Hi You are using HTTPS protocol for cloning your repository. You need to use SSH.
http://bioconductor.org/developers/how-to/git/new-package-workflow/ • SSH (developer) read / write access: g...@git.bioconductor.org • HTTPS (public) read only access: https://git.bioconductor.org Nitesh > On Sep 3, 2017, at 4:30 PM, Charles Warden <cwarde...@gmail.com> wrote: > > Hi Martin and Nitesh, > > Thanks for your help - I can now clone from the Bioconductor COHCAP git > repository, and I'm now working on syncing the GitHub repository and the > Bioconductor repository (or at least updating the Bioconductor repository). > > I'm testing making a minor change (not affecting functionality, in the > "CHANGES" text file) to one of the files from the Bioconductor repository > (without trying to sync the repositories), and I get the following error > message when I try to push the changes to the Bioconductor repository > (showing prior commands as well): > > cwarden$ git clone https://git.bioconductor.org/packages/COHCAP > > Cloning into 'COHCAP'... > > remote: Counting objects: 485, done. > > remote: Compressing objects: 100% (479/479), done. > > remote: Total 485 (delta 328), reused 0 (delta 0) > > Receiving objects: 100% (485/485), 107.97 KiB | 0 bytes/s, done. > > Resolving deltas: 100% (328/328), done. > > Checking connectivity... done. > > cwarden$ cd COHCAP > > COHCAP cwarden$ git checkout master > > Already on 'master' > > Your branch is up-to-date with 'origin/master'. > > [edit file] > > COHCAP cwarden$ git status > > On branch master > > Your branch is up-to-date with 'origin/master'. > > Changes not staged for commit: > > (use "git add <file>..." to update what will be committed) > > (use "git checkout -- <file>..." to discard changes in working directory) > > > > modified: CHANGES > > > > no changes added to commit (use "git add" and/or "git commit -a") > > COHCAP cwarden$ git commit -a -m "fake commit" > > [master 225f7ac] fake commit > > 1 file changed, 1 insertion(+) > > COHCAP cwarden$ git status > > On branch master > > Your branch is ahead of 'origin/master' by 1 commit. > > (use "git push" to publish your local commits) > > > nothing to commit, working directory clean > > COHCAP cwarden$ git push origin master > > fatal: remote error: FATAL: W any packages/COHCAP nobody DENIED by fallthru > > (or you mis-spelled the reponame) > > > I tried this on a couple computers and I get the same error message with the > "git push origin master" command. Can you please help me identify the > problem, so I can at least update the Bioconductor repository? > > Thanks, > Charles > > On Thu, Aug 24, 2017 at 11:07 AM, Charles Warden <cwarde...@gmail.com> wrote: > Hi Martin and Nitesh, > > Thanks for your help. > > I created a public ssh-key, I added it as a deploy key for the Bioconductor > package, and I provided that key in the git/svn transition Google Doc file. > > I was trying to provide a key what would only affect the COHCAP package, and > not the other projects that are not Bioconductor projects. Please let me > know if this still works. > > Thanks, > Charles > > On Thu, Aug 24, 2017 at 5:59 AM, Martin Morgan > <martin.mor...@roswellpark.org> wrote: > On 08/24/2017 07:27 AM, Turaga, Nitesh wrote: > http://bioconductor.org/developers/how-to/git/<http://bioconductor.org/developers/how-to/git/faq/>faq<http://bioconductor.org/developers/how-to/git/faq/>/<http://bioconductor.org/developers/how-to/git/faq/> > > Get Outlook for Android<https://aka.ms/ghei36> > > ________________________________ > From: Charles Warden <cwarde...@gmail.com> > Sent: Wednesday, August 23, 2017 11:32:42 PM > To: Turaga, Nitesh > Subject: Re: [Bioc-devel] COHCAP GitHub Update > > Hi Nitesh, > > I am getting a slightly different error message, now that I am changing to be > within the COHCAP directory: > > ###### Start Code ######## > > COHCAP cwarden$ git fetch --all > > Fetching origin > > Fetching upstream > > Permission denied (publickey). > > this means that you do not have permissions to access your repository. This > is probably because you, as an existing svn account holder, have not > submitted an 'ssh' key to Bioconductor. > > The things you need to do are > > 1. create an ssh key pair, and submit the public key to your github > account. Follow the link to 'add your public key to your GitHub account' in > step 2 of > > http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ > > 2. submit your request for ssh access to git.bioconductor.org, following > step 1 of > > http://bioconductor.org/developers/how-to/git/new-package-workflow/ > > (I will update the instructions at > http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ to > include this step. > > 3. Wait 24 hours for manual processing > > 4. Try again > > some more below... > > > > fatal: Could not read from remote repository. > > > Please make sure you have the correct access rights > > and the repository exists. > > error: Could not fetch upstream > > ###### End Code ######## > > I also don't see COHCAP when I search the Bioconductor repository (when > searching > https://github.com/Bioconductor?utf8=%E2%9C%93&q=COHCAP&type=&language=), and > I also can't clone anything directory from Bioconductor: > > github.com/Bioconductor contains public versions of repositories maintained > by the Bioconductor core team; yours will not appear there. > > > ###### Start Code ######## > > cwarden$ git clone g...@git.bioconductor.org:packages/COHCAP > > Cloning into 'COHCAP'... > > Permission denied (publickey). > > fatal: Could not read from remote repository. > > > Please make sure you have the correct access rights > > and the repository exists. > > ###### End Code ######## > > I have my Bioconductor SVN username and password, but does something need to > be initialized with the new git system (where I'll have a new Bioconductor > username and password)? > > Thanks, > Charles > > On Wed, Aug 23, 2017 at 2:18 PM, Turaga, Nitesh > <nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.org>> wrote: > Hi > > On Aug 23, 2017, at 5:13 PM, Charles Warden > <cwarde...@gmail.com<mailto:cwarde...@gmail.com>> wrote: > > Hi, > > I downloaded code for the COHCAP Bioconductor SVN repository ( > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COHCAP/), made > some changes, and then tried to commit those changes. However, I got an > error message that the SVN repository is locked, so the changes could not > be uploaded because of a switch to git. > > I have a GitHub account, and I uploaded the COHCAP code (with the latest > round of changes) to GitHub: > > https://github.com/cwarden45/COHCAP > > So far so good. > > However, I am not sure how to make this the new Bioconductor repository. I > am trying to follow the instructions available here: > > http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ > > However, if I run the command *git remote add upstream > g...@git.bioconductor.org:packages/COHCAP.gi**t*, then I get an error > message: *fatal: Not a git repository.* > > > Can you paste the command and the error message as is, this formatting seems > off. > > Can you please help me update the COHCAP Bioconductor repository and > understand how this is now managed through GitHub? > > Also, I posted this question on the Support forum, but that may have not > been the right venue. So, I apologize for the confusion. > > Thanks, > > Charles > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org<mailto: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. > > > > 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. > [[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. > > This email message may contain legally privileged and/or confidential information. 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