > Thanks,
> >
> > H.
> >
> >
> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__scikit-2Dlearn.org_stable_modules_generated_sklearn.decomposition.NMF.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz=DzxNJLg1ADaS3XDof9AnhKWeOBenp1DvnG6qt37swGk=
>
> > >
> > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.16_bioc-2DLATEST_seqArchR_palomino4-2Dchecksrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz=yJdY-LnSsA0-Xfh47DYFXIxLFxWOy8gQEQu4BiIwBA0=
>
> > >
> > > 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.git...@gmail.com
> >
> >
>
> --
>
> thanks!
> -Sarvesh
>
> 
> Q: Why is this email five sentences or less?
> A:
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>
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>
>


-- 

thanks!
-Sarvesh


Q: Why is this email five sentences or less?
A: http://five.sentenc.es

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Re: [Bioc-devel] Increase version of system dependency?

[Jennifer Wokaty]

Hi Sarvesh,

I've installed packaging on our devel Windows builder. We should see the issue 
resolved in the next build report.

Jen

From: Bioc-devel  on behalf of Sarvesh 
Nikumbh 
Sent: Thursday, October 20, 2022 12:08 PM
To: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Increase version of system dependency?

***ATTENTION: This email came from an external source. Do not open attachments 
or click on links from unknown senders or unexpected emails.***

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
be fine.
Thanks in advance.

Best wishes,
  Sarvesh

On Wed, 19 Oct 2022 at 02:36, Herv� Pag�s 
wrote:

> 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.
>
> Thanks,
>
> H.
>
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__scikit-2Dlearn.org_stable_modules_generated_sklearn.decomposition.NMF.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz=DzxNJLg1ADaS3XDof9AnhKWeOBenp1DvnG6qt37swGk=
> >
> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.16_bioc-2DLATEST_seqArchR_palomino4-2Dchecksrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=FGhgBnQ9LlkQNoTApdaferGM3XwiCSkJ4EzVsgcMz6Kg_q8PMDzOi1eB5M6JMqxz=yJdY-LnSsA0-Xfh47DYFXIxLFxWOy8gQEQu4BiIwBA0=
> >
> > 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
> >
> --
> Herv� Pag�s
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
>

--

thanks!
-Sarvesh


Q: Why is this email five sentences or less?
A: 
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Re: [Bioc-devel] Increase version of system dependency?

[Sarvesh Nikumbh]

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
be fine.
Thanks in advance.

Best wishes,
  Sarvesh

On Wed, 19 Oct 2022 at 02:36, Hervé Pagès 
wrote:

> 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.
>
> Thanks,
>
> H.
>
>
> 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
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
>

-- 

thanks!
-Sarvesh


Q: Why is this email five sentences or less?
A: http://five.sentenc.es

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Re: [Bioc-devel] Increase version of system dependency?

[Sarvesh Nikumbh]

Thanks for the reply, Hervé.
In the interest of available time for this release, I will include
'packaging' in the SystemRequirements, and look to using basilisk for the
next release.

Best,
  Sarvesh

On Wed, 19 Oct 2022 at 02:36, Hervé Pagès 
wrote:

> 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.
>
> Thanks,
>
> H.
>
>
> 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
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
>

-- 

thanks!
-Sarvesh


Q: Why is this email five sentences or less?
A: http://five.sentenc.es

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Increase version of system dependency?

[Hervé Pagès]

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.

Thanks,

H.


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

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

Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Increase version of system dependency?

[Sarvesh Nikumbh]

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.

Best,
  Sarvesh

On Tue, 18 Oct 2022 at 17:51, Vincent Carey 
wrote:

> 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.niku...@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]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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Re: [Bioc-devel] Increase version of system dependency?

[Vincent Carey]

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 
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]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] Increase version of system dependency?

[Sarvesh Nikumbh]

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

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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