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[Bioc-devel] troubles with fetching Bioconductor github

7 messages · Piotr, Turaga, Nitesh, Felix Ernst

Original
Piotr
# 
Dear All,

I try to follow instruction here:
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

however, I find the following
git fetch --all
Fetching origin
Fetching upstream
sign_and_send_pubkey: signing failed: agent refused operation
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

I have correct ssh keys and I am almost sure about 1 hr ago it worked.
What might have happened?

I created new ssh key but it is still not working

Kind regards,
Piotr
Turaga, Nitesh
# 
Please copy the result of this,

	git remote -v

and send it to us so we have more information.

http://bioconductor.org/developers/how-to/git/faq/ , check #14

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.
Piotr
# 
Dear Nitesh,
it is as follows:

dit at dit-N73Jn:~/Desktop/BRAIN$ git remote -v
origin    https://github.com/ditti2/BRAIN.git (fetch)
origin    https://github.com/ditti2/BRAIN.git (push)
upstream    git at git.bioconductor.org:packages/BRAIN.git (fetch)
upstream    git at git.bioconductor.org:packages/BRAIN.git (push)

bests,
Piotr

On Thu, Aug 2, 2018 at 11:35 PM Turaga, Nitesh <
Nitesh.Turaga at roswellpark.org> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Turaga, Nitesh
    

    

      
      #
    

  


  

      
Hi,

Can you upload a fresh key and try again? Everything on our end seems to be in good shape. Maybe you are using the wrong key.

After you upload a new key, please try to make sure you are using the right key.


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.

  
  


  


      

    

    

      
      

        


  

        

      Piotr
    

    

      
      #
    

  


  

      
Dear Nitesh,
now works ok, although I did not change anything.
maybe there is a time when I should not connect with Bioconductor git?


Piotr

On Thu, Aug 2, 2018 at 11:35 PM Turaga, Nitesh <

        
Nitesh.Turaga at roswellpark.org> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Turaga, Nitesh
    

    

      
      #
    

  


  

      
No, I'm not aware of any such issues.

Maybe someone else in the community can chip in with some information about this.

Best,

Nitesh

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13 days later

    

      
      

        


  

        

      Felix Ernst
    

    

      
      #
    

  


  

      
Hi all,

I had a problem accessing git at bioconductor yesterday as well from a Windows
1803 PC. With the same PC it worked in March, but not now.

The last bit about the version is important since the OpenSSH form Microsoft
is apparently in 1803 the default. I don't know, how the setup was
previously. 

How I diagnosed the problem:
- ssh-add -l does not show previously added keys (powershell or git bash
terminal in rstudio)
- re-adding keys works and is persistent after a restart without a .bashrc
script or anything ()
- ssh -T works
- git fetch does not

The last two information means, that there are to key stores at play.

There are two solutions, which worked for me:
- copy and rename the key file to ~/.ssh/id_rsa (git finds it then and ask
for passphrase. The config file in ~/.ssh/ was ignored)
- change core.sshCommand option in .gitconfig to
"C:/Windows/System32/OpenSSH/ssh.exe" (git uses the stored keys added with
ssh-add)

I don't know, where I found all the bits of information, but it was
basically a lot of googling. I am also not sure, whether this a specific
problem to my machine or a general Windows 1803 issue. I am also not sure,
what the underlying cause for the behaviour is. It is more a fix for the
symptom, not a cure.

Hope this helps some people.

Best regards,
Felix

---
Felix Ernst, PhD
Universit? Libre de Bruxelles
RNA MOLECULAR BIOLOGY
BIOPARK Charleroi Brussels-South CAMPUS
Rue Profs Jeener & Brachet, 12
B-6041 Charleroi - Gosselies
BELGIUM
+32(2)650 9774 (office phone)
felix.ernst at ulb.ac.be



-----Original Message-----
From: Bioc-devel <bioc-devel-bounces at r-project.org> On Behalf Of Turaga,
Nitesh
Sent: Freitag, 3. August 2018 12:21
To: Piotr <piotr.dittwald at gmail.com>
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] EXTERNAL: troubles with fetching Bioconductor
github

No, I'm not aware of any such issues.

Maybe someone else in the community can chip in with some information about
this.

Best,

Nitesh

Get Outlook for Android<https://aka.ms/ghei36>