[Bioc-devel] Pushing to Bioconductor repo gives errors

[Nitesh Turaga]

The RSS feed issue has been taken care of. The bug fix was issued today at 10 AM Eastern standard time. This should not be showing up on your push to the git server anymore.

Best,

Nitesh

> On Sep 7, 2020, at 8:44 AM, Nitesh Turaga <nturaga.bioc using gmail.com> wrote:
> 
> Your push went through. This is a different issue. I’ll look into it tomorrow.
> 
> Thanks,
> 
> Nitesh
> 
>> On Sep 6, 2020, at 12:44 PM, Alina Selega <alina.selega using gmail.com <mailto:alina.selega using gmail.com>> wrote:
>> 
>> Sorry, looks like the error got mangled. I pasted it in this gist:
>> https://gist.github.com/alinaselega/f5c4f724309211cc4a5bedd2a05bfd1e <https://gist.github.com/alinaselega/f5c4f724309211cc4a5bedd2a05bfd1e>
>> 
>> Thanks,
>> Alina
>> 
>> On Sun, 6 Sep 2020 at 12:36, Alina Selega <alina.selega using gmail.com> wrote:
>> 
>>> Hi,
>>> 
>>> I wanted to re-add a license file to my repository which got misplaced (no
>>> changes to code). I followed the instructions in this link (
>>> https://bioconductor.org/developers/how-to/git/pull-upstream-changes/) to
>>> pull upstream changes.
>>> 
>>> I then followed these instructions (
>>> https://bioconductor.org/developers/how-to/git/push-to-github-bioc/). I
>>> successfully pushed the file to my Github repo, but when I reached step 6
>>> to push the changes to Bioconductor, I got the following errors:
>>> 
>>> ```
>>> Counting objects: 3, done.
>>>                                      Delta compression using up to 8
>>> threads.
>>> Compressing objects: 100% (3/3), done.
>>>                        Writing objects: 100% (3/3), 12.11 KiB | 6.05
>>> MiB/s, done.                                  Total 3 (delta 1), reused 1
>>> (delta 0)
>>>    remote: fatal: this operation must be run in a work tree
>>>                        remote: ERROR:root:Exception: Command '['git',
>>> 'rev-parse', '--show-toplevel']' returned non-zero exit status 128
>>> remote: ERROR:root:local variable 'package_name' referenced before
>>> assignment
>>> remote: Note: failed to update RSS feed;git repository updated
>>> successfully.        To git.bioconductor.org:packages/BUMHMM.git
>>>                                          bbafa73..160b7a7  master -> master
>>> ```
>>> 
>>> It appears that the upstream updated successfully but can you advise about
>>> the errors?
>>> 
>>> Thank you,
>>> Alina
>>> 
>>> 
>> 
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>> 
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