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

Simina Boca smb310 at georgetown.edu
Wed Sep 6 05:40:37 CEST 2017

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:packages/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,' (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


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

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