[Bioc-devel] Do not push with merge conflicts to Bioconductor git repo.

[Nitesh Turaga]

Dear Developers,

Every time there is a release for Bioconductor we (the core team), face an 
issue where developers end up pushing code with the "merge conflicts". One of 
the reasons why we get the issue "Bad description" file in the build report is 
because of a merge which has gone bad and produced conflicts. 

To avoid this issue, we have taken a step to include a pre-receive hook in git 
which checks for the merge conflict markers and rejects your push.

Please note that, although this will keep our end of things (the Bioconductor 
git repo) clean, your local branch will need to be fixed before you try and 
push to Bioconductor again. To avoid having your push to Bioconductor rejected, 
it's easy to employ some good practices,

1. Check your code and DESCRIPTION file for merge conflict markers, i.e for 
anything that looks like

++<<< HEAD 
  +Version: 1.1.2 
++=== 
  + Version: 1.0.1 
++>>> origin/RELEASE_3_11

   Notice the <<< HEAD, ===, >>> markers in the files.

2. Before a commit, you can use "git diff --check", and it will show you the 
issues with your code.

   git diff --check   
   
  DESCRIPTION:4: leftover conflict marker
  DESCRIPTION:6: leftover conflict marker
  DESCRIPTION:8: leftover conflict marker

3. If you use an IDE there are certain "extensions" you can add to your IDE to 
make it detect merge conflicts for you automatically. Most editors have them 
(emacs, vim, visual-studio, atom, sublime etc). Please use these if they are 
your development environments. You can even get built in ones for bash or zsh.

If you need help resolving merge conflicts, please check,


https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/addressing-merge-conflicts

This is mostly an effort to avoid packages from breaking for needless reasons. 
As usual, thanks to everyone for the contributions.


Best regards,

Nitesh 
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Re: [Bioc-devel] How to use initializing functions correctly ?

[Charles Plessy]

Le Tue, May 12, 2020 at 10:18:24AM -0700, Hervé Pagès a écrit :
> 
> Note that the GPos() constructor is NOT the generator function returned by
> the setClass() statement that defines the GPos class. It's a constructor
> function defined in the GenomicRanges package and it implements a
> sophisticated logic.
…
> HOWEVER, please note that trying to support the 'stitch' argument does not
> make sense in a context where the newGPos class extends the UnstitchedGPos
> class. So you might want to do something like this instead:
> 
> ## newGPos() has the same arguments as the GPos() constructor **except**
> ## the 'stitch' argument.
> newGPos <- function (seqnames=NULL, pos=NULL, strand=NULL,
>  ..., seqinfo=NULL, seqlengths=NULL)
> {
> gpos <- GPos(seqnames=seqnames, pos=pos, strand=strand,
>  ..., seqinfo=seqinfo, seqlengths=seqlengths,
>  stitch=FALSE)
> new("newGPos", gpos)
> }

Thank you very much Hervé.  I think that I understand much better.  I
reformed my class to that it has a constructor that mimicks the
GPos(stitched = FALSE) one, plus an inializing function so that new()
can promote an UnstitchedGPos to the class, and finally a coerce method
so that GRanges can be converted.  The result is here:

https://github.com/charles-plessy/CAGEr/blob/fix-CTSS-GPos/R/CTSS.R

Not sure if you have time to have a look, but anybody's comments would
be appreciated if I am still doing things wrong.

Have a nice day,

Charles

-- 
Charles Plessy
Akano, Uruma, Okinawa, Japan

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Re: [Bioc-devel] Debugging not updated for coexnet package

[Shepherd, Lori]

There is lots of documentation on how to achieve this.

Most specifically for pushing changes to the RELEASE_3_11 branch following the 
documentation

http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Juan David 
Henao Sanchez 
Sent: Wednesday, May 13, 2020 8:27 AM
To: Herv� Pag�s 
Cc: Bioc-devel 
Subject: Re: [Bioc-devel] Debugging not updated for coexnet package

Hi.

Thanks for your help solving this issue. Could you please let me know how I
can fix the bug in the specific BioC version (3.11). How could I push my
current updated code into this specific version?

Thanks in advance.

I am looking forward to hearing from you soon.

Kind regards,

Juan

El mi�., 13 may. 2020 a las 0:44, Herv� Pag�s ()
escribi�:

> Hi Juan,
>
> On 5/12/20 13:37, Juan David Henao Sanchez wrote:
> > Dear all.
> >
> > I received an error regarding my package coexnet when it is checking for
> > multiple platforms. I already fix the problem a couple of days ago and I
> > push the solution like:
> >
> > git push origin master
>
> Indeed the package is now green in Bioc devel (the master branch of your
> package):
>
>
> https://secure-web.cisco.com/1zTvATemlXuwTsvdpt1GSyrR7oj4jKLSuVCFqEK8Bx3Ts3it5bWxLbK1v3PpyD_6tfq4WU4gWj_NQ04_TtwsZ2hK4RQsb-OaJIfEqhlWqhD6O12vKs2OpFOneeTYwcf0V4rEAScnuJQSvkfhFu6XiJLVfp5clHpKPE1EsKf8KipCDobKaXsexUyjocrgN51GAGQyUzjRKX03jeDLkmjhR7wk3ahdNWrf3UvYx4-dY19Qdt7lZTttHHk2N0caKsMImcktvRxlq5dfS0L6exoFpzt5f20YD3bnbtBUbCt9lFkOyesNr6TTka0_KFQ7GxPOIJhSPRvI7azRnoJ4I0x7HwE5Vn9g88HymJootFjCrME8/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2F
>
> However, as I mentioned in the email I sent you off list, the package is
> still broken in BioC 3.11 (the current release):
>
>
> https://secure-web.cisco.com/1qrz9-Njh-eGNyUg0E4PSo3kL_kE0PXtuHFxkeHDzLaJzY-F0pVmXz4t8eicwDp4CoICG3raQcKmB5kpD0h_ml52ivByFLPamaHcJ3vbS3DPxCewObxoXpIHuTGaSX_vzYA6JNHbnyeqchCQIjAua-8Y059kj0VR-mFNAxgMpRILLsRKNHkWLBSTbwIBhLzO4Dob3xuefzyua_mOvJU1X7O-9fYoTxuJg6MFAVUiR4L1Gmy_5d2o1_Mq6woySFk0fxC9RgZizOBdxyEX8qhb0-PgF37R2CZ4b7IceNwZLgXZJ7HJ0vvuYIa4rsSqcg-3mq5uXGxAxq_UMcWJIKUTxFACVnqB6DnzBUzmA6zawbCI/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2F
>
> So you also need to fix the RELEASE_3_11 branch of your package.
>
> Best,
> H.
>
> >
> > However, I continue receiving the same error message and it is the same
> > previous version of my package.
> >
> > There is something additional I have to do to update my package?
> >
> > Thanks on advance,
> >
> > I look forward to hearing from you soon.
> >
> > Juan
> >
>
> --
> Herv� Pag�s
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>


--
Juan David Henao
Magister in Bioinformatics
Universidad Nacional de Colombia

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Re: [Bioc-devel] Debugging not updated for coexnet package

[Juan David Henao Sanchez]

Hi.

Thanks for your help solving this issue. Could you please let me know how I
can fix the bug in the specific BioC version (3.11). How could I push my
current updated code into this specific version?

Thanks in advance.

I am looking forward to hearing from you soon.

Kind regards,

Juan

El mié., 13 may. 2020 a las 0:44, Hervé Pagès ()
escribió:

> Hi Juan,
>
> On 5/12/20 13:37, Juan David Henao Sanchez wrote:
> > Dear all.
> >
> > I received an error regarding my package coexnet when it is checking for
> > multiple platforms. I already fix the problem a couple of days ago and I
> > push the solution like:
> >
> > git push origin master
>
> Indeed the package is now green in Bioc devel (the master branch of your
> package):
>
>https://bioconductor.org/checkResults/3.12/bioc-LATEST/
>
> However, as I mentioned in the email I sent you off list, the package is
> still broken in BioC 3.11 (the current release):
>
>https://bioconductor.org/checkResults/3.11/bioc-LATEST/
>
> So you also need to fix the RELEASE_3_11 branch of your package.
>
> Best,
> H.
>
> >
> > However, I continue receiving the same error message and it is the same
> > previous version of my package.
> >
> > There is something additional I have to do to update my package?
> >
> > Thanks on advance,
> >
> > I look forward to hearing from you soon.
> >
> > Juan
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>


-- 
Juan David Henao
Magister in Bioinformatics
Universidad Nacional de Colombia

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Re: [Bioc-devel] BgeeCall package present twice

[Shepherd, Lori]

Yes looking at the links further it is a legacy version.

The one that resolves to a workflow page if you look closely is when 3.11 was 
in development phase

https://bioconductor.org/packages/release/workflows/html/BgeeCall.html


While the software page is the current release.

I'm not exactly sure why the development page still appears, this was 
surprising to me,  and is something I will try to track down.  Regardless the 
git link points to the same repository on git.bioconductor.org so users would 
download the correct version.  And yes I checked the repository locations and 
the only active one is in the Software  manifest so when users are doing 
BiocManager::install it would grab from the software repository.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Julien 
Wollbrett 
Sent: Wednesday, May 13, 2020 5:10 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BgeeCall package present twice

Hello,

For Bioconductor 3.11 I asked if it was possible to move BgeeCall from
workflow section to software section.
The package is now present in the software section. Thank you.
When I go to this page :
https://secure-web.cisco.com/1ifWHo9w6N8A_tWozVInX7SlCLk6o10Zy8eKyN4jISQTFiyxZw-Y9h4lXtl5NaB4oE44NT3efkyYu0lJPKEC0752nmSAxT5GNQWc18PwT5LOLHT-XloOsrmezREt-WImNjagRE5KsOUOGfmU2mvlIaOFsGtTHS4TNgy8LP12xxfkjSTFdDfjN_JYcDQYdMDzPVGTDITeY1HWFX0c08dPVqVruvdvpOH-n4pOEZ8lzE5PZYBBPWWAh0zpjWnx_7tbKvr4OAqGaYmq3KNUwteCIMmZpe4kLslEZI_8JXPkSfH_l-eUqOVNMsi_sgOlC2n3N4lKChf8FJ8PG4SlC0Smfr-AtetEnNwvQZVwPYRE8w38/https%3A%2F%2Fbioconductor.org%2Fhelp%2Fsearch%2Findex.html%3Fq%3Dbgeecall%2F
BgeeCall
appears twice (in workflow and software).

For both version the git URL is the same. Could you please confirm that
it is just an artefact? When updating the package do I update the one in
the Software section? When users install BgeeCall do they actually
install the package of the software section? Thank you.

Best Regards,

Julien Wollbrett


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distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] BgeeCall package present twice

[Julien Wollbrett]

Hello,

For Bioconductor 3.11 I asked if it was possible to move BgeeCall from 
workflow section to software section.
The package is now present in the software section. Thank you.
When I go to this page :
https://bioconductor.org/help/search/index.html?q=bgeecall/
BgeeCall 
appears twice (in workflow and software).

For both version the git URL is the same. Could you please confirm that 
it is just an artefact? When updating the package do I update the one in 
the Software section? When users install BgeeCall do they actually 
install the package of the software section? Thank you.

Best Regards,

Julien Wollbrett


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Re: [Bioc-devel] The new version of the package 'cbaf' is not downloadable for BioC 3.11

[Lluís Revilla]

Hi,

The maintainer is already aware of this error.
I reported it several months ago
https://github.com/colearendt/xlsx/issues/132 and is reported multiple
times (issues 154, 156, 159)
There is a fix on the github version of the package but the maintainter
hasn't updated the CRAN version yet.

Maybe if you present your case xlsx will be finally updated on CRAN.

Cheers,

Lluís

On Tue, 12 May 2020 at 23:44, Hervé Pagès  wrote:

> Hi Arman,
>
> On 5/7/20 08:57, Arman Shahrisa wrote:
> > Hi to all,
> >
> > I�m maintainer of the package  �cbaf�. I have pushed changes to both
> devel and stable branches almost two days ago. The package check has only
> been carried out for the stable release so far. There has been only one
> error on macOS server as a result of the version of Java used on the server.
>
> Not sure what is wrong with the version of Java used on our Mac server
> machv2. cbaf fails to load with the following error message:
>
>Error: .onLoad failed in loadNamespace() for 'xlsx', details:
>  call: fun(libname, pkgname)
>  error: Your java version is 14.  Need 1.5.0 or higher.
>Execution halted
>ERROR: lazy loading failed for package ‘cbaf’
>
> Obviously version 14 is higher than version 1.5.0 so to me it just looks
> like the Java checking code in xlsx is broken. Something you might want
> to report to the xlsx maintainer.
>
> Alternatively you might want to choose the packages you depend on more
> carefully.
>
> Cheers,
> H.
>
>
> > Despite this, the older version is listed on the cbaf web page for BioC
> 3.11.
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_release_bioc_html_cbaf.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=A59d3JuLgSK3niLkKLga7vyA-vcQsy8q7riknf75RJ0&s=UAhMnh0UmS_h5m4zNRZ_6GE4yemBR0PNGc1WWIARybI&e=
> >
> > Am I missing something?
> >
> > Best regards,
> > Arman
> >
> >
> >   [[alternative HTML version deleted]]
> >
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=A59d3JuLgSK3niLkKLga7vyA-vcQsy8q7riknf75RJ0&s=A-xLxbM3GGrLmBYZzTnC17RTyvyKEL4QRFNK8DoDq8A&e=
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>
> ___
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>

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