[Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)
Hi, Ok thank you. I do the commit as following: 'git commit -a #update CNORfeeder' and then I get the following: # Please enter the commit message for your changes. Lines starting # with '#' will be ignored, and an empty message aborts the commit. # # On branch master # Your branch is up to date with 'origin/master'. # # Changes to be committed: # modified: DESCRIPTION # modified: NAMESPACE # modified: vignettes/CNORfeeder-vignette.Rnw # # Untracked files: # R/buildFeederObjectDynamic.R # R/computeMSE.R # R/getLBodeContObjFunctionWeighted.R # R/identifyMisfitIndices.R # R/integrateLinks.R # R/parEstimationLBodeSSmWeighted.R # R/parEstimationLBodeWeighted.R # R/preprocessingWeighted.R # R/runDynamicFeeder.R # data/CNOlistToy_Gene.RData "~/CNORfeeder/.git/COMMIT_EDITMSG" 43L, 1176C However from this point the terminal becomes un-responsive and cannot type anything. Then I quit this dialog through :wq after which I get the following error: hint: Waiting for your editor to close the file... error: There was a problem with the editor 'vi'. Please supply the message using either -m or -F option. Please, how can I fix this issue? Cheers, On Mon, 30 Mar 2020 at 13:56, Shepherd, Lori <Lori.Shepherd at roswellpark.org> wrote:
I do not see any changes in the git.bioconductor.org server on the master branch. Did you remember to do the following to commit your changes before you tried pushing? git commit -a In general a good basic workflow for working on the devel (master) branch is git fetch --all git pull git pull upstream origin # make your changes including a version bump git commit -a # commit your changes and give an informative message git push git push upstream master Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ------------------------------ *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Enio Gjerga <enio.gjerga at gmail.com> *Sent:* Monday, March 30, 2020 6:05 AM *To:* Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> *Cc:* Herv? Pag?s <bioc-devel at r-project.org> *Subject:* Re: [Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access) Hi, Thank you very much. After following your suggestion I went to set up the SSH and I was also able to clone the packages I was maintaining locally. Next I did my desired changes to the cloned package locally and I wanted to push these changes to the Bioconductor repositories. For that I used the following commands: 1. git checkout master from where I got a list of files in the package labeled as M/D and the message: Already on 'master'. Your branch is up to date with 'origin/master'. 2. git push upstream master from where I got the message: Everything up-to-date. Does this mean that my changes are pushed to Bioconductor repositories correctly? Thank you again for all the help:)) Cheers, Enio On Fri, 27 Mar 2020 at 17:43, Turaga, Nitesh < Nitesh.Turaga at roswellpark.org> wrote:
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
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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-- Enio GJERGA PhD student JRC-COMBINE RWTH Aachen Tel : +4917685132057
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.
--
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057
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