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List: bioc-devel
Subject: Re: [Bioc-devel] R: R: R: Errors updating DaMiRseq package
From: Hervé Pagès <hpages () fredhutch ! org>
Date: 2017-09-27 20:16:16
Message-ID: 59CC0710.5010303 () fredhutch ! org
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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_BiocSt \
> yle_issues_36&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJ \
> JKaaPhzWA&m=cc7v28H-H8uZkc_NZj6sKslSYJv6SNAJjn_h8JIvxFk&s=JAqDcTJNbEguazxIeB5OANogrU9ZX4wkgCbSVGz79UM&e=>.
>
> Cheers,
> Andrzej
>
>
> On Wed, Sep 27, 2017 at 8:42 PM, Hervé Pagès <hpages@fredhutch.org
> <mailto:hpages@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_de \
> vel_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=eRAMFD45gAfqt84VtBcfh \
> Q&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@r-project.org
> <mailto:bioc-devel-bounces@r-project.org>> per conto di Mattia
> Chiesa <mattia.chiesa@hotmail.it
> <mailto:mattia.chiesa@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_wJYbW0WYiZv \
> SXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=kjSXw5R507jKhYdAltmXwTHpYelf2Vg9myNYk1zO9iI&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__go.microsoft.com_fwlink_-3FLi \
> nkId-3D550986&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJ \
> JKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=kjSXw5R507jKhYdAltmXwTHpYelf2Vg9myNYk1zO9iI&e=>>
> per Windows 10
>
> Da: Martin Morgan<mailto:martin.morgan@roswellpark.org
> <mailto:martin.morgan@roswellpark.org>>
> Inviato: sabato 23 settembre 2017 14:47
> A: Mattia Chiesa<mailto:mattia.chiesa@hotmail.it
> <mailto:mattia.chiesa@hotmail.it>>; Turaga,
> Nitesh<mailto:Nitesh.Turaga@RoswellPark.org
> <mailto:Nitesh.Turaga@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-H8uZ \
> kc_NZj6sKslSYJv6SNAJjn_h8JIvxFk&s=eghcfUexSOupg-OcZ6n38piTuCicFMVp4sdkDWirhGg&e=> \
> (and github).
> Martin
>
>
> Thanks again,
> Mattia
>
> Da: Turaga, Nitesh<mailto:Nitesh.Turaga@RoswellPark.org
> <mailto:Nitesh.Turaga@RoswellPark.org>>
> Inviato: venerd� 22 settembre 2017 17:10
> A: Mattia Chiesa<mailto:mattia.chiesa@hotmail.it
> <mailto:mattia.chiesa@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=BK7q3Xe \
> AvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=0n4nGvSEDZA5c17iqVnnrnnLgoKjhCHdPh_AU-srH3Y&e=
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_ho \
> w-2Dto_git_sync-2Dexisting-2Drepositories_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3 \
> XeAvimeWdGbWY_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@hotmail.it
> <mailto:mattia.chiesa@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_DaMiR \
> seq.git&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPh \
> zWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bCzeqCspPU38xGH0X-lU4evTE&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_DaM \
> iRseq.git&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaa \
> PhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bCzeqCspPU38xGH0X-lU4evTE&e=>
> (fetch)
> origin
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_DaMiR \
> seq.git&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPh \
> zWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bCzeqCspPU38xGH0X-lU4evTE&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_DaM \
> iRseq.git&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaa \
> PhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bCzeqCspPU38xGH0X-lU4evTE&e=>
> (push)
> upstream
> git@git.bioconductor.org:packages/DaMiRseq.git (fetch)
> upstream
> git@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
> www.bioconductor.org_packages_d" rel="nofollow">https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages_d> \
> evel_bioc_html_DaMiRseq.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_ \
> wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=dOIvyUAVEl7byqvhvs7VDnOfcDJthE5zb9y9opg4WQc&e=
> <www.bioconductor.org_packages" rel="nofollow">https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages> \
> _devel_bioc_html_DaMiRseq.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbW \
> Y_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_DaMiR \
> seq&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_DaM \
> iRseq&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzW \
> A&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=nJduMD4XtJ1lxSc2QbNl843gM0alPiHTvm8y-gLWiQY&e=>
> )<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_Da \
> MiRseq&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhz \
> WA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=nJduMD4XtJ1lxSc2QbNl843gM0alPiHTvm8y-gLWiQ
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_DaM \
> iRseq&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzW \
> A&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-5F \
> git-5Ftransition_blob_master_doc_scenario-2D2-2Dpush-2Dto-2Dgithub-2Dgitbioc.md&d=Dw \
> IGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7w \
> sCv56kYzezEzxrUikUbZS9ug9hKfvxut-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=AylM \
> 7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-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_DaMiR \
> seq.git&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPh \
> zWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=jRg9q1LljroQUCCLC2bCzeqCspPU38xGH0X-lU4evTE&e=
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BioinfoMonzino_DaM \
> iRseq.git&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaa \
> PhzWA&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@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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> 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@fredhutch.org <mailto:hpages@fredhutch.org>
> Phone: (206) 667-5791
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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@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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