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

Blattmann Peter blattmann at imsb.biol.ethz.ch
Fri Sep 1 11:09:32 CEST 2017

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<mailto:git at github.com:peterblattmann/SWATH2stats.git> (fetch)
origin  git at github.com:peterblattmann/SWATH2stats.git<mailto: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<mailto: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).

Therefore I am stuck here and any help how to solve this would be appreciated.

Thank you very much for your help

Kind regards



ETH Zurich
Dr. Peter Blattmann
Institute of Molecular Systems Biology
Aebersold group
Auguste-Piccard-Hof 1
8093 Zurich

phone: +41 44 633 0473
cellphone: +41 79 745 8061
e-mail: blattmann at imsb.biol.ethz.ch<mailto:blattmann at imsb.biol.ethz.ch>

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