Re: [Bioc-devel] reverting to a previous version

2022-10-19 Thread Hervé Pagès 
On 19/10/2022 19:48, Jason Ji wrote:

> Thanks Hervé,
>
> I am sorry I am not familiar with the Bioconductor git system. Could 
> you please advise the code I should use to revert to the last working 
> version? Thanks!

I'm not a git expert so maybe others have a better way to do this.

I would just identify the commit you want to revert (the fact that all 
the recent commit messages are "commit" won't necessarily help), then 
revert it with:

   git revert 

If you need to revert more than 1 commit, revert them in reverse 
chronological order.

This is just standard git stuff.

The only part that is specific to Bioconductor is that you need to 
finish the sequence with an additional commit that bumps the version to 
1.35.2.

Hope this helps,

H.


>
>
> Best,
> Jason
>
> --
> Zhicheng Ji, PhD.
> Assistant Professor
> Department of Biostatistics and Bioinformatics
> Duke University School of Medicine
> 2424 Erwin Road, Suite 1102 Hock Plaza Box 2721
> Durham, NC 27710, USA
>
>
>
> On Wed, Oct 19, 2022 at 10:29 PM Hervé Pagès 
>  wrote:
>
> Hi Jason,
>
> On 19/10/2022 19:10, Jason Ji wrote:
> > Dear admin,
> >
> > I am an author of a Bioconductor package (TSCAN) and recently I
> made a
> > mistake pushing a problematic version of the software to
> Bioconductor. I
> > wonder if there is a way to revert back to the previous working
> version?
>
> Yes but only for the master branch (BioC 3.16). The RELEASE_3_15
> branch
> got frozen recently and can no longer be touched.
>
> Also package versions can only go up. Note that the current devel
> version of  TSCAN (1.35.1) never got published (i.e. it didn't
> propagate), so, technically, you won't need to bump the version after
> you fix the package. Even though it wouldn't hurt to do so (i.e.
> to bump
> to 1.35.2).
>
> Cheers,
>
> H.
>
> >
> > Thanks!
> >
> >
> > Best,
> > Jason
> >
> > --
> > Zhicheng Ji, PhD.
> > Assistant Professor
> > Department of Biostatistics and Bioinformatics
> > Duke University School of Medicine
> > 2424 Erwin Road, Suite 1102 Hock Plaza Box 2721
> > Durham, NC 27710, USA
> >
> >       [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> -- 
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
-- 
Hervé Pagès

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

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Re: [Bioc-devel] reverting to a previous version

2022-10-19 Thread Jason Ji 
Thanks Hervé,

I am sorry I am not familiar with the Bioconductor git system. Could you
please advise the code I should use to revert to the last working version?
Thanks!


Best,
Jason

--
Zhicheng Ji, PhD.
Assistant Professor
Department of Biostatistics and Bioinformatics
Duke University School of Medicine
2424 Erwin Road, Suite 1102 Hock Plaza Box 2721
Durham, NC 27710, USA



On Wed, Oct 19, 2022 at 10:29 PM Hervé Pagès 
wrote:

> Hi Jason,
>
> On 19/10/2022 19:10, Jason Ji wrote:
> > Dear admin,
> >
> > I am an author of a Bioconductor package (TSCAN) and recently I made a
> > mistake pushing a problematic version of the software to Bioconductor. I
> > wonder if there is a way to revert back to the previous working version?
>
> Yes but only for the master branch (BioC 3.16). The RELEASE_3_15 branch
> got frozen recently and can no longer be touched.
>
> Also package versions can only go up. Note that the current devel
> version of  TSCAN (1.35.1) never got published (i.e. it didn't
> propagate), so, technically, you won't need to bump the version after
> you fix the package. Even though it wouldn't hurt to do so (i.e. to bump
> to 1.35.2).
>
> Cheers,
>
> H.
>
> >
> > Thanks!
> >
> >
> > Best,
> > Jason
> >
> > --
> > Zhicheng Ji, PhD.
> > Assistant Professor
> > Department of Biostatistics and Bioinformatics
> > Duke University School of Medicine
> > 2424 Erwin Road, Suite 1102 Hock Plaza Box 2721
> > Durham, NC 27710, USA
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
>

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Re: [Bioc-devel] reverting to a previous version

2022-10-19 Thread Hervé Pagès 

Hi Jason,

On 19/10/2022 19:10, Jason Ji wrote:

Dear admin,

I am an author of a Bioconductor package (TSCAN) and recently I made a
mistake pushing a problematic version of the software to Bioconductor. I
wonder if there is a way to revert back to the previous working version?


Yes but only for the master branch (BioC 3.16). The RELEASE_3_15 branch 
got frozen recently and can no longer be touched.


Also package versions can only go up. Note that the current devel 
version of  TSCAN (1.35.1) never got published (i.e. it didn't 
propagate), so, technically, you won't need to bump the version after 
you fix the package. Even though it wouldn't hurt to do so (i.e. to bump 
to 1.35.2).


Cheers,

H.



Thanks!


Best,
Jason

--
Zhicheng Ji, PhD.
Assistant Professor
Department of Biostatistics and Bioinformatics
Duke University School of Medicine
2424 Erwin Road, Suite 1102 Hock Plaza Box 2721
Durham, NC 27710, USA

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--
Hervé Pagès

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

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[Bioc-devel] reverting to a previous version

2022-10-19 Thread Jason Ji 
Dear admin,

I am an author of a Bioconductor package (TSCAN) and recently I made a
mistake pushing a problematic version of the software to Bioconductor. I
wonder if there is a way to revert back to the previous working version?

Thanks!


Best,
Jason

--
Zhicheng Ji, PhD.
Assistant Professor
Department of Biostatistics and Bioinformatics
Duke University School of Medicine
2424 Erwin Road, Suite 1102 Hock Plaza Box 2721
Durham, NC 27710, USA

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Re: [Bioc-devel] Problems pushing to release version of package

2022-10-19 Thread Russell Bainer 
Thank you very much!

My apologies to Lori for missing her email.

-R

On Wed, Oct 19, 2022 at 2:09 PM Steve Lianoglou 
wrote:

> Howdy,
>
> On Wed, Oct 19, 2022 at 1:55 PM Russell Bainer 
> wrote:
>
>> Hi Everyone,
>>
>> I am trying to update an error in the release version of my package, but
>> after following the instructions here:
>>
>>
>> https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories
>>
>> I am unable to push upstream:
>>
>>  git push upstream RELEASE_3_15
>> > Warning: remote port forwarding failed for listen port 52698
>>
>
> As of 2 days ago (Lori sent an email out then), the 3_15 branch is frozen,
> so I'm guessing this is what you're tripping up on. You can now only push
> to master in prep for the 3.16 release.
>
> -steve
>
>

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Re: [Bioc-devel] Problems pushing to release version of package

2022-10-19 Thread Steve Lianoglou 
Howdy,

On Wed, Oct 19, 2022 at 1:55 PM Russell Bainer 
wrote:

> Hi Everyone,
>
> I am trying to update an error in the release version of my package, but
> after following the instructions here:
>
>
> https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories
>
> I am unable to push upstream:
>
>  git push upstream RELEASE_3_15
> > Warning: remote port forwarding failed for listen port 52698
>

As of 2 days ago (Lori sent an email out then), the 3_15 branch is frozen,
so I'm guessing this is what you're tripping up on. You can now only push
to master in prep for the 3.16 release.

-steve

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[Bioc-devel] Problems pushing to release version of package

2022-10-19 Thread Russell Bainer 
Hi Everyone,

I am trying to update an error in the release version of my package, but
after following the instructions here:

https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories

I am unable to push upstream:

 git push upstream RELEASE_3_15
> Warning: remote port forwarding failed for listen port 52698
> Enumerating objects: 32, done.
> Counting objects: 100% (27/27), done.
> Delta compression using up to 8 threads
> Compressing objects: 100% (14/14), done.
> Writing objects: 100% (14/14), 1.31 KiB | 1.31 MiB/s, done.
> Total 14 (delta 11), reused 0 (delta 0), pack-reused 0
> remote: FATAL: W refs/heads/RELEASE_3_15 packages/gCrisprTools r.bainer
> DENIED by fallthru
> remote: error: hook declined to update refs/heads/RELEASE_3_15
> To git.bioconductor.org:packages/gCrisprTools.git
>  ! [remote rejected] RELEASE_3_15 -> RELEASE_3_15 (hook declined)


Can anyone advise on what I am doing wrong here? Sorry if this solution is
well known but I'm following Nitesh's recommendation
to someone who was
experiencing something similar.

Many Thanks,

-R

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

2022-10-19 Thread 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

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