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

Simina Boca smb310 at georgetown.edu
Wed Jan 31 04:51:39 CET 2018


Sure! This is for the MultiMed package, not swfdr, so I made that change
below:

~\Documents\GitHub\MultiMed [master ≡]> git remote -v
origin  https://github.com/SiminaB/MultiMed.git (fetch)
origin  https://github.com/SiminaB/MultiMed.git (push)
upstream        git at git.bioconductor.org:packages/MultiMed.git (fetch)
upstream        git at git.bioconductor.org:packages/MultiMed.git (push)

~\Documents\GitHub\MultiMed [master ≡]> ssh -T git at git.bioconductor.org |
grep MultiMed
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
 R      packages/MultiMed

The file containing my public key is named id_rsa.pub and the one
containing my private key is id_rsa, so I think that should be OK...

Best,
Simina


On Tue, Jan 30, 2018 at 9:36 PM, Turaga, Nitesh <
Nitesh.Turaga at roswellpark.org> wrote:

> Yes, that is the key we have.
>
> Please send me more information,( output of these commands)
>
>
>         git remote -v
>
>         ssh -T git at git.bioconductor.org | grep swfdr
>
> You might want to make sure you are using correct private key by setting
> up a config file in your SSH. (http://bioconductor.org/
> developers/how-to/git/faq/ section point 16)
>
>
> Nitesh
>
> > On Jan 30, 2018, at 8:47 PM, Simina Boca <smb310 at georgetown.edu> wrote:
> >
> > Hi Nitesh,
> >
> > I submitted this key as well a couple of days ago:
> > ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAACAQDP91Ifm9VtF76jYs4gPwJQx0nU3LBV
> rsWwX4Eba1SOIHlHiXb45RHFZ0tvwV4yMNb9IXGAA3Kg0OnJs1YS1ddXTVkK
> zyXAk4nlyiwSSSBe8gxhS1wPX5c8Zv8n28T71/bn90z61RKwkZc+hAZjrK/2Xiw/
> FwFsnJfcEIrEE3HT86WVDeXdNPDzIxb/MSmjRmjS4MVZ4tHqG5nC6du8SOSXFK
> gap5Z3YCL0SVO/2925LSbN4yiVHZQE5cY3iQoRBYtKCSr5/PBgsxrNxQhU8X//
> foqmLWGO0LVOV9Dk4Z3egHTrLXY+jVTm6wJICowrTFN5Db07roo66wc9Nb
> RAtb8lzDgc3u/GzYkQ5E2ZxA0r3j+XqrXRqa+qdl+sZTyBi2WixFEQKQGCs/
> xUg0AA5DB2mkNZtQpffGdWdHhsuY01ylS5gHaql/ciF18oMKJcdXIlQUtPTezT1hqHprx9
> 9WuHx+1HrBE50kU2rS3jsiFz7L2J1myt8jCqvpz1UirShD2cnLqmcwOgA7uu/bTx6gIAy/a/
> fbPGpQ5boYx6hEF5Qxrj0E5ZxcvW6Q1SxFbtSJsDyFHMvHafdZ3LpJdv9Fb/
> RtUEYl8zOxKqMZovdQVyy8XK1ZisSEKZ+FXGcT//cFFcEphSEGnJ04/
> 8u1r4uTn6mHriPQ5zYCr38a9TQPWCeQ== smb310 at georgetown.edu
> > Do you have this matched up with my account right now? I'm still getting
> the error message when trying to push upstream.
> >
> > Thanks so much for all your help!
> >
> > Best,
> > Simina
> >
> >
> > On Sun, Jan 28, 2018 at 9:53 AM, Simina Boca <smb310 at georgetown.edu>
> wrote:
> > 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/
> 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]]
> > > > >
> > > > > _______________________________________________
> > > > > 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
> >
> >
> >
> >
> > --
> > 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
> > https://sites.google.com/georgetown.edu/siminaboca/
> >
>
>
>
> 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
https://sites.google.com/georgetown.edu/siminaboca/

	[[alternative HTML version deleted]]



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