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

[Simina Boca]

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/1FAIpQLSdlTbNjsQJDp0BA480vo4tN
> ufs0ziNyNmexegNZgNieIovbAA/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/
> articles/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/Bioconductor/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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-- 
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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