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

Wed Sep 27 18:49:19 CEST 2017

Hi Mattia,

Please use BiocStyle::latex instead of BiocStyle::latex2 in your
vignette. The latter is deprecated.

That seems to make the LaTeX Error go away.

Cheers,
H.

On 09/26/2017 01:44 AM, Mattia Chiesa wrote:
> 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 ( https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_DaMiRseq_tokay1-2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=1ZZUhillF4Sx8Fodvq2XSUCoV2SlbHlbaQiFbkS0caU&e= ), 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 <bioc-devel-bounces at r-project.org> per conto di Mattia Chiesa <mattia.chiesa at hotmail.it>
> Inviato: sabato 23 settembre 2017 21:22
> A: Martin Morgan; Turaga, Nitesh
> Cc: bioc-devel at r-project.org
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__go.microsoft.com_fwlink_-3FLinkId-3D550986&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=kjSXw5R507jKhYdAltmXwTHpYelf2Vg9myNYk1zO9iI&e=> per Windows 10
>
> Da: Martin Morgan<mailto:martin.morgan at roswellpark.org>
> Inviato: sabato 23 settembre 2017 14:47
> A: Mattia Chiesa<mailto:mattia.chiesa at hotmail.it>; Turaga, Nitesh<mailto:Nitesh.Turaga at RoswellPark.org>
> Cc: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
> 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:Nitesh.Turaga at RoswellPark.org>
>> Inviato: venerd� 22 settembre 2017 17:10
>> A: Mattia Chiesa<mailto:mattia.chiesa at hotmail.it>
>> Cc: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
>> Oggetto: Re: [Bioc-devel] Errors updating DaMiRseq package
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_sync-2Dexisting-2Drepositories_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=0n4nGvSEDZA5c17iqVnnrnnLgoKjhCHdPh_AU-srH3Y&e=
>>
>> 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 at 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_DaMiRseq.git&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bCzeqCspPU38xGH0X-lU4evTE&e= (fetch)
>>> origin  https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_DaMiRseq.git&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bCzeqCspPU38xGH0X-lU4evTE&e= (push)
>>> upstream        git at git.bioconductor.org:packages/DaMiRseq.git (fetch)
>>> upstream        git at 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://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages_devel_bioc_html_DaMiRseq.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=dOIvyUAVEl7byqvhvs7VDnOfcDJthE5zb9y9opg4WQc&e= ) and try to update both the Bioconductor and the exixting GitHub repository ( https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_DaMiRseq&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=nJduMD4XtJ1lxSc2QbNl843gM0alPiHTvm8y-gLWiQY&e= )<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_DaMiRseq&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=nJduMD4XtJ1lxSc2QbNl843gM0alPiHTvm8y-gLWiQ
Y&e=>. So, following the "Scenario 2" for the git transition ( https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_bioc-5Fgit-5Ftransition_blob_master_doc_scenario-2D2-2Dpush-2Dto-2Dgithub-2Dgitbioc.md&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=0z84nLafAOk4yRk82Y2Lw70RaJfmqvI5zOuTIoRe3ko&e=) 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_DaMiRseq.git&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bCzeqCspPU38xGH0X-lU4evTE&e=
>>>     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 at 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]]
>>>
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>>
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Hervé Pagès

Program in Computational Biology
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