[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 15:40:35 CEST 2020 

Yes.  I see the changes pushed this morning.   They should be reflected on tomorrow's build report.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Enio Gjerga <enio.gjerga using gmail.com>
Sent: Monday, March 30, 2020 9:13 AM
To: Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org>
Cc: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>; Hervé Pagès <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

Hello,

Yes thank you. I am very new on git and will definitively have a look. However I think that I might have correctly pushed my changes to the CNORfeeder and the CNORode packages. Can someone please confirm if that the case? If not, I will carefully read the links before for the next time.

Best,

On Mon, 30 Mar 2020 at 14:46, Turaga, Nitesh <Nitesh.Turaga using roswellpark.org<mailto:Nitesh.Turaga using roswellpark.org>> wrote:
Hi Enio,

Based on the conversation you, Lori and I had, it seems that you are having a hard time with git as a version control system in general and not the Bioconductor git repository in general.

Please consider going through some good learning material so you can get started with git.

There are many resources where you can learn about git and GitHub.
        • git-and-github-learning-resources, https://help.github.com/articles/git-and-github-learning-resources/
        • git-scm, https://git-scm.com/
        • Guides, https://guides.github.com/


Best,

Nitesh

> On Mar 30, 2020, at 8:34 AM, Enio Gjerga <enio.gjerga using gmail.com<mailto:enio.gjerga using gmail.com>> wrote:
>
> Hi,
>
> Ok thank you. I do the commit as following: 'git commit -a #update CNORfeeder' and then I get the following:
>
> # Please enter the commit message for your changes. Lines starting
> # with '#' will be ignored, and an empty message aborts the commit.
> #
> # On branch master
> # Your branch is up to date with 'origin/master'.
> #
> # Changes to be committed:
> #       modified:   DESCRIPTION
> #       modified:   NAMESPACE
> #       modified:   vignettes/CNORfeeder-vignette.Rnw
> #
> # Untracked files:
> #       R/buildFeederObjectDynamic.R
> #       R/computeMSE.R
> #       R/getLBodeContObjFunctionWeighted.R
> #       R/identifyMisfitIndices.R
> #       R/integrateLinks.R
> #       R/parEstimationLBodeSSmWeighted.R
> #       R/parEstimationLBodeWeighted.R
> #       R/preprocessingWeighted.R
> #       R/runDynamicFeeder.R
> #       data/CNOlistToy_Gene.RData
> "~/CNORfeeder/.git/COMMIT_EDITMSG" 43L, 1176C
>
> However from this point the terminal becomes un-responsive and cannot type anything. Then I quit this dialog through :wq after which I get the following error:
>
> hint: Waiting for your editor to close the file... error: There was a problem with the editor 'vi'.
> Please supply the message using either -m or -F option.
>
> Please, how can I fix this issue?
>
> Cheers,
>
> On Mon, 30 Mar 2020 at 13:56, Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
> I do not see any changes in the git.bioconductor.org<http://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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Enio Gjerga <enio.gjerga using gmail.com<mailto: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<mailto: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<mailto: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<mailto: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<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: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<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: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: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
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> > > > > >
> > > > > >
> > > > > >
> > > > > >
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> > > > > > --
> > > > > > Enio GJERGA
> > > > > > PhD student
> > > > > > JRC-COMBINE RWTH Aachen
> > > > > > Tel : +4917685132057
> > > > > >
> > > > >
> > > > >
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> > > > >
> > > > > --
> > > > > Enio GJERGA
> > > > > PhD student
> > > > > JRC-COMBINE RWTH Aachen
> > > > > Tel : +4917685132057
> > > > >
> > > >
> > > >
> > > >
> > > > This email message may contain legally privileged and/or confidential
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> > > >
> > > > --
> > > > Enio GJERGA
> > > > PhD student
> > > > JRC-COMBINE RWTH Aachen
> > > > Tel : +4917685132057
> > > >
> > >
> > >
> > >
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> > >
> > >
> > > --
> > > Enio GJERGA
> > > PhD student
> > > JRC-COMBINE RWTH Aachen
> > > Tel : +4917685132057
> > >
> >
> >
> >
> > This email message may contain legally privileged and/or confidential
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>
>
> --
> Enio GJERGA
> PhD student
> JRC-COMBINE RWTH Aachen
> Tel : +4917685132057
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
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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, 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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