[Bioc-devel] Package changes not merging with upstream

Tiago Chedraoui Silva tiagochst at gmail.com
Thu Aug 31 00:20:13 CEST 2017


Hello,

I had the same problem with the ELMER.data package (Experiment package).

*> tiagochst at epigenomeFMRP3:~/ELMER.data$ git push upstream master*
FATAL: W any packages/ELMER.data t.silva DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.


*> origin  https://github.com/tiagochst/ELMER.data.git
<https://github.com/tiagochst/ELMER.data.git> (push)*
upstream        git at git.bioconductor.org:packages/ELMER.data.git (fetch)
upstream        git at git.bioconductor.org:packages/ELMER.data.git (push)

Best regards,
Tiago Chedraoui Silva

On Fri, Aug 25, 2017 at 10:48 AM, Matt Richards <
Matt.Richards at systemsbiology.org> wrote:

> Thanks Martin, I retried the push to upstream and it works just fine now.
>
> Thanks
> Matt
>
>
>
> On Fri, Aug 25, 2017 at 10:27 AM, Martin Morgan <
> martin.morgan at roswellpark.org> wrote:
>
> > On 08/25/2017 01:17 PM, Matt Richards wrote:
> >
> >> Hi all,
> >>
> >> I maintain the "trena" package and I'm attempting to sync the changes
> from
> >> my in-house Github repo with the Bioconductor version. I submitted my
> ssh
> >> keys last week, so essentially I'm following these instructions:
> >>
> >> https://www.bioconductor.org/developers/how-to/git/sync-
> >> existing-repositories/
> >>
> >> I've seemingly made it from #1-8 successfully, but in trying to push to
> >> the
> >> upstream branch, I get an error:
> >>
> >> ------
> >>
> >> buoy:trena mrichard$ git push upstream master
> >>
> >> FATAL: W any packages/trena m.richards 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.
> >>
> >> ------
> >> I checked on my remotes via git config as well:
> >>
> >> ------
> >>
> >> remote.bioc.url=https://hedgehog.fhcrc.org/bioconductor/trunk/madman/
> >> Rpacks/TReNA
> >>
> >> remote.bioc.fetch=+refs/heads/*:refs/remotes/bioc/*
> >>
> >> remote.upstream.url=git at git.bioconductor.org:packages/trena.git
> >>
> >> remote.upstream.fetch=+refs/heads/*:refs/remotes/upstream/*
> >>
> >> ------
> >>
> >> Any idea on how I can navigate this error? Ultimately, we've made a lot
> of
> >> changes to the repo (including changing the capitalization of the
> package
> >> from "TReNA" to "trena") and I definitely want to get in those updates
> for
> >> the next release.
> >>
> >
> > This was an error on our side and should be fixed now.
> >
> > We maintain a 'manifest' of packages in each Bioconductor release. The
> > package name was changed in the manifest and in the svn repository, but
> not
> > in the svn permissions file. When we made git permissions, the svn
> > permissions weren't copied over because the svn path wasn't in the
> manifest.
> >
> > Sorry for the inconvenience.
> >
> > Martin
> >
> >
> >> Thanks
> >> Matt
> >>
> >>
> >
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>
>
>
> --
> Matthew Richards
> Postdoctoral Fellow
> Institute for Systems Biology
>
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>
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