I'm trying to update a Mac OS X (10.6.8) AMBER installation from June 2012.
AmberTools12 patches bugfix.12 through bugfix.22 were sucessfully applied.
When I re-ran patch_amber.py -update I got this:
./patch_amber.py --update
Determining patches to download for AmberTools12
Downloading bugfix.23
Downloading bugfix.24
Downloading bugfix.25
Downloading bugfix.26
Downloading bugfix.27
Downloading bugfix.28
Downloading bugfix.29
Downloading bugfix.30
Downloading bugfix.31
Downloading bugfix.32
Downloading bugfix.33
Downloading bugfix.34
Downloading bugfix.35
Downloading bugfix.36
Downloading bugfix.37
Determining patches to download for Amber12
Downloading bugfix.8
Downloading bugfix.9.bz2_
Decompressing .patches/Amber_Unapplied_Patches/bugfix.9.bz2 with
/opt/local/bin/bunzip2
Downloading bugfix.10
Downloading bugfix.11
Downloading bugfix.12
Downloading bugfix.13
Downloading bugfix.14
Downloading bugfix.15
Downloading bugfix.16
Downloading bugfix.17
Applying AmberTools12 patches
Error or warning during patching process for
.patches/AmberTools_Unapplied_Patches/bugfix.23:
1 out of 15 hunks FAILED -- saving rejects to file
AmberTools/src/configure2.rej
Trying it again, I now get this:
./patch_amber.py --update
Determining patches to download for AmberTools12
Downloading bugfix.23
Downloading bugfix.24
Downloading bugfix.25
Downloading bugfix.26
Downloading bugfix.27
Downloading bugfix.28
Downloading bugfix.29
Downloading bugfix.30
Downloading bugfix.31
Downloading bugfix.32
Downloading bugfix.33
Downloading bugfix.34
Downloading bugfix.35
Downloading bugfix.36
Downloading bugfix.37
Determining patches to download for Amber12
Downloading bugfix.8
Downloading bugfix.9.bz2_
Decompressing .patches/Amber_Unapplied_Patches/bugfix.9.bz2 with
/opt/local/bin/bunzip2
Downloading bugfix.10
Downloading bugfix.11
Downloading bugfix.12
Downloading bugfix.13
Downloading bugfix.14
Downloading bugfix.15
Downloading bugfix.16
Downloading bugfix.17
Applying AmberTools12 patches
Error or warning during patching process for
.patches/AmberTools_Unapplied_Patches/bugfix.23:
Reversed (or previously applied) patch detected! Skipping patch.
15 out of 15 hunks ignored -- saving rejects to file
AmberTools/src/configure2.rej
Reversed (or previously applied) patch detected! Skipping patch.
6 out of 6 hunks ignored -- saving rejects to file
AmberTools/test/mmpbsa_py/04_Per_Residue_Decomp/FINAL_RESULTS_MMPBSA.dat.save.rej
Reversed (or previously applied) patch detected! Skipping patch.
6 out of 6 hunks ignored -- saving rejects to file
AmberTools/test/mmpbsa_py/05_Pairwise_Decomp/FINAL_RESULTS_MMPBSA.dat.save.rej
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file
AmberTools/test/mmpbsa_py/10_QM_MMGBSA/FINAL_RESULTS_MMPBSA.dat.save.rej
Here are the results of patch_amber.py --check-update
./patch_amber.py --check-update
AmberTools12 has 15 unapplied patches: 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37
Amber12 has 10 unapplied patches: 8, 9, 10, 11, 12, 13, 14, 15, 16, 17
Any suggestions?
Thanks for any help.
TG
--
Terry M. Gray, Ph.D.
Instructor, Colorado State University
Research Associate, Colorado State University
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Received on Thu Oct 10 2013 - 20:30:09 PDT
