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[Bioc-devel] Errors updating DaMiRseq package

10 messages · Turaga, Nitesh, Mattia Chiesa, Martin Morgan +2 more

Original
Mattia Chiesa
# 
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://github.com/BioinfoMonzino/DaMiRseq.git (fetch)
origin  https://github.com/BioinfoMonzino/DaMiRseq.git (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://www.bioconductor.org/packages/devel/bioc/html/DaMiRseq.html ) and try to update both the Bioconductor and the exixting GitHub repository ( https://github.com/BioinfoMonzino/DaMiRseq )<https://github.com/BioinfoMonzino/DaMiRseq>. So, following the "Scenario 2" for the git transition ( https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-2-push-to-github-gitbioc.md) 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://github.com/BioinfoMonzino/DaMiRseq.git
   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
Turaga, Nitesh
# 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

This should help you with the issue you are having. Please follow those steps.

Best,

Nitesh
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.
Mattia Chiesa
# 
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?
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

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

This should help you with the issue you are having. Please follow those steps.

Best,

Nitesh
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.
Martin Morgan
#
On 09/23/2017 08:44 AM, Mattia Chiesa wrote:
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
This email message may contain legally privileged and/or...{{dropped:2}}
Mattia Chiesa
# 
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://go.microsoft.com/fwlink/?LinkId=550986> 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:
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
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.
2 days later
Mattia Chiesa
# 
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 ( http://bioconductor.org/checkResults/devel/bioc-LATEST/DaMiRseq/tokay1-buildsrc.html ), 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
1 day later
Hervé Pagès
# 
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:
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:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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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, Herv? Pag?s wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Andrzej Oleś
    

    

      
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Thanks Herv? 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, Herv? Pag?s <hpages at fredhutch.org> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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Excellent! Thanks Andrzej.

H.

        
On 09/27/2017 01:05 PM, Andrzej Ole? wrote: