AMBER Archive (2008)

Subject: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2

From: Mike Hanby (mhanby_at_uab.edu)
Date: Thu Jul 24 2008 - 16:47:34 CDT

Howdy,

 

I use a scripted approach to building Amber10 (with AmberTools). With
AmberTools 1.2 released I downloaded it and ran my build script, it
fails during the patching process now.

 

I know that I probably don't need to run the bugfix.at.all patch for
1.2, however since this is scripted, it always downloads the latest
patch file and I'd prefer to not have to script in exceptions for when
to apply the patches and when not to. Here's the error:

 

$ tar -jxf AmberTools-1.2.tar.bz2

$ tar -jxf Amber10.tar.bz2

$ cd amber10

$ patch -p0 -N -r patch-rejects.at < bugfix.at.all

 

patching file src/nab/nblist.c

Reversed (or previously applied) patch detected! Skipping patch.

2 out of 2 hunks ignored -- saving rejects to file patch-rejects.at

patching file src/nab/prm.c

Reversed (or previously applied) patch detected! Skipping patch.

1 out of 1 hunk ignored -- saving rejects to file patch-rejects.at

patching file src/gleap/mortsrc/guilib/mainwin.cpp

Hunk #1 FAILED at 20.

1 out of 1 hunk FAILED -- saving rejects to file patch-rejects.at

patching file src/gleap/mortsrc/capbox.hpp

Reversed (or previously applied) patch detected! Skipping patch.

2 out of 2 hunks ignored -- saving rejects to file patch-rejects.at

patching file src/gleap/mortsrc/capbox/solvate.cpp

Hunk #1 FAILED at 75.

Hunk #2 FAILED at 87.

Hunk #3 FAILED at 235.

Hunk #4 FAILED at 276.

Hunk #5 FAILED at 288.

Hunk #6 FAILED at 317.

Hunk #7 FAILED at 389.

Hunk #8 FAILED at 464.

Hunk #9 FAILED at 472.

9 out of 9 hunks FAILED -- saving rejects to file patch-rejects.at

can't find file to patch at input line 660

Perhaps you used the wrong -p or --strip option?

The text leading up to this was:

--------------------------

|Index: mortsrc/capbox/solvate.hpp

|===================================================================

|RCS file:
/raid5/case/cvsroot/amber10/src/gleap/mortsrc/capbox/solvate.hpp,v

|retrieving revision 1.4

|diff -p -r1.4 solvate.hpp

|*** src/gleap/mortsrc/capbox/solvate.hpp 21 Dec 2006 17:27:15
-0000 1.4

|--- src/gleap/mortsrc/capbox/solvate.hpp 9 Apr 2008 22:48:48
-0000

--------------------------

File to patch:

 

I would expect the patching to skip all of the 7 patches in
bugfix.at.all since they should already be in the source code.

 

Any suggestions other than "just don't patch"?

 

Thanks, Mike

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