Hi Martin and Sean, Thanks for your help - I think the issue may be that I don't have a private key on the second computer (and the passcode still isn't recognized if I remove the .pub extension).
I was trying to set up a deploy key on GitHub that would only apply to the COHCAP repository, but I will test having a public account key for the account (and do more testing before asking another question). Thanks, Charles On Sep 9, 2017 7:34 PM, "Martin Morgan" <martin.mor...@roswellpark.org> wrote: > On 09/09/2017 09:06 PM, Sean Davis wrote: > >> Hi, Charles. >> >> See inline. >> >> On Sat, Sep 9, 2017 at 8:40 PM, Charles Warden <cwarde...@gmail.com> >> wrote: >> >> Hi, >>> >>> I'm sorry, but I am having an issue setting up my ssh key. In >>> particular, >>> it is not recognizing the passcode (and I've tried copying over a new >>> id_rsa.pub file as well as double-checking the passcode): >>> >>> :~/.ssh$ ssh-add id_rsa.pub >>> Enter passphrase for id_rsa.pub: >>> Bad passphrase, try again for id_rsa.pub: >>> >>> >> Many folks do not use a passphrase (just hit enter when creating a new >> key) >> for ssh keys. It is potentially not as secure (in reality, probably not by >> much), but it does simplify things at least to start. >> >> >> >>> I also tried following these github instructions ( >>> https://help.github.com/ >>> articles/error-permission-denied-publickey/): I didn't see a solution, >>> but I can confirm the problem: >>> >>> ~/.ssh$ ssh -T g...@github.com >>> Permission denied (publickey) >>> >>> >> I'm not sure what the problem is at this point, but it seems pretty likely >> that figuring out what is broken and trying to fix it might be >> challenging. >> I would suggest starting over from scratch, using Github as a starting >> place. >> >> https://help.github.com/articles/connecting-to-github-with-ssh/ >> >> Once you get your key working with github from your various machines, then >> you can move ahead with the Bioconductor git server. >> >> - While it is tempting to make new ssh keys every time you need one, that >> has some very real disadvantages. Note that the github article has some >> notes about finding existing ssh keys. That said, in your case, a clean >> slate might be the easiest way to go, particularly since it appears that >> you might have misplaced the passphrase. >> - The file permissions on key files are important, so pay attention to >> notes about setting those correctly. >> >> >> >>> Since Sean was able to run "git clone g...@git.bioconductor.org:packa >>> ges/COHCAP.git", is there some other modification I should make to ssh >>> key? >>> >>> >> Git clone does not require permissions for public github repositories or >> for bioconductor package repositories. Only operations that involving >> "writing" to the git server require authentication, so the fact that I was >> able to clone your repo has nothing to do with my having correctly used an >> ssh key. Anyone, even without ANY ssh key, could have done so. >> > > actually, the Bioconductor git repository does not support reading using > ssh keys, only https. So any could do > > git clone https://git.bioconductor.org/packages/COHCAP > > but only people with valid ssh keys AND permissions can use > > git clone g...@git.bioconductor.org:packages/COHCAP > > (Sean -- you've got magical powers that carry over from svn days). > > I notice, Charles, that there are no keys registered with github > > https://github.com/cwarden45.keys > > I suggest that you figure things out using github, where you can see your > keys and where there is more public documentation. Also, note that you can > look at your local key pairs, for instance on Linux > > $ ls ~/.ssh/id* > /home/mtmorgan/.ssh/id_rsa /home/mtmorgan/.ssh/id_rsa.pub > > and I can confirm that the public part of the key pair > > $ cat ~/.ssh/id_rsa.pub > ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAIEAwrnfSVn+lfnzSRwylWgC2Q7T0QJWvI8A > 0WHb8yMHF9OkgnldksS72OzjGr4qcz2kUsCb/ZsQTYj+g29zKUntbCSiLclEXBEz+lKUsdbG9z > awRiIypW60cfXKnbB3WfxkSqsiLDTtYDuaVAgS1htKwe6GV3aSYuMCge27ZlNhBWc= > mtmorgan@gopher4 > > matches the public part of the key pair registered on my github account. > (both github and Bioconductor support multiple key pairs). > > If you get to the point where your github public key is working, submit it > via the form using your svn id and github id. > > Martin > > > >> >> >> If it matters, the original computer was a Mac OSX and the computer I am >>> trying to manage COHCAP from is an Ubuntu VM (running within Windows). >>> Also, the error message is the same if using the bioconductor git instead >>> of the github: >>> >>> >> As for machine types and ssh, that does not matter. The ssh protocol is >> not >> machine-type dependent, although how to use ssh keys may vary a bit, >> particularly on windows. >> >> Sean >> >> >> >>> ~/.ssh$ ssh -T g...@git.bioconductor.org >>> Permission denied (publickey). >>> >>> Thanks, >>> Charles >>> >>> >>> >>> On Mon, Sep 4, 2017 at 5:28 PM, Sean Davis <seand...@gmail.com> wrote: >>> >>> Hi, Charles. See replies inline. >>>> >>>> On Mon, Sep 4, 2017 at 3:30 PM, Charles Warden <cwarde...@gmail.com> >>>> wrote: >>>> >>>> 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. >>>>> >>>>> >>>> This error means that there is a problem with your git ssh key. It could >>>> be that your private key is not present on the new computer or that the >>>> ssh >>>> key on Bioconductor has not been registered. Given the error below, it >>>> appears that at least one ssh key is working. >>>> >>>> >>>> >>>>> 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. >>>>> >>>>> >>>> You can often follow the instructions suggested by "hints" given by git. >>>> In this case, it appears that there are some commits present at >>>> Bioconductor that are not present in your local clone. Doing a `git >>>> pull` >>>> will fetch and merge those changes. Assuming there are no merge >>>> conflicts, >>>> you should then be able to push. >>>> >>>> >>>> >>>>> >>>>> 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? >>>>> >>>>> >>>> You have had a few separate issues on this thread. My last comment about >>>> `git pull` means that your first two problems (typo in the URL, missing >>>> or >>>> mismatched ssh key) were overcome already. I'd proceed from there. >>>> >>>> Hope that helps, >>>> Sean >>>> >>>> >>>> >>>> >>>>> 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.si >>>>>>> te.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-gith >>>>>>>>> >>>>>>>> ub-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-w >>>>>>>>> >>>>>>>> orkflow/ >>>>>>> >>>>>>>> >>>>>>>>> (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 >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> -- >>>> 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 >>>> >>>> >>> >>> >> >> > > 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