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.tur...@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.gje...@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.sheph...@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-boun...@r-project.org> on behalf of Enio > Gjerga <enio.gje...@gmail.com> > > Sent: Monday, March 30, 2020 6:05 AM > > To: Turaga, Nitesh <nitesh.tur...@roswellpark.org> > > Cc: Hervé Pagès <bioc-devel@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.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. 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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 > > > > 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
