[Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)
Shepherd, Lori
Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Mon Mar 30 13:56:27 CEST 2020
I do not see any changes in the git.bioconductor.org server on the master branch.
Did you remember to do the following to commit your changes before you tried pushing?
git commit -a
In general a good basic workflow for working on the devel (master) branch is
git fetch --all
git pull
git pull upstream origin
# make your changes including a version bump
git commit -a # commit your changes and give an informative message
git push
git push upstream master
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Enio Gjerga <enio.gjerga using gmail.com>
Sent: Monday, March 30, 2020 6:05 AM
To: Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org>
Cc: Hervé Pagès <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)
Hi,
Thank you very much. After following your suggestion I went to set up the
SSH and I was also able to clone the packages I was maintaining locally.
Next I did my desired changes to the cloned package locally and I wanted to
push these changes to the Bioconductor repositories. For that I used the
following commands:
1. git checkout master from where I got a list of files in the package
labeled as M/D and the message: Already on 'master'. Your branch is up to
date with 'origin/master'.
2. git push upstream master from where I got the message: Everything
up-to-date.
Does this mean that my changes are pushed to Bioconductor repositories
correctly?
Thank you again for all the help:))
Cheers,
Enio
On Fri, 27 Mar 2020 at 17:43, Turaga, Nitesh <Nitesh.Turaga using roswellpark.org>
wrote:
> You should try and set up your system using SSH from your Github account
> as well.
>
> > On Mar 27, 2020, at 12:25 PM, Enio Gjerga <enio.gjerga using gmail.com> wrote:
> >
> > 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> 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:<username>/<repository>`
> >
> > > On Mar 27, 2020, at 12:15 PM, Enio Gjerga <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> wrote:
> > > Ok, can you also show my the result of
> > >
> > > ssh - T git using git.bioconductor.org | grep CNORfeeder
> > >
> > > > On Mar 27, 2020, at 11:54 AM, Enio Gjerga <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:packages/CNORfeeder.git
> (fetch)
> > > > upstream 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" 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
> > > >
> > > > HostName
> > > > 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> 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>
> 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" command) or clone it locally
> (through "git clone 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> 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 on behalf of 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: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 mailing list
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> > > > >
> > > > >
> > > > >
> > > > >
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> > > > >
> > > > >
> > > > > --
> > > > > 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,
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> > > >
> > > >
> > > > --
> > > > 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
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> > >
> > >
> > > --
> > > 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,
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--
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057
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