AMBER Archive (2009)

Subject: Re: [AMBER] Trying to patch amber 9

From: Jack Shultz (js_at_drugdiscoveryathome.com)
Date: Wed Jun 24 2009 - 10:25:41 CDT

I think I figured it out I had the unix_utils in my path. I should use
the cygwin patch while in cygwin.

On Wed, Jun 24, 2009 at 11:18 AM, Jack Shultz<js_at_drugdiscoveryathome.com> wrote:
>
> I did this about a year ago on cygwin when I first got Amber9. So I'm
> surprised I have this error now.
>
> On Wed, Jun 24, 2009 at 10:58 AM, case <case_at_biomaps.rutgers.edu> wrote:
>>
>> On Wed, Jun 24, 2009, Jack Shultz wrote:
>> >
>> > $ patch -p0 -N -r patch_rejects < bugfix.all
>> > patching file `src/ptraj/ptraj.c'
>> > Assertion failed: hunk, file patch.c, line 321
>>
>> This appears to be some problem with patch, not with our files.  Do a
>> "which
>> patch" to make sure you are running the correct executable.
>
> $ which patch
> /cygdrive/c/unix_utils/usr/local/wbin/patch
>
>>
>> What OS are you
>> using?
>
> cygwin
>
>>
>> It's possible that line endings in the patch file might not match your
>> system -- use a text editor to be sure that the bugfix.all file looks OK.
>
> as far as I can tell the bugfixall looks fine.
> maybe version of patch???
>
> jshultz_at_Hydrogen /usr/local/amber9
> $ patch -v
> patch 2.5
> Copyright 1988 Larry Wall
> Copyright 1997 Free Software Foundation, Inc.
>
> This program comes with NO WARRANTY, to the extent permitted by law.
> You may redistribute copies of this program
> under the terms of the GNU General Public License.
> For more information about these matters, see the file named COPYING.
>
> written by Larry Wall with lots o' patches by Paul Eggert
>
>
>>
>> Even with bad input, patch should not exit with an assertion failure.
>>  And, I
>> just re-verified that the patch file for Amber9 works fine for me.  So
>> something weird is happening here.
>>
>> ...dac
>>
>>
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>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
> 

-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org

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