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=
), 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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=kjSXw5R507jKhYdAltmXwTHpYelf2Vg9myNYk1zO9iI&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__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> 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 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=
) 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
'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
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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
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E-mail: hpa...@fredhutch.org
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Fax: (206) 667-1319
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