[Bioc-devel] COHCAP GitHub Update

Mon Sep 4 04:07:38 CEST 2017

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: git at git.bioconductor.org
	• HTTPS (public) read only access: https://git.bioconductor.org

Nitesh

> On Sep 3, 2017, at 4:30 PM, Charles Warden <cwarden45 at 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 <cwarden45 at 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.morgan at 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 <cwarden45 at 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 git at 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.Turaga at roswellpark.org<mailto:Nitesh.Turaga at roswellpark.org>> wrote:
> Hi
> 
> On Aug 23, 2017, at 5:13 PM, Charles Warden <cwarden45 at gmail.com<mailto:cwarden45 at 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
> git at 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
> 
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> 
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