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

Sean Davis seandavi at gmail.com
Wed Sep 6 12:59:07 CEST 2017

Hi, Simina.

On Tue, Sep 5, 2017 at 11:40 PM, Simina Boca <smb310 at georgetown.edu> wrote:

> 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,' (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

Take a look at the FAQ, #3, here:


Have you submitted an SSH key somehow?

> 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.

When everything is working, you will "own" the bioconductor git repo, so
working it will be roughly equivalent to working with github. Opening an
issue on the package submission repo will not get you what you want and is
only for new packages.


> 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
>         [[alternative HTML version deleted]]
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> Bioc-devel at r-project.org mailing list
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Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892

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