[Bioc-devel] updating Bioconductor package that is already on Github

Fri, Jan 26, 2018 9:44 AM

Hi Simina,

I?m assuming your keys are stored in the folder ?.ssh?. If that is the case, try,

	 ssh-keygen -y -e -f <private_key>

That command will print out a public key. If that public key is the same as the one I?ve sent you, they you can use that. (Remember that public keys, don?t have ?.pub? ending. If your public key is called ?id_rsa.pub? then your private key is most likely, ?id_rsa?). 

If you have to configure your git login, please follow the link below to make sure that the same key is used

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

Best,

Nitesh

On Jan 26, 2018, at 12:36 PM, Simina Boca <smb310 at georgetown.edu> wrote:

Thank you Nitesh! Where should I use the private key? I only see the public key mentioned here: http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Sorry if I'm missing something very obvious!

Best,
Simina

On Fri, Jan 26, 2018 at 12:23 PM, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org> wrote:
Hi

You are using the wrong key.

The key we have on file for you is

ssh-rsa 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


You should use a private key corresponding to that public key.

Best,

Nitesh

On Jan 26, 2018, at 12:05 PM, Simina Boca <smb310 at georgetown.edu> wrote:

Dear all,
Thank you to Sean, Lori, and Nitesh for helping me out with a package update last year. I'm now trying to update another package, MultiMed. I have it set up on Github https://github.com/SiminaB/MultiMed - you can see that the contributors are Marc, Herve, and Dan Tenenbaum.
However, I get the same error as I got before when doing "git push upstream master":
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to the list of known hosts.
Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
FATAL: W any packages/swfdr SiminaB DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

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

Do I need to submit anything else or should BioC already know that I'm the same person who is managing these packages?

Thanks so much!

Cheers,
Simina


On Tue, Sep 12, 2017 at 10:17 AM, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org> wrote:
Hi Simina,

Please try again now.

The issue was you didn?t submit your SVN ID ?s.boca?. This is needed for people who have been maintainers before the Git transition, to associate your key to the package.

For new packages this issue doesn?t apply, because we just collect their Github IDs.

Hope this helps.

Best,

Nitesh

On Sep 11, 2017, at 2:50 PM, Simina Boca <smb310 at georgetown.edu> wrote:

Thank you again Sean and Lori! I am now past that initial stage. I now have
to resolve merge conflicts, primarily in the DESCRIPTION file. When
following the instructions here http://bioconductor.org/
developers/how-to/git/resolve-conflicts/ however, I ended up getting the
error below:

~\Documents\GitHub\swfdr [master ? +0 ~0 -1 !]> git push upstream master
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
Enter passphrase for key '/c/Users/sboca/.ssh/id_rsa':
FATAL: W any packages/swfdr SiminaB DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

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

Thank you so much!

Best,
Simina


On Wed, Sep 6, 2017 at 10:56 AM, Simina Boca <smb310 at georgetown.edu> wrote:

Thank you so much Sean and Lori! For some reason I thought the ssh key
part was only relevant if the package was submitted via svn, which is why i
had overlooked those instructions initially.

Cheers,
Simina

On Wed, Sep 6, 2017 at 7:01 AM, Shepherd, Lori <
Lori.Shepherd at roswellpark.org> wrote:

Have you submitted your ssh key


https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480v
o4tNufs0ziNyNmexegNZgNieIovbAA/viewform

<https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform>
git / svn transition: ssh keys
<https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform>
docs.google.com
Use this form to link your existing svn credentials with access
permissions to the new Bioconductor git repository. To do this, we need an
ssh public key. You might have added these to github, see
https://github.com/your-github-id.keys. Alternatively, you may provide
the ssh public key directly, e.g., copy-pasting ~/.ssh/id_rsa.pub. To
generate ssh key pairs, see https://help.github.com/articl
es/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
------------------------------
*From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of
Simina Boca <smb310 at georgetown.edu>
*Sent:* Tuesday, September 5, 2017 11:40:37 PM
*To:* bioc-devel at r-project.org
*Subject:* [Bioc-devel] updating Bioconductor package that is already on
Github

Dear all,

I hope this isn't a duplicate of another question. Here goes:

- I would like to update my swfdr package, which is already on
Bioconductor. It is also on Github and my submission process was via
opening an issue at https://github.com/Bioconducto
r/Contributions/issues/213

- At this point there are some slight differences between the Github and
Bioconductor versions, for example the Bioconductor version number got
automatically bumped to 1.0.0 upon acceptance

- I would like to first synchronize what is on Github to have the current
version that is on Bioconductor before updating and also include any
updates in the next version of the package on Bioconductor

- I did "git remote add upstream git at git.bioconductor.org:packa
ges/swfdr.git"
as per some of the instructions for developers, so that now I have:
~\Documents\GitHub\swfdr [master ? +0 ~0 -1 !]> git remote -v
origin  https://github.com/leekgroup/swfdr.git (fetch)
origin  https://github.com/leekgroup/swfdr.git (push)
upstream        git at git.bioconductor.org:packages/swfdr.git (fetch)
upstream        git at git.bioconductor.org:packages/swfdr.git (push)

*but* when I try to fetch upstream content, via:
git fetch upstream

I get an error:
~\Documents\GitHub\swfdr [master ? +0 ~0 -1 !]> git fetch upstream
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA)
to
the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights

Am I missing something here? Alternatively, I suppose I can just make the
changes I want and simply open another issue, although it would be nice to
have an easy to sync it with what is already on Bioconductor.

Thank you in advance for your help and I apologize if I missed anything
obvious!

Cheers,
Simina

--
Simina M. Boca
Assistant Professor
Innovation Center for Biomedical Informatics  (ICBI)
Department of Oncology | Georgetown University Medical Center
Department of Biostatistics, Bioinformatics and Biomathematics |
Georgetown
University Medical Center
Cancer Prevention and Control Program | Lombardi Comprehensive Cancer
Center

2115 Wisconsin Ave NW, Suite 110
Washington, DC 20007
Phone: (202) 687-1545
Fax: (202) 687-5011
http://icbi.georgetown.edu/boca

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[Bioc-devel] updating Bioconductor package that is already on Github

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