[Bioc-devel] git mirror fails

Martin Morgan martin.morgan at roswellpark.org
Fri Sep 2 12:46:41 CEST 2016

I'll inline an off-list exchange below, so that others with similar 
questions may benefit.

On 09/01/2016 08:09 AM, Martin Morgan wrote:
> On 08/31/2016 05:23 PM, Lara Urban wrote:
>> Dear All,
>> I hope this is the right platform to post my question: I am currently
>> trying to update my package on the devel branch. It is available via a
>> GitHub repo. I followed the instructions (
>> http://bioconductor.org/developers/how-to/git-mirror/) and can
>> commit/push
>> to GitHub, but when I switch to the devel branch and want to push
>> again, I
>> am "unable to access
>> 'https://github.com/Bioconductor-mirror/covRNA.git/': The
>> requested URL returned error: 403". However, I can access the URL via
>> browser. Does someone know what is going wring there? Please let me
>> know if
>> you need further information.
> Hi Lara -- I'm not really an expert on this so hopefully someone else
> will chime in.
> This
>   https://github.com/Bioconductor-mirror/covRNA.git
> is a read-only mirror of the svn repository; you should not be able to
> commit to it, and the instructions should not have lead you to need to
> commit to it.
> You should be doing the following on your own repository
>    git checkout devel
>    git svn rebase
>    git merge master --log
>    git svn dcommit
> maybe you could provide (cut and paste) the transcript of a session
> where you try do this. Also, it might help with diagnostics to report
>   git remove -v
>   git svn info
> again from within your cloned repository.

In off-list discussion Lara indicated that the next problem was the error

 > whenever I try
 > git svn rebase
 > or
 > git svn dcommit --add-author-from
 > I get:
 > Can't create session: Unable to connect to a repository at URL
 > 'https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/covRNA':
 > Unexpected server error 500 'Internal Server Error' on
 > '/bioconductor/trunk/madman/Rpacks/covRNA' at
 > /opt/local/lib/perl5/site_perl/5.22/Git/SVN.pm line 712.

this could be a problem on our end (e.g., misconfigured permissions) but 
it turned out that Lara needed to specify the username and password of 
the SVN account sent when the package was accepted, along the lines of

    git svn --username=<SVN user name> dcommit --add-author-from

Lara then indicated that

> Thanks a lot, it seems to have worked with adding just the username
> (and typing the password in afterwards). The versions on
> https://github.com/LaraUrban/covRNA and
> https://github.com/Bioconductor-mirror/covRNA are the same now.
> May I further ask how it long it will take until the new version is
> downloadable via biocLite? Currently, it is still the old version.

and the answer is that the 'devel' branch is built approximately every 
two days, and successful builds are pushed to the repos after that. The 
builds are summarized at



> Martin
>> Many thanks in advance.
>> Kind regards, Lara

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