If all else fails, clean out these files.
git clean -fxd
This deletes all untracked files (but does not touch any changes you made).
Note that "git status" will not show anything about this error if you
configured git to suppress printing untracked files (which is suggested on
the Amber wiki). Specifically, if you ran "git config
status.showUntrackedFiles no", then these 'untracked' files will not be
printed by 'git status'.
Alternatively, you can try a "git pull -f" to force through these safety
guards if you are certain you just want something that mirrors the main
repository.
All the best,
Jason
On Fri, Mar 22, 2013 at 11:27 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Mar 22, 2013, Scott Brozell wrote:
>
> > ...
> > %rm -fr AmberTools/src/paramfit/*
> > %git ls-files -d | xargs -t git checkout --
> > Your branch is behind the tracked remote branch 'origin/master' by 120
> commits,
> > and can be fast-forwarded.
> > %git pull
> > Updating c147f84..b185632
> > error: Untracked working tree file
> 'AmberTools/test/paramfit/dihedral_perfect_fit_NMA/Job_Control.in' would be
> overwritten by merge.
>
> Looks like you are making progress. "git status" is a good way to see what
> git thinks about the state of your tree.
>
> >
> > Various variations of above ultimately fail the same way.
>
> cf. the usual complaints we usually post to the Amber users' mailing list
> when
> there were not enough details for other people to be of much help.
>
> For example, what does git status report? Is Job_Control.in a new file?
> I'm
> guessing that it might be created during a test run, but is also under git
> control.
>
> > Note that I was uptodate a few days ago and had made no modifications.
>
> Did you run tests in this directory tree? That could introduce
> modifications.
> (Although that doesn't happen for me, as far as I can tell....)
>
> ...dac
>
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 22 2013 - 10:00:05 PDT
