[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

        [[alternative HTML version deleted]]

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Enio GJERGA
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JRC-COMBINE RWTH Aachen
Tel : +4917685132057

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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

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

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.
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
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

        [[alternative HTML version deleted]]

    _______________________________________________
    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.

--
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

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

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

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

	[[alternative HTML version deleted]]
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
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
> 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
> > > > >
> > > > >         [[alternative HTML version deleted]]
> > > > >
> > > > >     _______________________________________________
> > > > >     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.
> > > > >
> > > > >
> > > > > --
> > > > > 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
> > > >
> > >
> > >
> > >
> > > 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
> > >
> >
> >
> >
> > 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
> >
>
>
>
> 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

        [[alternative HTML version deleted]]

_______________________________________________
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.
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
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

        [[alternative HTML version deleted]]

    _______________________________________________
    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.

--
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

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

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

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

        [[alternative HTML version deleted]]

_______________________________________________
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.

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

	[[alternative HTML version deleted]]
That is asking you to make a commit message to summarize the changes.  It is traceable when you use git log.   You should type a commit message summarizing what you want to say

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
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<mailto:Lori.Shepherd at roswellpark.org>> wrote:
I do not see any changes in the git.bioconductor.org<http://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<mailto:bioc-devel-bounces at r-project.org>> on behalf of Enio Gjerga <enio.gjerga at gmail.com<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:git at github.com>:<username>/<repository>`
> >
> > > On Mar 27, 2020, at 12:15 PM, Enio Gjerga <enio.gjerga at gmail.com<mailto: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<mailto:Nitesh.Turaga at roswellpark.org>> wrote:
> > > Ok, can you also show my the result of
> > >
> > >         ssh - T git at git.bioconductor.org<mailto:git at git.bioconductor.org> | grep CNORfeeder
> > >
> > > > On Mar 27, 2020, at 11:54 AM, Enio Gjerga <enio.gjerga at gmail.com<mailto: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<mailto: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<http://git.bioconductor.org>
> > > >
> > > >      HostName
> > > > git.bioconductor.org<http://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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:bioc-devel-bounces at r-project.org> on behalf of enio.gjerga at gmail.com<mailto: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
> > > > >
> > > > >         [[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.
> > > > >
> > > > >
> > > > > --
> > > > > 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
> > > >
> > >
> > >
> > >
> > > 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
> > >
> >
> >
> >
> > 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
> >
>
>
>
> 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

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
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--
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057
[https://docs.google.com/uc?export=download&id=0B6mjZ0BJeekOeUgyQmpTQXYwWjg&revid=0B6mjZ0BJeekORUxnZ1VVS1ZjY25UTUc2VUU1dDA4N0lLUlM0PQ]

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.
Hi Enio,

Based on the conversation you, Lori and I had, it seems that you are having a hard time with git as a version control system in general and not the Bioconductor git repository in general. 

Please consider going through some good learning material so you can get started with git.

There are many resources where you can learn about git and GitHub.
	? git-and-github-learning-resources, https://help.github.com/articles/git-and-github-learning-resources/
	? git-scm, https://git-scm.com/
	? Guides, https://guides.github.com/

Best,

Nitesh
On Mar 30, 2020, at 8:34 AM, Enio Gjerga <enio.gjerga at gmail.com> wrote:

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
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

        [[alternative HTML version deleted]]

    _______________________________________________
    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.

--
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

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

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

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

        [[alternative HTML version deleted]]

_______________________________________________
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.

-- 
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.
Hello,

Yes thank you. I am very new on git and will definitively have a look.
However I think that I might have correctly pushed my changes to the
CNORfeeder and the CNORode packages. Can someone please confirm if that the
case? If not, I will carefully read the links before for the next time.

Best,

On Mon, 30 Mar 2020 at 14:46, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>
wrote:
Hi Enio,

Based on the conversation you, Lori and I had, it seems that you are
having a hard time with git as a version control system in general and not
the Bioconductor git repository in general.

Please consider going through some good learning material so you can get
started with git.

There are many resources where you can learn about git and GitHub.
        ? git-and-github-learning-resources,
https://help.github.com/articles/git-and-github-learning-resources/
        ? git-scm, https://git-scm.com/
        ? Guides, https://guides.github.com/

Best,

Nitesh

On Mar 30, 2020, at 8:34 AM, Enio Gjerga <enio.gjerga at gmail.com> wrote:

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
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

        [[alternative HTML version deleted]]

    _______________________________________________
    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.

--
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
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Yes.  I see the changes pushed this morning.   They should be reflected on tomorrow's build report.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Hello,

Yes thank you. I am very new on git and will definitively have a look. However I think that I might have correctly pushed my changes to the CNORfeeder and the CNORode packages. Can someone please confirm if that the case? If not, I will carefully read the links before for the next time.

Best,

On Mon, 30 Mar 2020 at 14:46, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org<mailto:Nitesh.Turaga at roswellpark.org>> wrote:
Hi Enio,

Based on the conversation you, Lori and I had, it seems that you are having a hard time with git as a version control system in general and not the Bioconductor git repository in general.

Please consider going through some good learning material so you can get started with git.

There are many resources where you can learn about git and GitHub.
        ? git-and-github-learning-resources, https://help.github.com/articles/git-and-github-learning-resources/
        ? git-scm, https://git-scm.com/
        ? Guides, https://guides.github.com/

Best,

Nitesh

> On Mar 30, 2020, at 8:34 AM, Enio Gjerga <enio.gjerga at gmail.com<mailto:enio.gjerga at gmail.com>> wrote:
>
> 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<mailto:Lori.Shepherd at roswellpark.org>> wrote:
> I do not see any changes in the git.bioconductor.org<http://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<mailto:bioc-devel-bounces at r-project.org>> on behalf of Enio Gjerga <enio.gjerga at gmail.com<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:git at github.com>:<username>/<repository>`
> > >
> > > > On Mar 27, 2020, at 12:15 PM, Enio Gjerga <enio.gjerga at gmail.com<mailto: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<mailto:Nitesh.Turaga at roswellpark.org>> wrote:
> > > > Ok, can you also show my the result of
> > > >
> > > >         ssh - T git at git.bioconductor.org<mailto:git at git.bioconductor.org> | grep CNORfeeder
> > > >
> > > > > On Mar 27, 2020, at 11:54 AM, Enio Gjerga <enio.gjerga at gmail.com<mailto: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<mailto: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<http://git.bioconductor.org>
> > > > >
> > > > >      HostName
> > > > > git.bioconductor.org<http://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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:bioc-devel-bounces at r-project.org> on behalf of enio.gjerga at gmail.com<mailto: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
> > > > > >
> > > > > >         [[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
> > > > > >
> > > > > >
> > > > > >
> > > > > >
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> > > > > >
> > > > > >
> > > > > > --
> > > > > > Enio GJERGA
> > > > > > PhD student
> > > > > > JRC-COMBINE RWTH Aachen
> > > > > > Tel : +4917685132057
> > > > > >
> > > > >
> > > > >
> > > > >
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> > > > >
> > > > >
> > > > > --
> > > > > Enio GJERGA
> > > > > PhD student
> > > > > JRC-COMBINE RWTH Aachen
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> > > > >
> > > >
> > > >
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> > > >
> > > > --
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> > > > PhD student
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> > > > Tel : +4917685132057
> > > >
> > >
> > >
> > >
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> > > --
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> >
> >
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> --
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> PhD student
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> Tel : +4917685132057
>
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>
> _______________________________________________
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>
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> --
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