[AMBER-Developers] Problems creating amber12 pbsa bugfix patch

From: <wmsmith.uci.edu>
Date: Mon, 30 Sep 2013 14:55:48 -0700

Hello everyone,
 I am trying to create a patch to fix a few bugs in pbsa for amber12. I
created the patch according to the instruction on
"http://ambermd.org/pmwiki/index.php/Main/Coding"
I started with a clean pull of amber12-with-patches branch, created and
checked out a temp branch, made added and commited the modifications and
then formatted the patch.
 Dr. Luo and I then tested it using the instructions on
"http://ambermd.org/pmwiki/index.php/Main/BugFixCreationInstructions"

It passes when running "./check_patches.py -b <bugfix>"
but fails for
"./check_patches.py -b path/to/your/bugfix -a -c <commit_id>"
where commit_id is the latest commit id.
(5d036abccbd94fc0c563674f4f7b92a18e27380a)

The error message is below. The patch itself is attached.

-Wes

"I will now try applying this patch.
You did not tell me what commit to apply the patch on. I'm guessing
you want the second-newest commit: 5d036abccbd94fc0c563674f4f7b92a18e27380a
Creating a new branch [am12-test-patch-apply] to test the patch
Created branch [am12-test-patch-apply] -- checking it out and applying the
patch

Error or warning during patching process for
0001-Minor-changes-to-pbsa-and-mmpbsa-to-fix-minor-bugs-a.patch:
2 out of 2 hunks FAILED -- saving rejects to file
b/AmberTools/src/mmpbsa_py/MMPBSA_mods/createinput.py.rej
1 out of 1 hunk FAILED -- saving rejects to file
b/AmberTools/src/mmpbsa_py/mmpbsa_energy.nab.rej
1 out of 1 hunk FAILED -- saving rejects to file
b/AmberTools/src/pbsa/force.F90.rej
3 out of 3 hunks FAILED -- saving rejects to file
b/AmberTools/src/pbsa/pb_init.F90.rej
2 out of 2 hunks FAILED -- saving rejects to file
b/AmberTools/src/pbsa/pb_read.F90.rej
1 out of 1 hunk FAILED -- saving rejects to file
b/AmberTools/test/mmpbsa_py/02_Poisson_Boltzmann/Run.PB.rej


0001-Minor-changes-to-pbsa-and-mmpbsa-to-fix-minor-bugs-a.patch did not
apply cleanly! See messages above and fix the errors.


Removing files I created above (but I am not deleting directories)
Resetting the branch to the original state.
I am (forcibly) going back to amber12-with-patches now
Deleted branch am12-test-patch-apply (was 5d036ab).

BAD PATCH -- please check why it did not apply cleanly"


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Received on Mon Sep 30 2013 - 15:00:04 PDT
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