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/>
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________________________________
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-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 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
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