Dear all,
I have seen that my package (DaMiRseq) is in status "ERROR" after my last
little modifications. It's a bit strange for me because locally everything is
all right.
Looking at the build report (
http://bioconductor.org/checkResults/devel/bioc-LATEST/DaMiRseq/tokay1-buildsrc.html
), it seems that the error occurs, compiling the vignette:
LaTeX errors:
vignettes/DaMiRseq.tex:43: LaTeX Error: Environment kframe undefined.
this correspond to this line in the TeX file:
\RequirePackage[]{Bioconductor2}
What should I do?
Thanks again,
Mattia
________________________________
Da: Bioc-devel <[email protected]> per conto di Mattia Chiesa
<[email protected]>
Inviato: sabato 23 settembre 2017 21:22
A: Martin Morgan; Turaga, Nitesh
Cc: [email protected]
Oggetto: [Bioc-devel] R: R: Errors updating DaMiRseq package
Thank you Martin for your reply. You are right: some files were not OK. Now
“build and check” end up without any errors.
I pushed again in both repositories.
Inviato da Posta<https://go.microsoft.com/fwlink/?LinkId=550986> per Windows 10
Da: Martin Morgan<mailto:[email protected]>
Inviato: sabato 23 settembre 2017 14:47
A: Mattia Chiesa<mailto:[email protected]>; Turaga,
Nitesh<mailto:[email protected]>
Cc: [email protected]<mailto:[email protected]>
Oggetto: Re: [Bioc-devel] R: Errors updating DaMiRseq package
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:[email protected]>
> Inviato: venerd� 22 settembre 2017 17:10
> A: Mattia Chiesa<mailto:[email protected]>
> Cc: [email protected]<mailto:[email protected]>
> 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 <[email protected]> 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 [email protected]:packages/DaMiRseq.git (fetch)
>> upstream [email protected]: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
>> '[email protected]: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]]
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
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