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.tur...@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.gje...@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.tur...@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 g...@github.com:<username>/<repository>` > > > > > On Mar 27, 2020, at 12:15 PM, Enio Gjerga <enio.gje...@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.tur...@roswellpark.org> wrote: > > > Ok, can you also show my the result of > > > > > > ssh - T g...@git.bioconductor.org | grep CNORfeeder > > > > > > > On Mar 27, 2020, at 11:54 AM, Enio Gjerga <enio.gje...@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 g...@git.bioconductor.org:packages/CNORfeeder.git > (fetch) > > > > upstream g...@git.bioconductor.org:packages/CNORfeeder.git > (push) > > > > > > > > 2. Then I check if I have access to the git serve by using "ssh -T > g...@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.tur...@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.gje...@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 g...@git.bioconductor.org" command) or clone it locally > (through "git clone g...@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.tur...@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-boun...@r-project.org on behalf of enio.gje...@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 g...@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@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 > > > > > > 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
