diff options
author | miwi <miwi@FreeBSD.org> | 2008-04-19 17:56:05 +0000 |
---|---|---|
committer | miwi <miwi@FreeBSD.org> | 2008-04-19 17:56:05 +0000 |
commit | bce9b81f9d6099820f3839d7809d6b08c1d2ae7b (patch) | |
tree | f5dd7c3a8dbebad79bdb5e844aeb69c59a9fd12c /biology | |
parent | 2eea5f1d2e44418020f8f4db08d40bea6915b6e8 (diff) | |
download | FreeBSD-ports-bce9b81f9d6099820f3839d7809d6b08c1d2ae7b.zip FreeBSD-ports-bce9b81f9d6099820f3839d7809d6b08c1d2ae7b.tar.gz |
- Remove unneeded dependency from gtk12/gtk20 [1]
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+
Thanks to all Helpers:
Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
ehaupt, nox, itetcu, flz, pav
PR: 116263
Tested on: pointyhat
Approved by: portmgr (pav)
Diffstat (limited to 'biology')
-rw-r--r-- | biology/L-Breeder/Makefile | 6 | ||||
-rw-r--r-- | biology/L-Breeder/files/patch-Unix-Makefile | 4 | ||||
-rw-r--r-- | biology/garlic/Makefile | 3 | ||||
-rw-r--r-- | biology/garlic/files/patch-Makefile | 4 | ||||
-rw-r--r-- | biology/gperiodic/Makefile | 2 | ||||
-rw-r--r-- | biology/kinemage/files/patch-Makefile | 4 | ||||
-rw-r--r-- | biology/molden/Makefile | 7 | ||||
-rw-r--r-- | biology/molden/distinfo | 6 | ||||
-rw-r--r-- | biology/molden/files/patch-aa | 8 | ||||
-rw-r--r-- | biology/ncbi-toolkit/Makefile | 2 | ||||
-rw-r--r-- | biology/ortep3/Makefile | 2 | ||||
-rw-r--r-- | biology/phylip/Makefile | 8 | ||||
-rw-r--r-- | biology/platon/Makefile | 6 | ||||
-rw-r--r-- | biology/platon/files/Makefile | 4 | ||||
-rw-r--r-- | biology/protomol/Makefile | 4 | ||||
-rw-r--r-- | biology/rasmol/Makefile | 3 | ||||
-rw-r--r-- | biology/seaview/files/patch-Makefile | 4 | ||||
-rw-r--r-- | biology/tinker/Makefile | 7 | ||||
-rw-r--r-- | biology/xdrawchem/Makefile | 9 |
19 files changed, 43 insertions, 50 deletions
diff --git a/biology/L-Breeder/Makefile b/biology/L-Breeder/Makefile index e83e6a0..c13374d 100644 --- a/biology/L-Breeder/Makefile +++ b/biology/L-Breeder/Makefile @@ -8,7 +8,7 @@ PORTNAME= LBreeder PORTVERSION= 1.0 -PORTREVISION= 9 +PORTREVISION= 10 CATEGORIES= biology MASTER_SITES= http://www.simonyi.ox.ac.uk/dawkins/software/yan/L-Breeder/ DISTNAME= ${PORTNAME}-source @@ -16,13 +16,11 @@ DISTNAME= ${PORTNAME}-source MAINTAINER= dyeske@gmail.com COMMENT= Allows you to display and breed L-system forms -LIB_DEPENDS= glut.4:${PORTSDIR}/graphics/libglut - NO_WRKSUBDIR= yes BUILD_WRKSRC= ${WRKSRC}/Unix USE_ZIP= yes -USE_GL= yes +USE_GL= glut USE_GMAKE= yes USE_WX= 2.4 diff --git a/biology/L-Breeder/files/patch-Unix-Makefile b/biology/L-Breeder/files/patch-Unix-Makefile index de7b0dd..2c59818 100644 --- a/biology/L-Breeder/files/patch-Unix-Makefile +++ b/biology/L-Breeder/files/patch-Unix-Makefile @@ -2,13 +2,13 @@ +++ Unix/Makefile Wed Dec 7 07:46:56 2005 @@ -1,9 +1,10 @@ src=../src/ -+C_FLAGS= -I$(X11BASE)/include -I$(LOCALBASE)/include ++C_FLAGS= -I$(LOCALBASE)/include .PHONY : clean all all : probability.o mutprobs.o trackball.o Lparse.o GL_Ldraw.o Lline.o Lsys.o GLUT_LBreeder.o - g++ probability.o mutprobs.o trackball.o Lparse.o GL_Ldraw.o Lline.o Lsys.o GLUT_LBreeder.o ${src}main.cpp -lGL -lGLU -lglut -o LBreeder-${OSTYPE} -+ g++ probability.o mutprobs.o trackball.o Lparse.o GL_Ldraw.o Lline.o Lsys.o GLUT_LBreeder.o ${src}main.cpp -L$(X11BASE)/lib -L$(LOCALBASE)/lib -lGL -lGLU -lglut -o LBreeder ++ g++ probability.o mutprobs.o trackball.o Lparse.o GL_Ldraw.o Lline.o Lsys.o GLUT_LBreeder.o ${src}main.cpp -L$(LOCALBASE)/lib -lGL -lGLU -lglut -o LBreeder GLUT_LBreeder.o : ${src}GLUT_LBreeder.cpp ${src}GLUT_LBreeder.h g++ -c ${src}GLUT_LBreeder.cpp ${C_FLAGS} diff --git a/biology/garlic/Makefile b/biology/garlic/Makefile index 497c008..b3e2654 100644 --- a/biology/garlic/Makefile +++ b/biology/garlic/Makefile @@ -31,8 +31,7 @@ CFLAGS+= -mfancy-math-387 -mpreferred-stack-boundary=3 .endif post-patch: - @${REINPLACE_CMD} -e 's|%%X11BASE%%|${X11BASE}|g ; \ - s|%%LOCALBASE%%|${LOCALBASE}|g ;\ + @${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g ;\ s|%%CC%%|${CC}|g ; \ s|%%CFLAGS%%|${CFLAGS}|g' ${WRKSRC}/Makefile .if !defined(WITH_OPTIMIZED_FLAGS) diff --git a/biology/garlic/files/patch-Makefile b/biology/garlic/files/patch-Makefile index 63eb7c7..b4d5e99 100644 --- a/biology/garlic/files/patch-Makefile +++ b/biology/garlic/files/patch-Makefile @@ -6,7 +6,7 @@ #CCOPT = -O -CCOPT = -O3 -+CCOPT = %%CFLAGS%% -I%%LOCALBASE%%/include -I%%X11BASE%%/include ++CCOPT = %%CFLAGS%% -I%%LOCALBASE%%/include #CCOPT = -O3 -g3 #CCOPT = -ansi -pedantic -g3 #CCOPT = -ansi -pedantic -O -Wall -Wstrict-prototypes -g3 @@ -14,7 +14,7 @@ HEADERS = defines.h typedefs.h -LIBPATH = -L/usr/X11R6/lib -+LIBPATH = -L%%X11BASE%%/lib ++LIBPATH = -L%%LOCALBASE%%/lib LINKOPT = -lX11 -lm diff --git a/biology/gperiodic/Makefile b/biology/gperiodic/Makefile index 792bfed..51777aa 100644 --- a/biology/gperiodic/Makefile +++ b/biology/gperiodic/Makefile @@ -7,13 +7,13 @@ PORTNAME= gperiodic PORTVERSION= 2.0.10 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= http://www.frantz.fi/software/ MAINTAINER= ports@FreeBSD.org COMMENT= Displays a periodic table of the elements -USE_XLIB= yes USE_GNOME= gtk20 USE_GETTEXT= yes diff --git a/biology/kinemage/files/patch-Makefile b/biology/kinemage/files/patch-Makefile index 4a4b60d..deb8db2 100644 --- a/biology/kinemage/files/patch-Makefile +++ b/biology/kinemage/files/patch-Makefile @@ -5,7 +5,7 @@ # for Linux, try: # CFLAGS = -I/usr/X11R6/LessTif/Motif2.0/include -CFLAGS = -g -I/usr/X11R6/LessTif/Motif2.0/include -+CFLAGS += -I$(X11BASE)/include ++CFLAGS += -I$(LOCALBASE)/include # for SGI use: # CFLAGS = -I/usr/include/X11 # CFLAGS = -g -I/usr/include/X11 @@ -16,7 +16,7 @@ -LIBS = -L/usr/X11R6/LessTif/Motif2.0/lib -L/usr/X11R6/lib -lXm -lXt -lX11 +# LIBS = -L/usr/X11R6/LessTif/Motif2.0/lib -L/usr/X11R6/lib -lXm -lXt -lX11 +# For FreeBSD: -+LIBS = -L$(X11BASE)/lib -lXm -lXt -lX11 ++LIBS = -L$(LOCALBASE)/lib -lXm -lXt -lX11 # ------------------------------------------------------------------------ diff --git a/biology/molden/Makefile b/biology/molden/Makefile index d3ae859..137ecf3 100644 --- a/biology/molden/Makefile +++ b/biology/molden/Makefile @@ -7,7 +7,7 @@ PORTNAME= molden PORTVERSION= 4.5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= ftp://ftp.cmbi.kun.nl/pub/molgraph/molden/ DISTNAME= ${PORTNAME}${PORTVERSION} @@ -18,9 +18,8 @@ EXTRACT_ONLY= ${PORTNAME}${PORTVERSION}.tar.Z MAINTAINER= ports@FreeBSD.org COMMENT= Display molecular orbitals and electron densities in 2D and 3D -LIB_DEPENDS= glut.4:${PORTSDIR}/graphics/libglut - -USE_XLIB= yes +USE_XORG= x11 xmu +USE_GL= glut RESTRICTED= free for academic, non profit usage; do not re-distribute source and executable. MAKEFILE= ${WRKSRC}/makefile diff --git a/biology/molden/distinfo b/biology/molden/distinfo index 7268a4f..3a06d43 100644 --- a/biology/molden/distinfo +++ b/biology/molden/distinfo @@ -1,3 +1,3 @@ -MD5 (molden-4.5_1/molden4.5.tar.Z) = 2706a205de011f2dca042f8c7fe95834 -SHA256 (molden-4.5_1/molden4.5.tar.Z) = 84b6905ec786bde9af8bfa6439b0c066b65a98028ffaf1ebc543e58b31fe2ca7 -SIZE (molden-4.5_1/molden4.5.tar.Z) = 3605279 +MD5 (molden-4.5_2/molden4.5.tar.Z) = 2706a205de011f2dca042f8c7fe95834 +SHA256 (molden-4.5_2/molden4.5.tar.Z) = 84b6905ec786bde9af8bfa6439b0c066b65a98028ffaf1ebc543e58b31fe2ca7 +SIZE (molden-4.5_2/molden4.5.tar.Z) = 3605279 diff --git a/biology/molden/files/patch-aa b/biology/molden/files/patch-aa index d8a7295..82a56ab 100644 --- a/biology/molden/files/patch-aa +++ b/biology/molden/files/patch-aa @@ -8,12 +8,12 @@ +#CC = cc LIBS = -lX11 -lm -LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm -+LIBSG = -L${X11BASE}/lib -lGLU -lGL -lXmu -lX11 -lm ++LIBSG = -L${LOCALBASE}/lib -lGLU -lGL -lXmu -lX11 -lm + +### +# FreeBSD +#CC = gcc -+CFLAGS += -c -DDOBACK -DHASTIMER -I${X11BASE}/include ++CFLAGS += -c -DDOBACK -DHASTIMER -I${LOCALBASE}/include +#FC = f77 +.if ${MACHINE_ARCH} == i386 +FFLAGS += -malign-double @@ -24,7 +24,7 @@ +.else +FFLAGS += #-Wno-globals -fno-globals +.endif -+LIBS = -L${X11BASE}/lib -lX11 -lm ++LIBS = -L${LOCALBASE}/lib -lX11 -lm +LDR = ${FC} +### @@ -52,7 +52,7 @@ # (make gmolden) # -LIBSOGL = -lglut -lGLU -lGL -lXmu -lX11 -lm -+LIBSOGL = -L${X11BASE}/lib -lglut -lGLU -lGL -lXmu -lX11 -lm ++LIBSOGL = -L${LOCALBASE}/lib -lglut -lGLU -lGL -lXmu -lX11 -lm # # on linux : # diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile index ba50ca9..b21507f 100644 --- a/biology/ncbi-toolkit/Makefile +++ b/biology/ncbi-toolkit/Makefile @@ -53,7 +53,7 @@ MLINKS= blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \ blast.1 seedtop.1 post-patch: - @${REINPLACE_CMD} -e 's,/usr/X11R6,${X11BASE},g' \ + @${REINPLACE_CMD} -e 's,/usr/X11R6,${LOCALBASE},g' \ ${WRKSRC}/make/makedis.csh \ ${WRKSRC}/platform/freebsd.ncbi.mk diff --git a/biology/ortep3/Makefile b/biology/ortep3/Makefile index 39b8b35..5741bd7 100644 --- a/biology/ortep3/Makefile +++ b/biology/ortep3/Makefile @@ -27,7 +27,7 @@ MAKE_ARGS= LFLAGS="${LFLAGS}" .if defined(WITH_PGPLOT) EXTRA_PATCHES= ${FILESDIR}/extra-patch-aa -LFLAGS= -L${LOCALBASE}/lib -lpgplot -L${X11BASE}/lib -lX11 +LFLAGS= -L${LOCALBASE}/lib -lpgplot -lX11 .endif post-extract: diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile index 9e21481..15794e1 100644 --- a/biology/phylip/Makefile +++ b/biology/phylip/Makefile @@ -7,7 +7,7 @@ PORTNAME= phylip PORTVERSION= 3.66 -PORTREVISION= 1 +PORTREVISION= 2 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/ \ @@ -19,12 +19,12 @@ MAINTAINER= ports@FreeBSD.org COMMENT= A Phylogeny Inference Package WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION} -USE_XLIB= yes +USE_XORG= x11 xaw xt BUILD_WRKSRC= ${WRKSRC}/src MAKE_ARGS= CC="${CC} ${CFLAGS}" \ - DC="${CC} -DX -I${X11BASE}/include ${CFLAGS}" \ - DLIBS="-L${X11BASE}/lib -lX11 -lXaw -lXt" + DC="${CC} -DX -I${LOCALBASE}/include ${CFLAGS}" \ + DLIBS="-L${LOCALBASE}/lib -lX11 -lXaw -lXt" PORTDOCS= * diff --git a/biology/platon/Makefile b/biology/platon/Makefile index 6f6cd35..97aa9f5 100644 --- a/biology/platon/Makefile +++ b/biology/platon/Makefile @@ -7,7 +7,7 @@ PORTNAME= platon PORTVERSION= 2007.01.09 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= ftp://xraysoft.chem.uu.nl/pub/unix/ DISTNAME= platon @@ -20,7 +20,7 @@ COMMENT= Tool for viewing molecular/crystallographic structures # There is a charge of US$ 5000 for commercial users. RESTRICTED= free for academic, US$ 5000 for commercial users -USE_XLIB= yes +USE_XORG= x11 USE_FORTRAN= yes # This port only has snapshot archive @@ -43,7 +43,7 @@ pre-patch: post-patch: ${CP} ${FILESDIR}/Makefile ${WRKSRC}/Makefile - ${REINPLACE_CMD} -e "s+%%X11BASE%%+${X11BASE}+" ${WRKSRC}/Makefile + ${REINPLACE_CMD} -e "s+%%LOCALBASE%%+${LOCALBASE}+" ${WRKSRC}/Makefile pre-install: ${STRIP_CMD} ${WRKDIR}/${DISTNAME}/platon diff --git a/biology/platon/files/Makefile b/biology/platon/files/Makefile index 4f6ca0b..2cda199 100644 --- a/biology/platon/files/Makefile +++ b/biology/platon/files/Makefile @@ -9,8 +9,8 @@ FOPT= ${FFLAGS} .else FOPT= ${FFLAGS} -Nx800 -NL400 -Nn802 .endif -COPT= ${CFLAGS} -I%%X11BASE%%/include -LOPT= -L%%X11BASE%%/lib -lX11 +COPT= ${CFLAGS} -I%%LOCALBASE%%/include +LOPT= -L%%LOCALBASE%%/lib -lX11 all: ${OBJS} ${FC} -o ${TARGET} ${OBJS} ${LOPT} diff --git a/biology/protomol/Makefile b/biology/protomol/Makefile index 45c82c0..d32a151 100644 --- a/biology/protomol/Makefile +++ b/biology/protomol/Makefile @@ -26,8 +26,8 @@ USE_GCC= 3.4+ # Hack to cure a misbehavior of the configure script CONFIGURE_ARGS+= --without-irix_mipspro_mpi -CPPFLAGS+= -I${LOCALBASE}/include -I${X11BASE}/include -CXXFLAGS+= -L${LOCALBASE}/lib -L${X11BASE}/lib +CPPFLAGS+= -I${LOCALBASE}/include +CXXFLAGS+= -L${LOCALBASE}/lib CONFIGURE_ENV+= CPPFLAGS="${CPPFLAGS}" CXXFLAGS="${CXXFLAGS}" diff --git a/biology/rasmol/Makefile b/biology/rasmol/Makefile index bea4f4e..40d7d25 100644 --- a/biology/rasmol/Makefile +++ b/biology/rasmol/Makefile @@ -7,7 +7,7 @@ PORTNAME= rasmol PORTVERSION= 2.7.2.1.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= ftp://ftp.bernstein-plus-sons.com/software/ DISTNAME= RasMol_${PORTVERSION} @@ -17,7 +17,6 @@ COMMENT= Fast Molecular Visualization Program WRKSRC= ${WRKDIR}/RasMol_${PORTVERSION}/src -USE_X_PREFIX= yes USE_IMAKE= yes MANCOMPRESSED= no XFREE86_HTML_MAN= no diff --git a/biology/seaview/files/patch-Makefile b/biology/seaview/files/patch-Makefile index a51cd4c..78eec35 100644 --- a/biology/seaview/files/patch-Makefile +++ b/biology/seaview/files/patch-Makefile @@ -7,7 +7,7 @@ CXX = g++ -CFLAGS = -Dunix -U__APPLE__ -c $(OPT) -I$(FLTK) -I$(PDF) -I$(X11)/include -+CFLAGS+= -Dunix -U__APPLE__ -c $(OPT) -I$(X11BASE)/include -I$(LOCALBASE)/include ++CFLAGS+= -Dunix -U__APPLE__ -c $(OPT) -I$(LOCALBASE)/include OBJECTS = seaview.o pdf.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o @@ -19,7 +19,7 @@ - -L$(X11)/lib -lX11 -lm + $(CXX) -o $@ $(OBJECTS) -L$(LOCALBASE)/lib -lfltk \ + -Xlinker -Bstatic -lpdf -Xlinker -Bdynamic \ -+ -L$(X11BASE)/lib -lX11 -lm ++ -L$(LOCALBASE)/lib -lX11 -lm strip $@ diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile index 5b94878..c08697f 100644 --- a/biology/tinker/Makefile +++ b/biology/tinker/Makefile @@ -7,7 +7,7 @@ PORTNAME= tinker PORTVERSION= 4.2.20040908 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GENTOO} \ ftp://dasher.wustl.edu/pub/ @@ -18,8 +18,6 @@ DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= A general purpose molecular modelling package -BUILD_DEPENDS= imake:${X_IMAKE_PORT} - MAKE_ENV+= HAVE_G2C=yes INSTALL_PROGRAM="${INSTALL_PROGRAM}" WRKSRC= ${WRKDIR}/tinker/source @@ -46,7 +44,8 @@ FFLAGS+= -mfancy-math-387 -malign-double .endif .if defined(WITH_VIEWER) -USE_XLIB= yes +BUILD_DEPENDS+= imake:${PORTSDIR}/devel/imake +USE_XORG= x11 xext xi PLIST_SUB+= WITH_VIEWER="" post-build: @${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/build_viewer diff --git a/biology/xdrawchem/Makefile b/biology/xdrawchem/Makefile index cff472c..a69783b 100644 --- a/biology/xdrawchem/Makefile +++ b/biology/xdrawchem/Makefile @@ -9,8 +9,7 @@ PORTNAME= xdrawchem PORTVERSION= 1.9.9 PORTREVISION= 4 CATEGORIES= biology -MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} -MASTER_SITE_SUBDIR= xdrawchem +MASTER_SITES= SF MAINTAINER= hemi@puresimplicity.net COMMENT= Chemical drawing program @@ -23,9 +22,9 @@ USE_QT_VER= 3 CONFIGURE_TARGET= --build=${ARCH}-portbld-freebsd${OSREL} -CONFIGURE_ENV= QTINCDIR="${X11BASE}/include" \ - QTLIBDIR="${X11BASE}/lib" \ - LDFLAGS="${LDFLAGS} -lm" +CONFIGURE_ENV= QTINCDIR="${LOCALBASE}/include" \ + QTLIBDIR="${LOCALBASE}/lib" \ + LDFLAGS="${LDFLAGS} -lm" MAKE_ARGS+= LDFLAGS+="-lqt-mt ${PTHREAD_LIBS}" |