'Re: [Bioc-devel] R: Errors updating DaMiRseq package'

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List:       bioc-devel
Subject:    Re: [Bioc-devel] R: Errors updating DaMiRseq package
From:       Martin Morgan <martin.morgan () roswellpark ! org>
Date:       2017-09-23 12:47:42
Message-ID: 2e9fe866-9ba4-638a-8e5f-0c6ef36ae272 () roswellpark ! org
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On 09/23/2017 08:44 AM, Mattia Chiesa wrote:
> Dear Nitesh,
> thank you! Now it seems to work perfectly. I will check the effect tomorrow after \
> the nighty build. Just another little question, related with my issue: I solve it \
> using 
> git merge --allow-unrelated-histories upstream/master
> 
> And then resolving conflicts:
> 
> git add DESCRIPTION
> git commit -m "Fixed conflicts in version change"
> 
> However, I didn�t delete any lines in DESCRIPTION. (between ===== and >>>>>>). Do \
> you think it would be OK?

The build system will simply check out your git repository and try to 
build your package; it will fail

$ R CMD build DaMiRseq/
Bioconductor version 3.6 (BiocInstaller 1.27.4), ?biocLite for help
* checking for file 'DaMiRseq/DESCRIPTION' ...Error : file 
'/home/mtmorgan/b/git/DaMiRseq/DESCRIPTION' is not in valid DCF format
  EXISTS but not correct format

Revise, build, and check your package (using Bioc-devel) locally, then 
push to git.bioconductor.org (and github).

Martin

> Thanks again,
> Mattia
> 
> Da: Turaga, Nitesh<mailto:Nitesh.Turaga@RoswellPark.org>
> Inviato: venerd� 22 settembre 2017 17:10
> A: Mattia Chiesa<mailto:mattia.chiesa@hotmail.it>
> Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
> Oggetto: Re: [Bioc-devel] Errors updating DaMiRseq package
> 
> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
> 
> This should help you with the issue you are having. Please follow those steps.
> 
> Best,
> 
> Nitesh
> 
> 
> > On Sep 22, 2017, at 11:02 AM, Mattia Chiesa <mattia.chiesa@hotmail.it> wrote:
> > 
> > Dear all,
> > I am the mantainer of the DaMiRseq package. I have some problems with GIT:
> > I filled the form for ssh key some weeks ago and I guess everthinks is ok.
> > 
> > $ git remote -v
> > origin  https://github.com/BioinfoMonzino/DaMiRseq.git (fetch)
> > origin  https://github.com/BioinfoMonzino/DaMiRseq.git (push)
> > upstream        git@git.bioconductor.org:packages/DaMiRseq.git (fetch)
> > upstream        git@git.bioconductor.org:packages/DaMiRseq.git (push)
> > 
> > Now, I want to fix some minor bugs in the package (e.g. some words in the \
> > vignette) for the next release. Therefore, I performed changes and bumped the \
> > version of DESCRIPTION FILE to 1.1.2 (it is 1.1.1 in devel \
> > https://www.bioconductor.org/packages/devel/bioc/html/DaMiRseq.html ) and try to \
> > update both the Bioconductor and the exixting GitHub repository ( \
> > https://github.com/BioinfoMonzino/DaMiRseq \
> > )<https://github.com/BioinfoMonzino/DaMiRseq>. So, following the "Scenario 2" for \
> > the git transition ( \
> > https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-2-push-to-github-gitbioc.md) \
> > I have just run: 
> > $ git add .
> > $ git commit -m  "message for commit"
> > $ git push origin master
> > 
> > Counting objects: 3, done.
> > Delta compression using up to 12 threads.
> > Compressing objects: 100% (3/3), done.
> > Writing objects: 100% (3/3), 327 bytes | 0 bytes/s, done.
> > Total 3 (delta 2), reused 0 (delta 0)
> > remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
> > To https://github.com/BioinfoMonzino/DaMiRseq.git
> > 21d32c2..1890325  master -> master
> > 
> > Everythink seems ok, but finally I ran:
> > 
> > $ git push upstream master
> > Enter passphrase for key '/c/Users/mchiesa/.ssh/id_rsa':
> > 
> > To git.bioconductor.org:packages/DaMiRseq.git
> > ! [rejected]        master -> master (non-fast-forward)
> > error: failed to push some refs to \
> >                 'git@git.bioconductor.org:packages/DaMiRseq.git'
> > hint: Updates were rejected because the tip of your current branch is behind
> > hint: its remote counterpart. Integrate the remote changes (e.g.
> > hint: 'git pull ...') before pushing again.
> > hint: See the 'Note about fast-forwards' in 'git push --help' for details.
> > 
> > I have also thought to "merge conflicts", but I got again an error message
> > 
> > $ git merge upstream/master
> > fatal: refusing to merge unrelated histories
> > 
> > What should I do?
> > Thank in advance,
> > Mattia
> > 
> > 
> > 
> > 
> > [[alternative HTML version deleted]]
> > 
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
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