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

Blattmann Peter blattmann at imsb.biol.ethz.ch
Wed Sep 6 19:35:31 CEST 2017

Dear Nitesh, 

Thank you for spotting that my upstream was wrong and fixing the form. I submitted my key (id_github) last weekend, but I still get stuck when I try to push changes to upstream. 
I'm not really sure from where the problem comes and if this might be because I have different .ssh keys (I have a config file that should sort this out) or if there is a problem with the username (it shows blattman in the error message, but I'm not sure where one defines a username or which one I would need to use)?

See below some print outs from the commands and thank you very much for any help. 



$ cat ~/.ssh/config
host git.bioconductor.com
user git
identityfile ~/.ssh/id_github

peterb at SYSBC-131 MINGW64 /c/ExchangeDrives/SWATH2stats (master)
$ git remote -v
origin  git at github.com:peterblattmann/SWATH2stats.git (fetch)
origin  git at github.com:peterblattmann/SWATH2stats.git (push)
upstream        git at git.bioconductor.org:packages/SWATH2stats.git (fetch)
upstream        git at git.bioconductor.org:packages/SWATH2stats.git (push)

peterb at SYSBC-131 MINGW64 /c/ExchangeDrives/SWATH2stats (master)
$ git fetch --all
Fetching origin
Fetching upstream

peterb at SYSBC-131 MINGW64 /c/ExchangeDrives/SWATH2stats (master)
$ git push origin master
Everything up-to-date

peterb at SYSBC-131 MINGW64 /c/ExchangeDrives/SWATH2stats (master)
$ git push upstream master
FATAL: W any packages/SWATH2stats blattman 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.

-----Original Message-----
From: Turaga, Nitesh [mailto:Nitesh.Turaga at RoswellPark.org] 
Sent: Friday, September 01, 2017 4:10 PM
To: Blattmann Peter
Cc: mailman, bioc-devel
Subject: Re: Problems pushing changes from github to git.bioconductor


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-repo
> sitories/) 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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