[Bioc-devel] COHCAP GitHub Update

[Turaga, Nitesh]

> http://bioconductor.org/developers/how-to/git/faq/


Sorry for the bad formatting, my mail client does that sometimes.

> On Aug 24, 2017, at 7:27 AM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> 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/>
> 
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> ________________________________
> 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).
> 
> 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:
> 
> ###### 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]]
>> 
>> _______________________________________________
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> 
> 
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