[Bioc-devel] pre-receive hook won't let me fix (very) old merge conflict

Nitesh Turaga ntur@g@@b|oc @end|ng |rom gm@||@com
Wed Sep 1 16:51:40 CEST 2021

Hi Alyssa,

I can help you with this. Merge conflicts are hard to deal with for a few reasons, and this makes the hook design a little challenging. We want to keep the hook simple, and straightforward without adding too many edge cases into it. 

The reason for your issue, is because the conflicts in your code were introduced in the ‘pre-git’ era. I can disable the hook for your package and we can resolve it.

I’ll send you a private email to coordinate.



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Sep 1, 2021, at 12:33 AM, Alyssa Frazee <alyssa.frazee using gmail.com> wrote:
> Hello!
> I have an old package up on Bioconductor, and as I was dusting it off
> fixing a build error this weekend, I ran into an issue where a commit with
> merge conflict markers (>>>>, ====, etc) was introduced into my repo in
> 2016. My new diff removes those characters and fixes the conflict, but I'm
> not able to push the fix to the git using git.bioconductor.org remote because the
> diff itself contains those characters, which is not allowed by pre-receive
> hooks (even if they are being removed and not added):
> https://github.com/Bioconductor/git-hooks/blob/916f2fd1ddc5f461f14ba8d7cb9fc077aea37e44/prevent_merge_markers.py#L96
> Is there a workaround for this? (any way to temporarily disable the hook to
> get out of a bad state? also open to other suggestions!)
> Thanks so much!
> -Alyssa
> details: package is polyester, commit containing the merge conflict
> characters is 2306e5b3e88c6156e091ff5cb9933a190f45d33c (2016-06-01) in the
> .travis.yml file, which isn't important for actual package
> functionality (but was being used on the github side).
> 	[[alternative HTML version deleted]]
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