19 files changed, 43 insertions, 50 deletions

diff --git a/biology/L-Breeder/Makefile b/biology/L-Breeder/Makefile
index e83e6a0d2058..c13374d94e86 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 de7b0dd89fed..2c598185d3dd 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 497c008bfed8..b3e26548fe0f 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 63eb7c755204..b4d5e99172a9 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 792bfedd3b37..51777aa0e6d1 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 4a4b60dd604b..deb8db205d83 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 d3ae85919f7c..137ecf323acb 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=	${WRKSRC}/makefile
diff --git a/biology/molden/distinfo b/biology/molden/distinfo
index 7268a4f6579c..3a06d430cc7c 100644
--- a/biology/molden/distinfo
+++ b/biology/molden/distinfo
@@ -1,3 +1,3 @@
-MD5 (molden-4.5_1/molden4.5.tar.Z) = 2706a205de011f2dca042f8c7fe95834
-SHA256 (molden-4.5_1/molden4.5.tar.Z) = 84b6905ec786bde9af8bfa6439b0c066b65a98028ffaf1ebc543e58b31fe2ca7
-SIZE (molden-4.5_1/molden4.5.tar.Z) = 3605279
+MD5 (molden-4.5_2/molden4.5.tar.Z) = 2706a205de011f2dca042f8c7fe95834
+SHA256 (molden-4.5_2/molden4.5.tar.Z) = 84b6905ec786bde9af8bfa6439b0c066b65a98028ffaf1ebc543e58b31fe2ca7
+SIZE (molden-4.5_2/molden4.5.tar.Z) = 3605279
diff --git a/biology/molden/files/patch-aa b/biology/molden/files/patch-aa
index d8a7295d1b34..82a56ab159df 100644
--- a/biology/molden/files/patch-aa
+++ b/biology/molden/files/patch-aa
@@ -8,12 +8,12 @@
 +#CC = cc
  LIBS =  -lX11 -lm
 -LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm
-+LIBSG = -L${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 ba50ca954b8b..b21507f81a0d 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 39b8b358c240..5741bd7d749d 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 9e21481d7033..15794e10adf1 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 6f6cd353b948..97aa9f5139e0 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 4f6ca0bfb445..2cda1996ee01 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 45c82c0d0492..d32a1516ebd2 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 bea4f4e3a1b6..40d7d256695e 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 a51cd4c3f54c..78eec35f57fb 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 5b948784bdbf..c08697fdb906 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 cff472c0e830..a69783b26ee2 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}"