Excellent! Thanks Andrzej. H.
On 09/27/2017 01:05 PM, Andrzej Oleś wrote:
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 <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_BiocStyle_issues_36&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cc7v28H-H8uZkc_NZj6sKslSYJv6SNAJjn_h8JIvxFk&s=JAqDcTJNbEguazxIeB5OANogrU9ZX4wkgCbSVGz79UM&e=>. Cheers, Andrzej On Wed, Sep 27, 2017 at 8:42 PM, Hervé Pagès <hpa...@fredhutch.org <mailto: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__bioconductor.org_checkResults_devel_bioc-2DLATEST_DaMiRseq_tokay1-2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=1ZZUhillF4Sx8Fodvq2XSUCoV2SlbHlbaQiFbkS0caU&e= <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-boun...@r-project.org <mailto:bioc-devel-boun...@r-project.org>> per conto di Mattia Chiesa <mattia.chi...@hotmail.it <mailto:mattia.chi...@hotmail.it>> Inviato: sabato 23 settembre 2017 21:22 A: Martin Morgan; Turaga, Nitesh Cc: bioc-devel@r-project.org <mailto: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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=kjSXw5R507jKhYdAltmXwTHpYelf2Vg9myNYk1zO9iI&e= <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.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>> Inviato: sabato 23 settembre 2017 14:47 A: Mattia Chiesa<mailto:mattia.chi...@hotmail.it <mailto:mattia.chi...@hotmail.it>>; Turaga, Nitesh<mailto:nitesh.tur...@roswellpark.org <mailto:nitesh.tur...@roswellpark.org>> Cc: bioc-devel@r-project.org <mailto:bioc-devel@r-project.org><mailto: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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__git.bioconductor.org&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cc7v28H-H8uZkc_NZj6sKslSYJv6SNAJjn_h8JIvxFk&s=eghcfUexSOupg-OcZ6n38piTuCicFMVp4sdkDWirhGg&e=> (and github). Martin Thanks again, Mattia Da: Turaga, Nitesh<mailto:nitesh.tur...@roswellpark.org <mailto:nitesh.tur...@roswellpark.org>> Inviato: venerd� 22 settembre 2017 17:10 A: Mattia Chiesa<mailto:mattia.chi...@hotmail.it <mailto:mattia.chi...@hotmail.it>> Cc: bioc-devel@r-project.org <mailto:bioc-devel@r-project.org><mailto: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__bioconductor.org_developers_how-2Dto_git_sync-2Dexisting-2Drepositories_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=0n4nGvSEDZA5c17iqVnnrnnLgoKjhCHdPh_AU-srH3Y&e= <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.chi...@hotmail.it <mailto: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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bCzeqCspPU38xGH0X-lU4evTE&e= <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= <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 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.bioconductor.org_packages_devel_bioc_html_DaMiRseq.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=dOIvyUAVEl7byqvhvs7VDnOfcDJthE5zb9y9opg4WQc&e= <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-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 <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= <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= <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 '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? 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[[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=XcDeJoXgJ7OmlgHmiJ1vYTLGouGYA0yljmrgZvoSQlU&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=XcDeJoXgJ7OmlgHmiJ1vYTLGouGYA0yljmrgZvoSQlU&e=> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=XcDeJoXgJ7OmlgHmiJ1vYTLGouGYA0yljmrgZvoSQlU&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=XcDeJoXgJ7OmlgHmiJ1vYTLGouGYA0yljmrgZvoSQlU&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 <mailto:hpa...@fredhutch.org> Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cc7v28H-H8uZkc_NZj6sKslSYJv6SNAJjn_h8JIvxFk&s=NY5DmVN9_uN7hUOJfrGXdJS1oOCUmPMK44tAaDCNIos&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
