[Bioc-devel] Problems pushing changes from github to git.bioconductor
Dear Nitesh, Here some addition to the previous e-mail. I saw that in the config file there was written by mistake git.bioconductor.com instead of .org. I changed this now, but still it doesn't work. But the ssh connection seems to work fine and it recognizes me as "blattman" (see below). Thanks Best Peter peterb at SYSBC-131 MINGW64 /c/ExchangeDrives/SWATH2stats (master) $ cat ~/.ssh/config host git.bioconductor.org user git identityfile ~/.ssh/id_github 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. peterb at SYSBC-131 MINGW64 /c/ExchangeDrives/SWATH2stats (master) $ 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 R packages/ABSSeq -----Original Message----- From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf Of Blattmann Peter Sent: Wednesday, September 06, 2017 7:36 PM To: Turaga, Nitesh Cc: mailman, bioc-devel Subject: Re: [Bioc-devel] Problems pushing changes from github to git.bioconductor 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. Best Peter $ 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 Hi, 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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