[Bioc-devel] Fwd: Trying to access the source repository of a bioconductor package (Developer Access)

Fri Mar 27 17:42:07 CET 2020

Seems the mailing list got dropped off.

Forwarding to make sure the community is in the know.

Begin forwarded message:

From: Enio Gjerga <enio.gjerga using gmail.com<mailto:enio.gjerga using gmail.com>>
Subject: Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)
Date: March 27, 2020 at 12:25:42 PM EDT
To: "Turaga, Nitesh" <Nitesh.Turaga using roswellpark.org<mailto:Nitesh.Turaga using roswellpark.org>>

Hi,

Ahh apparently I cannot. I tried to clone a random repo (PHONEMeS) locally through the command you provided, and then got the following:

Cloning into 'PHONEMeS'...
Permission denied (publickey).
fatal: Could not read from remote repository.

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

I usually rely on the Github Desktop which uses the HTTPS option. Might there be something wrong with my GitHub settings?

Cheers,

On Fri, 27 Mar 2020 at 17:18, Turaga, Nitesh <Nitesh.Turaga using roswellpark.org<mailto:Nitesh.Turaga using roswellpark.org>> wrote:
Can you access any git repository via the SSH protocol?

Not via HTTPS.

So you'll have to check if you can do something like, (from your own GitHub account).

`git clone git using github.com<mailto:git using github.com>:<username>/<repository>`

> On Mar 27, 2020, at 12:15 PM, Enio Gjerga <enio.gjerga using gmail.com<mailto:enio.gjerga using gmail.com>> wrote:
>
> Hi,
>
> Sure, I got the following: ssh: Could not resolve hostname -: nodename nor servname provided, or not known
>
> Thank you,
>
> On Fri, 27 Mar 2020 at 17:13, Turaga, Nitesh <Nitesh.Turaga using roswellpark.org<mailto:Nitesh.Turaga using roswellpark.org>> wrote:
> Ok, can you also show my the result of
>
>         ssh - T git using git.bioconductor.org<mailto:git using git.bioconductor.org> | grep CNORfeeder
>
> > On Mar 27, 2020, at 11:54 AM, Enio Gjerga <enio.gjerga using gmail.com<mailto:enio.gjerga using gmail.com>> wrote:
> >
> > Hi,
> >
> > Thank you for your reply. So according to #14:
> >
> > 1. I use "git remote -v" and then I get the following:
> >
> > origin        https://github.com/saezlab/CNOv2.git (fetch)
> > origin        https://github.com/saezlab/CNOv2.git (push)
> > upstream      git using git.bioconductor.org<mailto:git using git.bioconductor.org>:packages/CNORfeeder.git (fetch)
> > upstream      git using git.bioconductor.org<mailto:git using git.bioconductor.org>:packages/CNORfeeder.git (push)
> >
> > 2. Then I check if I have access to the git serve by using "ssh -T git using git.bioconductor.org<mailto:git using git.bioconductor.org>" after which I get:
> >
> > Permission denied (publickey).
> >
> > 3. According to #15, I have generated another key under the name id_rsa_bioc through the commands:
> >
> > mkdir -p ~/.ssh && chmod 700 ~/.ssh
> > touch ~/.ssh/config
> > chmod 600 ~/.ssh/config
> >
> > But it doesn't seem to generate anny ssh/config directory so was wondering how can I add the:
> >
> > host git.bioconductor.org<http://git.bioconductor.org/>
> >
> >      HostName
> > git.bioconductor.org<http://git.bioconductor.org/>
> >
> >      IdentityFile ~/.ssh/id_rsa_bioconductor
> >      User git
> >
> > The public key of id_rsa_bioc is already added on my profile in BiocCredentials and also on my GitHub account.
> >
> > As always any help is very much appreciated.
> >
> > Cheers,
> > Enio
> >
> > On Fri, 27 Mar 2020 at 16:03, Turaga, Nitesh <Nitesh.Turaga using roswellpark.org<mailto:Nitesh.Turaga using roswellpark.org>> wrote:
> > As given in #14 of the FAQ, please send me
> >
> >         git remote -v
> >
> >
> >
> >
> > > On Mar 27, 2020, at 10:54 AM, Enio Gjerga <enio.gjerga using gmail.com<mailto:enio.gjerga using gmail.com>> wrote:
> > >
> > > Hello,
> > >
> > > Thank you very much for your reply. I have added a new key on my BiocCredentials and on Github, however, I am afraid that the same issue still persists. If I try to check whether I have access to the package (using the "ssh -T git using git.bioconductor.org<mailto:git using git.bioconductor.org>" command) or clone it locally (through "git clone git using git.bioconductor.org<mailto:git using git.bioconductor.org>:packages/CNORfeeder" command) I still unfortunately get the same "permission denied (public key)" error.
> > >
> > > How can I check for my git set up?
> > >
> > > Sorry again, but quiet new on this.
> > >
> > > Cheers,
> > >
> > > On Fri, 27 Mar 2020 at 13:38, Turaga, Nitesh <Nitesh.Turaga using roswellpark.org<mailto:Nitesh.Turaga using roswellpark.org>> wrote:
> > > Try adding another key. If that doesn't work, show us your git set up.
> > >
> > > http://bioconductor.org/developers/how-to/git/faq/
> > >
> > > #13 and #14
> > >
> > > Best,
> > >
> > > Nitesh
> > >
> > >
> > > On 3/27/20, 6:15 AM, "Bioc-devel on behalf of Enio Gjerga" <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org> on behalf of enio.gjerga using gmail.com<mailto:enio.gjerga using gmail.com>> wrote:
> > >
> > >     Hello,
> > >
> > >     I am Enio Gjerga and I am the maintainer of the CNORfeeder and the CNORode
> > >     package, a role which I got recently. I am facing trouble trying to access
> > >     the source packages for then later syncing it with a Github repository and
> > >     do a few necessary updates. I try first to obtain developer access through
> > >     the "git clone git using git.bioconductor.org<mailto:git using git.bioconductor.org>:packages/CNORfeeder" command, but
> > >     then I get the error "Permission denied (publickey). fatal: Could not read
> > >     from remote repository.". I already have the GitHub id and the ssh-rsa key
> > >     on my user profile in https://git.bioconductor.org/BiocCredentials, but
> > >     apparently I still can't get the access to the package and not sure what
> > >     might be doing wrong.
> > >
> > >     Any help about this would be much appreciated.
> > >
> > >     Cheers,
> > >
> > >     Enio
> > >
> > >     --
> > >     Enio GJERGA
> > >     PhD student
> > >     JRC-COMBINE RWTH Aachen
> > >     Tel : +4917685132057
> > >
> > >         [[alternative HTML version deleted]]
> > >
> > >     _______________________________________________
> > >     Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
> > >     https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> > >
> > >
> > >
> > > 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.
> > >
> > >
> > > --
> > > Enio GJERGA
> > > PhD student
> > > JRC-COMBINE RWTH Aachen
> > > Tel : +4917685132057
> > >
> >
> >
> >
> > 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.
> >
> >
> > --
> > Enio GJERGA
> > PhD student
> > JRC-COMBINE RWTH Aachen
> > Tel : +4917685132057
> >
>
>
>
> 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.
>
>
> --
> Enio GJERGA
> PhD student
> JRC-COMBINE RWTH Aachen
> Tel : +4917685132057
>

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.

--
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057
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