[Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)
Enio Gjerga
en|o@gjerg@ @end|ng |rom gm@||@com
Mon Mar 30 15:13:43 CEST 2020
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>
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> 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> wrote:
> > 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
> > > > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
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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
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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
> > > >
> > >
> > >
> > >
> > > This email message may contain legally privileged and/or confidential
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> employee or
> > > agent responsible for the delivery of this message to the intended
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> >
> >
> >
> > --
> > Enio GJERGA
> > PhD student
> > JRC-COMBINE RWTH Aachen
> > Tel : +4917685132057
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
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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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