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(-)biology/molden/Makefile (-49 / +20 lines)
Lines 1-76 Link Here
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# Created by: Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
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# $FreeBSD$
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# $FreeBSD$
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PORTNAME=	molden
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PORTNAME=	molden
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DISTVERSION=	5.8.2
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DISTVERSION=	6.1
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PORTREVISION=	2
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PORTEPOCH=	1
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CATEGORIES=	biology
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CATEGORIES=	biology
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MASTER_SITES=	ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/
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MASTER_SITES=	ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/
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DISTNAME=	${PORTNAME}${PORTVERSION}
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DISTNAME=	${PORTNAME}${DISTVERSION}
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MAINTAINER=	jmd@FreeBSD.org
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MAINTAINER=	jmd@FreeBSD.org
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COMMENT=	Display molecular orbitals and electron densities in 2D and 3D
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COMMENT=	Display molecular orbitals and electron densities in 2D and 3D
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LICENSE=	Molden
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LICENSE=	Molden
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LICENSE_NAME=	Molden
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LICENSE_NAME=	Molden License
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LICENSE_FILE=	${WRKSRC}/CopyRight
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LICENSE_FILE=	${WRKSRC}/CopyRight
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LICENSE_PERMS=	auto-accept
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LICENSE_PERMS=	auto-accept dist-mirror pkg-mirror
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RESTRICTED=	free for academic, non profit usage; do not re-distribute source and executable.
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BUILD_DEPENDS=	makedepend:devel/makedepend
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WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION:R}
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USES=		fortran gl gmake localbase
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USE_GL=		gl glu
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USE_XORG=	x11 xmu
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USES=		fortran gl gmake
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USE_XORG=	x11
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USE_GL=		gl glu
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MAKEFILE=	makefile
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MAKEFILE=	makefile
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MAKE_JOBS_UNSAFE=yes
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MAKE_ARGS=	CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}"
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CFLAGS+=	-D${OPSYS:tu} -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 \
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CFLAGS+=	-DFREEBSD -DHASTIMER
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		-I${LOCALBASE}/include -Wno-return-type
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FFLAGS+=	-DFREEBSD
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PORTDOCS=	*
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EXES=		molden gmolden ambfor/ambfor ambfor/ambmd surf/surf
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PORTDATA=	*
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PLIST_FILES=	${EXES:C/.*\///:S/^/bin\//}
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PLIST_FILES=	bin/ambfor bin/gmolden bin/molden bin/surf
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PORTSCOUT=	limit:^5\.0\.
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OPTIONS_DEFINE=	DOCS
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OPTIONS_DEFINE=		DATA DOCS
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PORTDOCS=	*
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OPTIONS_DEFAULT=	DATA
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post-patch:
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	@${REINPLACE_CMD} -e \
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		's|^CC |#CC | ; \
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		 s|^FC |#FC | ; \
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		 s|/usr/X11R6|${LOCALBASE}| ; \
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		 s|$$(LIBS)|$$(LIBS) $$(LDFLAGS)| ; \
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		 s|-lXmu|| ; \
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		 /depend/s|^|#|' ${WRKSRC}/makefile
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post-configure:
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	@${ECHO_MSG} "********************"
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	@${ECHO_MSG} "**  If you want to use a larger MOLDEN,"
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	@${ECHO_MSG} "**  edit change_parameter.sh and run it,"
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	@${ECHO_MSG} "**  before \'make build\'."
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	@${ECHO_MSG} "********************"
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do-install:
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do-install:
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.for i in molden gmolden
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.for e in ${EXES}
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	(cd ${WRKSRC} && ${INSTALL_PROGRAM} ${i} ${STAGEDIR}${PREFIX}/bin)
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	${INSTALL_PROGRAM} ${WRKSRC}/${e} ${STAGEDIR}${PREFIX}/bin
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.endfor
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.endfor
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.for i in ambfor surf
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	(cd ${WRKSRC}/${i} && ${INSTALL_PROGRAM} ${i} ${STAGEDIR}/${PREFIX}/bin)
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.endfor
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do-install-DATA-on:
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	@${MKDIR} ${STAGEDIR}${DATADIR}/test
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	(cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/test)
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	${MKDIR} ${STAGEDIR}${DATADIR}/utils
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	(cd ${WRKSRC}/utils && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/utils)
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do-install-DOCS-on:
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do-install-DOCS-on:
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	${MKDIR} ${STAGEDIR}${DOCSDIR}
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	${MKDIR} ${STAGEDIR}${DOCSDIR}
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	(cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR})
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.for d in figures.ps.Z manual.ps.Z  manual.txt.Z
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	${INSTALL_DATA} ${WRKSRC}/doc/${d} ${STAGEDIR}${DOCSDIR}
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.endfor
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.include <bsd.port.mk>
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.include <bsd.port.mk>
(-)biology/molden/distinfo (-3 / +3 lines)
Lines 1-3 Link Here
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TIMESTAMP = 1541594934
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TIMESTAMP = 1561690466
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SHA256 (molden5.8.2.tar.gz) = 65a24db9e80b4fb6038cc1e57c7d6e2457414812c9389bc651af7cb33f01dbe9
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SHA256 (molden6.1.tar.gz) = ba228b863e8f405a9f6c9f6c502e50462a570daeff74661fb317338fcc6d7fb0
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SIZE (molden5.8.2.tar.gz) = 5770998
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SIZE (molden6.1.tar.gz) = 6263424
(-)biology/molden/files/patch-ambfor-makefile (-28 lines)
Lines 1-28 Link Here
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--- ambfor/makefile.orig	2015-05-02 19:49:10 UTC
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+++ ambfor/makefile
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@@ -12,12 +12,12 @@
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 #
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 # 
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-CFLAGS = -c -g ${EXT}
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+CFLAGS += -c
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 #FC = g77 
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-FC = gfortran
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-FFLAGS = -c -g -ffast-math -funroll-loops -O3
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+#FC = gfortran
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+#FFLAGS = -c -g -ffast-math -funroll-loops -O3
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 LIBS =  -lm
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-LDR = ${FC} -g
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+LDR = ${FC}
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 EXT :=
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 ifeq ($(uname), Darwin)
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@@ -56,7 +56,7 @@ ambmd:	md.o verlet.o qvdw.o allocmd.o $(
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 	$(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS)
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 ambfor.o:	ambfor.f
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-	${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f
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+	${FC} -c ${FFLAGS} -o ambfor.o ambfor.f
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 allocmd.o:	alloc.c
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 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o
(-)biology/molden/files/patch-makefile (+18 lines)
Line 0 Link Here
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--- makefile.orig	2019-06-28 03:02:40 UTC
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+++ makefile
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@@ -96,13 +96,13 @@ ifneq ($(comgcc), $(empty))
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    EXTRAZ = -Wno-implicit-function-declaration
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    EXT = ${EXTRAZ}
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 endif
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-FFLAGS = -g ${AFLAG}
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+FFLAGS += -g ${AFLAG}
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 LIBS =  -L/usr/X11R6/lib -lX11 -lm
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 ifeq ($(AFLAG),"-m64")
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 LIBS =  -L/usr/X11R6/lib64 -lX11 -lm
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 endif
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 LDR = ${FC} -g ${AFLAG}
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-CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
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+CFLAGS += ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
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  ifeq ($(os), Debian)
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     CFLAGS = ${AFLAG} ${EXTRAZ} -c -I/usr/include/X11 -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
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     LIBS =  -L/usr/lib/X11 -lX11 -lm
(-)biology/molden/files/patch-surf-Makefile (-789 lines)
Lines 1-789 Link Here
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--- surf/Makefile.orig	2015-05-02 19:48:48 UTC
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+++ surf/Makefile
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@@ -1,12 +1,8 @@
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 # Compilation flags
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-#CC	    = cc
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-CC	    = cc
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 INCLUDE     = -I. 
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 #LINCLUDE    = -lcurses -ltermcap -lm
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 LINCLUDE    = -lm
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-OPT_CFLAGS  = -O2 $(FLAGS) $(INCLUDE)
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 #CFLAGS	    = -g $(FLAGS) $(INCLUDE)
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-CFLAGS	    = -O2 $(FLAGS) $(INCLUDE) ${EXT}
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 ifeq ($(uname), Darwin)
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 #
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@@ -73,670 +69,117 @@ depend: $(DEPEND)
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 # DO NOT DELETE
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 surf.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
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-surf.o: /usr/include/sys/_symbol_aliasing.h
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-surf.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
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-surf.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
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-surf.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
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-surf.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
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-surf.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
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-surf.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
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-surf.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
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-surf.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
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-surf.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
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-surf.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
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-surf.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
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-surf.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
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-surf.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
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-surf.o: /usr/include/mach/i386/_structs.h
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-surf.o: /usr/include/sys/_pthread/_pthread_attr_t.h
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-surf.o: /usr/include/sys/_types/_sigaltstack.h
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-surf.o: /usr/include/sys/_types/_ucontext.h
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-surf.o: /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h
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-surf.o: /usr/include/sys/resource.h /usr/include/stdint.h
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-surf.o: /usr/include/sys/_types/_int8_t.h /usr/include/sys/_types/_int16_t.h
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-surf.o: /usr/include/sys/_types/_int32_t.h /usr/include/sys/_types/_int64_t.h
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-surf.o: /usr/include/_types/_uint8_t.h /usr/include/_types/_uint16_t.h
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-surf.o: /usr/include/_types/_uint32_t.h /usr/include/_types/_uint64_t.h
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-surf.o: /usr/include/sys/_types/_intptr_t.h
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-surf.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
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-surf.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
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-surf.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
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-surf.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
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-surf.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
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-surf.o: /usr/include/sys/_types/_ct_rune_t.h
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-surf.o: /usr/include/sys/_types/_rune_t.h /usr/include/sys/_types/_wchar_t.h
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-surf.o: /usr/include/machine/types.h /usr/include/i386/types.h
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-surf.o: /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h
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-surf.o: /usr/include/string.h /usr/include/sys/_types/_rsize_t.h
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-surf.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
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-surf.o: /usr/include/secure/_string.h /usr/include/sys/time.h
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-surf.o: /usr/include/sys/_types/_fd_def.h /usr/include/sys/_types/_timespec.h
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-surf.o: /usr/include/sys/_types/_time_t.h
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-surf.o: /usr/include/sys/_types/_suseconds_t.h
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-surf.o: /usr/include/sys/_types/_fd_setsize.h
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-surf.o: /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h
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-surf.o: /usr/include/sys/_types/_fd_isset.h
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-surf.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h
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-surf.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h
65
-surf.o: /usr/include/sys/_select.h linalg.h
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+surf.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
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+surf.o: /usr/include/machine/_types.h /usr/include/math.h
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+surf.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
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+surf.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
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+surf.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
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+surf.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
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+surf.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
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+surf.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
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 io.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
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-io.o: /usr/include/sys/_symbol_aliasing.h
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-io.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
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-io.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
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-io.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
79
-io.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
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-io.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
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-io.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
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-io.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
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-io.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
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-io.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
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-io.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
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-io.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
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-io.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
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-io.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
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-io.o: /usr/include/mach/i386/_structs.h
90
-io.o: /usr/include/sys/_pthread/_pthread_attr_t.h
91
-io.o: /usr/include/sys/_types/_sigaltstack.h
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-io.o: /usr/include/sys/_types/_ucontext.h /usr/include/sys/_types/_sigset_t.h
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-io.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
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-io.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
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-io.o: /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h
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-io.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h
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-io.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h
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-io.o: /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h
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-io.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
100
-io.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
101
-io.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
102
-io.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
103
-io.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
104
-io.o: /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h
105
-io.o: /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h
106
-io.o: /usr/include/i386/types.h /usr/include/sys/_types/_dev_t.h
107
-io.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
108
-io.o: /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h
109
-io.o: /usr/include/strings.h /usr/include/secure/_string.h
110
-io.o: /usr/include/sys/time.h /usr/include/sys/_types/_fd_def.h
111
-io.o: /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_time_t.h
112
-io.o: /usr/include/sys/_types/_suseconds_t.h
113
-io.o: /usr/include/sys/_types/_fd_setsize.h /usr/include/sys/_types/_fd_set.h
114
-io.o: /usr/include/sys/_types/_fd_clr.h /usr/include/sys/_types/_fd_isset.h
115
-io.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h
116
-io.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h
117
-io.o: /usr/include/sys/_select.h linalg.h
118
+io.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
119
+io.o: /usr/include/machine/_types.h /usr/include/math.h
120
+io.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
121
+io.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
122
+io.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
123
+io.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
124
+io.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
125
+io.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
126
 compute.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
127
-compute.o: /usr/include/sys/_symbol_aliasing.h
128
-compute.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
129
-compute.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
130
-compute.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
131
-compute.o: /usr/include/i386/_types.h
132
-compute.o: /usr/include/sys/_pthread/_pthread_types.h
133
-compute.o: /usr/include/sys/_types/_va_list.h
134
-compute.o: /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h
135
-compute.o: /usr/include/sys/stdio.h /usr/include/sys/_types/_off_t.h
136
-compute.o: /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h
137
-compute.o: /usr/include/secure/_common.h /usr/include/math.h
138
-compute.o: /usr/include/stdlib.h /usr/include/sys/wait.h
139
-compute.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
140
-compute.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
141
-compute.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
142
-compute.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
143
-compute.o: /usr/include/mach/i386/_structs.h
144
-compute.o: /usr/include/sys/_pthread/_pthread_attr_t.h
145
-compute.o: /usr/include/sys/_types/_sigaltstack.h
146
-compute.o: /usr/include/sys/_types/_ucontext.h
147
-compute.o: /usr/include/sys/_types/_sigset_t.h
148
-compute.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
149
-compute.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
150
-compute.o: /usr/include/sys/_types/_int16_t.h
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-compute.o: /usr/include/sys/_types/_int32_t.h
152
-compute.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h
153
-compute.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h
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-compute.o: /usr/include/_types/_uint64_t.h
155
-compute.o: /usr/include/sys/_types/_intptr_t.h
156
-compute.o: /usr/include/sys/_types/_uintptr_t.h
157
-compute.o: /usr/include/_types/_intmax_t.h /usr/include/_types/_uintmax_t.h
158
-compute.o: /usr/include/sys/_types/_timeval.h /usr/include/machine/endian.h
159
-compute.o: /usr/include/i386/endian.h /usr/include/sys/_endian.h
160
-compute.o: /usr/include/libkern/_OSByteOrder.h
161
-compute.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
162
-compute.o: /usr/include/sys/_types/_ct_rune_t.h
163
-compute.o: /usr/include/sys/_types/_rune_t.h
164
-compute.o: /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h
165
-compute.o: /usr/include/i386/types.h /usr/include/sys/_types/_dev_t.h
166
-compute.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
167
-compute.o: /usr/include/sys/_types/_rsize_t.h
168
-compute.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
169
-compute.o: /usr/include/secure/_string.h /usr/include/sys/time.h
170
-compute.o: /usr/include/sys/_types/_fd_def.h
171
-compute.o: /usr/include/sys/_types/_timespec.h
172
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 dual.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
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 utils.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
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+tessel_concave.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
704
+tessel_concave.o: /usr/include/machine/_types.h /usr/include/math.h
705
+tessel_concave.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
706
+tessel_concave.o: /usr/include/string.h /usr/include/strings.h
707
+tessel_concave.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
708
+tessel_concave.o: /usr/include/sys/types.h /usr/include/machine/endian.h
709
+tessel_concave.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
710
+tessel_concave.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
711
+tessel_concave.o: /usr/include/time.h linalg.h
712
 tessel_torus.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
713
-tessel_torus.o: /usr/include/sys/_symbol_aliasing.h
714
-tessel_torus.o: /usr/include/sys/_posix_availability.h
715
-tessel_torus.o: /usr/include/Availability.h
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-tessel_torus.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
717
-tessel_torus.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
718
-tessel_torus.o: /usr/include/i386/_types.h
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-tessel_torus.o: /usr/include/sys/_pthread/_pthread_types.h
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-tessel_torus.o: /usr/include/sys/_types/_va_list.h
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-tessel_torus.o: /usr/include/sys/_types/_size_t.h
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-tessel_torus.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
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-tessel_torus.o: /usr/include/sys/_types/_off_t.h
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-tessel_torus.o: /usr/include/sys/_types/_ssize_t.h
725
-tessel_torus.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
726
-tessel_torus.o: /usr/include/math.h /usr/include/stdlib.h
727
-tessel_torus.o: /usr/include/sys/wait.h /usr/include/sys/_types/_pid_t.h
728
-tessel_torus.o: /usr/include/sys/_types/_id_t.h /usr/include/sys/signal.h
729
-tessel_torus.o: /usr/include/sys/appleapiopts.h /usr/include/machine/signal.h
730
-tessel_torus.o: /usr/include/i386/signal.h /usr/include/machine/_mcontext.h
731
-tessel_torus.o: /usr/include/i386/_mcontext.h
732
-tessel_torus.o: /usr/include/mach/i386/_structs.h
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-tessel_torus.o: /usr/include/sys/_pthread/_pthread_attr_t.h
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-tessel_torus.o: /usr/include/sys/_types/_sigaltstack.h
735
-tessel_torus.o: /usr/include/sys/_types/_ucontext.h
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-tessel_torus.o: /usr/include/sys/_types/_sigset_t.h
737
-tessel_torus.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
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-tessel_torus.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
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-tessel_torus.o: /usr/include/sys/_types/_int16_t.h
740
-tessel_torus.o: /usr/include/sys/_types/_int32_t.h
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-tessel_torus.o: /usr/include/sys/_types/_int64_t.h
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-tessel_torus.o: /usr/include/_types/_uint8_t.h
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-tessel_torus.o: /usr/include/_types/_uint16_t.h
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-tessel_torus.o: /usr/include/_types/_uint32_t.h
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-tessel_torus.o: /usr/include/_types/_uint64_t.h
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-tessel_torus.o: /usr/include/sys/_types/_intptr_t.h
747
-tessel_torus.o: /usr/include/sys/_types/_uintptr_t.h
748
-tessel_torus.o: /usr/include/_types/_intmax_t.h
749
-tessel_torus.o: /usr/include/_types/_uintmax_t.h
750
-tessel_torus.o: /usr/include/sys/_types/_timeval.h
751
-tessel_torus.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
752
-tessel_torus.o: /usr/include/sys/_endian.h
753
-tessel_torus.o: /usr/include/libkern/_OSByteOrder.h
754
-tessel_torus.o: /usr/include/libkern/i386/_OSByteOrder.h
755
-tessel_torus.o: /usr/include/alloca.h /usr/include/sys/_types/_ct_rune_t.h
756
-tessel_torus.o: /usr/include/sys/_types/_rune_t.h
757
-tessel_torus.o: /usr/include/sys/_types/_wchar_t.h
758
-tessel_torus.o: /usr/include/machine/types.h /usr/include/i386/types.h
759
-tessel_torus.o: /usr/include/sys/_types/_dev_t.h
760
-tessel_torus.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
761
-tessel_torus.o: /usr/include/sys/_types/_rsize_t.h
762
-tessel_torus.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
763
-tessel_torus.o: /usr/include/secure/_string.h /usr/include/sys/time.h
764
-tessel_torus.o: /usr/include/sys/_types/_fd_def.h
765
-tessel_torus.o: /usr/include/sys/_types/_timespec.h
766
-tessel_torus.o: /usr/include/sys/_types/_time_t.h
767
-tessel_torus.o: /usr/include/sys/_types/_suseconds_t.h
768
-tessel_torus.o: /usr/include/sys/_types/_fd_setsize.h
769
-tessel_torus.o: /usr/include/sys/_types/_fd_set.h
770
-tessel_torus.o: /usr/include/sys/_types/_fd_clr.h
771
-tessel_torus.o: /usr/include/sys/_types/_fd_isset.h
772
-tessel_torus.o: /usr/include/sys/_types/_fd_zero.h
773
-tessel_torus.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h
774
-tessel_torus.o: /usr/include/sys/_types/_clock_t.h /usr/include/sys/_select.h
775
-tessel_torus.o: linalg.h
776
-  
777
-# DEPENDENCIES MUST END AT END OF FILE
778
-# IF YOU PUT STUFF HERE IT WILL GO AWAY
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-# see make depend above
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-  
781
+tessel_torus.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
782
+tessel_torus.o: /usr/include/machine/_types.h /usr/include/math.h
783
+tessel_torus.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
784
+tessel_torus.o: /usr/include/string.h /usr/include/strings.h
785
+tessel_torus.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
786
+tessel_torus.o: /usr/include/sys/types.h /usr/include/machine/endian.h
787
+tessel_torus.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
788
+tessel_torus.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
789
+tessel_torus.o: /usr/include/time.h linalg.h
(-)biology/molden/files/patch-surf_Makefile (+888 lines)
Line 0 Link Here
1
--- surf/Makefile.orig	2015-05-02 19:48:48 UTC
2
+++ surf/Makefile
3
@@ -53,12 +53,12 @@ DEPEND = $(SRCS)
4
 depend: $(DEPEND)
5
 	@ echo making dependencies...
6
 	@ echo ' ' > makedep
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-	@ makedepend $(INCLUDE) -f makedep $(DEPEND)
8
+	@ $(CC) $(INCLUDE) -M $(SRCS) > makedep
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 	@ echo '/^# DO NOT DELETE THIS LINE/+2,$$d' >eddep
10
 	@ echo '$$r makedep' >>eddep
11
 	@ echo 'w' >>eddep
12
 	@ cp Makefile Makefile.bak
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-	@ ex - Makefile < eddep
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+	#@ ex - Makefile < eddep
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 	@ rm eddep makedep 
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 	@ echo '  ' >> Makefile
17
 	@ echo '# DEPENDENCIES MUST END AT END OF FILE' >> Makefile
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@@ -69,672 +69,204 @@ depend: $(DEPEND)
19
 
20
 # DO NOT DELETE THIS LINE -- make depend depends on it.
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- 
23
-# DO NOT DELETE
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-
25
-surf.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
26
-surf.o: /usr/include/sys/_symbol_aliasing.h
27
-surf.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
28
-surf.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
29
-surf.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
30
-surf.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
31
-surf.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
32
-surf.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
33
-surf.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
34
-surf.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
35
-surf.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
36
-surf.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
37
-surf.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
38
-surf.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
39
-surf.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
40
-surf.o: /usr/include/mach/i386/_structs.h
41
-surf.o: /usr/include/sys/_pthread/_pthread_attr_t.h
42
-surf.o: /usr/include/sys/_types/_sigaltstack.h
43
-surf.o: /usr/include/sys/_types/_ucontext.h
44
-surf.o: /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h
45
-surf.o: /usr/include/sys/resource.h /usr/include/stdint.h
46
-surf.o: /usr/include/sys/_types/_int8_t.h /usr/include/sys/_types/_int16_t.h
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-surf.o: /usr/include/sys/_types/_int32_t.h /usr/include/sys/_types/_int64_t.h
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-surf.o: /usr/include/_types/_uint8_t.h /usr/include/_types/_uint16_t.h
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-surf.o: /usr/include/_types/_uint32_t.h /usr/include/_types/_uint64_t.h
50
-surf.o: /usr/include/sys/_types/_intptr_t.h
51
-surf.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
52
-surf.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
53
-surf.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
54
-surf.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
55
-surf.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
56
-surf.o: /usr/include/sys/_types/_ct_rune_t.h
57
-surf.o: /usr/include/sys/_types/_rune_t.h /usr/include/sys/_types/_wchar_t.h
58
-surf.o: /usr/include/machine/types.h /usr/include/i386/types.h
59
-surf.o: /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h
60
-surf.o: /usr/include/string.h /usr/include/sys/_types/_rsize_t.h
61
-surf.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
62
-surf.o: /usr/include/secure/_string.h /usr/include/sys/time.h
63
-surf.o: /usr/include/sys/_types/_fd_def.h /usr/include/sys/_types/_timespec.h
64
-surf.o: /usr/include/sys/_types/_time_t.h
65
-surf.o: /usr/include/sys/_types/_suseconds_t.h
66
-surf.o: /usr/include/sys/_types/_fd_setsize.h
67
-surf.o: /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h
68
-surf.o: /usr/include/sys/_types/_fd_isset.h
69
-surf.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h
70
-surf.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h
71
-surf.o: /usr/include/sys/_select.h linalg.h
72
-io.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
73
-io.o: /usr/include/sys/_symbol_aliasing.h
74
-io.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
75
-io.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
76
-io.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
77
-io.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
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-io.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
79
-io.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
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-io.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
81
-io.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
82
-io.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
83
-io.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
84
-io.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
85
-io.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
86
-io.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
87
-io.o: /usr/include/mach/i386/_structs.h
88
-io.o: /usr/include/sys/_pthread/_pthread_attr_t.h
89
-io.o: /usr/include/sys/_types/_sigaltstack.h
90
-io.o: /usr/include/sys/_types/_ucontext.h /usr/include/sys/_types/_sigset_t.h
91
-io.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
92
-io.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
93
-io.o: /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h
94
-io.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h
95
-io.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h
96
-io.o: /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h
97
-io.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
98
-io.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
99
-io.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
100
-io.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
101
-io.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
102
-io.o: /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h
103
-io.o: /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h
104
-io.o: /usr/include/i386/types.h /usr/include/sys/_types/_dev_t.h
105
-io.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
106
-io.o: /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h
107
-io.o: /usr/include/strings.h /usr/include/secure/_string.h
108
-io.o: /usr/include/sys/time.h /usr/include/sys/_types/_fd_def.h
109
-io.o: /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_time_t.h
110
-io.o: /usr/include/sys/_types/_suseconds_t.h
111
-io.o: /usr/include/sys/_types/_fd_setsize.h /usr/include/sys/_types/_fd_set.h
112
-io.o: /usr/include/sys/_types/_fd_clr.h /usr/include/sys/_types/_fd_isset.h
113
-io.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h
114
-io.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h
115
-io.o: /usr/include/sys/_select.h linalg.h
116
-compute.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
117
-compute.o: /usr/include/sys/_symbol_aliasing.h
118
-compute.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
119
-compute.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
120
-compute.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
121
-compute.o: /usr/include/i386/_types.h
122
-compute.o: /usr/include/sys/_pthread/_pthread_types.h
123
-compute.o: /usr/include/sys/_types/_va_list.h
124
-compute.o: /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h
125
-compute.o: /usr/include/sys/stdio.h /usr/include/sys/_types/_off_t.h
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-compute.o: /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h
127
-compute.o: /usr/include/secure/_common.h /usr/include/math.h
128
-compute.o: /usr/include/stdlib.h /usr/include/sys/wait.h
129
-compute.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
130
-compute.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
131
-compute.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
132
-compute.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
133
-compute.o: /usr/include/mach/i386/_structs.h
134
-compute.o: /usr/include/sys/_pthread/_pthread_attr_t.h
135
-compute.o: /usr/include/sys/_types/_sigaltstack.h
136
-compute.o: /usr/include/sys/_types/_ucontext.h
137
-compute.o: /usr/include/sys/_types/_sigset_t.h
138
-compute.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
139
-compute.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
140
-compute.o: /usr/include/sys/_types/_int16_t.h
141
-compute.o: /usr/include/sys/_types/_int32_t.h
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-compute.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h
143
-compute.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h
144
-compute.o: /usr/include/_types/_uint64_t.h
145
-compute.o: /usr/include/sys/_types/_intptr_t.h
146
-compute.o: /usr/include/sys/_types/_uintptr_t.h
147
-compute.o: /usr/include/_types/_intmax_t.h /usr/include/_types/_uintmax_t.h
148
-compute.o: /usr/include/sys/_types/_timeval.h /usr/include/machine/endian.h
149
-compute.o: /usr/include/i386/endian.h /usr/include/sys/_endian.h
150
-compute.o: /usr/include/libkern/_OSByteOrder.h
151
-compute.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
152
-compute.o: /usr/include/sys/_types/_ct_rune_t.h
153
-compute.o: /usr/include/sys/_types/_rune_t.h
154
-compute.o: /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h
155
-compute.o: /usr/include/i386/types.h /usr/include/sys/_types/_dev_t.h
156
-compute.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
157
-compute.o: /usr/include/sys/_types/_rsize_t.h
158
-compute.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
159
-compute.o: /usr/include/secure/_string.h /usr/include/sys/time.h
160
-compute.o: /usr/include/sys/_types/_fd_def.h
161
-compute.o: /usr/include/sys/_types/_timespec.h
162
-compute.o: /usr/include/sys/_types/_time_t.h
163
-compute.o: /usr/include/sys/_types/_suseconds_t.h
164
-compute.o: /usr/include/sys/_types/_fd_setsize.h
165
-compute.o: /usr/include/sys/_types/_fd_set.h
166
-compute.o: /usr/include/sys/_types/_fd_clr.h
167
-compute.o: /usr/include/sys/_types/_fd_isset.h
168
-compute.o: /usr/include/sys/_types/_fd_zero.h
169
-compute.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h
170
-compute.o: /usr/include/sys/_types/_clock_t.h /usr/include/sys/_select.h
171
-compute.o: linalg.h chull.h dual.h
172
-dual.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
173
-dual.o: /usr/include/sys/_symbol_aliasing.h
174
-dual.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
175
-dual.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
176
-dual.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
177
-dual.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
178
-dual.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
179
-dual.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
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-dual.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
181
-dual.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
182
-dual.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
183
-dual.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
184
-dual.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
185
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719
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
720
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
721
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
722
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
723
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
724
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
725
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
726
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h chull.h \
727
+  dual.h
728
+dual.o: dual.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
729
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
730
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
731
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
732
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
733
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
734
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
735
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
736
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
737
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
738
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
739
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
740
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h dual.h \
741
+  chull.h
742
+utils.o: utils.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
743
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
744
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
745
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
746
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
747
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
748
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
749
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
750
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
751
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
752
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
753
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
754
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h
755
+lp.o: lp.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
756
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
757
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
758
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
759
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
760
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
761
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
762
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
763
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
764
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
765
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
766
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
767
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h
768
+chull.o: chull.c surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h \
769
+  /usr/include/sys/_null.h /usr/include/sys/_types.h \
770
+  /usr/include/machine/_types.h /usr/include/x86/_types.h \
771
+  /usr/include/machine/_limits.h /usr/include/x86/_limits.h \
772
+  /usr/include/math.h /usr/include/stdlib.h /usr/include/string.h \
773
+  /usr/include/strings.h /usr/include/xlocale/_strings.h \
774
+  /usr/include/xlocale/_string.h /usr/include/sys/time.h \
775
+  /usr/include/sys/_timeval.h /usr/include/sys/types.h \
776
+  /usr/include/machine/endian.h /usr/include/x86/endian.h \
777
+  /usr/include/sys/_pthreadtypes.h /usr/include/sys/_stdint.h \
778
+  /usr/include/sys/select.h /usr/include/sys/_sigset.h \
779
+  /usr/include/sys/timespec.h /usr/include/sys/_timespec.h \
780
+  /usr/include/time.h /usr/include/xlocale/_time.h linalg.h chull.h
781
+tessel_cases.o: tessel_cases.c surf.h /usr/include/stdio.h \
782
+  /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
783
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
784
+  /usr/include/x86/_types.h /usr/include/machine/_limits.h \
785
+  /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
786
+  /usr/include/string.h /usr/include/strings.h \
787
+  /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
788
+  /usr/include/sys/time.h /usr/include/sys/_timeval.h \
789
+  /usr/include/sys/types.h /usr/include/machine/endian.h \
790
+  /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
791
+  /usr/include/sys/_stdint.h /usr/include/sys/select.h \
792
+  /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
793
+  /usr/include/sys/_timespec.h /usr/include/time.h \
794
+  /usr/include/xlocale/_time.h linalg.h dual.h
795
+tessel_patches.o: tessel_patches.c surf.h /usr/include/stdio.h \
796
+  /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
797
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
798
+  /usr/include/x86/_types.h /usr/include/machine/_limits.h \
799
+  /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
800
+  /usr/include/string.h /usr/include/strings.h \
801
+  /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
802
+  /usr/include/sys/time.h /usr/include/sys/_timeval.h \
803
+  /usr/include/sys/types.h /usr/include/machine/endian.h \
804
+  /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
805
+  /usr/include/sys/_stdint.h /usr/include/sys/select.h \
806
+  /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
807
+  /usr/include/sys/_timespec.h /usr/include/time.h \
808
+  /usr/include/xlocale/_time.h linalg.h
809
+tessel_convex.o: tessel_convex.c surf.h /usr/include/stdio.h \
810
+  /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
811
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
812
+  /usr/include/x86/_types.h /usr/include/machine/_limits.h \
813
+  /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
814
+  /usr/include/string.h /usr/include/strings.h \
815
+  /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
816
+  /usr/include/sys/time.h /usr/include/sys/_timeval.h \
817
+  /usr/include/sys/types.h /usr/include/machine/endian.h \
818
+  /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
819
+  /usr/include/sys/_stdint.h /usr/include/sys/select.h \
820
+  /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
821
+  /usr/include/sys/_timespec.h /usr/include/time.h \
822
+  /usr/include/xlocale/_time.h linalg.h
823
+tessel_concave.o: tessel_concave.c surf.h /usr/include/stdio.h \
824
+  /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
825
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
826
+  /usr/include/x86/_types.h /usr/include/machine/_limits.h \
827
+  /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
828
+  /usr/include/string.h /usr/include/strings.h \
829
+  /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
830
+  /usr/include/sys/time.h /usr/include/sys/_timeval.h \
831
+  /usr/include/sys/types.h /usr/include/machine/endian.h \
832
+  /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
833
+  /usr/include/sys/_stdint.h /usr/include/sys/select.h \
834
+  /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
835
+  /usr/include/sys/_timespec.h /usr/include/time.h \
836
+  /usr/include/xlocale/_time.h linalg.h
837
+tessel_torus.o: tessel_torus.c surf.h /usr/include/stdio.h \
838
+  /usr/include/sys/cdefs.h /usr/include/sys/_null.h \
839
+  /usr/include/sys/_types.h /usr/include/machine/_types.h \
840
+  /usr/include/x86/_types.h /usr/include/machine/_limits.h \
841
+  /usr/include/x86/_limits.h /usr/include/math.h /usr/include/stdlib.h \
842
+  /usr/include/string.h /usr/include/strings.h \
843
+  /usr/include/xlocale/_strings.h /usr/include/xlocale/_string.h \
844
+  /usr/include/sys/time.h /usr/include/sys/_timeval.h \
845
+  /usr/include/sys/types.h /usr/include/machine/endian.h \
846
+  /usr/include/x86/endian.h /usr/include/sys/_pthreadtypes.h \
847
+  /usr/include/sys/_stdint.h /usr/include/sys/select.h \
848
+  /usr/include/sys/_sigset.h /usr/include/sys/timespec.h \
849
+  /usr/include/sys/_timespec.h /usr/include/time.h \
850
+  /usr/include/xlocale/_time.h linalg.h
851
+  
852
+# DEPENDENCIES MUST END AT END OF FILE
853
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
854
+# see make depend above
855
+  
856
+  
857
+# DEPENDENCIES MUST END AT END OF FILE
858
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
859
+# see make depend above
860
+  
861
+  
862
+# DEPENDENCIES MUST END AT END OF FILE
863
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
864
+# see make depend above
865
+  
866
+  
867
+# DEPENDENCIES MUST END AT END OF FILE
868
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
869
+# see make depend above
870
+  
871
+  
872
+# DEPENDENCIES MUST END AT END OF FILE
873
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
874
+# see make depend above
875
+  
876
+  
877
+# DEPENDENCIES MUST END AT END OF FILE
878
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
879
+# see make depend above
880
+  
881
+  
882
+# DEPENDENCIES MUST END AT END OF FILE
883
+# IF YOU PUT STUFF HERE IT WILL GO AWAY
884
+# see make depend above
885
+  
886
   
887
 # DEPENDENCIES MUST END AT END OF FILE
888
 # IF YOU PUT STUFF HERE IT WILL GO AWAY
(-)biology/molden/files/patch-surf_utils.c (+10 lines)
Line 0 Link Here
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];
(-)biology/molden/files/patch-xwin.c (-32 lines)
Lines 1-32 Link Here
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;
(-)biology/molden/pkg-descr (-13 / +23 lines)
Lines 1-14 Link Here
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/

Return to bug 238858