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[Bioc-devel] updating Bioconductor package that is already on Github

6 messages · Simina Boca, Sean Davis, Shepherd, Lori +1 more

Original
Simina Boca
# 
Dear all,

I hope this isn't a duplicate of another question. Here goes:

- I would like to update my swfdr package, which is already on
Bioconductor. It is also on Github and my submission process was via
opening an issue at https://github.com/Bioconductor/Contributions/issues/213

- At this point there are some slight differences between the Github and
Bioconductor versions, for example the Bioconductor version number got
automatically bumped to 1.0.0 upon acceptance

- I would like to first synchronize what is on Github to have the current
version that is on Bioconductor before updating and also include any
updates in the next version of the package on Bioconductor

- I did "git remote add upstream git at git.bioconductor.org:packages/swfdr.git"
as per some of the instructions for developers, so that now I have:
~\Documents\GitHub\swfdr [master ? +0 ~0 -1 !]> git remote -v
origin  https://github.com/leekgroup/swfdr.git (fetch)
origin  https://github.com/leekgroup/swfdr.git (push)
upstream        git at git.bioconductor.org:packages/swfdr.git (fetch)
upstream        git at git.bioconductor.org:packages/swfdr.git (push)

*but* when I try to fetch upstream content, via:
git fetch upstream

I get an error:
~\Documents\GitHub\swfdr [master ? +0 ~0 -1 !]> git fetch upstream
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights

Am I missing something here? Alternatively, I suppose I can just make the
changes I want and simply open another issue, although it would be nice to
have an easy to sync it with what is already on Bioconductor.

Thank you in advance for your help and I apologize if I missed anything
obvious!

Cheers,
Simina
Sean Davis
# 
Hi, Simina.
On Tue, Sep 5, 2017 at 11:40 PM, Simina Boca <smb310 at georgetown.edu> wrote:

            

      
      
      
    

        
Take a look at the FAQ, #3, here:

http://bioconductor.org/developers/how-to/git/faq/

Have you submitted an SSH key somehow?

            

      
      
      
    

        
When everything is working, you will "own" the bioconductor git repo, so
working it will be roughly equivalent to working with github. Opening an
issue on the package submission repo will not get you what you want and is
only for new packages.

Sean

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Shepherd, Lori
    

    

      
      #
    

  


  

      
Have you submitted your ssh key


https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform

[https://lh6.googleusercontent.com/aTIh4yWF4TsFYR95qIA_lBuCgvLJ88Q4WzDmdBuie6ndQirxWI0jhfRBF7eO-n3W6SE=w1200-h630-p]<https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform>

git / svn transition: ssh keys<https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform>
docs.google.com
Use this form to link your existing svn credentials with access permissions to the new Bioconductor git repository. To do this, we need an ssh public key. You might have added these to github, see https://github.com/your-github-id.keys. Alternatively, you may provide the ssh public key directly, e.g., copy-pasting ~/.ssh/id_rsa.pub. To generate ssh key pairs, see https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/






Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simina Boca
    

    

      
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Thank you so much Sean and Lori! For some reason I thought the ssh key part
was only relevant if the package was submitted via svn, which is why i had
overlooked those instructions initially.

Cheers,
Simina

On Wed, Sep 6, 2017 at 7:01 AM, Shepherd, Lori <

        
Lori.Shepherd at roswellpark.org> wrote:

        

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    
5 days later

    

      
      

        


  

        

      Simina Boca
    

    

      
      #
    

  


  

      
Thank you again Sean and Lori! I am now past that initial stage. I now have
to resolve merge conflicts, primarily in the DESCRIPTION file. When
following the instructions here http://bioconductor.org/
developers/how-to/git/resolve-conflicts/ however, I ended up getting the
error below:

~\Documents\GitHub\swfdr [master ? +0 ~0 -1 !]> git push upstream master
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
FATAL: W any packages/swfdr SiminaB DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

Thank you so much!

Best,
Simina

        
On Wed, Sep 6, 2017 at 10:56 AM, Simina Boca <smb310 at georgetown.edu> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Turaga, Nitesh
    

    

      
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Hi Simina,

Please try again now.

The issue was you didn?t submit your SVN ID ?s.boca?. This is needed for people who have been maintainers before the Git transition, to associate your key to the package.

For new packages this issue doesn?t apply, because we just collect their Github IDs. 

Hope this helps.

Best,

Nitesh

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
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