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

[Simina Boca]

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
>>
>>         [[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]]