[Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

You should try and set up your system using SSH from your Github account
as well.

On Mar 27, 2020, at 12:25 PM, Enio Gjerga <enio.gjerga at gmail.com> wrote:

Hi,

Ahh apparently I cannot. I tried to clone a random repo (PHONEMeS)

locally through the command you provided, and then got the following:

Cloning into 'PHONEMeS'...
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

I usually rely on the Github Desktop which uses the HTTPS option. Might

there be something wrong with my GitHub settings?

Cheers,

On Fri, 27 Mar 2020 at 17:18, Turaga, Nitesh <

Nitesh.Turaga at roswellpark.org> wrote:

Can you access any git repository via the SSH protocol?

Not via HTTPS.

So you'll have to check if you can do something like, (from your own

GitHub account).

`git clone git at github.com:<username>/<repository>`

On Mar 27, 2020, at 12:15 PM, Enio Gjerga <enio.gjerga at gmail.com>

wrote:

Hi,

Sure, I got the following: ssh: Could not resolve hostname -: nodename

nor servname provided, or not known

Thank you,

On Fri, 27 Mar 2020 at 17:13, Turaga, Nitesh <

Nitesh.Turaga at roswellpark.org> wrote:

Ok, can you also show my the result of

        ssh - T git at git.bioconductor.org | grep CNORfeeder

On Mar 27, 2020, at 11:54 AM, Enio Gjerga <enio.gjerga at gmail.com>

wrote:

Hi,

Thank you for your reply. So according to #14:

1. I use "git remote -v" and then I get the following:

origin        https://github.com/saezlab/CNOv2.git (fetch)
origin        https://github.com/saezlab/CNOv2.git (push)
upstream      git at git.bioconductor.org:packages/CNORfeeder.git

(fetch)

upstream      git at git.bioconductor.org:packages/CNORfeeder.git

(push)

2. Then I check if I have access to the git serve by using "ssh -T

git at git.bioconductor.org" after which I get:

Permission denied (publickey).

3. According to #15, I have generated another key under the name

id_rsa_bioc through the commands:

mkdir -p ~/.ssh && chmod 700 ~/.ssh
touch ~/.ssh/config
chmod 600 ~/.ssh/config

But it doesn't seem to generate anny ssh/config directory so was

wondering how can I add the:

host git.bioconductor.org

     HostName
git.bioconductor.org

     IdentityFile ~/.ssh/id_rsa_bioconductor
     User git

The public key of id_rsa_bioc is already added on my profile in

BiocCredentials and also on my GitHub account.

As always any help is very much appreciated.

Cheers,
Enio

On Fri, 27 Mar 2020 at 16:03, Turaga, Nitesh <

Nitesh.Turaga at roswellpark.org> wrote:

As given in #14 of the FAQ, please send me

        git remote -v

On Mar 27, 2020, at 10:54 AM, Enio Gjerga <enio.gjerga at gmail.com>

wrote:

Hello,

Thank you very much for your reply. I have added a new key on my

BiocCredentials and on Github, however, I am afraid that the same issue
still persists. If I try to check whether I have access to the package
(using the "ssh -T git at git.bioconductor.org" command) or clone it locally
(through "git clone git at git.bioconductor.org:packages/CNORfeeder"
command) I still unfortunately get the same "permission denied (public
key)" error.

How can I check for my git set up?

Sorry again, but quiet new on this.

Cheers,

On Fri, 27 Mar 2020 at 13:38, Turaga, Nitesh <

Nitesh.Turaga at roswellpark.org> wrote:

Try adding another key. If that doesn't work, show us your git set

up.

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

#13 and #14

Best,

Nitesh


?On 3/27/20, 6:15 AM, "Bioc-devel on behalf of Enio Gjerga" <

bioc-devel-bounces at r-project.org on behalf of enio.gjerga at gmail.com>
wrote:

    Hello,

    I am Enio Gjerga and I am the maintainer of the CNORfeeder and

the CNORode

    package, a role which I got recently. I am facing trouble

trying to access

    the source packages for then later syncing it with a Github

repository and

    do a few necessary updates. I try first to obtain developer

access through

    the "git clone git at git.bioconductor.org:packages/CNORfeeder"

command, but

    then I get the error "Permission denied (publickey). fatal:

Could not read

    from remote repository.". I already have the GitHub id and the

ssh-rsa key

    on my user profile in

https://git.bioconductor.org/BiocCredentials, but

    apparently I still can't get the access to the package and not

sure what

    might be doing wrong.

    Any help about this would be much appreciated.

    Cheers,

    Enio

    --
    Enio GJERGA
    PhD student
    JRC-COMBINE RWTH Aachen
    Tel : +4917685132057

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