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[Bioc-devel] Update data in data package, pcxnData

6 messages · Sokratis Kariotis, Turaga, Nitesh, Shepherd, Lori

Original
Shepherd, Lori
# 
Where you able to update master?  Or are you having access trouble for both branches?  Please use reply all so that other members on the team can answer when appropriate and the responses go to the mailing list.

Your package is in the git repository and has access with the ID s.kariotis.  Can you please copy the commands with the output you are receiving that make you think that you do not have access?

Please also include the output of

git remote -v

and

ssh -T git at git.bioconductor.org
(you should see RW access next to your package)


Please




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Sokratis Kariotis
# 
Hey Lori,

While under the RELEASE_3_6 branch and using git fetch upstream or git push
upstream/RELEASE_3_6:






*Warning: Permanently added 'git.bioconductor.org
<http://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 rightsand the
repository exists.*


git remove -v results to:






*origin  https://github.com/hidelab/pcxn.git
<https://github.com/hidelab/pcxn.git> (fetch)origin
https://github.com/hidelab/pcxn.git <https://github.com/hidelab/pcxn.git>
(push)upstream        git at git.bioconductor.org:packages/pcxn.git
(fetch)upstream        git at git.bioconductor.org:packages/pcxn.git (push)*
The ssh command also gives:




*Warning: Permanently added 'git.bioconductor.org
<http://git.bioconductor.org>,34.192.48.227' (ECDSA) to the list of known
hosts.Permission denied (publickey).*

*Cheers,*

*Sokratis*


On 23 March 2018 at 11:35, Shepherd, Lori <Lori.Shepherd at roswellpark.org>
wrote:

  
    

      
      
    

  


  


      

    

    
3 days later

    

      
      

        


  

        

      Turaga, Nitesh
    

    

      
      #
    

  


  

      
Hi Sokratis,

Your key(s) on file is 

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCmaqfMSKr3AtAPpMz5m4pITFaq6AVp+v8ABp7FfTvcirdZz834ECUsnlsvkLZL2uWtelNo7TFgaIo0Jfi21IDSZ3R0Oyl49vsYXqHAB9CtH3yItiaddq+nLG4s+jnlAftWyQOFa/02LyYwBvEnuacLxxZimveZ6VywBF9Q7pz3v+pGXZb9LDmK9khr6RvO+mRcD7dJyFt1CySEbxVZj/TKHwn4Vs9lQIISxeeKo9ypxFzW8YDzmACLga7u2BVX622/UjrrXanZhmNWcEEgxw3B8rgzDZi2YcwbBG3RqXncE29a6gEvsjqJbUh5jIyk9cLunUjQpVwqrnlHXcRGjkLB

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC9G4NrGqxmHJj26MBW4A2EJLCD8z+QV5fRehTPiNzwHztQiJzj8Kakesk8FcfZt1Y3cPZRhwzyuwxiZQRrB1qidg6nFfLwjHBi24xLo9RWQBxTfgCDWyUKb5WLFZn6wQWhWp10ooRz0oGX9Syh6rw+rCiHiFwE+CxTWjELwlASiuDUa/599MBe7Q2mMVmtP4QXFyaOGsq46I16k80Ta0YzM1bbIZlY+YFbmw8GhDrZ//z+2FJ241AR4nuTx8QJ6fXLMnfo8IgZtDxJYw3G24ZduP93Q47ptl4u5IElZzEceXN53VD1WQkphk4+SDr24Fm4qkYkQ2s5VaPk6Yh3oXYd

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC7QB8rwK1n7/cD5rfDoZe/uSVGVqkBCHOEbfReiEt8dQCx1KqrjPFRv2geTDkhmQpSmVSWxKbrmbgMmogGQZykKmT2CybrGQZavOgwsFNzvkJYW8InfQ6eO09ovHKxW8u/kPBxuR8tUQAqWLaMVDp0UZseC79zqMAZRVOxvy4Esa5E/gIPDPrrhAVraTTqZjLGKOvii2WnInYZP4oR2KsBck5sIdYUFIdkDU73oHbTlvTl8ic7s5uiW94+VM5Cj8oi5sZtQKptdLK8cQWGerCcYj/ZzlvMpn1wXKbmGYiGVWDZy5qtO42UsW5EIVb1QlGXh//ppBJRnZ9ORSZahFsf

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAACAQDdEiGtAz6nXBAaGbUCLQFMWYE9mKRtKf+20GTGAt83aM7uMpIH9fiHIFpe+5ghm3+68fKVTuprG2PYosiy3Nvk79/WZ02IZuYGfFHXEIhsa1aIVMNsofvOrwBhFezbvoZ3b9oPakFbQFiAtjPkN6h4drr+iQq4to4jc5wvYw07uqIEEG8nZfiB+QWa5s+rplTS3zJZzr7xpEDT/7ZHpKVduZUg34tzaN4+vONgofgOthUMWArO3oO69wPwAdoAUACRmXT02xknrcWZm4UtuhzT98FHLznSowZMLG3jm8vKgsgbH8UGGtz478UZW5xE4qS5LHiKJbcZFBCLFABUjCajuYF3z+bZF0cxbT9d+25kpp/p89lvljsvlE7vbxdqFmeobGSQ6ftDq5btdEHfD2rc++iWEZgmOGjcHtDxUem3nNGCOYtDkPAIKES5oCCtlD9sBL5gLFHTkl3KyxNdIsH9j0iNFdJmEHySZh2ePdrqG7ZE/FOKf77XTX+acqgydF+Dsep16lTIxk94MXLk7Sz2v8XQqFtETa5q0Gkm70Ok/qht/O80nWUT3QX44sPM4ivPckOHwnZjywpZyBONas26hP0M1pZSEvB5qLCMKyD4YmTJ5aZkeCHh6wsW7CDZvNJl7dWyn2kxrxgin4nhqSrDryEYl3qYZxwOG0XzfHGVfQ==

Are you sure you are using a private key which corresponds to any of these public keys? I?d start with that. 

Best 

Nitesh

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
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      Sokratis Kariotis
    

    

      
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Hey all,

Thanks for the advice. I managed to fix the problem of no permissions! My
windows machine, after an update, changed the paths to my github keys and
had to reposition them.  I have now succesfully pushed in both master and
RELEASE_3_6 branches.

Cheers,
Sokratis

On 26 March 2018 at 15:47, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    
1 day later

    

      
      

        


  

        

      Sokratis Kariotis
    

    

      
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Hey all,

The packages' changes went through to the 3_6 branch, but since pcxn and
pcxnData depend on each other, there are errors when they get built as they
see the old version of the other package. In the current example:
https://www.bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-buildsrc.htm
l , the pathCor_pathprint_v1.2.3_unadjusted_frame file is now located in
the new pcxnData package but during build the old pcxnData is being used
and the error occurs since the file is not there. I have checked both
packages locally and they work when both are in their updated form. How can
we bypass this? Thanks.

Cheers,
Sokratis

On 27 March 2018 at 14:02, Sokratis Kariotis <s.kariotis at sheffield.ac.uk>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    
1 day later

    

      
      

        


  

        

      Shepherd, Lori
    

    

      
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I believe this should clear up in a few days.  Because of the circular dependencies, it will require a few passes through the build system.


For example:


First pass:

The pcxnData package has a force install, so it will get installed even if it fails the build and check. The pcxn package will also fail its first pass through.


Second pass:

the pcxn package will find the newly installed version of the pcxnData package and pass.  The pcxnData package will still fail


Third pass:

pcxnData will find the newly built software package and pass as will the linux version of the software package.


Forth pass:

May be needed for the mac and windows versions to find the new data package.



The last update to the software package was on March 27 - which probably missed being pulled for the March 28th report so probably included for the March 29th build report

March 29th  - both fail (but there was a force install behind the scenes)

March 30th -  data package fails, but the linux version of the software package built and propagated

http://bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/malbec1-buildsrc.html


My guess is that by Sunday's or Monday's build reports everything will be okay.

I will keep an eye on this to make sure its the case and please let us know if you still are seeing issues next week.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263