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