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Date: Sat, 9 Jan 2010 05:23:18 GMT
From: Ben Kaduk <kaduk@mit.edu>
To: freebsd-gnats-submit@FreeBSD.org
Subject: [update port] science/vmd -- upgrade from 1.8.3 to 1.8.7
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>Number:         142513
>Category:       ports
>Synopsis:       [update port] science/vmd -- upgrade from 1.8.3 to 1.8.7
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    wxs
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Sat Jan 09 05:30:01 UTC 2010
>Closed-Date:    Mon Feb 22 14:23:02 UTC 2010
>Last-Modified:  Mon Feb 22 14:30:02 UTC 2010
>Originator:     Ben Kaduk
>Release:        8-current
>Organization:
MIT Student Information Processing Board
>Environment:
FreeBSD periphrasis.mit.edu 8.0-CURRENT FreeBSD 8.0-CURRENT #12: Fri Jun 26 23:33:14 EDT 2009     kaduk@periphrasis.mit.edu:/usr/obj/usr/src/sys/PERIPHRASIS  amd64
>Description:
Upgrade from VMD 1.8.3 to 1.8.7.  I'm not entirely sure what new features this provides, since I was not able to install 1.8.3 (The tachyon 0.97 that the port wanted was no longer available on the upstream site).  As such, I also can't tell if there are any regressions in the new packaging.
I guess I will assert maintainership and take one for ports@ ...
I changed the master site for the stride tarball to one hosted on the www.ks.uiuc.edu site that is upstream for vmd.
A couple of tweaks to the Makefile to make portlint less unhappy, but there are still several spurious warnings issued.
Upstream has updated from Tcl/Tk 8.4 to 8.5, so we'll follow that.

I have only tested on an amd64 system, as I don't have a 32-bit install with graphics handy.

In addition to the patch, I'll also attach a copy of the diagnostic errors that are printed on startup (some modules can't be found); as mentioned above, I don't know if this is a regression from the 1.8.3 port.
>How-To-Repeat:

>Fix:


Patch attached with submission follows:

diff -ru vmd-old/Makefile vmd/Makefile
--- vmd-old/Makefile	2009-03-10 01:30:56.000000000 -0400
+++ vmd/Makefile	2010-01-08 23:54:43.000000000 -0500
@@ -6,23 +6,23 @@
 #
 
 PORTNAME=		vmd
-PORTVERSION=		1.8.3
-PORTREVISION=		2
+PORTVERSION=		1.8.7
 CATEGORIES=		science graphics python tcl tk
-MASTER_SITES=		http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.97/:tachyon \
-			ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/:stride
+MASTER_SITES=		http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.98.7/:tachyon \
+			http://www.ks.uiuc.edu/Research/vmd/extsrcs/:stride
 DISTFILES=		${VMD_DIST} \
 			${TACHYON_DIST}:tachyon \
 			${STRIDE_DIST}:stride
 
-MAINTAINER=		ports@FreeBSD.org
+MAINTAINER=		kaduk-fbsd@mit.edu
 COMMENT=		A molecular visualization program
 
 BUILD_DEPENDS=		makedepend:${PORTSDIR}/devel/makedepend \
 			${PYNUMERIC}
-LIB_DEPENDS=		tcl84:${PORTSDIR}/lang/tcl84 \
-			tk84:${PORTSDIR}/x11-toolkits/tk84 \
-			fltk:${PORTSDIR}/x11-toolkits/fltk
+LIB_DEPENDS=		tcl85:${PORTSDIR}/lang/tcl85 \
+			tk85:${PORTSDIR}/x11-toolkits/tk85 \
+			fltk:${PORTSDIR}/x11-toolkits/fltk \
+			netcdf:${PORTSDIR}/science/netcdf
 RUN_DEPENDS=		${PYNUMERIC}
 
 USE_PERL5_BUILD=	yes
@@ -30,11 +30,15 @@
 USE_GL=			glu
 USE_PYTHON=		yes
 
-RESTRICTED=		"License has restrictions"
+RESTRICTED=		License has restrictions
 
 VMD_DIST=		${PORTNAME}-${PORTVERSION}.src.tar.gz
-TACHYON_DIST=		tachyon-0.97.tar.gz
-STRIDE_DIST=		stride.tar.gz
+TACHYON_DIST=		tachyon-0.98.7.tar.gz
+# I get stride.tar.gz from ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/
+# but the www.ks.uiuc.edu site (that gives Stride_src.tar.Z) is closer
+# to vmd upstream (and google actually knows about it).
+#STRIDE_DIST=		stride.tar.gz
+STRIDE_DIST=		Stride_src.tar.Z
 
 .include <bsd.port.pre.mk>
 
@@ -51,14 +55,13 @@
 # Check for VMD sources
 .if !exists(${DISTDIR}/${VMD_DIST}) # && !defined(PACKAGE_BUILDING)
 ECHO_MSG=	${PRINTF}
-IGNORE=	:\n\
-Because of licensing restrictions, you must fetch the source distribution\n\
-manually.  Please access\n\
+IGNORE=	because of licensing restrictions, you must fetch the source\n\
+distribution manually.  Please access\n\
 http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD\n\
 with a web browser.  You will be required to log in and register,\n\
 but you can create an account on this page.  After registration and\n\
 accepting the University of Illinois agreement, download the source file,\n\
-${VMD_DIST}.  Please place this file in ${DISTDIR}.\n
+${VMD_DIST}.  Please place this file in ${DISTDIR}.
 .endif
 
 do-extract:
@@ -70,17 +73,20 @@
 
 post-patch:
 	${REINPLACE_CMD} "s/-lpthread/${PTHREAD_LIBS}/" ${WRKSRC}/configure
-	${REINPLACE_CMD} "s/-ltk8.4/-ltk84/" ${WRKSRC}/configure
-	${REINPLACE_CMD} "s/-ltcl8.4/-ltcl84/" ${WRKSRC}/configure
+	${REINPLACE_CMD} "s/-ltk8.5/-ltk85/" ${WRKSRC}/configure
+	${REINPLACE_CMD} "s/-ltcl8.5/-ltcl85/" ${WRKSRC}/configure
 	${REINPLACE_CMD} "s%\$$python_dir/lib_\$$config_arch%${PREFIX}%" ${WRKSRC}/configure
 	${REINPLACE_CMD} "s/python2.2/${PYTHON_VERSION}/" ${WRKSRC}/configure
 	${REINPLACE_CMD} "s/.SILENT:/#.SILENT:/" ${WRKDIR}/plugins/Makefile
 	${REINPLACE_CMD} "s/.SILENT:/#.SILENT:/" ${WRKDIR}/plugins/*/Makefile
+	${REINPLACE_CMD} "s%log2f(\([^ ,]*\))%logf(\1)/(float)M_LN2%g" ${WRKSRC}/src/Orbital.C
+	${REINPLACE_CMD} -e "s|%%PREFIX%%|${PREFIX}|g" \
+		-e "s|/usr/local|${LOCALBASE}|g" ${WRKSRC}/configure
 
 do-build:
 	${SETENV} ${MAKE_ENV} ${GMAKE} bsd -C ${WRKSRC}/lib/tachyon/unix && ${MV} ${WRKSRC}/lib/tachyon/compile/bsd/tachyon ${WRKSRC}/lib/tachyon/tachyon_${VMD_ARCH}
 	${SETENV} ${MAKE_ENV} PLUGINDIR=${WRKSRC}/plugins ${GMAKE} ${VMD_ARCH} distrib -C ${WRKDIR}/plugins
-	${SETENV} ${MAKE_ENV} TCL_INCLUDE_DIR=${PREFIX}/include/tcl8.4 TK_INCLUDE_DIR=${PREFIX}/include/tk8.4 ${GMAKE} ${VMD_TARGET} -C ${WRKSRC}
+	${SETENV} ${MAKE_ENV} TCL_INCLUDE_DIR=${PREFIX}/include/tcl8.5 TK_INCLUDE_DIR=${PREFIX}/include/tk8.5 ${GMAKE} ${VMD_TARGET} -C ${WRKSRC}
 	${SETENV} ${MAKE_ENV} ${GMAKE} all -C ${WRKSRC}/src
 	${SETENV} ${MAKE_ENV} ${GMAKE} depend -C ${WRKSRC}/lib/surf && ${SETENV} ${MAKE_ENV} ${GMAKE} surf -C ${WRKSRC}/lib/surf && ${MV} ${WRKSRC}/lib/surf/surf ${WRKSRC}/lib/surf/surf_${VMD_ARCH}
 	${SETENV} ${MAKE_ENV} ${GMAKE} -C ${WRKSRC}/lib/stride && ${MV} ${WRKSRC}/lib/stride/stride ${WRKSRC}/lib/stride/stride_${VMD_ARCH}
diff -ru vmd-old/distinfo vmd/distinfo
--- vmd-old/distinfo	2005-05-06 11:19:35.000000000 -0400
+++ vmd/distinfo	2010-01-08 23:49:29.000000000 -0500
@@ -1,6 +1,9 @@
-MD5 (vmd-1.8.3.src.tar.gz) = 8fb3fa55a54bcc3e41dbbd53c1c2cc59
-SIZE (vmd-1.8.3.src.tar.gz) = 8590337
-MD5 (tachyon-0.97.tar.gz) = 198953aea283a7158eef2ee079e909f6
-SIZE (tachyon-0.97.tar.gz) = 2485223
-MD5 (stride.tar.gz) = bdef3a3e1af8cbdf8fbfefacfa9a929f
-SIZE (stride.tar.gz) = 56441
+MD5 (vmd-1.8.7.src.tar.gz) = e8da2f2a5ffd5b4b2562eec77bbea8a3
+SHA256 (vmd-1.8.7.src.tar.gz) = 72fe2fb7eff4c805a886ea929c7e143a3a1be57cc817b5d1719d29e591d80316
+SIZE (vmd-1.8.7.src.tar.gz) = 23853864
+MD5 (tachyon-0.98.7.tar.gz) = 17b41c7042a2d3a75531a4979f643d15
+SHA256 (tachyon-0.98.7.tar.gz) = f22b86ed8c85bb12abc20c703f01238bce676c097dae66c81a6bbb7c08a60341
+SIZE (tachyon-0.98.7.tar.gz) = 3269840
+MD5 (Stride_src.tar.Z) = 96507c2bdc16d4b152278ad7a0cb0389
+SHA256 (Stride_src.tar.Z) = c40f7de64947ebab7ec49511c0d264b08bc0fcbc703014bdc85d83a7389be230
+SIZE (Stride_src.tar.Z) = 100329
Only in vmd/files: old-patch-configure
diff -ru vmd-old/files/patch-AtomParser.C vmd/files/patch-AtomParser.C
--- vmd-old/files/patch-AtomParser.C	2005-03-14 07:21:32.000000000 -0500
+++ vmd/files/patch-AtomParser.C	2010-01-07 18:50:58.000000000 -0500
@@ -1,11 +1,11 @@
 --- src/AtomParser.C-xxx	Fri Dec  5 13:21:53 2003
 +++ src/AtomParser.C	Thu Aug 12 00:24:00 2004
-@@ -109,7 +109,7 @@
+@@ -114,7 +114,7 @@
  #define	YYCONST
  #endif
  
--#if !defined(_MSC_VER) && !defined(ARCH_MACOSX)
-+#if !defined(_MSC_VER) && !defined(ARCH_MACOSX) && !defined(ARCH_FREEBSD) && !defined(ARCH_FREEBSDAMD64)
+-#if !defined(_MSC_VER) && !defined(__APPLE__)
++#if !defined(_MSC_VER) && !defined(__APPLE__) && !defined(ARCH_FREEBSD) && !defined(ARCH_FREEBSDAMD64)
  #include <values.h>
  #endif
  
diff -ru vmd-old/files/patch-Make-arch vmd/files/patch-Make-arch
--- vmd-old/files/patch-Make-arch	2005-05-06 11:19:35.000000000 -0400
+++ vmd/files/patch-Make-arch	2010-01-08 14:48:33.000000000 -0500
@@ -1,22 +1,24 @@
 --- Make-arch.orig	Mon Feb  7 13:09:55 2005
 +++ ../plugins/Make-arch	Fri Mar 25 16:54:01 2005
-@@ -9,6 +9,7 @@
- 	@echo "--------------------------------------"
- 	@echo " AIX4"
+@@ -12,6 +12,7 @@
+ 	@echo " AIX5_64"
+ 	@echo " AIX6_64"
  	@echo " FREEBSD"
 +	@echo " FREEBSDAMD64"
  	@echo " HPUX11"
  	@echo " IRIX6"
  	@echo " IRIX6_64"
-@@ -142,8 +143,22 @@
- 	"LOPTO = -o " \
+@@ -259,8 +260,25 @@
  	"CC = gcc" \
  	"CXX = g++" \
--	"CCFLAGS = -O2 -Wall -I/usr/local/include/tcl8.4" \
+	"DEF = -D" \
+-	"CCFLAGS = -O2 -Wall -I/usr/local/include/tcl8.5" \
 -	"CXXFLAGS = -O2 -Wall" \
-+	"CCFLAGS = ${CFLAGS} -O2 -Wall -I/usr/local/include/tcl8.4" \
-+	"CXXFLAGS = ${CFLAGS} -O2 -Wall" \
-+	"TCLLDFLAGS = -L/usr/local/lib -ltcl84" \
++	"CCFLAGS = ${CFLAGS} -O2 -Wall -I/usr/local/include/tcl8.5" \
++	"CXXFLAGS = ${CFLAGS} -O2 -Wall -I/usr/local/include/tcl8.5" \
++	"TCLLDFLAGS = -L/usr/local/lib -ltcl85" \
++	"NETCDFLDFLAGS = -lnetcdf " \
++	"AR = ar" \
 +	"NM = nm -p" \
 +	"RANLIB = touch" \
 +	"SHLD = gcc -shared"
@@ -28,8 +30,9 @@
 +	"LOPTO = -fPIC -m64 -o " \
 +	"CC = gcc" \
 +	"CXX = g++" \
-+	"CCFLAGS = ${CFLAGS} -m64 -O2 -Wall -I/usr/local/include/tcl8.4" \
-+	"CXXFLAGS = ${CFLAGS} -m64 -O2 -Wall" \
- 	"TCLLDFLAGS = -L/usr/local/lib -ltcl84" \
- 	"NM = nm -p" \
- 	"RANLIB = touch" \
++	"DEF = -D" \
++	"CCFLAGS = ${CFLAGS} -m64 -O2 -Wall -I/usr/local/include/tcl8.5" \
++	"CXXFLAGS = ${CFLAGS} -m64 -O2 -Wall -I/usr/local/include/tcl8.5" \
+ 	"TCLLDFLAGS = -L/usr/local/lib -ltcl85" \
+	"NETCDFLDFLAGS = -lnetcdf " \
+ 	"AR = ar" \
diff -ru vmd-old/files/patch-Makefile vmd/files/patch-Makefile
--- vmd-old/files/patch-Makefile	2005-05-06 11:19:35.000000000 -0400
+++ vmd/files/patch-Makefile	2010-01-07 21:54:06.000000000 -0500
@@ -1,19 +1,18 @@
 --- Makefile.orig	Sat Dec  6 04:20:58 2003
 +++ Makefile	Wed Feb  2 21:30:13 2005
-@@ -52,11 +52,14 @@
- 
+@@ -86,10 +86,13 @@
  ## FreeBSD builds
+ ##
  freebsd.mesa:
--	./configure FREEBSD MESA FLTK TK TCL IMD VRPN PYTHON PTHREADS LIBTACHYON NUMPY SILENT
-+	./configure FREEBSD MESA FLTK TK TCL IMD PYTHON PTHREADS LIBTACHYON NUMPY
+-	./configure FREEBSD MESA FLTK TK TCL IMD VRPN PTHREADS LIBTACHYON NETCDF SILENT
++	./configure FREEBSD MESA FLTK TK TCL IMD PTHREADS LIBTACHYON NETCDF
  
- # FreeBSD doesn't have hardware good accelleration support
  freebsd.opengl:
--	./configure FREEBSD OPENGL FLTK TK IMD VRPN SILENT SPACEBALL TCL PTHREADS ACTC LIBTACHYON PYTHON NUMPY
-+	./configure FREEBSD OPENGL FLTK TK IMD TCL PTHREADS LIBTACHYON PYTHON NUMPY
+-	./configure FREEBSD OPENGL FLTK TK IMD VRPN SILENT LIBSBALL TCL PTHREADS ACTC LIBTACHYON NETCDF
++	./configure FREEBSD OPENGL FLTK TK IMD TCL PTHREADS LIBTACHYON NETCDF
 +
 +freebsd.amd64.opengl:
-+	./configure FREEBSDAMD64 OPENGL FLTK TK IMD SILENT TCL PTHREADS LIBTACHYON PYTHON NUMPY
++	./configure FREEBSDAMD64 OPENGL FLTK TK IMD TCL PTHREADS LIBTACHYON NETCDF
  
  
  
diff -ru vmd-old/files/patch-OpenGLExtensions.C vmd/files/patch-OpenGLExtensions.C
--- vmd-old/files/patch-OpenGLExtensions.C	2004-09-03 05:02:31.000000000 -0400
+++ vmd/files/patch-OpenGLExtensions.C	2010-01-07 22:01:22.000000000 -0500
@@ -1,10 +1,10 @@
 --- src/OpenGLExtensions.C-xxx	Fri Dec  5 13:21:59 2003
 +++ src/OpenGLExtensions.C	Fri Aug 27 16:42:14 2004
-@@ -117,7 +117,17 @@
+@@ -157,7 +157,17 @@
  #endif
  
  #if !defined(_MSC_VER) && !defined(__APPLE__)
--#if !defined(ARCH_LINUX) && !defined(ARCH_LINUXALPHA) && !defined(ARCH_LINUXAMD64) && !defined(ARCH_LINUXPPC) && (defined(GLX_VERSION_1_4) || defined(ARCH_SOLARIS2))
+-#if !defined(__linux) && !defined(ARCH_SOLARISX86) && !defined(ARCH_SOLARISX86_64) && (defined(GLX_VERSION_1_4) || defined(ARCH_SOLARIS2))
 +/*
 +   Why the !defined(ARCH_FREEBSD)?  Typically the X libraries that
 +   come with FreeBSD work with glXGetProcAddress.  However, if the
@@ -15,7 +15,7 @@
 +   that bridge when we come to it - email me at stephen@math.missouri.edu
 +   about it.)
 +*/
-+#if !defined(ARCH_FREEBSD) && !defined(ARCH_LINUX) && !defined(ARCH_LINUXALPHA) && !defined(ARCH_LINUXAMD64) && !defined(ARCH_LINUXPPC) && (defined(GLX_VERSION_1_4) || defined(ARCH_SOLARIS2))
++#if !defined(ARCH_FREEBSD) && !defined(__linux) && !defined(ARCH_SOLARISX86) && !defined(ARCH_SOLARISX86_64) && (defined(GLX_VERSION_1_4) || defined(ARCH_SOLARIS2))
    // GLX 1.4 form found on commercial Unix systems that
    // don't bother providing the ARB extension version that Linux prefers.
    return glXGetProcAddress((const GLubyte *) procname);
diff -ru vmd-old/files/patch-configure vmd/files/patch-configure
--- vmd-old/files/patch-configure	2005-05-06 11:19:35.000000000 -0400
+++ vmd/files/patch-configure	2010-01-08 22:01:57.000000000 -0500
@@ -1,39 +1,54 @@
---- configure.orig	Sat Dec  6 04:20:58 2003
-+++ configure	Wed Feb  2 21:16:23 2005
-@@ -46,6 +46,7 @@
- # ---------------------------------------------------------------
- # AIX4        - compile on an RS/6000 machine (gcc/g++/xlc/xlC)
- # FREEBSD     - compile on a FreeBSD machine (gcc/g++)
-+# FREEBSDAMD64- compile on a FreeBSD machine (gcc/g++)
- # HPUX11      - compile on an HP-UX 11.0 machine (cc/CC/cc/aCC)
- # IRIX6       - compile on an SGI, IRIX 6.X or later, 32-bit ABI
- # IRIX6_64    - compile on an SGI, IRIX 6.X or later, 64-bit ABI
-@@ -116,7 +117,7 @@
+--- configure.orig	2009-08-01 03:19:34.000000000 -0400
++++ configure	2010-01-08 22:01:38.000000000 -0500
+@@ -13,10 +13,10 @@
+ $install_name = "vmd";
+ 
+ # Directory where VMD startup script is installed, should be in users' paths.
+-$install_bin_dir="/usr/local/bin";
++$install_bin_dir="%%PREFIX%%/bin";
+ 
+ # Directory where VMD files and executables are installed
+-$install_library_dir="/usr/local/lib/$install_name";
++$install_library_dir="%%PREFIX%%/lib/$install_name";
+ 
+ 
+ # optionally override hard-coded defaults above with environment variables
+@@ -48,6 +48,7 @@
+ # AIX5          - compile on an RS/6000 machine (gcc/g++/xlc/xlC)
+ # AIX6          - compile on an RS/6000 machine (gcc/g++/xlc/xlC)
+ # FREEBSD       - compile on a FreeBSD machine (gcc/g++)
++# FREEBSDAMD64  - compile on a FreeBSD machine (gcc/g++)
+ # HPUX11        - compile on an HP-UX 11.0 machine (cc/CC/cc/aCC)
+ # IRIX6         - compile on an SGI, IRIX 6.X or later, 32-bit ABI
+ # IRIX6_64      - compile on an SGI, IRIX 6.X or later, 64-bit ABI
+@@ -153,7 +154,7 @@
  
  #################### Parse command line options   ###########
  # list of allowed architectures
--@archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXPPC', 'MACOSX', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'WIN32');
-+@archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'FREEBSDAMD64', 'HPUX11', 'AIX4', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXPPC', 'MACOSX', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'WIN32');
+-@archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
++@archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'FREEBSDAMD64', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
  
  if ($#ARGV == -1) {
      $text = `cat configure.options`;
-@@ -624,8 +625,8 @@
+@@ -747,8 +748,8 @@
  # This may be commented out if not required.
- $libtachyon_defines        = "-DVMDLIBTACHYON";
+ $libtachyon_defines     = "-DVMDLIBTACHYON";
  $libtachyon_dir         = "$vmd_library_dir/tachyon";
 -$libtachyon_include     = "-I$libtachyon_dir/include";
 -$libtachyon_library     = "-L$libtachyon_dir/lib_$config_arch";
 +$libtachyon_include     = "-I$libtachyon_dir/src";
 +$libtachyon_library     = "-L$libtachyon_dir/compile/bsd";
  $libtachyon_libs        = "-ltachyon";
- @libtachyon_cc             = ();
- @libtachyon_ccpp           = ('LibTachyonDisplayDevice.C'
-@@ -1174,8 +1175,10 @@
+ @libtachyon_cc          = ();
+ @libtachyon_cu          = ();
+@@ -1478,9 +1479,11 @@
+     $def_imageviewer="display %s";
  
      # XFree 4.0 Direct Rendering Interface and GLX 
-     $opengl_dir         = "/usr/X11R6";
+-    $opengl_dir         = "/usr/X11R6";
 -    $opengl_include     = "-I$opengl_dir/include";
 -    $opengl_library     = "-L$opengl_dir/lib";
++    $opengl_dir         = "/usr/local";
 +# -DGLX_GLXEXT_LEGACY is required for patched OpenGLExtensions.C to compile.
 +# See patched OpenGLExtensions.C for explanation.
 +    $opengl_include     = "-DGLX_GLXEXT_LEGACY -I$opengl_dir/include";
@@ -41,7 +56,28 @@
      $opengl_libs        = "-lGL -lGLU"; 
  
      $arch_lex      = "flex";
-@@ -1209,7 +1212,66 @@
+@@ -1492,17 +1495,17 @@
+     $arch_shld        = "g++ -shared";
+     $arch_shlibname   = "so";
+     $arch_shcppopts   = "-fPIC";
+-    $arch_shldopts    = "-L/usr/local/lib -L/usr/X11R6/lib";
++    $arch_shldopts    = "-L/usr/local/lib";
+ 
+     $arch_opt_flag    = "-m32 -fno-for-scope -Wno-deprecated -Wall -O3";
+     $arch_copts       = "-m32 -Wall -O3";
+ 
+     if ($config_static) {
+       $arch_lopts       = "-static";
+-      $mesa_libs        = "-lMesaGL -lMesaGLU -L/usr/X11R6/lib -lXext -lX11";
++      $mesa_libs        = "-lMesaGL -lMesaGLU -L/usr/local/lib -lXext -lX11";
+     } else {
+       $arch_lopts       = "";
+-      $mesa_libs        = "-lGL -lGLU -L/usr/X11R6/lib -lXext -lX11";
++      $mesa_libs        = "-lGL -lGLU -L/usr/local/lib -lXext -lX11";
+     }
+ 
+     if ($config_shared) {
+@@ -1515,7 +1518,66 @@
  
      # this is to make tcl happy,
      # also needed for plugins
@@ -67,7 +103,7 @@
 +    }
 +
 +    # XFree 4.0 Direct Rendering Interface and GLX 
-+    $opengl_dir         = "/usr/X11R6";
++    $opengl_dir         = "/usr/local";
 +# -DGLX_GLXEXT_LEGACY is required for patched OpenGLExtensions.C to compile.
 +# See patched OpenGLExtensions.C for explanation.
 +    $opengl_include     = "-DGLX_GLXEXT_LEGACY -I$opengl_dir/include";
@@ -83,17 +119,17 @@
 +    $arch_shld        = "ld -shared";
 +    $arch_shlibname   = "so";
 +    $arch_shcppopts   = "-fPIC";
-+    $arch_shldopts    = "-L/usr/local/lib -L/usr/X11R6/lib";
++    $arch_shldopts    = "-L/usr/local/lib -L/usr/local/lib";
 +
-+    $arch_opt_flag	= "-m64 -Wall -O6 -ffast-math";
-+    $arch_copts	        = "-m64 -Wall -O6 -ffast-math";
++    $arch_opt_flag	= "-m64 -Wall -O3 -ffast-math";
++    $arch_copts	        = "-m64 -Wall -O3 -ffast-math";
 +
 +    if ($config_static) {
 +      $arch_lopts       = "-static";
-+      $mesa_libs        = "-lMesaGL -lMesaGLU -L/usr/X11R6/lib -lXext -lX11";
++      $mesa_libs        = "-lMesaGL -lMesaGLU -L/usr/local/lib -lXext -lX11";
 +    } else {
 +      $arch_lopts       = "";
-+      $mesa_libs        = "-lGL -lGLU -L/usr/X11R6/lib -lXext -lX11";
++      $mesa_libs        = "-lGL -lGLU -L/usr/local/lib -lXext -lX11";
 +    }
 +
 +    if ($config_shared) {
@@ -109,17 +145,16 @@
   
      if ($config_python) {
        # this is to make python happy
-@@ -2052,11 +2114,11 @@
+@@ -2715,10 +2777,10 @@
  
  # compiler and compiler directives 
  CC          = $arch_cc
--CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
- COMPILERC   = $arch_compilerc
- RCFLAGS     = $arch_rcflags
+-CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
++CFLAGS      += $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
+ 
  CCPP	    = $arch_ccpp
--CPPFLAGS    = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
+-CPPFLAGS    = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
 +CPPFLAGS    = \${CXXFLAGS} $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
-+CFLAGS      += $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
  
- DEPEND      = $arch_depend_flag
- DEPENDFILE  = Makedata.depend
+ NVCC        = $arch_nvcc
+ NVCCFLAGS   = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
diff -ru vmd-old/files/patch-lib_tachyon_unix_Make-arch vmd/files/patch-lib_tachyon_unix_Make-arch
--- vmd-old/files/patch-lib_tachyon_unix_Make-arch	2005-05-06 11:19:35.000000000 -0400
+++ vmd/files/patch-lib_tachyon_unix_Make-arch	2010-01-08 13:12:00.000000000 -0500
@@ -1,11 +1,11 @@
 --- Make-arch-orig	Fri Mar 25 14:34:38 2005
 +++ lib/tachyon/unix/Make-arch	Fri Mar 25 14:34:50 2005
-@@ -859,7 +859,7 @@
+@@ -950,7 +950,7 @@
  	$(MAKE) all \
  	"ARCH = bsd" \
  	"CC = gcc" \
--	"CFLAGS = -O6 -fomit-frame-pointer -ffast-math -DBsd  $(MISCFLAGS)" \
-+	"CFLAGS += -O6 -fomit-frame-pointer -ffast-math -DBsd  $(MISCFLAGS)" \
+-	"CFLAGS = -O3 -fomit-frame-pointer -ffast-math -DBsd  $(MISCFLAGS)" \
++	"CFLAGS += -O3 -fomit-frame-pointer -ffast-math -DBsd  $(MISCFLAGS)" \
  	"AR = ar" \
  	"ARFLAGS = r" \
  	"STRIP = strip" \
diff -ru vmd-old/files/patch-stride.h vmd/files/patch-stride.h
--- vmd-old/files/patch-stride.h	2005-01-30 17:42:12.000000000 -0500
+++ vmd/files/patch-stride.h	2010-01-08 13:18:40.000000000 -0500
@@ -3,7 +3,7 @@
 @@ -40,7 +40,7 @@
  #define MAX_BOND                  100
  #define MAX_ASSIGN                300
- #define MAX_INFO                  1000
+ #define MAX_INFO                  100
 -#define MAX_AT_IN_RES             50
 +#define MAX_AT_IN_RES             75
  #define MAX_AT_IN_HETERORES       200
diff -ru vmd-old/files/patch-utilities.C vmd/files/patch-utilities.C
--- vmd-old/files/patch-utilities.C	2005-03-14 07:21:32.000000000 -0500
+++ vmd/files/patch-utilities.C	2010-01-08 13:24:30.000000000 -0500
@@ -1,11 +1,11 @@
 --- src/utilities.C.orig	Sat Jan 22 16:15:24 2005
 +++ src/utilities.C	Sat Jan 22 16:15:45 2005
-@@ -275,7 +275,7 @@
+@@ -396,7 +396,7 @@
      return stringdup("Windows User");
    }
  #else
--#if defined(ARCH_FREEBSD) || defined(ARCH_MACOSX) || defined(ARCH_LINUX) || defined(ARCH_LINUXALPHA) || defined(ARCH_LINUXAMD64) || defined(ARCH_LINUXPPC)
-+#if defined(ARCH_FREEBSD) || defined(ARCH_FREEBSDAMD64) || defined(ARCH_MACOSX) || defined(ARCH_LINUX) || defined(ARCH_LINUXALPHA) || defined(ARCH_LINUXAMD64) || defined(ARCH_LINUXPPC)
+-#if defined(ARCH_FREEBSD) || defined(__APPLE__) || defined(__linux)
++#if defined(ARCH_FREEBSD) || defined(ARCH_FREEBSDAMD64) || defined(__APPLE__) || defined(__linux)
    return stringdup(getlogin());
  #else
    return stringdup(cuserid(NULL));
Only in vmd-old/files: patch-vmd
Only in vmd/files: patch-vmd.csh
Only in vmd/files: sub-patch-configure.in
diff -ru vmd-old/pkg-plist vmd/pkg-plist
--- vmd-old/pkg-plist	2005-05-06 11:19:35.000000000 -0400
+++ vmd/pkg-plist	2010-01-08 20:30:16.000000000 -0500
@@ -1,14 +1,16 @@
 bin/vmd
+lib/vmd/.vmdrc
+lib/vmd/.vmdsensors
 lib/vmd/Announcement
 lib/vmd/LICENSE
 lib/vmd/README
-lib/vmd/.vmdrc
-lib/vmd/.vmdsensors
 lib/vmd/doc/ug.pdf
-lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd4.0/catdcd
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/avsplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/babelplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/basissetplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/bgfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/binposplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/biomoccaplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/brixplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/carplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/ccp4plugin.so
@@ -19,6 +21,7 @@
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/dcdplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/dlpolyplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/dsn6plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/dtrplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/dxplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/edmplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/fs4plugin.so
@@ -27,16 +30,20 @@
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/grdplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/gridplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/gromacsplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/jsplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/lammpsplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/libmolfile_plugin.a
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/libmolfile_plugin.h
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/maeffplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/mapplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/mdfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/mol2plugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/moldenplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/msmsplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/namdbinplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/parm7plugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/parmplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/pbeqplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/pdbplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/phiplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/pltplugin.so
@@ -44,43 +51,146 @@
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/psfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/raster3dplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/rst7plugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/situsplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/spiderplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/stlplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/tinkerplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/molfile/webpdbplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/uhbdplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspchgcarplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspoutcarplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspparchgplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspposcarplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspxdatcarplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vaspxmlplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/vtfplugin.so
+lib/vmd/plugins/%%VMD_ARCH%%/molfile/xbgfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/xsfplugin.so
 lib/vmd/plugins/%%VMD_ARCH%%/molfile/xyzplugin.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/libpmepot.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pmepot.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0/pmepot_gui.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/libpsfgen.so
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/pkgIndex.tcl
-lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3/ug.pdf
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hessTest.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hesstrans.so
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/hesstrans.tcl
+lib/vmd/plugins/%%VMD_ARCH%%/tcl/hesstrans1.0/pkgIndex.tcl
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/color_func.tcl
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/intersurf_gui.tcl
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/license.txt
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/nicostuf.tcl
+lib/vmd/plugins/LINUX/tcl/intersurf1.1/pkgIndex.tcl
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/bin/intersurf.dll
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/color_func.tcl
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/intersurf_gui.tcl
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/license.txt
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/nicostuf.tcl
+lib/vmd/plugins/WIN32/tcl/intersurf1.1/pkgIndex.tcl
 lib/vmd/plugins/include/molfile_plugin.h
+lib/vmd/plugins/include/vmdconio.h
 lib/vmd/plugins/include/vmdplugin.h
-lib/vmd/plugins/noarch/tcl/apbsrun1.0/apbsrun.tcl
-lib/vmd/plugins/noarch/tcl/apbsrun1.0/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/apbsrun1.0/radii.dat
-lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-api.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-gui.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-settings.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd-template.namd
-lib/vmd/plugins/noarch/tcl/autoimd1.4/autoimd.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/namdrun.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/autoimd1.4/ug.pdf
-lib/vmd/plugins/noarch/tcl/autoionize1.1/autoionize.tcl
-lib/vmd/plugins/noarch/tcl/autoionize1.1/ions.top
-lib/vmd/plugins/noarch/tcl/autoionize1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/apbsrun1.3/apbsrun.tcl
+lib/vmd/plugins/noarch/tcl/apbsrun1.3/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/apbsrun1.3/radii.dat
+lib/vmd/plugins/noarch/tcl/atomedit1.0/atomedit.tcl
+lib/vmd/plugins/noarch/tcl/atomedit1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-api.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-gui.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-settings.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd-template.namd
+lib/vmd/plugins/noarch/tcl/autoimd1.6/autoimd.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/namdrun.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/autoimd1.6/ug.pdf
+lib/vmd/plugins/noarch/tcl/autoionize1.2/autoionize.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.2/autoionizegui.tcl
+lib/vmd/plugins/noarch/tcl/autoionize1.2/ions.top
+lib/vmd/plugins/noarch/tcl/autoionize1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/bignum1.0/bignum.tcl
+lib/vmd/plugins/noarch/tcl/bignum1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocore.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocoreHelper.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocorechat.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocorelogin.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocorepubsync.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/biocoreutil.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/locked.gif
+lib/vmd/plugins/noarch/tcl/biocore1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/biocore1.1/unlocked.gif
+lib/vmd/plugins/noarch/tcl/blast1.1/blast.tcl
+lib/vmd/plugins/noarch/tcl/blast1.1/blast_resultviewer.tcl
+lib/vmd/plugins/noarch/tcl/blast1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.0/cggui.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.0/cgnetworking.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.0/cgtools.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/cgtools1.0/protein.cgc
+lib/vmd/plugins/noarch/tcl/cgtools1.0/rbcg-2007.par
+lib/vmd/plugins/noarch/tcl/cgtools1.0/rbcg-2007.top
+lib/vmd/plugins/noarch/tcl/cgtools1.0/water.cgc
 lib/vmd/plugins/noarch/tcl/cliptool1.0/cliptool.tcl
 lib/vmd/plugins/noarch/tcl/cliptool1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/clonerep1.1/clonerep.tcl
+lib/vmd/plugins/noarch/tcl/clonerep1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/colorscalebar1.2/colorscalebar.tcl
+lib/vmd/plugins/noarch/tcl/colorscalebar1.2/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/contactmap1.1/contactmap.tcl
 lib/vmd/plugins/noarch/tcl/contactmap1.1/pkgIndex.tcl
-lib/vmd/plugins/noarch/tcl/exectool1.0/exectool.tcl
-lib/vmd/plugins/noarch/tcl/exectool1.0/jobmanager.tcl
-lib/vmd/plugins/noarch/tcl/exectool1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/dataimport1.0/dataimport.tcl
+lib/vmd/plugins/noarch/tcl/dataimport1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/demomaster1.0/demomaster.tcl
+lib/vmd/plugins/noarch/tcl/demomaster1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/dipwatch1.2/dipwatch.tcl
+lib/vmd/plugins/noarch/tcl/dipwatch1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/dowser1.0/dowser.tcl
+lib/vmd/plugins/noarch/tcl/dowser1.0/dowser_gui.tcl
+lib/vmd/plugins/noarch/tcl/dowser1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/exectool1.2/exectool.tcl
+lib/vmd/plugins/noarch/tcl/exectool1.2/jobmanager.tcl
+lib/vmd/plugins/noarch/tcl/exectool1.2/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/extendedpdb1.0/extendedpdb.tcl
+lib/vmd/plugins/noarch/tcl/extendedpdb1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/gofrgui1.1/gofrgui.tcl
+lib/vmd/plugins/noarch/tcl/gofrgui1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/hbonds1.1/hbonds.tcl
+lib/vmd/plugins/noarch/tcl/hbonds1.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/idatm0.1/idatm.tcl
+lib/vmd/plugins/noarch/tcl/idatm0.1/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/ilstools1.2/acetylene.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/carbondioxide.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/carbonmonoxide.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/ethene.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/hydrogen.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/ilstools.tcl
+lib/vmd/plugins/noarch/tcl/ilstools1.2/methane.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/nitricoxide.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/nitrogen.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/nitrogendioxide.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/nitrousoxide.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/oxygen.xyz
+lib/vmd/plugins/noarch/tcl/ilstools1.2/pkgIndex.tcl
 lib/vmd/plugins/noarch/tcl/imdmenu1.0/imdmenu.tcl
 lib/vmd/plugins/noarch/tcl/imdmenu1.0/pkgIndex.tcl
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/inorganicbuilder.tcl
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/CVS/Entries
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/CVS/Repository
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/CVS/Root
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/asio2.inp
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/asio2.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/asio2.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/au.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/au.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/graphite.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/graphite.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/quartz_alpha.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/quartz_alpha.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/si.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/si.top
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/si3n4.inp
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/si3n4.pdb
+lib/vmd/plugins/noarch/tcl/inorganicbuilder0.1/materials/si3n4.top
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 lib/vmd/scripts/vmd/atomselect.tcl
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+@dirrm lib/vmd/plugins/noarch/tcl/trunctraj1.5
+@dirrm lib/vmd/plugins/noarch/tcl/utilities1.0
+@dirrm lib/vmd/plugins/noarch/tcl/vdna2.0
+@dirrm lib/vmd/plugins/noarch/tcl/viewmaster2.2
+@dirrm lib/vmd/plugins/noarch/tcl/vmdmovie1.7
+@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-2.3/CVS
+@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-2.3/docs/CVS
+@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-2.3/docs
+@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.1/tkcon-2.3
+@dirrm lib/vmd/plugins/noarch/tcl/vmdtkcon1.1
+@dirrm lib/vmd/plugins/noarch/tcl/volmapgui1.1
+@dirrm lib/vmd/plugins/noarch/tcl/zoomseq1.1
 @dirrm lib/vmd/plugins/noarch/tcl
 @dirrm lib/vmd/plugins/noarch
-@dirrm lib/vmd/plugins/include
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd4.0
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/bin
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.3
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl/pmepot1.0
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/tcl
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%/molfile
-@dirrm lib/vmd/plugins/%%VMD_ARCH%%
 @dirrm lib/vmd/plugins
-@dirrm lib/vmd/doc
+@dirrm lib/vmd/scripts/CVS
+@dirrm lib/vmd/scripts/python
+@dirrm lib/vmd/scripts/tcl8.5/encoding
+@dirrm lib/vmd/scripts/tcl8.5/http1.0
+@dirrm lib/vmd/scripts/tcl8.5/msgs
+@dirrm lib/vmd/scripts/tcl8.5/opt0.4
+@exec mkdir -p %D/lib/vmd/scripts/tcl8/8.3
+@dirrm lib/vmd/scripts/tcl8/8.3
+@dirrm lib/vmd/scripts/tcl8/8.4/platform
+@dirrm lib/vmd/scripts/tcl8/8.4
+@dirrm lib/vmd/scripts/tcl8/8.5
+@dirrm lib/vmd/scripts/tcl8
+@dirrm lib/vmd/scripts/tcl8.5
+@dirrm lib/vmd/scripts/tk8.5/demos/images
+@dirrm lib/vmd/scripts/tk8.5/demos
+@dirrm lib/vmd/scripts/tk8.5/images
+@dirrm lib/vmd/scripts/tk8.5/msgs
+@dirrm lib/vmd/scripts/tk8.5/ttk
+@dirrm lib/vmd/scripts/tk8.5
+@dirrm lib/vmd/scripts/vmd/CVS
+@dirrm lib/vmd/scripts/vmd
+@dirrm lib/vmd/scripts
+@dirrm lib/vmd/shaders/CVS
+@dirrm lib/vmd/shaders
 @dirrm lib/vmd


>Release-Note:
>Audit-Trail:

From: Benjamin Kaduk <kaduk@MIT.EDU>
To: bug-followup@freebsd.org
Cc:  
Subject: Re: ports/142513: [update port] science/vmd -- upgrade from 1.8.3
 to 1.8.7
Date: Sat, 9 Jan 2010 00:42:39 -0500 (EST)

   This message is in MIME format.  The first part should be readable text,
   while the remaining parts are likely unreadable without MIME-aware tools.
 
 ---559023410-516110268-1263015759=:29136
 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
 
 And here's the promised log.
 --kaduk
 ---559023410-516110268-1263015759=:29136
 Content-Type: TEXT/PLAIN; charset=US-ASCII; name=vmd-errors.txt
 Content-Transfer-Encoding: BASE64
 Content-ID: <alpine.GSO.1.10.1001090042390.29136@multics.mit.edu>
 Content-Description: 
 Content-Disposition: attachment; filename=vmd-errors.txt
 
 VGhlIGlyc3BlY2d1aSBwYWNrYWdlIGNvdWxkIG5vdCBiZSBsb2FkZWQ6DQoN
 ClRoZSBtdWx0aXNlcSBwYWNrYWdlIGNvdWxkIG5vdCBiZSBsb2FkZWQ6DQoN
 ClRoZSBwbWVwb3RfZ3VpIHBhY2thZ2UgY291bGQgbm90IGJlIGxvYWRlZDoN
 Cg0KVGhlIHNvbHZhdGUgcGFja2FnZSBjb3VsZCBub3QgYmUgbG9hZGVkOg0K
 DQpUaGUgYXV0b3BzZiBwYWNrYWdlIGNvdWxkIG5vdCBiZSBsb2FkZWQ6DQoN
 ClRoZSBjZ2d1aSBwYWNrYWdlIGNvdWxkIG5vdCBiZSBsb2FkZWQ6DQoNClRo
 ZSBkb3dzZXJfZ3VpIHBhY2thZ2UgY291bGQgbm90IGJlIGxvYWRlZDoNCg0K
 VGhlIG1lbWJyYW5lIHBhY2thZ2UgY291bGQgbm90IGJlIGxvYWRlZDoNCg0K
 VGhlIG11dGF0b3IgcGFja2FnZSBjb3VsZCBub3QgYmUgbG9hZGVkOg0KDQpU
 aGUgYXV0b2ltZCBwYWNrYWdlIGNvdWxkIG5vdCBiZSBsb2FkZWQ6DQoNCg==
 
 ---559023410-516110268-1263015759=:29136--
Responsible-Changed-From-To: freebsd-ports-bugs->pgollucci 
Responsible-Changed-By: pgollucci 
Responsible-Changed-When: Sun Jan 10 00:30:59 UTC 2010 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=142513 
Responsible-Changed-From-To: pgollucci->freebsd-ports-bugs 
Responsible-Changed-By: pgollucci 
Responsible-Changed-When: Sat Feb 13 05:14:51 UTC 2010 
Responsible-Changed-Why:  requested by linimon


http://www.freebsd.org/cgi/query-pr.cgi?pr=142513 
State-Changed-From-To: open->feedback 
State-Changed-By: pgollucci 
State-Changed-When: Sat Feb 13 06:41:19 UTC 2010 
State-Changed-Why:  
Ask for maintainer fix. 

ls -l /pr/distfiles/vmd-1.8.* /pr/distfiles/tachyon-0.98.7.tar.gz /pr/distfiles/Stride_src.tar.Z 
-rw-r--r--  1 root  wheel  -   98K Feb 13 00:52:53 2010 /pr/distfiles/Stride_src.tar.Z
-rw-r--r--  1 root  wheel  -  3.1M Feb 13 00:54:55 2010 /pr/distfiles/tachyon-0.98.7.tar.gz
-rw-rw-r--  1 root  wheel  -  8.2M Feb 13 00:40:14 2010 /pr/distfiles/vmd-1.8.3.src.tar.gz
-rw-r--r--  1 root  wheel  -   23M Feb 13 00:45:35 2010 /pr/distfiles/vmd-1.8.7.src.tar.gz

http://tb.p6m7g8.net//errors/9-CURRENT-amd64/vmd-1.8.7.log

Also, an updated patch that applies

http://people.freebsd.org/~pgollucci/FreeBSD/diffs/science_vmd-1.8.7.diff

http://www.freebsd.org/cgi/query-pr.cgi?pr=142513 

From: Benjamin Kaduk <kaduk@MIT.EDU>
To: pgollucci@freebsd.org
Cc: bug-followup@freebsd.org
Subject: Re: ports/142513: [update port] science/vmd -- upgrade from 1.8.3
 to 1.8.7
Date: Sat, 13 Feb 2010 15:23:18 -0500 (EST)

 On Sat, 13 Feb 2010, pgollucci@freebsd.org wrote:
 
 > Synopsis: [update port] science/vmd -- upgrade from 1.8.3 to 1.8.7
 >
 > State-Changed-From-To: open->feedback
 > State-Changed-By: pgollucci
 > State-Changed-When: Sat Feb 13 06:41:19 UTC 2010
 > State-Changed-Why:
 > Ask for maintainer fix.
 >
 > http://www.freebsd.org/cgi/query-pr.cgi?pr=142513
 >
 
 The comment includes a link to a log at
 http://tb.p6m7g8.net//errors/9-CURRENT-amd64/vmd-1.8.7.log
 but tb.p6m7g8.net seems to be off the net at the moment.
 
 -Ben Kaduk

From: "Philip M. Gollucci" <pgollucci@FreeBSD.org>
To: Benjamin Kaduk <kaduk@mit.edu>
Cc: bug-followup@freebsd.org
Subject: Re: ports/142513: [update port] science/vmd -- upgrade from 1.8.3
 to 1.8.7
Date: Sun, 14 Feb 2010 13:09:22 -0500

 On 2/13/2010 3:23 PM, Benjamin Kaduk wrote:
 > On Sat, 13 Feb 2010, pgollucci@freebsd.org wrote:
 > 
 >> Synopsis: [update port] science/vmd -- upgrade from 1.8.3 to 1.8.7
 >>
 >> State-Changed-From-To: open->feedback
 >> State-Changed-By: pgollucci
 >> State-Changed-When: Sat Feb 13 06:41:19 UTC 2010
 >> State-Changed-Why:
 >> Ask for maintainer fix.
 >>
 >> http://www.freebsd.org/cgi/query-pr.cgi?pr=142513
 >>
 > 
 > The comment includes a link to a log at
 > http://tb.p6m7g8.net//errors/9-CURRENT-amd64/vmd-1.8.7.log
 > but tb.p6m7g8.net seems to be off the net at the moment.
 > 
 > -Ben Kaduk
 
 Mumble, I wanted to use it today too.  Its my $work, I won't be there
 again until Monday.
 

From: Benjamin Kaduk <kaduk@MIT.EDU>
To: "Philip M. Gollucci" <pgollucci@freebsd.org>
Cc: bug-followup@freebsd.org
Subject: Re: ports/142513: [update port] science/vmd -- upgrade from 1.8.3
 to 1.8.7
Date: Wed, 17 Feb 2010 01:48:26 -0500 (EST)

 On Sun, 14 Feb 2010, Philip M. Gollucci wrote:
 
 > On 2/13/2010 3:23 PM, Benjamin Kaduk wrote:
 >>
 >> The comment includes a link to a log at
 >> http://tb.p6m7g8.net//errors/9-CURRENT-amd64/vmd-1.8.7.log
 >> but tb.p6m7g8.net seems to be off the net at the moment.
 >>
 >> -Ben Kaduk
 >
 > Mumble, I wanted to use it today too.  Its my $work, I won't be there
 > again until Monday.
 
 
 (I couldn't get Philip on IRC for a couple days, so resorting to mail.)
 
 So, the error on your tinderbox is just that it couldn't fetch the 
 distfile.  Are you sure you put it in the right place?
 
 -Ben Kaduk
State-Changed-From-To: feedback->open 
State-Changed-By: linimon 
State-Changed-When: Sat Feb 20 22:43:13 UTC 2010 
State-Changed-Why:  
Feedback received. 


Responsible-Changed-From-To: freebsd-ports-bugs->wxs 
Responsible-Changed-By: linimon 
Responsible-Changed-When: Sat Feb 20 22:43:13 UTC 2010 
Responsible-Changed-Why:  
wxs expressed an interest. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=142513 
State-Changed-From-To: open->closed 
State-Changed-By: wxs 
State-Changed-When: Mon Feb 22 14:23:01 UTC 2010 
State-Changed-Why:  
Committed, with minor changes. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=142513 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/142513: commit references a PR
Date: Mon, 22 Feb 2010 14:23:00 +0000 (UTC)

 wxs         2010-02-22 14:22:45 UTC
 
   FreeBSD ports repository
 
   Modified files:
     science/vmd          Makefile distinfo pkg-plist 
     science/vmd/files    patch-AtomParser.C patch-Make-arch 
                          patch-Makefile patch-OpenGLExtensions.C 
                          patch-configure 
                          patch-lib_tachyon_unix_Make-arch 
                          patch-stride.h patch-utilities.C 
   Removed files:
     science/vmd/files    patch-vmd 
   Log:
   - Update to 1.8.7
   - Pass maintainer to submitter
   
   PR:             ports/142513
   Submitted by:   Ben Kaduk <kaduk@mit.edu>
   Feature safe:   yes
   
   Revision  Changes     Path
   1.17      +27 -21     ports/science/vmd/Makefile
   1.4       +9 -6       ports/science/vmd/distinfo
   1.3       +3 -3       ports/science/vmd/files/patch-AtomParser.C
   1.3       +17 -14     ports/science/vmd/files/patch-Make-arch
   1.5       +7 -8       ports/science/vmd/files/patch-Makefile
   1.2       +3 -3       ports/science/vmd/files/patch-OpenGLExtensions.C
   1.6       +69 -34     ports/science/vmd/files/patch-configure
   1.2       +3 -3       ports/science/vmd/files/patch-lib_tachyon_unix_Make-arch
   1.2       +1 -1       ports/science/vmd/files/patch-stride.h
   1.2       +3 -3       ports/science/vmd/files/patch-utilities.C
   1.2       +0 -11      ports/science/vmd/files/patch-vmd (dead)
   1.5       +1057 -344  ports/science/vmd/pkg-plist
 _______________________________________________
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>Unformatted:
