[Bioc-devel] Problems pushing changes from github to git.bioconductor

Turaga, Nitesh Nitesh.Turaga at RoswellPark.org
Fri Sep 1 16:09:47 CEST 2017


The form is fixed now. You should be able to submit. 

But your upstream remote is wrong. You need to be using SSH protocol for access to the git.bioconductor.org server.

i.e your upstream should be `git at git.bioconductor.org:packages/SWATH2stats.git`.

Please see the documentation http://bioconductor.org/developers/how-to/git/new-package-workflow/

• SSH (developer) read / write access: git at git.bioconductor.org
• HTTPS (public) read only access: https://git.bioconductor.org

> On Sep 1, 2017, at 5:02 AM, Blattmann Peter <blattmann at imsb.biol.ethz.ch> wrote:
> Dear Nitesh, 
> I wanted to make some changes to our R/Bioconductor package but whereas I could successfully push it to my github account, it seems it did not propagate to bioconductor github / upstream. I guess I maybe didn’t set up something correctly or something with the ssh keys did not work correctly? 
> Here is my setup  and one can see that the c105413 commit has not been successfully pushed to upstream/master.
> $ git remote -v
> origin  git at github.com:peterblattmann/SWATH2stats.git (fetch)
> origin  git at github.com:peterblattmann/SWATH2stats.git (push)
> upstream        https://git.bioconductor.org/packages/SWATH2stats.git (fetch)
> upstream        https://git.bioconductor.org/packages/SWATH2stats.git (push)
> ¨
> $ git show-ref
> 53409d69584bf4742540ea2961dc4abdd2e2a9aa refs/heads/RELEASE_3_5
> c10541339b01352190c873e83840fdedccc04eca refs/heads/master
> c10541339b01352190c873e83840fdedccc04eca refs/remotes/origin/master
> 15b158f36fc7bf2acdf1d844e0def61e8cf4ce04 refs/remotes/upstream/RELEASE_3_2
> 29504fb0a7c95b0e7ebb5ac7ba924f291eaa9402 refs/remotes/upstream/RELEASE_3_3
> d857a511489fdf2fa5c5854fdbc3d1f49a7234e4 refs/remotes/upstream/RELEASE_3_4
> 53409d69584bf4742540ea2961dc4abdd2e2a9aa refs/remotes/upstream/RELEASE_3_5
> 0f4feef6f4105928a2ef40e695f37a2ec4f87b04 refs/remotes/upstream/master
> To solve this I tried to go along the steps outlined on the website to sync the repositories (https://www.bioconductor.org/developers/how-to/git/sync-existing-repositories/)
> But, I get then an error when trying to push to the upstream.
> $ git push upstream master
> fatal: remote error: FATAL: W any packages/SWATH2stats nobody DENIED by fallthru
> (or you mis-spelled the reponame)
> So I thought the problem might be with the ssh connection. However when I connect to git.bioconductor it seems to work.
> $ ssh -T git at git.bioconductor.org
> hello blattman, this is git at ip-172-30-0-33 running gitolite3 v3.6.6-6-g7c8f0ab on git 2.13.0
> R      admin/..*
> R      packages/..*
> R      admin/manifest
> R      packages/ABAData
> R      packages/ABAEnrichment
> However, I think the username should be p.blattmann (I think I wrongly submitted my bioconductor instead of SVN user id in the Google form some weeks ago). Therefore I wanted to fill in another google form, but it doesn’t accept my SVN identifier (it tells me it contains spaces which it doesn’t). 
> <image002.jpg>
> Therefore I am stuck here and any help how to solve this would be appreciated.
> Thank you very much for your help
> Kind regards
> Peter
> __________________________________________
> ETH Zurich
> Dr. Peter Blattmann
> Institute of Molecular Systems Biology
> Aebersold group
> HPT E58
> Auguste-Piccard-Hof 1
> 8093 Zurich
> Switzerland
> phone: +41 44 633 0473
> cellphone: +41 79 745 8061
> e-mail: blattmann at imsb.biol.ethz.ch

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