[Bioc-devel] R: R: R: Errors updating DaMiRseq package
Hervé Pagès
hpages at fredhutch.org
Wed Sep 27 20:42:09 CEST 2017
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-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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AylM7wsCv56kYzezEzxrUikUbZS9ug9hKfvxut-TDqY&s=kjSXw5R507jKhYdAltmXwTHpYelf2Vg9myNYk1zO9iI&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__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.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=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 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.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
>>>> '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
>>>> 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=
>>>>
>>>
>>>
>>>
>>> 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. Thank you.
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioc-devel at 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=
>>>
>>>
>>
>>
>> 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. Thank you.
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at 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=
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at 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=
>>
>>
>
--
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
More information about the Bioc-devel
mailing list