Attachment #205391 for bug #238858




# Created by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
# $FreeBSD$

PORTNAME=	molden
DISTVERSION=	6.1
PORTREVISION=	2
PORTEPOCH=	1
CATEGORIES=	biology
MASTER_SITES=	ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/
DISTNAME=	${PORTNAME}${DISTVERSION}

MAINTAINER=	jmd@FreeBSD.org
COMMENT=	Display molecular orbitals and electron densities in 2D and 3D

LICENSE=	Molden
LICENSE_NAME=	Molden License
LICENSE_FILE=	${WRKSRC}/CopyRight
LICENSE_PERMS=	auto-accept dist-mirror pkg-mirror

BUILD_DEPENDS=	makedepend:devel/makedepend

USES=		fortran gl gmake localbase
USE_GL=		gl glu
USE_XORG=	x11 xmu

USES=		fortran gl gmake
USE_XORG=	x11
USE_GL=		gl glu
MAKEFILE=	makefile
MAKE_ARGS=	CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}"

CFLAGS+=	-DFREEBSD -DHASTIMER
FFLAGS+=	-DFREEBSD

EXES=		molden gmolden ambfor/ambfor ambfor/ambmd surf/surf
PLIST_FILES=	${EXES:C/.*\///:S/^/bin\//}
PLIST_FILES=	bin/ambfor bin/gmolden bin/molden bin/surf

OPTIONS_DEFINE=	DOCS

PORTDOCS=	*
OPTIONS_DEFAULT=	DATA

post-patch:
	@${REINPLACE_CMD} -e \
		's|^CC |#CC | ; \
		 s|^FC |#FC | ; \
		 s|/usr/X11R6|${LOCALBASE}| ; \
		 s|$$(LIBS)|$$(LIBS) $$(LDFLAGS)| ; \
		 s|-lXmu|| ; \
		 /depend/s|^|#|' ${WRKSRC}/makefile

post-configure:
	@${ECHO_MSG} "********************"
	@${ECHO_MSG} "**  If you want to use a larger MOLDEN,"
	@${ECHO_MSG} "**  edit change_parameter.sh and run it,"
	@${ECHO_MSG} "**  before \'make build\'."
	@${ECHO_MSG} "********************"

do-install:
.for e in ${EXES}
	${INSTALL_PROGRAM} ${WRKSRC}/${e} ${STAGEDIR}${PREFIX}/bin
.endfor
.for i in ambfor surf
	(cd ${WRKSRC}/${i} && ${INSTALL_PROGRAM} ${i} ${STAGEDIR}/${PREFIX}/bin)
.endfor

do-install-DATA-on:
	@${MKDIR} ${STAGEDIR}${DATADIR}/test
	(cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/test)
	${MKDIR} ${STAGEDIR}${DATADIR}/utils
	(cd ${WRKSRC}/utils && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/utils)

do-install-DOCS-on:
	${MKDIR} ${STAGEDIR}${DOCSDIR}
.for d in figures.ps.Z manual.ps.Z  manual.txt.Z
	${INSTALL_DATA} ${WRKSRC}/doc/${d} ${STAGEDIR}${DOCSDIR}
.endfor

.include <bsd.port.mk>

Lines 1-3 Link Here

(-)biology/molden/distinfo (-3 / +3 lines)
1	TIMESTAMP = 1541594934	1	TIMESTAMP = 1561690466
2	SHA256 (molden5.8.2.tar.gz) = 65a24db9e80b4fb6038cc1e57c7d6e2457414812c9389bc651af7cb33f01dbe9	2	SHA256 (molden6.1.tar.gz) = ba228b863e8f405a9f6c9f6c502e50462a570daeff74661fb317338fcc6d7fb0
3	SIZE (molden5.8.2.tar.gz) = 5770998	3	SIZE (molden6.1.tar.gz) = 6263424




--- ambfor/makefile.orig	2015-05-02 19:49:10 UTC
+++ ambfor/makefile
@@ -12,12 +12,12 @@
 #
 # 
 
-CFLAGS = -c -g ${EXT}
+CFLAGS += -c
 #FC = g77 
-FC = gfortran
-FFLAGS = -c -g -ffast-math -funroll-loops -O3
+#FC = gfortran
+#FFLAGS = -c -g -ffast-math -funroll-loops -O3
 LIBS =  -lm
-LDR = ${FC} -g
+LDR = ${FC}
 EXT :=
 
 ifeq ($(uname), Darwin)
@@ -56,7 +56,7 @@ ambmd:	md.o verlet.o qvdw.o allocmd.o $(
 	$(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS)
 
 ambfor.o:	ambfor.f
-	${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f
+	${FC} -c ${FFLAGS} -o ambfor.o ambfor.f
 
 allocmd.o:	alloc.c
 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o




--- makefile.orig	2019-06-28 03:02:40 UTC
+++ makefile
@@ -96,13 +96,13 @@ ifneq ($(comgcc), $(empty))
    EXTRAZ = -Wno-implicit-function-declaration
    EXT = ${EXTRAZ}
 endif
-FFLAGS = -g ${AFLAG}
+FFLAGS += -g ${AFLAG}
 LIBS =  -L/usr/X11R6/lib -lX11 -lm
 ifeq ($(AFLAG),"-m64")
 LIBS =  -L/usr/X11R6/lib64 -lX11 -lm
 endif
 LDR = ${FC} -g ${AFLAG}
-CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
+CFLAGS += ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
  ifeq ($(os), Debian)
     CFLAGS = ${AFLAG} ${EXTRAZ} -c -I/usr/include/X11 -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
     LIBS =  -L/usr/lib/X11 -lX11 -lm




--- surf/Makefile.orig	2015-05-02 19:48:48 UTC
+++ surf/Makefile
@@ -1,12 +1,8 @@
 # Compilation flags
-#CC	    = cc
-CC	    = cc
 INCLUDE     = -I. 
 #LINCLUDE    = -lcurses -ltermcap -lm
 LINCLUDE    = -lm
-OPT_CFLAGS  = -O2 $(FLAGS) $(INCLUDE)
 #CFLAGS	    = -g $(FLAGS) $(INCLUDE)
-CFLAGS	    = -O2 $(FLAGS) $(INCLUDE) ${EXT}
 
 ifeq ($(uname), Darwin)
 #
@@ -73,670 +69,117 @@ depend: $(DEPEND)
 # DO NOT DELETE
 
 surf.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-surf.o: /usr/include/sys/_symbol_aliasing.h
-surf.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
-surf.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-surf.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-surf.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
-surf.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
-surf.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-surf.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
-surf.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-surf.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
-surf.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
-surf.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
-surf.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-surf.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
-surf.o: /usr/include/mach/i386/_structs.h
-surf.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-surf.o: /usr/include/sys/_types/_sigaltstack.h
-surf.o: /usr/include/sys/_types/_ucontext.h
-surf.o: /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h
-surf.o: /usr/include/sys/resource.h /usr/include/stdint.h
-surf.o: /usr/include/sys/_types/_int8_t.h /usr/include/sys/_types/_int16_t.h
-surf.o: /usr/include/sys/_types/_int32_t.h /usr/include/sys/_types/_int64_t.h
-surf.o: /usr/include/_types/_uint8_t.h /usr/include/_types/_uint16_t.h
-surf.o: /usr/include/_types/_uint32_t.h /usr/include/_types/_uint64_t.h
-surf.o: /usr/include/sys/_types/_intptr_t.h
-surf.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
-surf.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
-surf.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-surf.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
-surf.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
-surf.o: /usr/include/sys/_types/_ct_rune_t.h
-surf.o: /usr/include/sys/_types/_rune_t.h /usr/include/sys/_types/_wchar_t.h
-surf.o: /usr/include/machine/types.h /usr/include/i386/types.h
-surf.o: /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h
-surf.o: /usr/include/string.h /usr/include/sys/_types/_rsize_t.h
-surf.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-surf.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-surf.o: /usr/include/sys/_types/_fd_def.h /usr/include/sys/_types/_timespec.h
-surf.o: /usr/include/sys/_types/_time_t.h
-surf.o: /usr/include/sys/_types/_suseconds_t.h
-surf.o: /usr/include/sys/_types/_fd_setsize.h
-surf.o: /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h
-surf.o: /usr/include/sys/_types/_fd_isset.h
-surf.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h
-surf.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h
-surf.o: /usr/include/sys/_select.h linalg.h
+surf.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+surf.o: /usr/include/machine/_types.h /usr/include/math.h
+surf.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+surf.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
+surf.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
+surf.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
+surf.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
+surf.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
 io.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-io.o: /usr/include/sys/_symbol_aliasing.h
-io.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
-io.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-io.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-io.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
-io.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
-io.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-io.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
-io.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-io.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
-io.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
-io.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
-io.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-io.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
-io.o: /usr/include/mach/i386/_structs.h
-io.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-io.o: /usr/include/sys/_types/_sigaltstack.h
-io.o: /usr/include/sys/_types/_ucontext.h /usr/include/sys/_types/_sigset_t.h
-io.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
-io.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
-io.o: /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h
-io.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h
-io.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h
-io.o: /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h
-io.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
-io.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
-io.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-io.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
-io.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
-io.o: /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h
-io.o: /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h
-io.o: /usr/include/i386/types.h /usr/include/sys/_types/_dev_t.h
-io.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
-io.o: /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h
-io.o: /usr/include/strings.h /usr/include/secure/_string.h
-io.o: /usr/include/sys/time.h /usr/include/sys/_types/_fd_def.h
-io.o: /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_time_t.h
-io.o: /usr/include/sys/_types/_suseconds_t.h
-io.o: /usr/include/sys/_types/_fd_setsize.h /usr/include/sys/_types/_fd_set.h
-io.o: /usr/include/sys/_types/_fd_clr.h /usr/include/sys/_types/_fd_isset.h
-io.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h
-io.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h
-io.o: /usr/include/sys/_select.h linalg.h
+io.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+io.o: /usr/include/machine/_types.h /usr/include/math.h
+io.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+io.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
+io.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
+io.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
+io.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
+io.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
 compute.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-compute.o: /usr/include/sys/_symbol_aliasing.h
-compute.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
-compute.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-compute.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-compute.o: /usr/include/i386/_types.h
-compute.o: /usr/include/sys/_pthread/_pthread_types.h
-compute.o: /usr/include/sys/_types/_va_list.h
-compute.o: /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h
-compute.o: /usr/include/sys/stdio.h /usr/include/sys/_types/_off_t.h
-compute.o: /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h
-compute.o: /usr/include/secure/_common.h /usr/include/math.h
-compute.o: /usr/include/stdlib.h /usr/include/sys/wait.h
-compute.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
-compute.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
-compute.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-compute.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
-compute.o: /usr/include/mach/i386/_structs.h
-compute.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-compute.o: /usr/include/sys/_types/_sigaltstack.h
-compute.o: /usr/include/sys/_types/_ucontext.h
-compute.o: /usr/include/sys/_types/_sigset_t.h
-compute.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
-compute.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
-compute.o: /usr/include/sys/_types/_int16_t.h
-compute.o: /usr/include/sys/_types/_int32_t.h
-compute.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h
-compute.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h
-compute.o: /usr/include/_types/_uint64_t.h
-compute.o: /usr/include/sys/_types/_intptr_t.h
-compute.o: /usr/include/sys/_types/_uintptr_t.h
-compute.o: /usr/include/_types/_intmax_t.h /usr/include/_types/_uintmax_t.h
-compute.o: /usr/include/sys/_types/_timeval.h /usr/include/machine/endian.h
-compute.o: /usr/include/i386/endian.h /usr/include/sys/_endian.h
-compute.o: /usr/include/libkern/_OSByteOrder.h
-compute.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
-compute.o: /usr/include/sys/_types/_ct_rune_t.h
-compute.o: /usr/include/sys/_types/_rune_t.h
-compute.o: /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h
-compute.o: /usr/include/i386/types.h /usr/include/sys/_types/_dev_t.h
-compute.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
-compute.o: /usr/include/sys/_types/_rsize_t.h
-compute.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-compute.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-compute.o: /usr/include/sys/_types/_fd_def.h
-compute.o: /usr/include/sys/_types/_timespec.h
-compute.o: /usr/include/sys/_types/_time_t.h
-compute.o: /usr/include/sys/_types/_suseconds_t.h
-compute.o: /usr/include/sys/_types/_fd_setsize.h
-compute.o: /usr/include/sys/_types/_fd_set.h
-compute.o: /usr/include/sys/_types/_fd_clr.h
-compute.o: /usr/include/sys/_types/_fd_isset.h
-compute.o: /usr/include/sys/_types/_fd_zero.h
-compute.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h
-compute.o: /usr/include/sys/_types/_clock_t.h /usr/include/sys/_select.h
-compute.o: linalg.h chull.h dual.h
+compute.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+compute.o: /usr/include/machine/_types.h /usr/include/math.h
+compute.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+compute.o: /usr/include/string.h /usr/include/strings.h
+compute.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
+compute.o: /usr/include/sys/types.h /usr/include/machine/endian.h
+compute.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
+compute.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
+compute.o: /usr/include/time.h linalg.h chull.h dual.h
 dual.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-dual.o: /usr/include/sys/_symbol_aliasing.h
-dual.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
-dual.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-dual.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-dual.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
-dual.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
-dual.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-dual.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
-dual.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-dual.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
-dual.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
-dual.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
-dual.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-dual.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
-dual.o: /usr/include/mach/i386/_structs.h
-dual.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-dual.o: /usr/include/sys/_types/_sigaltstack.h
-dual.o: /usr/include/sys/_types/_ucontext.h
-dual.o: /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h
-dual.o: /usr/include/sys/resource.h /usr/include/stdint.h
-dual.o: /usr/include/sys/_types/_int8_t.h /usr/include/sys/_types/_int16_t.h
-dual.o: /usr/include/sys/_types/_int32_t.h /usr/include/sys/_types/_int64_t.h
-dual.o: /usr/include/_types/_uint8_t.h /usr/include/_types/_uint16_t.h
-dual.o: /usr/include/_types/_uint32_t.h /usr/include/_types/_uint64_t.h
-dual.o: /usr/include/sys/_types/_intptr_t.h
-dual.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
-dual.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
-dual.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-dual.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
-dual.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
-dual.o: /usr/include/sys/_types/_ct_rune_t.h
-dual.o: /usr/include/sys/_types/_rune_t.h /usr/include/sys/_types/_wchar_t.h
-dual.o: /usr/include/machine/types.h /usr/include/i386/types.h
-dual.o: /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h
-dual.o: /usr/include/string.h /usr/include/sys/_types/_rsize_t.h
-dual.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-dual.o: /usr/include/secure/_string.h /usr/include/sys/time.h
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-tessel_patches.o: /usr/include/sys/_types/_int32_t.h
-tessel_patches.o: /usr/include/sys/_types/_int64_t.h
-tessel_patches.o: /usr/include/_types/_uint8_t.h
-tessel_patches.o: /usr/include/_types/_uint16_t.h
-tessel_patches.o: /usr/include/_types/_uint32_t.h
-tessel_patches.o: /usr/include/_types/_uint64_t.h
-tessel_patches.o: /usr/include/sys/_types/_intptr_t.h
-tessel_patches.o: /usr/include/sys/_types/_uintptr_t.h
-tessel_patches.o: /usr/include/_types/_intmax_t.h
-tessel_patches.o: /usr/include/_types/_uintmax_t.h
-tessel_patches.o: /usr/include/sys/_types/_timeval.h
-tessel_patches.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-tessel_patches.o: /usr/include/sys/_endian.h
-tessel_patches.o: /usr/include/libkern/_OSByteOrder.h
-tessel_patches.o: /usr/include/libkern/i386/_OSByteOrder.h
-tessel_patches.o: /usr/include/alloca.h /usr/include/sys/_types/_ct_rune_t.h
-tessel_patches.o: /usr/include/sys/_types/_rune_t.h
-tessel_patches.o: /usr/include/sys/_types/_wchar_t.h
-tessel_patches.o: /usr/include/machine/types.h /usr/include/i386/types.h
-tessel_patches.o: /usr/include/sys/_types/_dev_t.h
-tessel_patches.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
-tessel_patches.o: /usr/include/sys/_types/_rsize_t.h
-tessel_patches.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-tessel_patches.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-tessel_patches.o: /usr/include/sys/_types/_fd_def.h
-tessel_patches.o: /usr/include/sys/_types/_timespec.h
-tessel_patches.o: /usr/include/sys/_types/_time_t.h
-tessel_patches.o: /usr/include/sys/_types/_suseconds_t.h
-tessel_patches.o: /usr/include/sys/_types/_fd_setsize.h
-tessel_patches.o: /usr/include/sys/_types/_fd_set.h
-tessel_patches.o: /usr/include/sys/_types/_fd_clr.h
-tessel_patches.o: /usr/include/sys/_types/_fd_isset.h
-tessel_patches.o: /usr/include/sys/_types/_fd_zero.h
-tessel_patches.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h
-tessel_patches.o: /usr/include/sys/_types/_clock_t.h
-tessel_patches.o: /usr/include/sys/_select.h linalg.h
+tessel_patches.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+tessel_patches.o: /usr/include/machine/_types.h /usr/include/math.h
+tessel_patches.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+tessel_patches.o: /usr/include/string.h /usr/include/strings.h
+tessel_patches.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
+tessel_patches.o: /usr/include/sys/types.h /usr/include/machine/endian.h
+tessel_patches.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
+tessel_patches.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
+tessel_patches.o: /usr/include/time.h linalg.h
 tessel_convex.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-tessel_convex.o: /usr/include/sys/_symbol_aliasing.h
-tessel_convex.o: /usr/include/sys/_posix_availability.h
-tessel_convex.o: /usr/include/Availability.h
-tessel_convex.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-tessel_convex.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-tessel_convex.o: /usr/include/i386/_types.h
-tessel_convex.o: /usr/include/sys/_pthread/_pthread_types.h
-tessel_convex.o: /usr/include/sys/_types/_va_list.h
-tessel_convex.o: /usr/include/sys/_types/_size_t.h
-tessel_convex.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-tessel_convex.o: /usr/include/sys/_types/_off_t.h
-tessel_convex.o: /usr/include/sys/_types/_ssize_t.h
-tessel_convex.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-tessel_convex.o: /usr/include/math.h /usr/include/stdlib.h
-tessel_convex.o: /usr/include/sys/wait.h /usr/include/sys/_types/_pid_t.h
-tessel_convex.o: /usr/include/sys/_types/_id_t.h /usr/include/sys/signal.h
-tessel_convex.o: /usr/include/sys/appleapiopts.h
-tessel_convex.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-tessel_convex.o: /usr/include/machine/_mcontext.h
-tessel_convex.o: /usr/include/i386/_mcontext.h
-tessel_convex.o: /usr/include/mach/i386/_structs.h
-tessel_convex.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-tessel_convex.o: /usr/include/sys/_types/_sigaltstack.h
-tessel_convex.o: /usr/include/sys/_types/_ucontext.h
-tessel_convex.o: /usr/include/sys/_types/_sigset_t.h
-tessel_convex.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
-tessel_convex.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
-tessel_convex.o: /usr/include/sys/_types/_int16_t.h
-tessel_convex.o: /usr/include/sys/_types/_int32_t.h
-tessel_convex.o: /usr/include/sys/_types/_int64_t.h
-tessel_convex.o: /usr/include/_types/_uint8_t.h
-tessel_convex.o: /usr/include/_types/_uint16_t.h
-tessel_convex.o: /usr/include/_types/_uint32_t.h
-tessel_convex.o: /usr/include/_types/_uint64_t.h
-tessel_convex.o: /usr/include/sys/_types/_intptr_t.h
-tessel_convex.o: /usr/include/sys/_types/_uintptr_t.h
-tessel_convex.o: /usr/include/_types/_intmax_t.h
-tessel_convex.o: /usr/include/_types/_uintmax_t.h
-tessel_convex.o: /usr/include/sys/_types/_timeval.h
-tessel_convex.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-tessel_convex.o: /usr/include/sys/_endian.h
-tessel_convex.o: /usr/include/libkern/_OSByteOrder.h
-tessel_convex.o: /usr/include/libkern/i386/_OSByteOrder.h
-tessel_convex.o: /usr/include/alloca.h /usr/include/sys/_types/_ct_rune_t.h
-tessel_convex.o: /usr/include/sys/_types/_rune_t.h
-tessel_convex.o: /usr/include/sys/_types/_wchar_t.h
-tessel_convex.o: /usr/include/machine/types.h /usr/include/i386/types.h
-tessel_convex.o: /usr/include/sys/_types/_dev_t.h
-tessel_convex.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
-tessel_convex.o: /usr/include/sys/_types/_rsize_t.h
-tessel_convex.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-tessel_convex.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-tessel_convex.o: /usr/include/sys/_types/_fd_def.h
-tessel_convex.o: /usr/include/sys/_types/_timespec.h
-tessel_convex.o: /usr/include/sys/_types/_time_t.h
-tessel_convex.o: /usr/include/sys/_types/_suseconds_t.h
-tessel_convex.o: /usr/include/sys/_types/_fd_setsize.h
-tessel_convex.o: /usr/include/sys/_types/_fd_set.h
-tessel_convex.o: /usr/include/sys/_types/_fd_clr.h
-tessel_convex.o: /usr/include/sys/_types/_fd_isset.h
-tessel_convex.o: /usr/include/sys/_types/_fd_zero.h
-tessel_convex.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h
-tessel_convex.o: /usr/include/sys/_types/_clock_t.h
-tessel_convex.o: /usr/include/sys/_select.h linalg.h
+tessel_convex.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+tessel_convex.o: /usr/include/machine/_types.h /usr/include/math.h
+tessel_convex.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+tessel_convex.o: /usr/include/string.h /usr/include/strings.h
+tessel_convex.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
+tessel_convex.o: /usr/include/sys/types.h /usr/include/machine/endian.h
+tessel_convex.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
+tessel_convex.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
+tessel_convex.o: /usr/include/time.h linalg.h
 tessel_concave.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-tessel_concave.o: /usr/include/sys/_symbol_aliasing.h
-tessel_concave.o: /usr/include/sys/_posix_availability.h
-tessel_concave.o: /usr/include/Availability.h
-tessel_concave.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-tessel_concave.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-tessel_concave.o: /usr/include/i386/_types.h
-tessel_concave.o: /usr/include/sys/_pthread/_pthread_types.h
-tessel_concave.o: /usr/include/sys/_types/_va_list.h
-tessel_concave.o: /usr/include/sys/_types/_size_t.h
-tessel_concave.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-tessel_concave.o: /usr/include/sys/_types/_off_t.h
-tessel_concave.o: /usr/include/sys/_types/_ssize_t.h
-tessel_concave.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-tessel_concave.o: /usr/include/math.h /usr/include/stdlib.h
-tessel_concave.o: /usr/include/sys/wait.h /usr/include/sys/_types/_pid_t.h
-tessel_concave.o: /usr/include/sys/_types/_id_t.h /usr/include/sys/signal.h
-tessel_concave.o: /usr/include/sys/appleapiopts.h
-tessel_concave.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-tessel_concave.o: /usr/include/machine/_mcontext.h
-tessel_concave.o: /usr/include/i386/_mcontext.h
-tessel_concave.o: /usr/include/mach/i386/_structs.h
-tessel_concave.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-tessel_concave.o: /usr/include/sys/_types/_sigaltstack.h
-tessel_concave.o: /usr/include/sys/_types/_ucontext.h
-tessel_concave.o: /usr/include/sys/_types/_sigset_t.h
-tessel_concave.o: /usr/include/sys/_types/_uid_t.h
-tessel_concave.o: /usr/include/sys/resource.h /usr/include/stdint.h
-tessel_concave.o: /usr/include/sys/_types/_int8_t.h
-tessel_concave.o: /usr/include/sys/_types/_int16_t.h
-tessel_concave.o: /usr/include/sys/_types/_int32_t.h
-tessel_concave.o: /usr/include/sys/_types/_int64_t.h
-tessel_concave.o: /usr/include/_types/_uint8_t.h
-tessel_concave.o: /usr/include/_types/_uint16_t.h
-tessel_concave.o: /usr/include/_types/_uint32_t.h
-tessel_concave.o: /usr/include/_types/_uint64_t.h
-tessel_concave.o: /usr/include/sys/_types/_intptr_t.h
-tessel_concave.o: /usr/include/sys/_types/_uintptr_t.h
-tessel_concave.o: /usr/include/_types/_intmax_t.h
-tessel_concave.o: /usr/include/_types/_uintmax_t.h
-tessel_concave.o: /usr/include/sys/_types/_timeval.h
-tessel_concave.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-tessel_concave.o: /usr/include/sys/_endian.h
-tessel_concave.o: /usr/include/libkern/_OSByteOrder.h
-tessel_concave.o: /usr/include/libkern/i386/_OSByteOrder.h
-tessel_concave.o: /usr/include/alloca.h /usr/include/sys/_types/_ct_rune_t.h
-tessel_concave.o: /usr/include/sys/_types/_rune_t.h
-tessel_concave.o: /usr/include/sys/_types/_wchar_t.h
-tessel_concave.o: /usr/include/machine/types.h /usr/include/i386/types.h
-tessel_concave.o: /usr/include/sys/_types/_dev_t.h
-tessel_concave.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
-tessel_concave.o: /usr/include/sys/_types/_rsize_t.h
-tessel_concave.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-tessel_concave.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-tessel_concave.o: /usr/include/sys/_types/_fd_def.h
-tessel_concave.o: /usr/include/sys/_types/_timespec.h
-tessel_concave.o: /usr/include/sys/_types/_time_t.h
-tessel_concave.o: /usr/include/sys/_types/_suseconds_t.h
-tessel_concave.o: /usr/include/sys/_types/_fd_setsize.h
-tessel_concave.o: /usr/include/sys/_types/_fd_set.h
-tessel_concave.o: /usr/include/sys/_types/_fd_clr.h
-tessel_concave.o: /usr/include/sys/_types/_fd_isset.h
-tessel_concave.o: /usr/include/sys/_types/_fd_zero.h
-tessel_concave.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h
-tessel_concave.o: /usr/include/sys/_types/_clock_t.h
-tessel_concave.o: /usr/include/sys/_select.h linalg.h
+tessel_concave.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+tessel_concave.o: /usr/include/machine/_types.h /usr/include/math.h
+tessel_concave.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+tessel_concave.o: /usr/include/string.h /usr/include/strings.h
+tessel_concave.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
+tessel_concave.o: /usr/include/sys/types.h /usr/include/machine/endian.h
+tessel_concave.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
+tessel_concave.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
+tessel_concave.o: /usr/include/time.h linalg.h
 tessel_torus.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-tessel_torus.o: /usr/include/sys/_symbol_aliasing.h
-tessel_torus.o: /usr/include/sys/_posix_availability.h
-tessel_torus.o: /usr/include/Availability.h
-tessel_torus.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-tessel_torus.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-tessel_torus.o: /usr/include/i386/_types.h
-tessel_torus.o: /usr/include/sys/_pthread/_pthread_types.h
-tessel_torus.o: /usr/include/sys/_types/_va_list.h
-tessel_torus.o: /usr/include/sys/_types/_size_t.h
-tessel_torus.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-tessel_torus.o: /usr/include/sys/_types/_off_t.h
-tessel_torus.o: /usr/include/sys/_types/_ssize_t.h
-tessel_torus.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-tessel_torus.o: /usr/include/math.h /usr/include/stdlib.h
-tessel_torus.o: /usr/include/sys/wait.h /usr/include/sys/_types/_pid_t.h
-tessel_torus.o: /usr/include/sys/_types/_id_t.h /usr/include/sys/signal.h
-tessel_torus.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
-tessel_torus.o: /usr/include/i386/signal.h /usr/include/machine/_mcontext.h
-tessel_torus.o: /usr/include/i386/_mcontext.h
-tessel_torus.o: /usr/include/mach/i386/_structs.h
-tessel_torus.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-tessel_torus.o: /usr/include/sys/_types/_sigaltstack.h
-tessel_torus.o: /usr/include/sys/_types/_ucontext.h
-tessel_torus.o: /usr/include/sys/_types/_sigset_t.h
-tessel_torus.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
-tessel_torus.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
-tessel_torus.o: /usr/include/sys/_types/_int16_t.h
-tessel_torus.o: /usr/include/sys/_types/_int32_t.h
-tessel_torus.o: /usr/include/sys/_types/_int64_t.h
-tessel_torus.o: /usr/include/_types/_uint8_t.h
-tessel_torus.o: /usr/include/_types/_uint16_t.h
-tessel_torus.o: /usr/include/_types/_uint32_t.h
-tessel_torus.o: /usr/include/_types/_uint64_t.h
-tessel_torus.o: /usr/include/sys/_types/_intptr_t.h
-tessel_torus.o: /usr/include/sys/_types/_uintptr_t.h
-tessel_torus.o: /usr/include/_types/_intmax_t.h
-tessel_torus.o: /usr/include/_types/_uintmax_t.h
-tessel_torus.o: /usr/include/sys/_types/_timeval.h
-tessel_torus.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-tessel_torus.o: /usr/include/sys/_endian.h
-tessel_torus.o: /usr/include/libkern/_OSByteOrder.h
-tessel_torus.o: /usr/include/libkern/i386/_OSByteOrder.h
-tessel_torus.o: /usr/include/alloca.h /usr/include/sys/_types/_ct_rune_t.h
-tessel_torus.o: /usr/include/sys/_types/_rune_t.h
-tessel_torus.o: /usr/include/sys/_types/_wchar_t.h
-tessel_torus.o: /usr/include/machine/types.h /usr/include/i386/types.h
-tessel_torus.o: /usr/include/sys/_types/_dev_t.h
-tessel_torus.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
-tessel_torus.o: /usr/include/sys/_types/_rsize_t.h
-tessel_torus.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-tessel_torus.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-tessel_torus.o: /usr/include/sys/_types/_fd_def.h
-tessel_torus.o: /usr/include/sys/_types/_timespec.h
-tessel_torus.o: /usr/include/sys/_types/_time_t.h
-tessel_torus.o: /usr/include/sys/_types/_suseconds_t.h
-tessel_torus.o: /usr/include/sys/_types/_fd_setsize.h
-tessel_torus.o: /usr/include/sys/_types/_fd_set.h
-tessel_torus.o: /usr/include/sys/_types/_fd_clr.h
-tessel_torus.o: /usr/include/sys/_types/_fd_isset.h
-tessel_torus.o: /usr/include/sys/_types/_fd_zero.h
-tessel_torus.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h
-tessel_torus.o: /usr/include/sys/_types/_clock_t.h /usr/include/sys/_select.h
-tessel_torus.o: linalg.h
-  
-# DEPENDENCIES MUST END AT END OF FILE
-# IF YOU PUT STUFF HERE IT WILL GO AWAY
-# see make depend above
-  
+tessel_torus.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+tessel_torus.o: /usr/include/machine/_types.h /usr/include/math.h
+tessel_torus.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+tessel_torus.o: /usr/include/string.h /usr/include/strings.h
+tessel_torus.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
+tessel_torus.o: /usr/include/sys/types.h /usr/include/machine/endian.h
+tessel_torus.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
+tessel_torus.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
+tessel_torus.o: /usr/include/time.h linalg.h




--- surf/Makefile.orig	2015-05-02 19:48:48 UTC
+++ surf/Makefile
@@ -53,12 +53,12 @@ DEPEND = $(SRCS)
 depend: $(DEPEND)
 	@ echo making dependencies...
 	@ echo ' ' > makedep
-	@ makedepend $(INCLUDE) -f makedep $(DEPEND)
+	@ $(CC) $(INCLUDE) -M $(SRCS) > makedep
 	@ echo '/^# DO NOT DELETE THIS LINE/+2,$$d' >eddep
 	@ echo '$$r makedep' >>eddep
 	@ echo 'w' >>eddep
 	@ cp Makefile Makefile.bak
-	@ ex - Makefile < eddep
+	#@ ex - Makefile < eddep
 	@ rm eddep makedep 
 	@ echo '  ' >> Makefile
 	@ echo '# DEPENDENCIES MUST END AT END OF FILE' >> Makefile
@@ -69,672 +69,204 @@ depend: $(DEPEND)
 
 # DO NOT DELETE THIS LINE -- make depend depends on it.
   
- 
-# DO NOT DELETE
-
-surf.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-surf.o: /usr/include/sys/_symbol_aliasing.h
-surf.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
-surf.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-surf.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-surf.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
-surf.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
-surf.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-surf.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
-surf.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-surf.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
-surf.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
-surf.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
-surf.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-surf.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
-surf.o: /usr/include/mach/i386/_structs.h
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-tessel_torus.o: /usr/include/sys/_posix_availability.h
-tessel_torus.o: /usr/include/Availability.h
-tessel_torus.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-tessel_torus.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-tessel_torus.o: /usr/include/i386/_types.h
-tessel_torus.o: /usr/include/sys/_pthread/_pthread_types.h
-tessel_torus.o: /usr/include/sys/_types/_va_list.h
-tessel_torus.o: /usr/include/sys/_types/_size_t.h
-tessel_torus.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-tessel_torus.o: /usr/include/sys/_types/_off_t.h
-tessel_torus.o: /usr/include/sys/_types/_ssize_t.h
-tessel_torus.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-tessel_torus.o: /usr/include/math.h /usr/include/stdlib.h
-tessel_torus.o: /usr/include/sys/wait.h /usr/include/sys/_types/_pid_t.h
-tessel_torus.o: /usr/include/sys/_types/_id_t.h /usr/include/sys/signal.h
-tessel_torus.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
-tessel_torus.o: /usr/include/i386/signal.h /usr/include/machine/_mcontext.h
-tessel_torus.o: /usr/include/i386/_mcontext.h
-tessel_torus.o: /usr/include/mach/i386/_structs.h
-tessel_torus.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-tessel_torus.o: /usr/include/sys/_types/_sigaltstack.h
-tessel_torus.o: /usr/include/sys/_types/_ucontext.h
-tessel_torus.o: /usr/include/sys/_types/_sigset_t.h
-tessel_torus.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
-tessel_torus.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
-tessel_torus.o: /usr/include/sys/_types/_int16_t.h
-tessel_torus.o: /usr/include/sys/_types/_int32_t.h
-tessel_torus.o: /usr/include/sys/_types/_int64_t.h
-tessel_torus.o: /usr/include/_types/_uint8_t.h
-tessel_torus.o: /usr/include/_types/_uint16_t.h
-tessel_torus.o: /usr/include/_types/_uint32_t.h
-tessel_torus.o: /usr/include/_types/_uint64_t.h
-tessel_torus.o: /usr/include/sys/_types/_intptr_t.h
-tessel_torus.o: /usr/include/sys/_types/_uintptr_t.h
-tessel_torus.o: /usr/include/_types/_intmax_t.h
-tessel_torus.o: /usr/include/_types/_uintmax_t.h
-tessel_torus.o: /usr/include/sys/_types/_timeval.h
-tessel_torus.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-tessel_torus.o: /usr/include/sys/_endian.h
-tessel_torus.o: /usr/include/libkern/_OSByteOrder.h
-tessel_torus.o: /usr/include/libkern/i386/_OSByteOrder.h
-tessel_torus.o: /usr/include/alloca.h /usr/include/sys/_types/_ct_rune_t.h
-tessel_torus.o: /usr/include/sys/_types/_rune_t.h
-tessel_torus.o: /usr/include/sys/_types/_wchar_t.h
-tessel_torus.o: /usr/include/machine/types.h /usr/include/i386/types.h
-tessel_torus.o: /usr/include/sys/_types/_dev_t.h
-tessel_torus.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
-tessel_torus.o: /usr/include/sys/_types/_rsize_t.h
-tessel_torus.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-tessel_torus.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-tessel_torus.o: /usr/include/sys/_types/_fd_def.h
-tessel_torus.o: /usr/include/sys/_types/_timespec.h
-tessel_torus.o: /usr/include/sys/_types/_time_t.h
-tessel_torus.o: /usr/include/sys/_types/_suseconds_t.h
-tessel_torus.o: /usr/include/sys/_types/_fd_setsize.h
-tessel_torus.o: /usr/include/sys/_types/_fd_set.h
-tessel_torus.o: /usr/include/sys/_types/_fd_clr.h
-tessel_torus.o: /usr/include/sys/_types/_fd_isset.h
-tessel_torus.o: /usr/include/sys/_types/_fd_zero.h
-tessel_torus.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h
-tessel_torus.o: /usr/include/sys/_types/_clock_t.h /usr/include/sys/_select.h
-tessel_torus.o: linalg.h
+surf.o: surf.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h
+io.o: io.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h
+compute.o: compute.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h chull.h \
+  dual.h
+dual.o: dual.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h dual.h \
+  chull.h
+utils.o: utils.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h
+lp.o: lp.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h
+chull.o: chull.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h chull.h
+tessel_cases.o: tessel_cases.c surf.h /usr/include/stdio.h \
+  /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/x86/_types.h /usr/include/machine/_limits.h \
+  /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
+  /usr/include/string.h /usr/include/strings.h \
+  /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
+  /usr/include/sys/time.h /usr/include/sys/_timeval.h \
+  /usr/include/sys/types.h /usr/include/machine/endian.h \
+  /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
+  /usr/include/sys/_stdint.h /usr/include/sys/select.h \
+  /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
+  /usr/include/sys/_timespec.h /usr/include/time.h \
+  /usr/include/xlocale/_time.h linalg.h dual.h
+tessel_patches.o: tessel_patches.c surf.h /usr/include/stdio.h \
+  /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/x86/_types.h /usr/include/machine/_limits.h \
+  /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
+  /usr/include/string.h /usr/include/strings.h \
+  /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
+  /usr/include/sys/time.h /usr/include/sys/_timeval.h \
+  /usr/include/sys/types.h /usr/include/machine/endian.h \
+  /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
+  /usr/include/sys/_stdint.h /usr/include/sys/select.h \
+  /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
+  /usr/include/sys/_timespec.h /usr/include/time.h \
+  /usr/include/xlocale/_time.h linalg.h
+tessel_convex.o: tessel_convex.c surf.h /usr/include/stdio.h \
+  /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/x86/_types.h /usr/include/machine/_limits.h \
+  /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
+  /usr/include/string.h /usr/include/strings.h \
+  /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
+  /usr/include/sys/time.h /usr/include/sys/_timeval.h \
+  /usr/include/sys/types.h /usr/include/machine/endian.h \
+  /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
+  /usr/include/sys/_stdint.h /usr/include/sys/select.h \
+  /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
+  /usr/include/sys/_timespec.h /usr/include/time.h \
+  /usr/include/xlocale/_time.h linalg.h
+tessel_concave.o: tessel_concave.c surf.h /usr/include/stdio.h \
+  /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/x86/_types.h /usr/include/machine/_limits.h \
+  /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
+  /usr/include/string.h /usr/include/strings.h \
+  /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
+  /usr/include/sys/time.h /usr/include/sys/_timeval.h \
+  /usr/include/sys/types.h /usr/include/machine/endian.h \
+  /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
+  /usr/include/sys/_stdint.h /usr/include/sys/select.h \
+  /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
+  /usr/include/sys/_timespec.h /usr/include/time.h \
+  /usr/include/xlocale/_time.h linalg.h
+tessel_torus.o: tessel_torus.c surf.h /usr/include/stdio.h \
+  /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
+  /usr/include/x86/_types.h /usr/include/machine/_limits.h \
+  /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
+  /usr/include/string.h /usr/include/strings.h \
+  /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
+  /usr/include/sys/time.h /usr/include/sys/_timeval.h \
+  /usr/include/sys/types.h /usr/include/machine/endian.h \
+  /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
+  /usr/include/sys/_stdint.h /usr/include/sys/select.h \
+  /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
+  /usr/include/sys/_timespec.h /usr/include/time.h \
+  /usr/include/xlocale/_time.h linalg.h
+  
+# DEPENDENCIES MUST END AT END OF FILE
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
+# see make depend above
+  
+  
+# DEPENDENCIES MUST END AT END OF FILE
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
+# see make depend above
+  
+  
+# DEPENDENCIES MUST END AT END OF FILE
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
+# see make depend above
+  
+  
+# DEPENDENCIES MUST END AT END OF FILE
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
+# see make depend above
+  
+  
+# DEPENDENCIES MUST END AT END OF FILE
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
+# see make depend above
+  
+  
+# DEPENDENCIES MUST END AT END OF FILE
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
+# see make depend above
+  
+  
+# DEPENDENCIES MUST END AT END OF FILE
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
+# see make depend above
+  
   
 # DEPENDENCIES MUST END AT END OF FILE
 # IF YOU PUT STUFF HERE IT WILL GO AWAY

Line 0 Link Here

(-)biology/molden/files/patch-surf_utils.c (+10 lines)
	1	--- surf/utils.c.orig 2019-06-28 03:23:08 UTC
	2	+++ surf/utils.c
	3	@@ -76,6 +76,7 @@ find_ray_sphere_int computes the intersection of a ra
	4	uses method given in Graphics Gems I, pp 388-389.
	5	the direction vector of the ray need not be normalized.
	6	----------------------------------------------------------------------------------*/
	7	+void
	8	find_ray_sphere_int(int_point, ray_pt, ray_dir, center, radius)
	9	float int_point[3], center[3];
	10	float ray_pt[3], ray_dir[3];




--- xwin.c.orig	2018-11-07 12:54:20 UTC
+++ xwin.c
@@ -4218,8 +4218,12 @@ void makeRasterFont(Display *dpy);
 #include <math.h>
 
 #include <fcntl.h>
-#if defined(__APPLE__) || defined(__FreeBSD__)
+#if defined(__APPLE__)
 #include <copyfile.h>
+#elif defined(__FreeBSD__)
+#include <sys/types.h>
+#include <sys/socket.h>
+#include <sys/uio.h>
 #else
 #include <sys/sendfile.h>
 #endif
@@ -4238,9 +4242,14 @@ int OSCopyFile(const char* source, const
     }
 
     //Here we use kernel-space copying for performance reasons
-#if defined(__APPLE__) || defined(__FreeBSD__)
+#if defined(__APPLE__)
     //fcopyfile works on FreeBSD and OS X 10.5+ 
     int result = fcopyfile(input, output, 0, COPYFILE_ALL);
+#elif defined(__FreeBSD__)
+    off_t bytesCopied = 0;
+    struct stat fileinfo = {0};
+    fstat(input, &fileinfo);
+    int result = sendfile(output, input, 0/*ofset*/, fileinfo.st_size, 0/*hdtr*/, &bytesCopied, 0/*flags*/);
 #else
     //sendfile will work with non-socket output (i.e. regular file) on Linux 2.6.33+
     off_t bytesCopied = 0;




Molden is a package for displaying Molecular Density from the Ab Initio packages
GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac,
it also supports a number of other programs via the Molden Format. Molden reads
all the required information from the GAMESS / GAUSSIAN outputfile. Molden is
capable of displaying Molecular Orbitals, the electron density and the Molecular
minus Atomic density. Either the spherically averaged atomic density or the
oriented ground state atomic density can be subtracted for a number of standard
basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and
a combination of both. It can write a variety of graphics instructions;
postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and
Figure. Both Xwindows and OpenGL versions of Molden are also capable of
importing and displaying of chemx, PDB, and a variety of mopac/ampac files and
lots of other formats. Molden also can animate reaction paths and molecular
vibrations. It can calculate and display the true or Multipole Derived
Electrostatic Potential and atomic charges can be fitted to the Electrostatic
Potential calculated on a Connolly surface. Molden also features an stand alone
forcefield program ambfor, which can optimise geometries with the combined Amber
(protein) and GAFF (small molecules) force fields. Atom typing can be done
automatically and interactively from within Molden, as well as firing
optimisation jobs. Molden has a powerful Z-matrix editor which give full control
over the geometry and allows you to build molecules from scratch, including
polypeptides.

WWW: http://cheminf.cmbi.ru.nl/molden/
 * Only the latest version is supplied.
 * Users must get the `distfiles' from the original site.
 * Do not re-distribute the source and the executable.
 * Using a not-so-latest version is prohibited, because
   the author may only respond about the latest version.

WWW: http://www.cmbi.ru.nl/molden/

Return to bug 238858

Lines 1-76 Link Here

(-)biology/molden/Makefile (-49 / +20 lines)
1	# Created by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
2	# $FreeBSD$	1	# $FreeBSD$
3		2
4	PORTNAME= molden	3	PORTNAME= molden
5	DISTVERSION= 5.8.2	4	DISTVERSION= 6.1
6	PORTREVISION= 2
7	PORTEPOCH= 1
8	CATEGORIES= biology	5	CATEGORIES= biology
9	MASTER_SITES= ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/	6	MASTER_SITES= ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/
10	DISTNAME= ${PORTNAME}${PORTVERSION}	7	DISTNAME= ${PORTNAME}${DISTVERSION}
11		8
12	MAINTAINER= jmd@FreeBSD.org	9	MAINTAINER= jmd@FreeBSD.org
13	COMMENT= Display molecular orbitals and electron densities in 2D and 3D	10	COMMENT= Display molecular orbitals and electron densities in 2D and 3D
14		11
15	LICENSE= Molden	12	LICENSE= Molden
16	LICENSE_NAME= Molden	13	LICENSE_NAME= Molden License
17	LICENSE_FILE= ${WRKSRC}/CopyRight	14	LICENSE_FILE= ${WRKSRC}/CopyRight
18	LICENSE_PERMS= auto-accept	15	LICENSE_PERMS= auto-accept dist-mirror pkg-mirror
19		16
20	RESTRICTED= free for academic, non profit usage; do not re-distribute source and executable.	17	BUILD_DEPENDS= makedepend:devel/makedepend
21		18
22	WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION:R}	19	USES= fortran gl gmake localbase
		20	USE_GL= gl glu
		21	USE_XORG= x11 xmu
23		22
24	USES= fortran gl gmake
25	USE_XORG= x11
26	USE_GL= gl glu
27	MAKEFILE= makefile	23	MAKEFILE= makefile
28	MAKE_JOBS_UNSAFE=yes	24	MAKE_ARGS= CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}"
29		25
30	CFLAGS+= -D${OPSYS:tu} -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 \	26	CFLAGS+= -DFREEBSD -DHASTIMER
31	-I${LOCALBASE}/include -Wno-return-type	27	FFLAGS+= -DFREEBSD
32		28
33	PORTDOCS= *	29	EXES= molden gmolden ambfor/ambfor ambfor/ambmd surf/surf
34	PORTDATA= *	30	PLIST_FILES= ${EXES:C/.*\///:S/^/bin\//}
35	PLIST_FILES= bin/ambfor bin/gmolden bin/molden bin/surf
36		31
37	PORTSCOUT= limit:^5\.0\.	32	OPTIONS_DEFINE= DOCS
38		33
39	OPTIONS_DEFINE= DATA DOCS	34	PORTDOCS= *
40	OPTIONS_DEFAULT= DATA
41		35
42	post-patch:
43	@${REINPLACE_CMD} -e \
44	's\|^CC \|#CC \| ; \
45	s\|^FC \|#FC \| ; \
46	s\|/usr/X11R6\|${LOCALBASE}\| ; \
47	s\|$$(LIBS)\|$$(LIBS) $$(LDFLAGS)\| ; \
48	s\|-lXmu\|\| ; \
49	/depend/s\|^\|#\|' ${WRKSRC}/makefile
50
51	post-configure:
52	@${ECHO_MSG} "********************"
53	@${ECHO_MSG} "** If you want to use a larger MOLDEN,"
54	@${ECHO_MSG} "** edit change_parameter.sh and run it,"
55	@${ECHO_MSG} "** before \'make build\'."
56	@${ECHO_MSG} "********************"
57
58	do-install:	36	do-install:
59	.for i in molden gmolden	37	.for e in ${EXES}
60	(cd ${WRKSRC} && ${INSTALL_PROGRAM} ${i} ${STAGEDIR}${PREFIX}/bin)	38	${INSTALL_PROGRAM} ${WRKSRC}/${e} ${STAGEDIR}${PREFIX}/bin
61	.endfor	39	.endfor
62	.for i in ambfor surf
63	(cd ${WRKSRC}/${i} && ${INSTALL_PROGRAM} ${i} ${STAGEDIR}/${PREFIX}/bin)
64	.endfor
65		40
66	do-install-DATA-on:
67	@${MKDIR} ${STAGEDIR}${DATADIR}/test
68	(cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/test)
69	${MKDIR} ${STAGEDIR}${DATADIR}/utils
70	(cd ${WRKSRC}/utils && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/utils)
71
72	do-install-DOCS-on:	41	do-install-DOCS-on:
73	${MKDIR} ${STAGEDIR}${DOCSDIR}	42	${MKDIR} ${STAGEDIR}${DOCSDIR}
74	(cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR})	43	.for d in figures.ps.Z manual.ps.Z manual.txt.Z
		44	${INSTALL_DATA} ${WRKSRC}/doc/${d} ${STAGEDIR}${DOCSDIR}
		45	.endfor
75		46
76	.include <bsd.port.mk>	47	.include <bsd.port.mk>

Lines 1-28 Link Here

(-)biology/molden/files/patch-ambfor-makefile (-28 lines)
1	--- ambfor/makefile.orig 2015-05-02 19:49:10 UTC
2	+++ ambfor/makefile
3	@@ -12,12 +12,12 @@
4	#
5	#
6
7	-CFLAGS = -c -g ${EXT}
8	+CFLAGS += -c
9	#FC = g77
10	-FC = gfortran
11	-FFLAGS = -c -g -ffast-math -funroll-loops -O3
12	+#FC = gfortran
13	+#FFLAGS = -c -g -ffast-math -funroll-loops -O3
14	LIBS = -lm
15	-LDR = ${FC} -g
16	+LDR = ${FC}
17	EXT :=
18
19	ifeq ($(uname), Darwin)
20	@@ -56,7 +56,7 @@ ambmd: md.o verlet.o qvdw.o allocmd.o $(
21	$(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS)
22
23	ambfor.o: ambfor.f
24	- ${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f
25	+ ${FC} -c ${FFLAGS} -o ambfor.o ambfor.f
26
27	allocmd.o: alloc.c
28	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o

Line 0 Link Here

(-)biology/molden/files/patch-makefile (+18 lines)
	1	--- makefile.orig 2019-06-28 03:02:40 UTC
	2	+++ makefile
	3	@@ -96,13 +96,13 @@ ifneq ($(comgcc), $(empty))
	4	EXTRAZ = -Wno-implicit-function-declaration
	5	EXT = ${EXTRAZ}
	6	endif
	7	-FFLAGS = -g ${AFLAG}
	8	+FFLAGS += -g ${AFLAG}
	9	LIBS = -L/usr/X11R6/lib -lX11 -lm
	10	ifeq ($(AFLAG),"-m64")
	11	LIBS = -L/usr/X11R6/lib64 -lX11 -lm
	12	endif
	13	LDR = ${FC} -g ${AFLAG}
	14	-CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
	15	+CFLAGS += ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
	16	ifeq ($(os), Debian)
	17	CFLAGS = ${AFLAG} ${EXTRAZ} -c -I/usr/include/X11 -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
	18	LIBS = -L/usr/lib/X11 -lX11 -lm

Lines 1-32 Link Here

(-)biology/molden/files/patch-xwin.c (-32 lines)
1	--- xwin.c.orig 2018-11-07 12:54:20 UTC
2	+++ xwin.c
3	@@ -4218,8 +4218,12 @@ void makeRasterFont(Display *dpy);
4	#include <math.h>
5
6	#include <fcntl.h>
7	-#if defined(__APPLE__) \|\| defined(__FreeBSD__)
8	+#if defined(__APPLE__)
9	#include <copyfile.h>
10	+#elif defined(__FreeBSD__)
11	+#include <sys/types.h>
12	+#include <sys/socket.h>
13	+#include <sys/uio.h>
14	#else
15	#include <sys/sendfile.h>
16	#endif
17	@@ -4238,9 +4242,14 @@ int OSCopyFile(const char* source, const
18	}
19
20	//Here we use kernel-space copying for performance reasons
21	-#if defined(__APPLE__) \|\| defined(__FreeBSD__)
22	+#if defined(__APPLE__)
23	//fcopyfile works on FreeBSD and OS X 10.5+
24	int result = fcopyfile(input, output, 0, COPYFILE_ALL);
25	+#elif defined(__FreeBSD__)
26	+ off_t bytesCopied = 0;
27	+ struct stat fileinfo = {0};
28	+ fstat(input, &fileinfo);
29	+ int result = sendfile(output, input, 0/ofset/, fileinfo.st_size, 0/hdtr/, &bytesCopied, 0/flags/);
30	#else
31	//sendfile will work with non-socket output (i.e. regular file) on Linux 2.6.33+
32	off_t bytesCopied = 0;

Lines 1-14 Link Here

(-)biology/molden/pkg-descr (-13 / +23 lines)
1	Visualizing the results of molecular orbital calculations	1	Molden is a package for displaying Molecular Density from the Ab Initio packages
2	1) MO program: gaussian, gamess, mopac, etc.	2	GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac,
3	2) display molecule in 3D: geo-opt, single-point, nomal mode (animation)	3	it also supports a number of other programs via the Molden Format. Molden reads
4	3) density: contour plot or 3D view for electron density and MO coefficient	4	all the required information from the GAMESS / GAUSSIAN outputfile. Molden is
5	Everything what you want about MO calculation can be seen.	5	capable of displaying Molecular Orbitals, the electron density and the Molecular
		6	minus Atomic density. Either the spherically averaged atomic density or the
		7	oriented ground state atomic density can be subtracted for a number of standard
		8	basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and
		9	a combination of both. It can write a variety of graphics instructions;
		10	postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and
		11	Figure. Both Xwindows and OpenGL versions of Molden are also capable of
		12	importing and displaying of chemx, PDB, and a variety of mopac/ampac files and
		13	lots of other formats. Molden also can animate reaction paths and molecular
		14	vibrations. It can calculate and display the true or Multipole Derived
		15	Electrostatic Potential and atomic charges can be fitted to the Electrostatic
		16	Potential calculated on a Connolly surface. Molden also features an stand alone
		17	forcefield program ambfor, which can optimise geometries with the combined Amber
		18	(protein) and GAFF (small molecules) force fields. Atom typing can be done
		19	automatically and interactively from within Molden, as well as firing
		20	optimisation jobs. Molden has a powerful Z-matrix editor which give full control
		21	over the geometry and allows you to build molecules from scratch, including
		22	polypeptides.
6		23
7	By the distribution policy of the author;	24	WWW: http://cheminf.cmbi.ru.nl/molden/
8	* Only the latest version is supplied.
9	* Users must get the `distfiles' from the original site.
10	* Do not re-distribute the source and the executable.
11	* Using a not-so-latest version is prohibited, because
12	the author may only respond about the latest version.
13
14	WWW: http://www.cmbi.ru.nl/molden/