AMBER Archive (2008)

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

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Jul 31 2008 - 17:04:55 CDT

Hi,

This is already solved, but a couple of comments:

One can use the -f option to patch
patch -f -p0 -N -r patch_rejects <bugfix.a...
This will avoid pausing for
File to patch:
Skip this patch? [y]

But it won't change the exit status.

As far as amber tools 1.2 being patched by bugfix.at.all-1.0, only
src/gleap/mortsrc/capbox/octree.hpp
truely fails since there was lots of activity between 1.0 and 1.2.
The other complaints can be safely ignored.

In addition, applying the patch command to the current effectively
empty bugfix.at.all-1.2 file is safe; just ignore the patch comment:
patch: **** Only garbage was found in the patch input.

Scott

On Fri, 25 Jul 2008, Mike Hanby wrote:

> Thanks Dave,
>
> For those of you using a bash script to compile Amber 10 and AmberTools,
> something like this should help:
>
> if [[ ! $(grep "THERE ARE NO BUGFIXES" $SOURCEDIR/bugfix.at.all-1.2) ]];
> then
> patch -p0 -N -r patch-rejects.at < $SOURCEDIR/bugfix.at.all-1.2
> else
> echo "AmberTools does not need patching, skipping the patch process!"
> fi
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of David A. Case
> Sent: Thursday, July 24, 2008 18:38
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2
>
> On Thu, Jul 24, 2008, Mike Hanby wrote:
> >
> > 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.
>
> > Any suggestions other than "just don't patch"?
>
> nope. There are updates in version 1.2 that were not deemed crucial
> enough
> to post as bugfixes. I'll rename the patch file to indicate that it is
> intended for AmberTools1.0.
>
> ...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu