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

Fri Jan 26 18:05:20 CET 2018

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/1FAIpQLSdlTbNjsQJDp0BA480vo4tN
> ufs0ziNyNmexegNZgNieIovbAA/viewform>
> >>> git / svn transition: ssh keys
> >>> <https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tN
> ufs0ziNyNmexegNZgNieIovbAA/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
> >>>
> >>>        [[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.
> >>
> >>
> >>
> >>
> >> --
> >> 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
> >>
> >>
> >
> >
> >
> > --
> > 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]]
> >
> > _______________________________________________
> > 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.
>

-- 
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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