[Bioc-devel] R: R: R: Errors updating DaMiRseq package
Andrzej Oleś
andrzej.oles at gmail.com
Wed Sep 27 22:05:57 CEST 2017
Thanks Hervé for troubleshooting!
This should be now fixed in BiocStyle 2.5.39, for details see the
discussion at https://github.com/Bioconductor/BiocStyle/issues/36.
Cheers,
Andrzej
On Wed, Sep 27, 2017 at 8:42 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> It's better to discuss this on the bioc-devel list, Others might
> benefit.
>
> > I really did not know that latex2 was deprecated. I will modify
> > the vignette ASAP.
> >
> > Many thanks in advance.
> >
> > Mattia
>
> To troubleshoot this you can proceed in 2 steps:
>
> 1) First generate the .tex file with 'R CMD Sweave DaMiRseq.Rnw'
>
> 2) Then try to render it with 'pdflatex DaMiRseq.tex'
>
> I did this on my laptop. Step 1) worked fine but step 2) produced the
> same error as reported by our build system:
>
> ! LaTeX Error: Environment kframe undefined.
>
> See the LaTeX manual or LaTeX Companion for explanation.
> Type H <return> for immediate help.
> ...
>
> l.43 \begin{kframe}
>
> So I opened the .tex file with an editor, and went to line 43 which is
> where the LaTex error is happening. There I saw the deprecation warning
> message right below line 43:
>
> \begin{kframe}
>
> {\ttfamily\noindent\color{warningcolor}{\#\# Warning: 'latex2' is
> deprecated.\\\#\# Use 'latex' instead.\\\#\# See help("{}Deprecated"{})}}
>
> \end{kframe}
>
> Unfortunately you never got to see this message because you never got
> to see the rendered version of the vignette. In the rendered version,
> you wouldn't miss it because it would get displayed at the top of the
> document and with special font and color.
>
> Anyway, what's interesting here is that it's the LaTeX code for the
> warning itself that seems to be causing the LaTeX error. If I remove
> it, then step 2) works!
>
> To reproduce all this, and like with any problem reported on the build
> report for Bioc devel, you need to use Bioc devel and to make sure that
> all your packages are up-to-date. In particular here, you want to make
> sure that you have the latest devel version of BiocStyle (which is
> 2.5.38 at the moment).
>
> Hope this helps,
> H.
>
>
>
>
> On 09/27/2017 09:49 AM, Hervé Pagès wrote:
>
>> 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__biocondu
>>> ctor.org_checkResults_devel_bioc-2DLATEST_DaMiRseq_tokay1-
>>> 2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
>>> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUi
>>> kUbZS9ug9hKfvxut-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=eRAMFD
>>> 45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhz
>>> WA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=kjSXw5R50
>>> 7jKhYdAltmXwTHpYelf2Vg9myNYk1zO9iI&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__biocondu
>>>> ctor.org_developers_how-2Dto_git_sync-2Dexisting-2Dreposito
>>>> ries_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY
>>>> _wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9h
>>>> Kfvxut-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=eRAMFD45gAfqt84Vt
>>>>> BcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7w
>>>>> sCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bC
>>>>> zeqCspPU38xGH0X-lU4evTE&e=
>>>>> (fetch)
>>>>> origin
>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>>>>> com_BioinfoMonzino_DaMiRseq.git&d=DwIGaQ&c=eRAMFD45gAfqt84Vt
>>>>> BcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7w
>>>>> sCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bC
>>>>> zeqCspPU38xGH0X-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.bio
>>>>> conductor.org_packages_devel_bioc_html_DaMiRseq.html&d=
>>>>> DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W
>>>>> YiZvSXAJJKaaPhzWA&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=eRAMFD45gAfqt84VtBcfh
>>>>> Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv5
>>>>> 6kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=nJduMD4XtJ1lxSc2QbNl843
>>>>> gM0alPiHTvm8y-gLWiQY&e=
>>>>> )<https://urldefense.proofpoint.com/v2/url?u=https-3A__
>>>>> github.com_BioinfoMonzino_DaMiRseq&d=DwIGaQ&c=eRAMFD45gAfqt8
>>>>> 4VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Ayl
>>>>> M7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=nJduMD4XtJ1lxSc2Q
>>>>> bNl843gM0alPiHTvm8y-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_sce
>> nario-2D2-2Dpush-2Dto-2Dgithub-2Dgitbioc.md&d=DwIGaQ&c=eRAMF
>> D45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPh
>> zWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=0z84nLaf
>> AOk4yRk82Y2Lw70RaJfmqvI5zOuTIoRe3ko&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=eRAMFD45gAfqt84Vt
>>>>> BcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7w
>>>>> sCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bC
>>>>> zeqCspPU38xGH0X-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]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
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>>>>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt
>>>>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Ay
>>>>> lM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=XcDeJoXgJ7OmlgHm
>>>>> iJ1vYTLGouGYA0yljmrgZvoSQlU&e=
>>>>>
>>>>>
>>>>
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>>
> --
> 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: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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