Hi, Charles. The command is slightly off. Note the first '/' is a ':'. This worked for me:
git clone g...@git.bioconductor.org:packages/COHCAP.git Cloning into 'COHCAP'... remote: Counting objects: 485, done. remote: Compressing objects: 100% (479/479), done. remote: Total 485 (delta 329), reused 0 (delta 0) Receiving objects: 100% (485/485), 104.78 KiB | 0 bytes/s, done. Resolving deltas: 100% (329/329), done. Sean On Mon, Sep 4, 2017 at 2:15 PM, Charles Warden <cwarde...@gmail.com> wrote: > Hi Nitesh, > > Thanks. Unfortunately, I can't connect to the Bioconductor repository that > way: > > > *cwarden$ git clone g...@git.bioconductor.org/packages/COHCAP.git > <http://g...@git.bioconductor.org/packages/COHCAP.git>* > > *fatal: repository 'g...@git.bioconductor.org/packages/COHCAP.git > <http://g...@git.bioconductor.org/packages/COHCAP.git>' does not exist* > > However, I can connect and update the GitHub repository with the SSH > commands: > > cwarden$ git clone g...@github.com:cwarden45/COHCAP.git > > Cloning into 'COHCAP'... > > Saving password to keychain failed > > Identity added: /Users/cwarden/.ssh/id_rsa ((null)) > > remote: Counting objects: 59, done. > > remote: Compressing objects: 100% (53/53), done. > > remote: Total 59 (delta 9), reused 3 (delta 2), pack-reused 0 > > Receiving objects: 100% (59/59), 56.83 KiB | 0 bytes/s, done. > > Resolving deltas: 100% (9/9), done. > > Checking connectivity... done. > > BR11252: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") > > BR11252:COHCAP cwarden$ git commit -a -m "test commit" > > [master f2aded7] test commit > > 1 file changed, 1 insertion(+) > > BR11252:COHCAP cwarden$ git push > > Warning: Permanently added the RSA host key for IP address '192.30.255.112' > to the list of known hosts. > > Counting objects: 3, done. > > Delta compression using up to 8 threads. > > Compressing objects: 100% (3/3), done. > > Writing objects: 100% (3/3), 302 bytes | 0 bytes/s, done. > > Total 3 (delta 2), reused 0 (delta 0) > > remote: Resolving deltas: 100% (2/2), completed with 2 local objects. > > To g...@github.com:cwarden45/COHCAP.git > > 5285d59..f2aded7 master -> master > > *If it helps with troubleshooting, I can also try to update the > Bioconductor repository as an upstream link to the GitHub repository, but > that also does not work (at the push step, see below):* > > cwarden$ git clone g...@github.com:cwarden45/COHCAP.git > > Cloning into 'COHCAP'... > > remote: Counting objects: 63, done. > > remote: Compressing objects: 100% (55/55), done. > > remote: Total 63 (delta 12), reused 7 (delta 4), pack-reused 0 > > Receiving objects: 100% (63/63), 57.24 KiB | 0 bytes/s, done. > > Resolving deltas: 100% (12/12), done. > > Checking connectivity... done. > > cwarden$ cd COHCAP > > COHCAP cwarden$ git remote -v > > origin g...@github.com:cwarden45/COHCAP.git (fetch) > > origin g...@github.com:cwarden45/COHCAP.git (push) > > COHCAP cwarden$ git remote add upstream g...@git.bioconductor.org: > packages/COHCAP.git > > BR11252:COHCAP cwarden$ git remote -v > > origin g...@github.com:cwarden45/COHCAP.git (fetch) > > origin g...@github.com:cwarden45/COHCAP.git (push) > > upstream g...@git.bioconductor.org:packages/COHCAP.git (fetch) > > upstream g...@git.bioconductor.org:packages/COHCAP.git (push) > > COHCAP cwarden$ git fetch upstream > > warning: no common commits > > 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), 110.22 KiB | 0 bytes/s, done. > > Resolving deltas: 100% (328/328), done. > > From git.bioconductor.org:packages/COHCAP > > * [new branch] RELEASE_2_14 -> upstream/RELEASE_2_14 > > * [new branch] RELEASE_3_0 -> upstream/RELEASE_3_0 > > * [new branch] RELEASE_3_1 -> upstream/RELEASE_3_1 > > * [new branch] RELEASE_3_2 -> upstream/RELEASE_3_2 > > * [new branch] RELEASE_3_3 -> upstream/RELEASE_3_3 > > * [new branch] RELEASE_3_4 -> upstream/RELEASE_3_4 > > * [new branch] RELEASE_3_5 -> upstream/RELEASE_3_5 > > * [new branch] master -> upstream/master > > COHCAP cwarden$ git merge upstream/master > > Auto-merging vignettes/COHCAP.Rnw > > CONFLICT (add/add): Merge conflict in vignettes/COHCAP.Rnw > > Auto-merging man/COHCAP.site.Rd > > CONFLICT (add/add): Merge conflict in man/COHCAP.site.Rd > > Auto-merging man/COHCAP.qc.Rd > > CONFLICT (add/add): Merge conflict in man/COHCAP.qc.Rd > > Auto-merging man/COHCAP.integrate.avg.by.site.Rd > > CONFLICT (add/add): Merge conflict in man/COHCAP.integrate.avg.by.site.Rd > > Auto-merging man/COHCAP.integrate.avg.by.island.Rd > > CONFLICT (add/add): Merge conflict in man/COHCAP.integrate.avg.by. > island.Rd > > Auto-merging man/COHCAP.denovo.Rd > > CONFLICT (add/add): Merge conflict in man/COHCAP.denovo.Rd > > Auto-merging man/COHCAP.avg.by.site.Rd > > CONFLICT (add/add): Merge conflict in man/COHCAP.avg.by.site.Rd > > Auto-merging man/COHCAP.avg.by.island.Rd > > CONFLICT (add/add): Merge conflict in man/COHCAP.avg.by.island.Rd > > Auto-merging man/COHCAP.annotate.Rd > > CONFLICT (add/add): Merge conflict in man/COHCAP.annotate.Rd > > Auto-merging man/COHCAP.BSSeq.preprocess.Rd > > CONFLICT (add/add): Merge conflict in man/COHCAP.BSSeq.preprocess.Rd > > Auto-merging NAMESPACE > > CONFLICT (add/add): Merge conflict in NAMESPACE > > Auto-merging DESCRIPTION > > CONFLICT (add/add): Merge conflict in DESCRIPTION > > Auto-merging CHANGES > > CONFLICT (add/add): Merge conflict in CHANGES > > [modified files to keep changes intended for SVN Bioconductor repository] > > COHCAP cwarden$ git add CHANGES > > COHCAP cwarden$ git add DESCRIPTION > > COHCAP cwarden$ git add NAMESPACE > > COHCAP cwarden$ git add man/COHCAP.BSSeq.preprocess.Rd > > COHCAP cwarden$ git add man/COHCAP.annotate.Rd > > COHCAP cwarden$ git add man/COHCAP.avg.by.island.Rd > > COHCAP cwarden$ git add man/COHCAP.avg.by.site.Rd > > COHCAP cwarden$ git add man/COHCAP.denovo.Rd > > COHCAP cwarden$ git add man/COHCAP.integrate.avg.by.island.Rd > > COHCAP cwarden$ git add man/COHCAP.integrate.avg.by.site.Rd > > COHCAP cwarden$ git add man/COHCAP.qc.Rd > > COHCAP cwarden$ git add man/COHCAP.site.Rd > > COHCAP cwarden$ git add man/COHCAP.reformatFinalReport.Rd > > COHCAP cwarden$ git add vignettes/COHCAP.Rnw > > COHCAP cwarden$ git add R/COHCAP.reformatFinalReport.R > > COHCAP cwarden$ git push upstream master > > To g...@git.bioconductor.org:packages/COHCAP.git > > ! [rejected] master -> master (non-fast-forward) > > error: failed to push some refs to 'g...@git.bioconductor.org: > packages/COHCAP.git' > > hint: Updates were rejected because the tip of your current branch is > behind > > hint: its remote counterpart. Integrate the remote changes (e.g. > > hint: 'git pull ...') before pushing again. > > hint: See the 'Note about fast-forwards' in 'git push --help' for details. > > Can you please help me troubleshoot updating the Bioconductor COHCAP > repository via SSH? > > Thanks, > > Charles > > On Sun, Sep 3, 2017 at 7:07 PM, Turaga, Nitesh < > nitesh.tur...@roswellpark.org> wrote: > > > 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. 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 -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
