[Bioc-devel] updating Bioconductor package that is already on Github
Thanks so much Nitesh! I had submitted my public key last time I did this (a few months ago) so I thought I didn't have to do it again. However, for whatever reason, the public key you sent is a bit different from mine (not sure why, since I haven't generated any more since then). In any case, I just used the google form to submit my public key. Cheers, Simina On Fri, Jan 26, 2018 at 12:44 PM, Turaga, Nitesh <
Nitesh.Turaga at roswellpark.org> wrote:
Hi Simina,
I?m assuming your keys are stored in the folder ?.ssh?. If that is the
case, try,
ssh-keygen -y -e -f <private_key>
That command will print out a public key. If that public key is the same
as the one I?ve sent you, they you can use that. (Remember that public
keys, don?t have ?.pub? ending. If your public key is called ?id_rsa.pub?
then your private key is most likely, ?id_rsa?).
If you have to configure your git login, please follow the link below to
make sure that the same key is used
http://bioconductor.org/developers/how-to/git/faq/
Best,
Nitesh
On Jan 26, 2018, at 12:36 PM, Simina Boca <smb310 at georgetown.edu> wrote: Thank you Nitesh! Where should I use the private key? I only see the
public key mentioned here: http://bioconductor.org/developers/how-to/git/ maintain-github-bioc/ Sorry if I'm missing something very obvious!
Best, Simina On Fri, Jan 26, 2018 at 12:23 PM, Turaga, Nitesh <
Nitesh.Turaga at roswellpark.org> wrote:
Hi You are using the wrong key. The key we have on file for you is ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAACAQDk1ywCtjVfC0wewYRCvzEiAac3so7n
nRISC6xj3RkEerAUaOHHSA2RjlrG60TYjnEZGPyeN79oKNDP0NhCelsNR2us gviCVeS04Qs2RhyzQVf5iNP/pJIBt21pwIvsW3CBqB1bTECUG8E9pK 3Gtm77uyRAwLImJtH1RioJ1JpGWKZ0r0ZU0O9c//zwr+Ae8OB94kSEuQ0yTXZj1nHfzL3vHsDt I8SsF3UE22RhS/sClW7s3raAlGNbmVdURZ2726JW2jIm40jeLDScdfO8UGEr5bWgVo7bnl6bzY UBsS2l8I2DZZHKIC+A1wBngNFpKNJ6dTpKzadkRudGbvU5q cIoX2zQNGzs/IyTh3LnX1TbCR1TbG/zC1BwoLB64yyjYI0O2nb+ ZhhRyXyoljX6AtoMgr16vwUfO+ts3HoD060WTFx29jucqV8rtYXNhDzZmqQs8Z5Ajk++ 8A0x7fxtuAR1FTVNByaTmH3PAIW6WU9wXXpQEz72mSm7FpQgQDkOfjRBQKqR nGbhaay8qltMYaqzjQLA8pBl7YIa5Km5UvyvV2DbAHS0B1R8w7c8L3kmPj5M PJZdAcRc6Nc0ByE4pYVwv8mosMB4gt12Lzuj0hz5ID9SDUPq8QghGJiWhVyb ZpKafu8VQ7E5QvqBC6DHhpKhdodt16BymxkEWk380yODUQ==
You should use a private key corresponding to that public key. Best, Nitesh
On Jan 26, 2018, at 12:05 PM, Simina Boca <smb310 at georgetown.edu>
wrote:
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
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
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 [[alternative HTML version deleted]]