On Mon, Sep 24, 2012 at 4:15 PM, Nadeem A. Vellore <vnadeem.gmail.com>wrote:
> Hi,
> I downloaded the new bugfix9 (
> http://ambermd.org/bugfixes/12.0/bugfix.9.bz2_)
> and 10 from the amebrmd website for patching the Amber12 code (for GPU
> fixes)
> The file **.bz2_ *I renamed to .bz2 and unzipped it and placed it in the
> ./patch/Amber_Unapplied_Patches folder.
>
Why did you do this? Why not just use
./patch_amber.py --update
> Using the patch_amber.py command I tried to apply the patch and got error.
> Could you help me resolve this.
>
> *> ./patch_amber.py
> --apply-patch=./.patches/Amber_Unapplied_Patches/bugfix.9*
> Traceback (most recent call last):
> File "./patch_amber.py", line 747, in <module>
> if not single_patch.files_edited():
> File "./patch_amber.py", line 231, in files_edited
> "path: [%s] -- For security this is not allowed." % filename)
> TypeError: exceptions must be old-style classes or derived from
> BaseException, not NoneType
>
What version of Python are you using? (python --version) This has been
tested with Python as old as 2.4, and I do not see how this error is
possible unless you modified the patch_amber.py script.
I would like to discourage you from trying to use patch_amber.py this way,
since it can cause a lot of problems. If you are doing it to pick out
individual patches to download and apply rather than just applying all of
them, then this will *not* work (and never has). Each patch is intended to
apply on top of the source code that results from all previous patches.
Therefore, if 2 patches affect the same file, and are not applied in
order, the patch will fail. (Also, patch_amber.py has had to be fixed
twice already, so these bug fixes need to be applied as well).
Lastly, the error you're getting indicates that a modified file begins with
"/" (i.e., it has an absolute path). Unless the file is /dev/null (which
means it's either deleted or added), this can potentially modify files
outside AMBERHOME (protections were put in to prevent this from happening).
Since there are no such files from bugfix.9, my guess is that it was
modified somehow, which is dangerous.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Sep 24 2012 - 15:00:03 PDT
