science/vmd: Update to 1.9.4a57

Unbreak build: 1.9.3 incompatible with latest python tools
Clean up portlint and stage qa issues

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 \
@@ -17,13 +17,22 @@ 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 \
 		libfltk.so:x11-toolkits/fltk \
 		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
 

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

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" \

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
 
 
-
+ ##

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

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

science/vmd/files/patch-surf_Makefile → 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)