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[Bioc-devel] Permission denied when fetching from BioC GitHub repository

6 messages · Federico C, Obenchain, Valerie, Turaga, Nitesh

Original
Federico C
# 
Dear all,

I?m trying to push a bug fix for wavClusteR to the BioC GitHub repository. I currently pushed the latest package version to the devel and master branch of my GitHub repository (https://github.com/FedericoComoglio/wavClusteR <https://github.com/FedericoComoglio/wavClusteR>).

To sync these changes with the bioC GitHub repository, I have followed the documentation at https://bioconductor.org/developers/how-to/git/ <https://bioconductor.org/developers/how-to/git/> . However, even though I added an upstream remote to my repository and added a public key as described, when I fetch updates from all (see https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ <https://bioconductor.org/developers/how-to/git/sync-existing-repositories/>) I get

| => git fetch --all
Fetching origin
Fetching upstream
git at git.bioconductor.org <mailto:git at git.bioconductor.org>: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

Could you please help me with this issue?

Thanks a lot for your time and patience.

Best wishes,
Federico
Obenchain, Valerie
# 
Hi Federico,

We don't have an ssh key on file for you. Please add one by following instructions at the link below and use the ID of 'f.comoglio':

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

You will get an email in the next 24 hours if the submission was successful.

Valerie
On 01/23/2018 09:47 AM, Federico C wrote:
Dear all,

I?m trying to push a bug fix for wavClusteR to the BioC GitHub repository. I currently pushed the latest package version to the devel and master branch of my GitHub repository (https://github.com/FedericoComoglio/wavClusteR <https://github.com/FedericoComoglio/wavClusteR><https://github.com/FedericoComoglio/wavClusteR>).

To sync these changes with the bioC GitHub repository, I have followed the documentation at https://bioconductor.org/developers/how-to/git/ <https://bioconductor.org/developers/how-to/git/><https://bioconductor.org/developers/how-to/git/> . However, even though I added an upstream remote to my repository and added a public key as described, when I fetch updates from all (see https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ <https://bioconductor.org/developers/how-to/git/sync-existing-repositories/><https://bioconductor.org/developers/how-to/git/sync-existing-repositories/>) I get

| => git fetch --all
Fetching origin
Fetching upstream
git at git.bioconductor.org<mailto:git at git.bioconductor.org> <mailto:git at git.bioconductor.org><mailto:git at git.bioconductor.org>: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

Could you please help me with this issue?

Thanks a lot for your time and patience.

Best wishes,
Federico

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Federico C
# 
Hi Valerie,

done. Thanks a lot,

Federico

  
  


  


      

    

    

      
      

        


  

        

      Federico C
    

    

      
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Hi Valerie,

the ssh key has now been setup and it works. I had some issues with merging but at the end I decided to force BioC master to GitHub master (following https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github- <https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github->). Afterwards, I pushed the bug fix to both origin and upstream remotes (master branch). Indeed:

| => git status
On branch master
Your branch is up-to-date with 'upstream/master'.

nothing to commit, working tree clean

However, shouldn?t wavClusteR be listed at https://github.com/Bioconductor <https://github.com/Bioconductor> at this point?

Thanks a lot for your help.
Best wishes,

Federico

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Turaga, Nitesh
    

    

      
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Hi 

Only packages maintained by Bioconductor are at that location gitHub.com/Bioconductor.  Your package is not maintained by the core-team in Bioconductor, so, it does not belong in that location.

We follow the same process as all the maintainers, we have a Github repo to take advantage of the social coding practices, and the canonical Bioconductor git server which acts as the central server for bioconductor packages.

I hope this answers your question.

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.

  
  


  


      

    

    

      
      

        


  

        

      Federico C
    

    

      
      #
    

  


  

      
Hi Nitesh,

thanks a lot for your message. It makes perfect sense.

Best wishes,

Federico