[Bioc-devel] COHCAP GitHub Update

[Martin Morgan]

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
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
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