[Bioc-devel] COHCAP GitHub Update

[Turaga, Nitesh]

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).

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]]
>
> _______________________________________________
> Bioc-devel at r-project.org<mailto:Bioc-devel at 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]]