diff options
| -rw-r--r-- | science/vmd/Makefile | 48 | ||||
| -rw-r--r-- | science/vmd/distinfo | 15 | ||||
| -rw-r--r-- | science/vmd/files/patch-AtomParser.C | 6 | ||||
| -rw-r--r-- | science/vmd/files/patch-Make-arch | 31 | ||||
| -rw-r--r-- | science/vmd/files/patch-Makefile | 15 | ||||
| -rw-r--r-- | science/vmd/files/patch-OpenGLExtensions.C | 6 | ||||
| -rw-r--r-- | science/vmd/files/patch-configure | 103 | ||||
| -rw-r--r-- | science/vmd/files/patch-lib_tachyon_unix_Make-arch | 6 | ||||
| -rw-r--r-- | science/vmd/files/patch-stride.h | 2 | ||||
| -rw-r--r-- | science/vmd/files/patch-utilities.C | 6 | ||||
| -rw-r--r-- | science/vmd/files/patch-vmd | 11 | ||||
| -rw-r--r-- | science/vmd/pkg-plist | 1401 |
12 files changed, 1199 insertions, 451 deletions
diff --git a/science/vmd/Makefile b/science/vmd/Makefile index 59044b1622cc..da5687bc859d 100644 --- a/science/vmd/Makefile +++ b/science/vmd/Makefile @@ -6,23 +6,23 @@ # PORTNAME= vmd -PORTVERSION= 1.8.3 -PORTREVISION= 4 +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_GMAKE= yes 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> @@ -49,17 +53,16 @@ VMD_TARGET= freebsd.opengl PLIST_SUB+= VMD_ARCH=${VMD_ARCH} # Check for VMD sources -.if !exists(${DISTDIR}/${VMD_DIST}) # && !defined(PACKAGE_BUILDING) -ECHO_MSG= ${PRINTF} -IGNORE= :\n\ -Because of licensing restrictions, you must fetch the source distribution\n\ -manually. Please access\n\ +#.if !exists(${DISTDIR}/${VMD_DIST}) # && !defined(PACKAGE_BUILDING) +#ECHO_MSG= ${PRINTF} +#IGNORE= because of licensing restrictions, you must fetch the source\n\ +distribution manually. Please access\n\ http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD\n\ with a web browser. You will be required to log in and register,\n\ but you can create an account on this page. After registration and\n\ accepting the University of Illinois agreement, download the source file,\n\ -${VMD_DIST}. Please place this file in ${DISTDIR}.\n -.endif +${VMD_DIST}. Please place this file in ${DISTDIR}. +#.endif do-extract: ${MKDIR} ${WRKDIR} @@ -70,17 +73,20 @@ do-extract: 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 --git a/science/vmd/distinfo b/science/vmd/distinfo index d98d34e7fce8..92d082e7ccf6 100644 --- a/science/vmd/distinfo +++ b/science/vmd/distinfo @@ -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 diff --git a/science/vmd/files/patch-AtomParser.C b/science/vmd/files/patch-AtomParser.C index 370f2b407319..b27d2b19b3ec 100644 --- a/science/vmd/files/patch-AtomParser.C +++ b/science/vmd/files/patch-AtomParser.C @@ -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 --git a/science/vmd/files/patch-Make-arch b/science/vmd/files/patch-Make-arch index f476206f9363..f981afc108cf 100644 --- a/science/vmd/files/patch-Make-arch +++ b/science/vmd/files/patch-Make-arch @@ -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 --git a/science/vmd/files/patch-Makefile b/science/vmd/files/patch-Makefile index 59ad76f3cc4e..53675de7524b 100644 --- a/science/vmd/files/patch-Makefile +++ b/science/vmd/files/patch-Makefile @@ -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 --git a/science/vmd/files/patch-OpenGLExtensions.C b/science/vmd/files/patch-OpenGLExtensions.C index 5b7510a2695a..5f24ce33c59c 100644 --- a/science/vmd/files/patch-OpenGLExtensions.C +++ b/science/vmd/files/patch-OpenGLExtensions.C @@ -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 --git a/science/vmd/files/patch-configure b/science/vmd/files/patch-configure index 72a717480095..ce3c93112e3c 100644 --- a/science/vmd/files/patch-configure +++ b/science/vmd/files/patch-configure @@ -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 --git a/science/vmd/files/patch-lib_tachyon_unix_Make-arch b/science/vmd/files/patch-lib_tachyon_unix_Make-arch index 2d67afb4b77c..ade246db35aa 100644 --- a/science/vmd/files/patch-lib_tachyon_unix_Make-arch +++ b/science/vmd/files/patch-lib_tachyon_unix_Make-arch @@ -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 --git a/science/vmd/files/patch-stride.h b/science/vmd/files/patch-stride.h index 3b95be662753..9241199c87ca 100644 --- a/science/vmd/files/patch-stride.h +++ b/science/vmd/files/patch-stride.h @@ -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 --git a/science/vmd/files/patch-utilities.C b/science/vmd/files/patch-utilities.C index 907676f7548b..41abe5f0c839 100644 --- a/science/vmd/files/patch-utilities.C +++ b/science/vmd/files/patch-utilities.C @@ -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)); diff --git a/science/vmd/files/patch-vmd b/science/vmd/files/patch-vmd deleted file mode 100644 index ec90285e80de..000000000000 --- a/science/vmd/files/patch-vmd +++ /dev/null @@ -1,11 +0,0 @@ ---- bin/vmd.orig Tue Feb 1 14:05:15 2005 -+++ bin/vmd Tue Feb 1 14:05:59 2005 -@@ -194,6 +194,8 @@ - # The standard options - if (`uname -m` == "i386") then - set ARCH=FREEBSD -+ else if (`uname -m` == "amd64") then -+ set ARCH=FREEBSDAMD64 - endif - set VMD_WINTERM=xterm - set VMD_WINOPTS='-sb -sl 1000 -e' diff --git a/science/vmd/pkg-plist b/science/vmd/pkg-plist index b78504ff706c..daff3ee26865 100644 --- a/science/vmd/pkg-plist +++ b/science/vmd/pkg-plist @@ -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/cubeplugin.so 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/graspplugin.so 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/pqrplugin.so 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 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+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 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+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 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