Hi,
This is actually an issue with dos line endings in the patch file
confusing 'patch' under cygwin. If you remove the dos line endings
from the patch, updating should occur successfully:
$> cd $AMBERHOME
$> ./configure -cygwin gnu
...
Applying AmberTools 13/update.4
PatchingError: .patches/AmberTools13_Unapplied_Patches/update.4 failed
to apply. No changes made from this patch
Automatic patching failed! Check the errors before re-configuring
$> dos2unix.exe .patches/AmberTools13_Unapplied_Patches/update.4
dos2unix: converting file
.patches/AmberTools13_Unapplied_Patches/update.4 to Unix format ...
$> ./configure -cygwin gnu
...
A fix to update_amber is also in the works to correct this.
-Dan
On Fri, Jun 14, 2013 at 4:41 PM, Hunter Brown <bassoongoon.earthlink.net> wrote:
> Hello, I am having difficulty compiling amber12 and ambertools 13. I am a windows user, so I am working via Cygwin.
>
> When I try to apply patches I get this message:
>
>
>
> PatchingError: .patches/AmberTools13_Unapplied_Patches/update.4 failed to apply. No changes made from this patch
> Automatic patching failed! Check the errors before re-configuring
>
>
>
>
> When I try to skip the patches using './configure cygwin' I get this message:
>
>
>
>
>
> NOT updating your tree and continuing anyway.
> Could not find the X11 libraries; you may need to edit config.h
> to set the XHOME and XLIBS variables.
> Searching for python2... Found python2.7: /usr/bin/python2.7
> Error: Architecture/compiler 'cygwin' is not supported!
> Type './configure -help' for options.
> Configure failed due to the errors above!
>
>
>
>
>
>
>
>
> I have tried using './configure gnu -cygwin' as well. The patches still fail to apply. If I try to skip the patches with './configure gnu -cygwin' I get this message (by the way, the single quotes are to make the commands I enter stand out from the rest of my text. I did not actually put single quotes into my Cygwin bash) :
>
>
>
>
> NOT updating your tree and continuing anyway.
> Error: unknown compiler: gnu
> Type './configure -help' for options.
> Configure failed due to the errors above!
>
>
>
>
>
>
> If somebody could help me get that sorted out I would really appreciate it. I need to learn Amber/Ambertools so that I can start running simulations. Because I have had difficulty configuring/compiling Amber, I cannot even reach the stage where I can begin learning how to use it; its frustrating!
>
>
>
>
>
> Anyways, thanks for reading and I hope that someone can be of assistance to me.
>
>
> -Hunter
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Jun 17 2013 - 09:30:02 PDT
