[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 14:34:13 CEST 2020
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
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > This email message may contain legally privileged and/or
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> > employee or agent responsible for the delivery of this message to the
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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
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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,
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> > 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
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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> information. If you are not the intended recipient(s), or the employee or
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> 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
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