Hi Sean, I'm admittedly on a different computer now, but I still get an error message (although it is different than the last one):
git clone g...@git.bioconductor.org:packages/COHCAP.git 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. Also, there was a lot of text in the previous message, but I tried following the commands to merge and update the Bioconductor and GitHub COHCAP repositories. On that computer (the computer where I defined the ssh key), I could run "git remote add upstream g...@git.bioconductor.org: packages/COHCAP.git", but I ran into a problem at the push step: 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. Is there a way that I should modify the ssh "git clone g...@git.bioconductor.org:packages/COHCAP.git" command? Thanks, Charles On Mon, Sep 4, 2017 at 11:41 AM, Sean Davis <seand...@gmail.com> wrote: > 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.is >> land.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
