diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2022-11-16 00:32:46 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2022-11-16 00:36:16 +0000 |
| commit | 9d387d6d8e68d73411813a0c70f3295d514aee6f (patch) | |
| tree | be58886a7a9cab34c016ca40a8c40460e4f9124a | |
| parent | faab0eb2bebff16152b11515792d1953301fdbde (diff) | |
| download | ports-9d387d6d8e68d73411813a0c70f3295d514aee6f.tar.gz ports-9d387d6d8e68d73411813a0c70f3295d514aee6f.zip | |
science/vmd: Update to 1.9.4a57
Unbreak build: 1.9.3 incompatible with latest python tools
Clean up portlint and stage qa issues
| -rw-r--r-- | science/vmd/Makefile | 46 | ||||
| -rw-r--r-- | science/vmd/distinfo | 6 | ||||
| -rw-r--r-- | science/vmd/files/patch-Make-arch | 2 | ||||
| -rw-r--r-- | science/vmd/files/patch-Makefile | 8 | ||||
| -rw-r--r-- | science/vmd/files/patch-configure | 205 | ||||
| -rw-r--r-- | science/vmd/files/patch-lib_stride_Makefile | 2 | ||||
| -rw-r--r-- | science/vmd/files/patch-lib_surf_Makefile (renamed from science/vmd/files/patch-surf_Makefile) | 6 | ||||
| -rw-r--r-- | science/vmd/files/patch-lib_tachyon_unix_Make-arch | 258 | ||||
| -rw-r--r-- | science/vmd/pkg-plist | 806 |
9 files changed, 952 insertions, 387 deletions
diff --git a/science/vmd/Makefile b/science/vmd/Makefile index 7ef3fc782db0..c5d758ac0042 100644 --- a/science/vmd/Makefile +++ b/science/vmd/Makefile @@ -1,6 +1,6 @@ PORTNAME= vmd -DISTVERSION= 1.9.3 -PORTREVISION= 11 +DISTVERSION= 1.9.4 +DISTVERSIONSUFFIX= a57 CATEGORIES= science graphics python tcl tk MASTER_SITES= http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.99b6/:tachyon \ http://www.photonlimited.com/~johns/tachyon/files/0.99b6/:tachyon \ @@ -17,6 +17,8 @@ WWW= http://www.ks.uiuc.edu/Research/vmd/ LICENSE= VMD BSD3CLAUSE STRIDE LICENSE_COMB= multi +ONLY_FOR_ARCHS= amd64 i386 + BUILD_DEPENDS= makedepend:devel/makedepend \ ${PYNUMPY} LIB_DEPENDS= libexpat.so:textproc/expat2 \ @@ -24,6 +26,13 @@ LIB_DEPENDS= libexpat.so:textproc/expat2 \ libnetcdf.so:science/netcdf RUN_DEPENDS= ${PYNUMPY} +USES= gl gmake perl5 python shebangfix sqlite tcl tk xorg +SHEBANG_FILES= ${WRKDIR}/plugins/topotools/*.tcl \ + ${WRKDIR}/plugins/mdff/resetmaps.sh +USE_PERL5= build +USE_GL= gl glu +USE_XORG= x11 + LICENSE_FILE_VMD= ${WRKSRC}/LICENSE LICENSE_PERMS_VMD= no-auto-accept LICENSE_NAME_VMD= Visual Molecular Dynamics Software License Agreement @@ -37,14 +46,6 @@ LICENSE_PERMS_STRIDE= dist-mirror pkg-mirror auto-accept LICENSE_NAME_STRIDE= Stride Copyright Notice LICENSE_DISTFILES_STRIDE=${STRIDE_DIST} -USES= gl gmake perl5 python shebangfix sqlite tcl tk xorg -SHEBANG_FILES= ${WRKDIR}/plugins/topotools/*.tcl -USE_PERL5= build -USE_GL= gl glu -USE_XORG= x11 - -ONLY_FOR_ARCHS= amd64 i386 - CONFIGURE_ENV= PYTHON_INCLUDE_DIR=${PYTHON_INCLUDEDIR} \ PYTHON_LIBRARY_DIR=${PYTHON_LIBDIR} \ NUMPY_INCLUDE_DIR=${PYTHON_SITELIBDIR}/numpy/core/include \ @@ -71,13 +72,21 @@ MAKE_ENV= EXPATINC=-I${LOCALBASE}/include \ TCLLDFLAGS=-ltcl${TCL_VER:S/.//} \ TKLDFLAGS="-ltk${TK_VER:S/.//} -lX11" -VMD_DIST= ${PORTNAME}-${DISTVERSION}.src.tar.gz +VMD_DIST= ${PORTNAME}-${DISTVERSION}${DISTVERSIONSUFFIX}.src.tar.gz TACHYON_DIST= tachyon-0.99b6.tar.gz STRIDE_DIST= stride.tar.gz STRIDE_DOC= stride.doc .include <bsd.port.pre.mk> +.if !exists(${DISTDIR}/${VMD_DIST}) +IGNORE= license restrictions require manual fetching of the distribution\ + source. Please visit http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD\ + with a browser. You will be required to register, log in, and accept\ + the University of Illinois agreement before you can download the\ + ${VMD_DIST} source. Place this distfile in ${DISTDIR} and try again. +.endif + .if ${ARCH} == "amd64" VMD_ARCH= FREEBSDAMD64 .else @@ -86,15 +95,6 @@ VMD_ARCH= FREEBSD PLIST_SUB+= VMD_ARCH=${VMD_ARCH} -# Check for VMD sources -.if !exists(${DISTDIR}/${VMD_DIST}) -IGNORE= license restrictions require manual fetching of the distribution\ - source. Please visit http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD\ - with a browser. You will be required to register, log in, and accept\ - the University of Illinois agreement before you can download the\ - ${VMD_DIST} source file. Place this file in ${DISTDIR} and try again. -.endif - do-extract: ${MKDIR} ${WRKDIR} ${WRKSRC}/lib/stride ${TAR} -xzf ${DISTDIR}/${VMD_DIST} -C ${WRKDIR} @@ -148,9 +148,9 @@ post-install: ${REINPLACE_CMD} -i '' -e 's|${STAGEDIR}||g' ${STAGEDIR}${PREFIX}/bin/vmd ${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/*${VMD_ARCH} \ ${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/molfile/*.so -.for f in tcl/autopsf1.6/psfcheck.so tcl/hesstrans1.0/hesstrans.so \ +.for f in tcl/autopsf1.8/psfcheck.so tcl/hesstrans1.0/hesstrans.so \ tcl/mutator1.5/libalchemify.so tcl/pmepot1.0/libpmepot.so \ - tcl/psfgen1.6/libpsfgen.so tcl/rnaview1.1/rnaview \ + tcl/psfgen2.0/libpsfgen.so tcl/rnaview1.1/rnaview \ tcl/signalproc1.1/specden.so tcl/signalproc1.1/fftcmds.so \ tcl/signalproc1.1/sgsmooth.so tcl/volutil1.3/volutil \ tcl/clustalw1.1/clustalw tcl/libbiokit1.1/tcl_libbiokit.so \ @@ -159,7 +159,7 @@ post-install: tcl/libbiokit1.1/rmsd tcl/libbiokit1.1/percid \ tcl/phylotree1.2/upgmaclu tcl/stamp1.2/stamp \ tcl/bossconvert1.0/Topology \ - bin/catdcd5.1/catdcd bin/cionize1.0/cionize + bin/catdcd5.2/catdcd bin/cionize1.0/cionize ${STRIP_CMD} ${STAGEDIR}${LOCALBASE}/lib/vmd/plugins/${VMD_ARCH}/${f} .endfor diff --git a/science/vmd/distinfo b/science/vmd/distinfo index 5d42d032ddd2..1d36dd1916e4 100644 --- a/science/vmd/distinfo +++ b/science/vmd/distinfo @@ -1,6 +1,6 @@ -TIMESTAMP = 1482469862 -SHA256 (vmd-1.9.3.src.tar.gz) = 5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128 -SIZE (vmd-1.9.3.src.tar.gz) = 43981314 +TIMESTAMP = 1668527587 +SHA256 (vmd-1.9.4a57.src.tar.gz) = de278d0c5d969336d89068e0806fb50aaa0cb0f546ba985d840b279357860679 +SIZE (vmd-1.9.4a57.src.tar.gz) = 43155120 SHA256 (tachyon-0.99b6.tar.gz) = f4dcaf9c76a4f49310f56254390f9611c22e353947a1745a8c623e8bc8119b97 SIZE (tachyon-0.99b6.tar.gz) = 2981568 SHA256 (stride.tar.gz) = 51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a diff --git a/science/vmd/files/patch-Make-arch b/science/vmd/files/patch-Make-arch index fc680cffc2c7..adbec96b2b27 100644 --- a/science/vmd/files/patch-Make-arch +++ b/science/vmd/files/patch-Make-arch @@ -1,4 +1,4 @@ ---- ../plugins/Make-arch.orig 2016-10-21 23:34:39.000000000 +0200 +--- ../plugins/Make-arch.orig 2016-10-21 23:34:39 UTC +++ ../plugins/Make-arch @@ -272,10 +272,8 @@ "CC = gcc" \ diff --git a/science/vmd/files/patch-Makefile b/science/vmd/files/patch-Makefile index 53675de7524b..8088f99782f5 100644 --- a/science/vmd/files/patch-Makefile +++ b/science/vmd/files/patch-Makefile @@ -1,6 +1,6 @@ ---- Makefile.orig Sat Dec 6 04:20:58 2003 -+++ Makefile Wed Feb 2 21:30:13 2005 -@@ -86,10 +86,13 @@ +--- Makefile.orig 2022-04-27 06:21:11 UTC ++++ Makefile +@@ -95,10 +95,13 @@ android.armv7a.text: ## FreeBSD builds ## freebsd.mesa: @@ -15,4 +15,4 @@ + ./configure FREEBSDAMD64 OPENGL FLTK TK IMD TCL PTHREADS LIBTACHYON NETCDF - + ## diff --git a/science/vmd/files/patch-configure b/science/vmd/files/patch-configure index 33ca9e23ce8f..229aa6aead6b 100644 --- a/science/vmd/files/patch-configure +++ b/science/vmd/files/patch-configure @@ -1,4 +1,4 @@ ---- configure.orig 2016-12-01 07:11:33 UTC +--- configure.orig 2022-04-27 06:21:11 UTC +++ configure @@ -13,10 +13,10 @@ $install_name = "vmd"; @@ -13,7 +13,27 @@ # optionally override hard-coded defaults above with environment variables -@@ -729,8 +729,8 @@ $tcl_include = "-I$stock_tcl_includ +@@ -491,7 +491,7 @@ $arch_deletedir = "rm -rf"; + $arch_echo = "echo"; + $arch_tar = "tar"; + $arch_compress = "compress"; +-$arch_gnucompress = "/usr/local/bin/gzip"; ++$arch_gnucompress = "/usr/bin/gzip"; + $arch_latex = "latex"; + $arch_compilerc = $arch_echo; + $arch_rcflags = "No resource compiler required on this platform."; +@@ -511,8 +511,8 @@ $arch_nvccflags = "-lineinfo --ptxas-options=-v " . + "-gencode arch=compute_70,code=sm_70 " . + "--ftz=true "; + # "-gencode arch=compute_75,code=sm_75 " . +-$arch_gcc = "gcc"; +-$arch_gccpp = "g++"; ++$arch_gcc = "cc"; ++$arch_gccpp = "c++"; + $arch_lex = "lex"; + $arch_yacc = "yacc"; + $arch_yflags = "-d"; +@@ -783,9 +783,10 @@ $tcl_include = "-I$stock_tcl_include_dir"; if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; } $tcl_library = "-L$stock_tcl_library_dir"; if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; } @@ -22,9 +42,11 @@ +$tcl_libs = "\${TCLLDFLAGS}"; +if ($config_tk) { $tcl_libs = "\${TKLDFLAGS} " . $tcl_libs; } ++ @tcl_cc = (); @tcl_cu = (); -@@ -1105,8 +1105,8 @@ if ($config_liboptix) { + @tcl_ccpp = ('ColorInfo.C', +@@ -1353,8 +1354,8 @@ if ($config_liboptix) { # This may be commented out if not required. $libtachyon_defines = "-DVMDLIBTACHYON"; $libtachyon_dir = "$vmd_library_dir/tachyon"; @@ -35,7 +57,174 @@ $libtachyon_libs = "-ltachyon"; @libtachyon_cc = (); @libtachyon_cu = (); -@@ -3187,10 +3187,10 @@ DEFINES = $DEFINES +@@ -1673,7 +1674,7 @@ if ($ENV{_CONDA_ROOT}) { + # $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib"; + $stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "$vmd_library_dir/numpy/lib_$config_arch/include"; + $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include"; +- $python_libs = "-lpython2.5 -lpthread"; ++ $python_libs = "-lpython3.9 -lpthread"; + } + + $python_defines = "-DVMDPYTHON"; +@@ -2147,8 +2148,8 @@ if ($config_arch eq "ANDROIDARMV7A") { + $androidlibs = "-L/home/kvandivo/Proj/android-ndk-r8b/platforms/android-14/arch-arm/usr/lib -L/home/kvandivo/Proj/android-ndk-r8b/sources/cxx-stl/stlport/libs/armeabi-v7a/"; + $androidsysroot = "--sysroot=/home/kvandivo/Proj/android-ndk-r8b/platforms/android-14/arch-arm"; + $androidabi = "arm-linux-androideabi-"; +- $arch_cc = $androidbins . $androidabi . "gcc"; +- $arch_ccpp = $androidbins . $androidabi . "g++"; ++ $arch_cc = $androidbins . $androidabi . "cc"; ++ $arch_ccpp = $androidbins . $androidabi . "c++"; + $arch_copts = "-Wall -Wno-unknown-pragmas -Wno-psabi -MMD -MP -fpic -ffunction-sections -funwind-tables -fstack-protector -D__ARM_ARCH_5__ -D__ARM_ARCH_5T__ -D__ARM_ARCH_5E__ -D__ARM_ARCH_5TE__ -march=armv7-a -msoft-float -mfpu=vfp -fno-exceptions -mthumb -Os -fomit-frame-pointer -fno-strict-aliasing -finline-limit=64 -Wa,--noexecstac"; + $arch_opt_flag = "-Wall -Wno-unknown-pragmas -Wno-psabi -MMD -MP -fpic -ffunction-sections -funwind-tables -fstack-protector -D__ARM_ARCH_5__ -D__ARM_ARCH_5T__ -D__ARM_ARCH_5E__ -D__ARM_ARCH_5TE__ -march=armv7-a -msoft-float -mfpu=vfp -fno-exceptions -mthumb -Os -fomit-frame-pointer -fno-strict-aliasing -finline-limit=64 -Wa,--noexecstac"; + $arch_copts = $androidincs; +@@ -2220,7 +2221,7 @@ if ($config_arch eq "BLUEWATERS" || + $arch_cc = "cc"; + $arch_ccpp = "CC"; + $arch_copts = "-m64 -Wall -Wno-unknown-pragmas -O6 -ffast-math"; +- $arch_opt_flag = "-m64 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O6 -ffast-math"; ++ $arch_opt_flag = "-m64 -Wno-deprecated -Wall -Wno-unknown-pragmas -O6 -ffast-math"; + } + + if ($config_mpi) { +@@ -2321,15 +2322,15 @@ if ($config_arch eq "FREEBSD") { + $arch_lex = "flex"; + $arch_yacc = "bison -b y -d "; # If standard yacc doesn't work + +- $arch_cc = "gcc"; +- $arch_ccpp = "g++"; ++ $arch_cc = "cc"; ++ $arch_ccpp = "c++"; + $arch_depend_flag = "-MM"; + $arch_shld = "g++ -shared"; + $arch_shlibname = "so"; + $arch_shcppopts = "-fPIC"; + $arch_shldopts = "-L/usr/local/lib"; + +- $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3"; ++ $arch_opt_flag = "-m32 -Wno-deprecated -Wall -Wno-unknown-pragmas -O3"; + $arch_copts = "-m32 -Wall -Wno-unknown-pragmas -O3"; + + if ($config_static) { +@@ -2377,8 +2378,8 @@ if ($config_arch eq "FREEBSDAMD64") { + $arch_lex = "flex"; + $arch_yacc = "bison -b y -d "; # If standard yacc doesn't work + +- $arch_cc = "gcc"; +- $arch_ccpp = "g++"; ++ $arch_cc = "cc"; ++ $arch_ccpp = "c++"; + $arch_depend_flag = "-MM"; + $arch_shld = "ld -shared"; + $arch_shlibname = "so"; +@@ -2456,14 +2457,14 @@ if ($config_arch eq "LINUX") { + $arch_lopts .= "-i-static "; + } else { + # compling with GCC +- $arch_cc = "gcc"; +- $arch_ccpp = "g++"; ++ $arch_cc = "cc"; ++ $arch_ccpp = "c++"; + $arch_depend_flag = "-MM"; + $arch_shld = "g++ -shared"; + $arch_shlibname = "so"; + $arch_shcppopts = "-fPIC"; + $arch_shldopts = ""; +- $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3"; ++ $arch_opt_flag = "-m32 -Wno-deprecated -Wall -Wno-unknown-pragmas -O3"; + $arch_copts = "-m32 -Wall -Wno-unknown-pragmas -O3"; + + if ($config_static) { +@@ -2573,9 +2574,9 @@ if ($config_arch eq "LINUXAMD64") { + $arch_depend_flag = "-MM"; + } else { + # for compiling with g++: +- $arch_cc = "gcc"; +- $arch_ccpp = "g++"; +- $arch_opt_flag = "-m64 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O6 -ffast-math"; ++ $arch_cc = "cc"; ++ $arch_ccpp = "c++"; ++ $arch_opt_flag = "-m64 -Wno-deprecated -Wall -Wno-unknown-pragmas -O6 -ffast-math"; + $arch_depend_flag = "-MM"; + $arch_copts = "-m64 -Wall -Wno-unknown-pragmas -O6 -ffast-math"; + +@@ -2680,8 +2681,8 @@ if ($config_arch eq "LINUXPPC64") { + print "No LP64 ABI on this platform currently.\n"; + } + +- $arch_cc = "gcc"; +- $arch_ccpp = "g++"; ++ $arch_cc = "cc"; ++ $arch_ccpp = "c++"; + $arch_depend_flag = "-MM"; + $arch_opt_flag = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math"; + $arch_copts = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math"; +@@ -3056,8 +3057,8 @@ if ($config_arch eq "SUMMIT") { + # $arch_cppopts = "-D_H_ACCESS=1"; + $arch_depend_flag = "-MM"; + } elsif ($config_gcc) { +- $arch_cc = "gcc"; +- $arch_ccpp = "g++"; ++ $arch_cc = "cc"; ++ $arch_ccpp = "c++"; + $arch_opt_flag = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math -mtune=power8"; + $arch_copts = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math -mtune=power8"; + $arch_depend_flag = "-MM"; +@@ -3131,8 +3132,8 @@ if ($config_arch eq "OPENPOWER" || $config_arch eq "SU + # $arch_cppopts = "-D_H_ACCESS=1"; + $arch_depend_flag = "-MM"; + } else { +- $arch_cc = "gcc"; +- $arch_ccpp = "g++"; ++ $arch_cc = "cc"; ++ $arch_ccpp = "c++"; + $arch_opt_flag = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math -mtune=power8"; + $arch_copts = "-m64 -Wall -Wno-unknown-pragmas -O3 -ffast-math -mtune=power8"; + $arch_depend_flag = "-MM"; +@@ -3185,8 +3186,8 @@ if ($config_arch eq "SOLARIS2" || $config_arch eq "SOL + if ($config_lp64) { + print "GCC doesn't support LP64 ABI on this platform currently.\n"; + } +- $arch_ccpp = "g++"; +- $arch_cc = "gcc"; ++ $arch_ccpp = "c++"; ++ $arch_cc = "cc"; + $arch_opt_flag = "-O"; + $arch_copts = "-O"; + $arch_debug_flag = "-g"; +@@ -3258,8 +3259,8 @@ if ($config_arch eq "SOLARISX86" || $config_arch eq "S + if ($config_lp64) { + die "No LP64 gcc for this platform currently.\n"; + } +- $arch_ccpp = "g++"; +- $arch_cc = "gcc"; ++ $arch_ccpp = "c++"; ++ $arch_cc = "cc"; + # XXX gcc/g++ 2.95 and newer need -fpermissive since the X11 headers + # on Solaris (and other systems) are broken and still assume that missing + # types will default to int.... When they fix this in future revs of Solaris, +@@ -3349,8 +3350,8 @@ if ($config_arch eq "WIN32") { + $arch_cppopts = "/TP"; + $arch_coptout = "/Fo"; + } else { +- $arch_ccpp = "g++"; +- $arch_cc = "gcc"; ++ $arch_ccpp = "c++"; ++ $arch_cc = "cc"; + $arch_opt_flag = "-O"; + $arch_debug_flag = "-g"; + $arch_depend_flag = "-M"; +@@ -3366,8 +3367,8 @@ if ($config_arch eq "WIN32") { + + + if ($config_arch eq "WIN64") { +- $arch_ccpp = "g++"; +- $arch_cc = "gcc"; ++ $arch_ccpp = "c++"; ++ $arch_cc = "cc"; + $arch_opt_flag = "-O"; + $arch_debug_flag = "-g"; + $arch_depend_flag = "-M"; +@@ -3721,10 +3722,10 @@ DEFINES = $DEFINES # compiler and compiler directives CC = $arch_cc @@ -44,7 +233,7 @@ CCPP = $arch_ccpp -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) - - NVCC = $arch_nvcc - NVCCFLAGS = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) ++CPPFLAGS = \${CXXFLAGS} $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags + CPPAVXFLAGS = $arch_opt_flag $arch_cppopts -mavx -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags + CPPAVX2FLAGS = $arch_opt_flag $arch_cppopts -mfma -mavx -mavx2 -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags + CPPAVX512FLAGS = $arch_opt_flag $arch_cppopts -mavx512f -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags diff --git a/science/vmd/files/patch-lib_stride_Makefile b/science/vmd/files/patch-lib_stride_Makefile index b9beb1655e68..8a07fd85789e 100644 --- a/science/vmd/files/patch-lib_stride_Makefile +++ b/science/vmd/files/patch-lib_stride_Makefile @@ -5,7 +5,7 @@ #CC = cc -O2 -fullwarn -TENV:large_GOT #CC = cc -g -Wall -CC = gcc -O2 # at least for SunOS -+#CC = gcc -O2 # at least for SunOS ++#CC = cc -O2 # at least for SunOS #CC = cc -g #CC = cc -O2 -fullwarn diff --git a/science/vmd/files/patch-surf_Makefile b/science/vmd/files/patch-lib_surf_Makefile index f8136f812ce7..a548100fa31f 100644 --- a/science/vmd/files/patch-surf_Makefile +++ b/science/vmd/files/patch-lib_surf_Makefile @@ -1,6 +1,6 @@ ---- lib/surf/Makefile.orig Fri Mar 25 17:52:40 2005 -+++ lib/surf/Makefile Fri Mar 25 17:50:20 2005 -@@ -6,7 +6,7 @@ +--- lib/surf/Makefile.orig 2022-11-15 15:32:58 UTC ++++ lib/surf/Makefile +@@ -6,7 +6,7 @@ INCLUDE = -I. LINCLUDE = -lm OPT_CFLAGS = -O2 $(FLAGS) $(INCLUDE) #CFLAGS = -g $(FLAGS) $(INCLUDE) diff --git a/science/vmd/files/patch-lib_tachyon_unix_Make-arch b/science/vmd/files/patch-lib_tachyon_unix_Make-arch index ef1aade136ff..56b2f0a699c7 100644 --- a/science/vmd/files/patch-lib_tachyon_unix_Make-arch +++ b/science/vmd/files/patch-lib_tachyon_unix_Make-arch @@ -1,11 +1,265 @@ --- lib/tachyon/unix/Make-arch.orig 2013-04-21 19:09:28 UTC +++ lib/tachyon/unix/Make-arch -@@ -1103,7 +1103,7 @@ bsd: +@@ -134,7 +134,7 @@ android-armv7a-thr: + linux-carma-thr: + $(MAKE) all \ + "ARCH = linux-carma-thr" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -Wall -march=armv7-a -mcpu=cortex-a9 -mtune=cortex-a9 -mfpu=vfpv3-d16 -ffast-math -fomit-frame-pointer -fno-strict-aliasing -O3 -DLinux $(THREADSFLAGS) -DUSEPHYSCPUCOUNT -D_REENTRANT $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -145,7 +145,7 @@ linux-carma-thr: + linux-carma-thr-fast: + $(MAKE) all \ + "ARCH = linux-carma-thr-fast" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -Wall -fexpensive-optimizations -funsafe-math-optimizations -march=armv7-a -mcpu=cortex-a9 -mtune=cortex-a9 -mfpu=vfpv3 -ffast-math -fomit-frame-pointer -fno-strict-aliasing -O3 -DLinux $(THREADSFLAGS) -DUSEPHYSCPUCOUNT -D_REENTRANT $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -156,7 +156,7 @@ linux-carma-thr-fast: + linux-carma-thr-neon: + $(MAKE) all \ + "ARCH = linux-carma-thr-neon" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -Wall -fexpensive-optimizations -funsafe-math-optimizations -march=armv7-a -mcpu=cortex-a9 -mtune=cortex-a9 -mfpu=neon -ffast-math -fomit-frame-pointer -fno-strict-aliasing -O3 -DLinux $(THREADSFLAGS) -DUSEPHYSCPUCOUNT -D_REENTRANT $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -174,7 +174,7 @@ linux-carma-thr-neon: + linux-carma-softfp-thr: + $(MAKE) all \ + "ARCH = linux-carma-softfp-thr" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -Wall -march=armv7-a -mcpu=cortex-a9 -mtune=cortex-a9 -msoft-float -mfpu=vfpv3-d16 -ffast-math -fomit-frame-pointer -fno-strict-aliasing -finline-limit=64 -Wa,--noexecstack -O -DLinux $(THREADSFLAGS) -DUSEPHYSCPUCOUNT -D_REENTRANT $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -611,7 +611,7 @@ solaris-thr: + solaris-pthreads-gcc: + $(MAKE) all \ + "ARCH = solaris-pthreads-gcc" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -Wall -O3 -fomit-frame-pointer -ffast-math -D_REENTRANT -DSunOS $(MISCFLAGS) $(THREADSFLAGS) -DUSEPOSIXTHREADS" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -791,7 +791,7 @@ solaris-apcc-ultra-thr: + solaris-gcc-thr: + $(MAKE) all \ + "ARCH = solaris-gcc-thr" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -ansi -Wall -pedantic -O4 -mv8 -msupersparc -DSunOS $(MISCFLAGS) $(THREADSFLAGS) -D_REENTRANT" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -801,7 +801,7 @@ solaris-gcc-thr: + solaris-gcc-thr-x11: + $(MAKE) all \ + "ARCH = solaris-gcc-thr-x11" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -ansi -Wall -pedantic -O4 -mv8 -msupersparc $(X11INC) -DSunOS $(MISCFLAGS) $(THREADSFLAGS) -D_REENTRANT -DUSEX11" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1086,7 +1086,7 @@ macosx-x86-thr-ogl: + beos: + $(MAKE) all \ + "ARCH = beos" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -O3 -fomit-frame-pointer -ffast-math $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1102,8 +1102,8 @@ beos: + bsd: $(MAKE) all \ "ARCH = bsd" \ - "CC = gcc" \ +- "CC = gcc" \ - "CFLAGS = -O3 -fomit-frame-pointer -ffast-math -DBsd $(MISCFLAGS)" \ ++ "CC = cc" \ + "CFLAGS += -O3 -fomit-frame-pointer -ffast-math -DBsd $(MISCFLAGS)" \ "AR = ar" \ "ARFLAGS = r" \ "STRIP = strip" \ +@@ -1113,7 +1113,7 @@ bsd: + bsd-sparc: + $(MAKE) all \ + "ARCH = bsd-sparc" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -mv8 -msupersparc -O3 -fomit-frame-pointer -ffast-math -DBsd $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1128,7 +1128,7 @@ bsd-sparc: + win32: + $(MAKE) all \ + "ARCH = win32" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -mpentium -Wall -O3 -fomit-frame-pointer -ffast-math -DWIN32 $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1139,7 +1139,7 @@ win32: + win32-mpi: + $(MAKE) all \ + "ARCH = win32-mpi" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -mpentium -Wall -O3 -fomit-frame-pointer -ffast-math -DWIN32 $(MISCFLAGS) -I'/Program files/MPIPro/INCLUDE' $(MPIFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1155,7 +1155,7 @@ win32-mpi: + linux: + $(MAKE) all \ + "ARCH = linux" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -m32 -Wall -O3 -g -ffast-math -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1167,7 +1167,7 @@ linux: + linux-profile: + $(MAKE) all \ + "ARCH = linux-profile" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -m32 -Wall -O3 -g -pg -ffast-math -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1179,7 +1179,7 @@ linux-profile: + linux-debug: + $(MAKE) all \ + "ARCH = linux-debug" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -m32 -Wall -g -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1191,7 +1191,7 @@ linux-debug: + linux-64: + $(MAKE) all \ + "ARCH = linux-64" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -m64 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1203,7 +1203,7 @@ linux-64: + linux-64-debug: + $(MAKE) all \ + "ARCH = linux-64-debug" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -m64 -Wall -O -g -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1216,7 +1216,7 @@ linux-64-debug: + linux-64-thr: + $(MAKE) all \ + "ARCH = linux-64-thr" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -m64 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(THREADSFLAGS) -D_REENTRANT $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1240,7 +1240,7 @@ linux-icc-64-thr: + linux-64-openmp: + $(MAKE) all \ + "ARCH = linux-64-openmp" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -m64 -Wall -O3 -fopenmp -fomit-frame-pointer -ffast-math -DLinux -D_REENTRANT $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1277,7 +1277,7 @@ linux-mic-thr: + linux-p4: + $(MAKE) all \ + "ARCH = linux-p4" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -mcpu=i686 -march=i686 -funroll-loops -fexpensive-optimizations -malign-double -fschedule-insns2 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1315,7 +1315,7 @@ linux-p4-icc-thr: + linux-athlon: + $(MAKE) all \ + "ARCH = linux-athlon" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -mcpu=athlon -march=athlon -funroll-loops -fexpensive-optimizations -malign-double -fschedule-insns2 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1326,7 +1326,7 @@ linux-athlon: + linux-athlon-thr: + $(MAKE) all \ + "ARCH = linux-athlon-thr" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -mcpu=athlon -march=athlon -funroll-loops -fexpensive-optimizations -malign-double -fschedule-insns2 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(THREADSFLAGS) -D_REENTRANT $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1363,7 +1363,7 @@ linux-athlon-pgcc: + linux-thr: + $(MAKE) all \ + "ARCH = linux-thr" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -m32 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(THREADSFLAGS) -D_REENTRANT $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1422,7 +1422,7 @@ linux-icc-thr-ogl: + linux-beowulf-mpi-ogl: + $(MAKE) all \ + "ARCH = linux-beowulf-mpi" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -m32 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS) $(MPIFLAGS) -DUSEOPENGL $(LINUX_GLX_INCS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1434,7 +1434,7 @@ linux-beowulf-mpi-ogl: + linux-beowulf-mpi: + $(MAKE) all \ + "ARCH = linux-beowulf-mpi" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -m32 -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS) $(MPIFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1551,7 +1551,7 @@ linux-lam-thr: + linux-ipaq: + $(MAKE) all \ + "ARCH = linux-ipaq" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1563,7 +1563,7 @@ linux-ipaq: + linux-ppc: + $(MAKE) all \ + "ARCH = linux-ppc" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1575,7 +1575,7 @@ linux-ppc: + linux-ps2: + $(MAKE) all \ + "ARCH = linux-ps2" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ +@@ -1587,7 +1587,7 @@ linux-ps2: + linux-alpha: + $(MAKE) all \ + "ARCH = linux-alpha" \ +- "CC = gcc" \ ++ "CC = cc" \ + "CFLAGS = -Wall -O3 -fomit-frame-pointer -ffast-math -DLinux $(MISCFLAGS)" \ + "AR = ar" \ + "ARFLAGS = r" \ diff --git a/science/vmd/pkg-plist b/science/vmd/pkg-plist index 46a5ba2c0aab..023779be50ae 100644 --- a/science/vmd/pkg-plist +++ b/science/vmd/pkg-plist @@ -5,9 +5,10 @@ lib/vmd/Announcement lib/vmd/LICENSE lib/vmd/README lib/vmd/doc/ug.pdf -lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd5.1/catdcd +lib/vmd/plugins/%%VMD_ARCH%%/bin/catdcd5.2/catdcd lib/vmd/plugins/%%VMD_ARCH%%/bin/cionize1.0/cionize lib/vmd/plugins/%%VMD_ARCH%%/molfile/abinitplugin.so +lib/vmd/plugins/%%VMD_ARCH%%/molfile/amiraplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/avsplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/babelplugin.so lib/vmd/plugins/%%VMD_ARCH%%/molfile/basissetplugin.so @@ -79,9 +80,9 @@ lib/vmd/plugins/%%VMD_ARCH%%/molfile/webpdbplugin.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/autopsf1.6/autopsf.tcl -lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.6/pkgIndex.tcl -lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.6/psfcheck.so +lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.8/autopsf.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.8/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/autopsf1.8/psfcheck.so lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/Topology lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/bossconvert.tcl lib/vmd/plugins/%%VMD_ARCH%%/tcl/bossconvert1.0/imprlist @@ -131,9 +132,9 @@ 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/psfgen1.6/libpsfgen.so -lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6/pkgIndex.tcl -lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen1.6/ug.pdf +lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen2.0/libpsfgen.so +lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen2.0/pkgIndex.tcl +lib/vmd/plugins/%%VMD_ARCH%%/tcl/psfgen2.0/ug.pdf lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_A.pdb lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_C.pdb lib/vmd/plugins/%%VMD_ARCH%%/tcl/rnaview1.1/BASEPARS/Atomic_G.pdb @@ -187,9 +188,9 @@ lib/vmd/plugins/noarch/tcl/autoimd1.7/autoimd.tcl lib/vmd/plugins/noarch/tcl/autoimd1.7/namdrun.tcl lib/vmd/plugins/noarch/tcl/autoimd1.7/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/autoimd1.7/ug.pdf -lib/vmd/plugins/noarch/tcl/autoionize1.4/autoionize.tcl -lib/vmd/plugins/noarch/tcl/autoionize1.4/autoionizegui.tcl -lib/vmd/plugins/noarch/tcl/autoionize1.4/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/autoionize1.5/autoionize.tcl +lib/vmd/plugins/noarch/tcl/autoionize1.5/autoionizegui.tcl +lib/vmd/plugins/noarch/tcl/autoionize1.5/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk.tcl lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk_gui.tcl lib/vmd/plugins/noarch/tcl/bdtk1.0/bdtk_procs.tcl @@ -219,6 +220,8 @@ lib/vmd/plugins/noarch/tcl/bendix1.1/GUI-tips.gif lib/vmd/plugins/noarch/tcl/bendix1.1/Monsieur_Bendix_smaller_still.gif lib/vmd/plugins/noarch/tcl/bendix1.1/bendix.tcl lib/vmd/plugins/noarch/tcl/bendix1.1/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/bfeestimator1.0/bfee.tcl +lib/vmd/plugins/noarch/tcl/bfeestimator1.0/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 @@ -233,28 +236,44 @@ lib/vmd/plugins/noarch/tcl/biocore1.1/unlocked.gif lib/vmd/plugins/noarch/tcl/blast1.11/blast.tcl lib/vmd/plugins/noarch/tcl/blast1.11/blast_resultviewer.tcl lib/vmd/plugins/noarch/tcl/blast1.11/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/cgtools1.2/cggui.tcl -lib/vmd/plugins/noarch/tcl/cgtools1.2/cgnetworking.tcl -lib/vmd/plugins/noarch/tcl/cgtools1.2/cgtools.tcl -lib/vmd/plugins/noarch/tcl/cgtools1.2/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/cgtools1.2/protein.cgc -lib/vmd/plugins/noarch/tcl/cgtools1.2/rbcg-2007.par -lib/vmd/plugins/noarch/tcl/cgtools1.2/rbcg-2007.top -lib/vmd/plugins/noarch/tcl/cgtools1.2/water.cgc -lib/vmd/plugins/noarch/tcl/chirality1.2/chirality.tcl -lib/vmd/plugins/noarch/tcl/chirality1.2/chirality_gui.tcl -lib/vmd/plugins/noarch/tcl/chirality1.2/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/cispeptide1.3/cispeptide.tcl -lib/vmd/plugins/noarch/tcl/cispeptide1.3/cispeptide_gui.tcl -lib/vmd/plugins/noarch/tcl/cispeptide1.3/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/cgenffcaller1.0/cgenffcaller.tcl +lib/vmd/plugins/noarch/tcl/cgenffcaller1.0/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/cgtools1.3/cggui.tcl +lib/vmd/plugins/noarch/tcl/cgtools1.3/cgnetworking.tcl +lib/vmd/plugins/noarch/tcl/cgtools1.3/cgtools.tcl +lib/vmd/plugins/noarch/tcl/cgtools1.3/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/cgtools1.3/protein.cgc +lib/vmd/plugins/noarch/tcl/cgtools1.3/rbcg-2007.par +lib/vmd/plugins/noarch/tcl/cgtools1.3/rbcg-2007.top +lib/vmd/plugins/noarch/tcl/cgtools1.3/water.cgc +lib/vmd/plugins/noarch/tcl/chirality1.4/chirality.tcl +lib/vmd/plugins/noarch/tcl/chirality1.4/chirality_gui.tcl +lib/vmd/plugins/noarch/tcl/chirality1.4/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/cispeptide1.4/cispeptide.tcl +lib/vmd/plugins/noarch/tcl/cispeptide1.4/cispeptide_gui.tcl +lib/vmd/plugins/noarch/tcl/cispeptide1.4/pkgIndex.tcl lib/vmd/plugins/noarch/tcl/cliptool1.0/cliptool.tcl lib/vmd/plugins/noarch/tcl/cliptool1.0/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/clonerep1.3/clonerep.tcl -lib/vmd/plugins/noarch/tcl/clonerep1.3/pkgIndex.tcl -lib/vmd/plugins/noarch/tcl/colorscalebar1.4/colorscalebar.tcl -lib/vmd/plugins/noarch/tcl/colorscalebar1.4/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/clonerep1.4/clonerep.tcl +lib/vmd/plugins/noarch/tcl/clonerep1.4/pkgIndex.tcl +lib/vmd/plugins/noarch/tcl/colorscalebar3.0/colorscalebar.tcl +lib/vmd/plugins/noarch/tcl/colorscalebar3.0/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/cv_dashboard1.5/cv_dashboard.tcl 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lib/vmd/plugins/noarch/tcl/demomaster1.0/demomaster.tcl @@ -269,28 +288,32 @@ 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/fftk1.1/fftk.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_BondAngleOpt.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_BuildPar.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_ChargeOpt.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_DihOpt.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GenBonded.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GenDihScan.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GenZMatrix.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_GeomOpt.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_SharedFcns.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_distort.tcl -lib/vmd/plugins/noarch/tcl/fftk1.1/fftk_guiInterface.tcl 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