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 <hpa...@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-boun...@r-project.org> per conto di Mattia >>> Chiesa <mattia.chi...@hotmail.it> >>> Inviato: sabato 23 settembre 2017 21:22 >>> A: Martin Morgan; Turaga, Nitesh >>> Cc: bioc-devel@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.mor...@roswellpark.org> >>> Inviato: sabato 23 settembre 2017 14:47 >>> A: Mattia Chiesa<mailto:mattia.chi...@hotmail.it>; Turaga, >>> Nitesh<mailto:nitesh.tur...@roswellpark.org> >>> Cc: bioc-devel@r-project.org<mailto:bioc-devel@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.tur...@roswellpark.org> >>>> Inviato: venerd� 22 settembre 2017 17:10 >>>> A: Mattia Chiesa<mailto:mattia.chi...@hotmail.it> >>>> Cc: bioc-devel@r-project.org<mailto:bioc-devel@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.chi...@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 g...@git.bioconductor.org:packages/DaMiRseq.git (fetch) >>>>> upstream g...@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 >>>>> 'g...@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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et >>>>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt >>>>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Ay >>>>> lM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=XcDeJoXgJ7OmlgHm >>>>> iJ1vYTLGouGYA0yljmrgZvoSQlU&e= >>>>> >>>>> >>>> >>>> >>>> This email message may contain legally privileged and/or confidential >>>> information. If you are not the intended recipient(s), or the >>>> employee or agent responsible for the delivery of this message to the >>>> intended recipient(s), you are hereby notified that any disclosure, >>>> copying, 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 delete this email message from your >>>> computer. 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If >>> you have received this message in error, please notify the sender >>> immediately by e-mail and delete this email message from your >>> computer. Thank you. >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et >>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt >>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Ay >>> lM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=XcDeJoXgJ7OmlgHm >>> iJ1vYTLGouGYA0yljmrgZvoSQlU&e= >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et >>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt >>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Ay >>> lM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=XcDeJoXgJ7OmlgHm >>> iJ1vYTLGouGYA0yljmrgZvoSQlU&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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel