24 files changed, 46 insertions, 48 deletions

diff --git a/science/afni/Makefile b/science/afni/Makefile
index d1fef2283320..435110c25e54 100644
--- a/science/afni/Makefile
+++ b/science/afni/Makefile
@@ -74,7 +74,7 @@ X11R6_FILES=	coxplot/Makefile \
 post-extract:
 	@${CP} -f ${FILESDIR}/Makefile.FreeBSD_PORT ${WRKSRC}
 .for f in ${X11R6_FILES}
-	@${REINPLACE_CMD} -e 's|/usr/X11R6|$${X11BASE}|g' ${WRKSRC}/${f}
+	@${REINPLACE_CMD} -e 's|/usr/X11R6|$${LOCALBASE}|g' ${WRKSRC}/${f}
 .endfor
 	@${REINPLACE_CMD} -e 's|AFNI_2007_05_29_1644|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h
 	@${CP} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${WRKDIR}
diff --git a/science/afni/files/Makefile.FreeBSD_PORT b/science/afni/files/Makefile.FreeBSD_PORT
index fbd29dd9a198..55f96ce90860 100644
--- a/science/afni/files/Makefile.FreeBSD_PORT
+++ b/science/afni/files/Makefile.FreeBSD_PORT
@@ -62,15 +62,15 @@ CCMIN  = ${CC}
 CCD    = ${CC} ${CCDEBS}
 CCSVD  = ${CC} -O0
 
-IFLAGS = -I. -I${X11BASE}/include -I/usr/local/include
-LFLAGS = -s -L. -L${X11BASE}/lib
+IFLAGS = -I. -I${LOCALBASE}/include -I/usr/local/include
+LFLAGS = -s -L. -L${LOCALBASE}/lib
 
 MAKE   = gmake
 
 PLUGIN_SUFFIX = so
 PLUGIN_LFLAGS = -shared
 PLUGIN_CC     = ${CC}
-PLFLAGS       = -s -rdynamic -L. -L${X11BASE}/lib
+PLFLAGS       = -s -rdynamic -L. -L${LOCALBASE}/lib
 
 AR     = /usr/bin/ar
 RANLIB = /usr/bin/ranlib
@@ -94,8 +94,8 @@ LLIBS  = -lmri -lXm -lXp -lXpm -lXext -lXmu -lXt -lX11 -lm $(LZLIB)
 
 # vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
 # For suma (NO STATIC LINKING OF GL libs)
-SUMA_INCLUDE_PATH = -I${X11BASE}/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src 
-SUMA_LINK_PATH = -L/usr/lib -L${X11BASE}/lib -L../
+SUMA_INCLUDE_PATH = -I${LOCALBASE}/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src 
+SUMA_LINK_PATH = -L/usr/lib -L${LOCALBASE}/lib -L../
 #use -lGLw if you have libGLw.a or libGLw.so* or 
 #  -lMesaGLw if you have Mesa's version (libMesaGLw*) of libGLw
 SUMA_LINK_LIB = -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm $(LZLIB)
diff --git a/science/buddy/Makefile b/science/buddy/Makefile
index f909f6138523..2f2d235f3b04 100644
--- a/science/buddy/Makefile
+++ b/science/buddy/Makefile
@@ -19,7 +19,7 @@ USE_AUTOTOOLS=	libtool:15
 GNU_CONFIGURE=	yes
 CONFIGURE_TARGET=	--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
 USE_GMAKE=	yes
-INSTALLS_SHLIB=	yes
+USE_LDCONFIG=	yes
 
 DOCS=		doc/bddnotes.ps doc/buddy.ps doc/tech.txt README AUTHORS
 
diff --git a/science/dtiquery/files/patch-Makefile.definitions b/science/dtiquery/files/patch-Makefile.definitions
index 593cefc32b3f..80334a3527fc 100644
--- a/science/dtiquery/files/patch-Makefile.definitions
+++ b/science/dtiquery/files/patch-Makefile.definitions
@@ -14,7 +14,7 @@
  ifdef FreeBSD
  
 -WX_CONFIG_BIN		?= /usr/X11R6/bin/wxgtk2-2.8-config
-+WX_CONFIG_BIN		?= ${X11BASE}/bin/wxgtk2-2.8-config
++WX_CONFIG_BIN		?= ${LOCALBASE}/bin/wxgtk2-2.8-config
  VTK_INCLUDE_PATHS	?= -I/usr/local/include/vtk-5.0/
  VTK_LIB_PATHS		?= -L/usr/local/lib/vtk-5.0/
  WX_INCLUDE_PATHS	?= `$(WX_CONFIG_BIN) --cxxflags`
@@ -27,7 +27,7 @@
  JAMA_INCLUDE_PATH	?= -I/usr/local/include/
  ZLIB_INCLUDE_PATH	?= -I/usr/include
 -SYS_INCLUDE_PATHS	?= -I/usr/include -I/usr/X11R6/include -I/usr/local/include/gtk-2.0 -I/usr/X11R6/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I/usr/X11R6/include/pango-1.0 -I/usr/local/include/atk-1.0 
-+SYS_INCLUDE_PATHS	?= -I/usr/include -I${X11BASE}/include -I/usr/local/include/gtk-2.0 -I${X11BASE}/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I${X11BASE}/include/pango-1.0 -I/usr/local/include/atk-1.0 
++SYS_INCLUDE_PATHS	?= -I/usr/include -I${LOCALBASE}/include -I/usr/local/include/gtk-2.0 -I${LOCALBASE}/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I${LOCALBASE}/include/pango-1.0 -I/usr/local/include/atk-1.0 
 +SYS_CXXFLAGS 		?= -g
  SYS_LIBS		?= -L/usr/local/lib -lXt -lGL -lpng
  
diff --git a/science/felt/Makefile b/science/felt/Makefile
index 6c0fd074c7b1..3052f371a1d9 100644
--- a/science/felt/Makefile
+++ b/science/felt/Makefile
@@ -22,7 +22,7 @@ WRKSRC=		${WRKDIR}/FElt-${PORTVERSION}
 USE_MOTIF=	yes
 USE_GL=		glu
 GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--x-defaults=${X11BASE}/lib/X11/app-defaults
+CONFIGURE_ARGS=	--x-defaults=${LOCALBASE}/lib/X11/app-defaults
 CFLAGS+=	-D__GLX_MOTIF
 
 MAN1=		burlap.1 corduroy.1 felt.1 patchwork.1 velvet.1 yardstick.1
diff --git a/science/flounder/Makefile b/science/flounder/Makefile
index 4c7d453f403c..078f5a928eed 100644
--- a/science/flounder/Makefile
+++ b/science/flounder/Makefile
@@ -22,8 +22,8 @@ LIB_DEPENDS=	fltk:${PORTSDIR}/x11-toolkits/fltk \
 		glut.4:${PORTSDIR}/graphics/libglut
 
 GNU_CONFIGURE=	yes
-CONFIGURE_ENV=	CPPFLAGS="-I${LOCALBASE}/include -I${X11BASE}/include" \
-		LDFLAGS="-L${LOCALBASE}/lib -L${X11BASE}/lib ${PTHREAD_LIBS} -lstdc++"
+CONFIGURE_ENV=	CPPFLAGS="-I${LOCALBASE}/include" \
+		LDFLAGS="-L${LOCALBASE}/lib ${PTHREAD_LIBS} -lstdc++"
 USE_GMAKE=	yes
 
 .if !defined(WITHOUT_AVIFILE)
diff --git a/science/gnudatalanguage/Makefile b/science/gnudatalanguage/Makefile
index b01dda6c7125..df7af8c782f3 100644
--- a/science/gnudatalanguage/Makefile
+++ b/science/gnudatalanguage/Makefile
@@ -37,8 +37,8 @@ LIB_DEPENDS+=	plplotd.11:${PORTSDIR}/math/plplot	\
 
 USE_AUTOTOOLS=	libtool:15
 CONFIGURE_TARGET=	--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
-CONFIGURE_ENV=	CPPFLAGS="${CFLAGS} ${PTHREAD_CFLAGS} -I${LOCALBASE}/include -I${X11BASE}/include"	\
-		LDFLAGS="${LDFLAGS} ${PTHREAD_LIBS} -L${LOCALBASE}/lib -L${X11BASE}/lib"
+CONFIGURE_ENV=	CPPFLAGS="${CFLAGS} ${PTHREAD_CFLAGS} -I${LOCALBASE}/include"	\
+		LDFLAGS="${LDFLAGS} ${PTHREAD_LIBS} -L${LOCALBASE}/lib"
 
 SLAVEDIRS=	science/py-gnudatalanguage
 
diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile
index d82139c702e8..ad4893927215 100644
--- a/science/gromacs/Makefile
+++ b/science/gromacs/Makefile
@@ -24,7 +24,7 @@ RUN_DEPENDS=	${LOCALBASE}/mpich/bin/mpicc:${PORTSDIR}/net/mpich
 
 USE_GMAKE=	yes
 USE_AUTOTOOLS=	libtool:15
-INSTALLS_SHLIB=	yes
+USE_LDCONFIG=	yes
 CONFIGURE_TARGET=	--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
 CONFIGURE_ENV=	CPPFLAGS=-I${LOCALBASE}/include LDFLAGS=-L${LOCALBASE}/lib
 CONFIGURE_ARGS=	--exec-prefix=${PREFIX}
diff --git a/science/gsystem/Makefile b/science/gsystem/Makefile
index 0a303e7ab1e0..0be1ed376605 100644
--- a/science/gsystem/Makefile
+++ b/science/gsystem/Makefile
@@ -21,7 +21,7 @@ USE_BZIP2=	yes
 
 USE_KDELIBS_VER=	3
 
-INSTALLS_SHLIB=	yes
+USE_LDCONFIG=	yes
 
 QTDIR=		${QT_PREFIX}
 QMAKESPEC=	freebsd-g++
diff --git a/science/kmovisto/Makefile b/science/kmovisto/Makefile
index 61a0310321b1..b7333772f2a0 100644
--- a/science/kmovisto/Makefile
+++ b/science/kmovisto/Makefile
@@ -8,19 +8,19 @@
 
 PORTNAME=	kmovisto
 PORTVERSION=	0.7.0
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	science
 MASTER_SITES=	http://mitglied.lycos.de/pageofmh/download/
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	A real 3-D molecule viewer
 
+USE_XORG=	x11 ice xext
 USE_QT_VER=	3
 USE_GL=		yes
 USE_GMAKE=	yes
 GNU_CONFIGURE=	yes
 CONFIGURE_TARGET=	--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
-CONFIGURE_ARGS=	--x-libraries=${X11BASE}/lib --x-includes=${X11BASE}/include
 
 post-patch:
 	@${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|g ; \
diff --git a/science/medit/files/patch-makefile b/science/medit/files/patch-makefile
index 1feffe06e74f..0612fe6b02b8 100644
--- a/science/medit/files/patch-makefile
+++ b/science/medit/files/patch-makefile
@@ -16,8 +16,8 @@
 +FreeBSD:
 +	$(MAKE) $(MFLAGS) -f Makefile.arch \
 +        "prog   = medit" \
-+        "INCDIR = -I. -I$(WRKSRC)/sources -I$(X11BASE)/include" \
-+	"XLIBS  = -L$(X11BASE)/lib -lXmu -lXext -lX11" \
++        "INCDIR = -I. -I$(WRKSRC)/sources -I$(LOCALBASE)/include" \
++	"XLIBS  = -L$(LOCALBASE)/lib -lXmu -lXext -lX11" \
 +        "GL_LIB   = -lGL" \
 +	"GLU_LIB  = -lGLU" \
 +	"GLUT_LIB = -lglut" \
diff --git a/science/minc/Makefile b/science/minc/Makefile
index 52a7497bd20b..770bc188f4ec 100644
--- a/science/minc/Makefile
+++ b/science/minc/Makefile
@@ -28,7 +28,7 @@ COMMENT=	Medical Imaging NetCDF
 LIB_DEPENDS=	netcdf.4:${PORTSDIR}/science/netcdf
 
 USE_AUTOTOOLS=	libtool:15
-INSTALLS_SHLIB=	yes
+USE_LDCONFIG=	yes
 GNU_CONFIGURE=	yes
 USE_GCC=	3.2+
 CONFIGURE_ENV=	CPPFLAGS="-I${LOCALBASE}/include" \
diff --git a/science/ncs/Makefile b/science/ncs/Makefile
index 992ae9c88edd..cdee469eb340 100644
--- a/science/ncs/Makefile
+++ b/science/ncs/Makefile
@@ -90,7 +90,7 @@ LIB_DEPENDS+=	blas.2:${PORTSDIR}/math/blas
 BLAS_LIB=	-lblas
 .endif
 
-.if exists(${X11BASE}/bin/acroread)
+.if exists(${LOCALBASE}/bin/acroread)
 RUN_DEPENDS+=	acroread:${PORTSDIR}/print/acroreadwrapper
 .else
 RUN_DEPENDS+=	xpdf:${PORTSDIR}/graphics/xpdf
diff --git a/science/oases/Makefile b/science/oases/Makefile
index 921c3f6f5004..9b5d2229fb0b 100644
--- a/science/oases/Makefile
+++ b/science/oases/Makefile
@@ -34,7 +34,7 @@ post-patch:
 		 s|%%FFLAGS%%|${FFLAGS}|g ; \
 		 s|%%CFLAGS%%|${CFLAGS}|g ; \
 		 s|%%LDFLAGS%%|${LDFLAGS}|g ; \
-		 s|%%X11BASE%%|${X11BASE}|g' ${WRKSRC}/Makefile
+		 s|%%LOCALBASE%%|${LOCALBASE}|g' ${WRKSRC}/Makefile
 
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/bin/FreeBSD-FreeBSD/* ${PREFIX}/bin
diff --git a/science/oases/files/patch-aa b/science/oases/files/patch-aa
index 95db14108d5c..2c1f3ccdd6d8 100644
--- a/science/oases/files/patch-aa
+++ b/science/oases/files/patch-aa
@@ -30,8 +30,8 @@
 +FC.FreeBSD-FreeBSD	= %%FC%%
 +CC.FreeBSD-FreeBSD	= %%CC%%
 +FFLAGS.FreeBSD-FreeBSD	= %%FFLAGS%% 
-+CFLAGS.FreeBSD-FreeBSD	= %%CFLAGS%% -I%%X11BASE%%/include
-+LFLAGS.FreeBSD-FreeBSD	= %%LDFLAGS%% -L%%X11BASE%%/lib
++CFLAGS.FreeBSD-FreeBSD	= %%CFLAGS%% -I%%LOCALBASE%%/include
++LFLAGS.FreeBSD-FreeBSD	= %%LDFLAGS%% -L%%LOCALBASE%%/lib
 +RANLIB.FreeBSD-FreeBSD	= ranlib
 +LIB_MISC.FreeBSD-FreeBSD	= 	
 +MISC.FreeBSD-FreeBSD	= 
diff --git a/science/omnetpp/Makefile b/science/omnetpp/Makefile
index 97c8258e38d6..f4d7b1b32a47 100644
--- a/science/omnetpp/Makefile
+++ b/science/omnetpp/Makefile
@@ -32,7 +32,7 @@ LIB_DEPENDS=	${TCL_NODOT}:${PORTSDIR}/lang/${TCL_NODOT} \
 
 COMPONENTS=	libs progs
 
-INSTALLS_SHLIB=	yes
+USE_LDCONFIG=	yes
 HAS_CONFIGURE=	yes
 
 LIB_FILES=	cmdenv envir nedxml sim_std tkenv
@@ -55,8 +55,8 @@ pre-configure:
 	@${ECHO} "OMNETPP_PLOVE_DIR=${DATADIR}/plove" >> ${CONFIGUREUSER}
 	@${ECHO} "OMNETPP_TKENV_DIR=${DATADIR}/tkenv" >> ${CONFIGUREUSER}
 	@${ECHO} "OMNETPP_BITMAP_PATH=${DATADIR}/bitmaps" >> ${CONFIGUREUSER}
-	@${ECHO} "TK_CFLAGS=\"-I${X11BASE}/include -I${LOCALBASE}/include/${TCL_VERSION} -I${LOCALBASE}/include/${TK_VERSION}\"" >> ${CONFIGUREUSER}
-	@${ECHO} "TK_LIBS=\"-L${X11BASE}/lib -L${LOCALBASE}/lib -lX11 -l${TCL_NODOT} -l${TK_NODOT}\"" >> ${CONFIGUREUSER}
+	@${ECHO} "TK_CFLAGS=\"-I${LOCALBASE}/include -I${LOCALBASE}/include/${TCL_VERSION} -I${LOCALBASE}/include/${TK_VERSION}\"" >> ${CONFIGUREUSER}
+	@${ECHO} "TK_LIBS=\"-L${LOCALBASE}/lib -L${LOCALBASE}/lib -lX11 -l${TCL_NODOT} -l${TK_NODOT}\"" >> ${CONFIGUREUSER}
 	@${ECHO} "EXPAT_CFLAGS=\"-I${LOCALBASE}/include\"" >> ${CONFIGUREUSER}
 	@${ECHO} "EXPAT_LIBS=\"-L${LOCALBASE}/lib -lexpat\"" >> ${CONFIGUREUSER}
 	@${ECHO} "WISH=wish${TK_VERSION}" | ${SED} 's,tk,,' >> ${CONFIGUREUSER}
diff --git a/science/oof/Makefile b/science/oof/Makefile
index db5d471b0898..6a46a390aba0 100644
--- a/science/oof/Makefile
+++ b/science/oof/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	oof
 PORTVERSION=	1.037
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	science
 MASTER_SITES=	http://www.ctcms.nist.gov/~langer/OOFdownload/SRC/
 DISTNAME=	${PORTNAME}-dist${PORTVERSION}
@@ -40,10 +40,8 @@ CXXFLAGS+=	-Wno-deprecated
 GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--with-cxxflags='${CXXFLAGS}'	\
 		--with-libdirs=-L${LOCALBASE}/lib	\
-		--with-blas="-L${LOCALBASE}/lib ${BLAS_LIBS} -L/usr/local/lib -L${FORTRANLIBDIR} -L${FORTRANLIBDIR2} ${FORTRANLIBS}" \
-		--x-includes=${X11BASE}/include \
-		--x-libraries=${X11BASE}/lib
-USE_GCC=	3.2+
+		--with-blas="-L${LOCALBASE}/lib ${BLAS_LIBS} -L/usr/local/lib -L${FORTRANLIBDIR} -L${FORTRANLIBDIR2} ${FORTRANLIBS}"
+
 ALL_TARGET=	all
 PLIST_FILES=	bin/oof bin/ppm2oof
 
diff --git a/science/openfoam/Makefile b/science/openfoam/Makefile
index b4cf05a9226c..776dfbc0d38a 100644
--- a/science/openfoam/Makefile
+++ b/science/openfoam/Makefile
@@ -19,12 +19,12 @@ COMMENT=	Open Field Operation and Manipulation - CFD Simulation Toolbox
 BUILD_DEPENDS=	micod:${PORTSDIR}/devel/mico						\
 		bash:${PORTSDIR}/shells/bash						\
 		cmake:${PORTSDIR}/devel/cmake						\
-		${X11BASE}/lib/libode.a:${PORTSDIR}/devel/ode				\
+		${LOCALBASE}/lib/libode.a:${PORTSDIR}/devel/ode				\
 		${PARAVIEW_LIB}/ParaViewConfig.cmake:${PORTSDIR}/science/paraview	\
 		${LOCALBASE}/share/java/java3d/jar/j3dutils.jar:${PORTSDIR}/java/java3d	\
 		${LOCALBASE}/include/libiberty/demangle.h:${PORTSDIR}/devel/gnulibiberty\
 		${LOCALBASE}/include/vtk/vtkDataSetSource.h:${PORTSDIR}/math/vtk-headers\
-		${X11BASE}/lib/X11/fonts/freefont-ttf/FreeSans.ttf:${PORTSDIR}/x11-fonts/freefont-ttf
+		${LOCALBASE}/lib/X11/fonts/freefont-ttf/FreeSans.ttf:${PORTSDIR}/x11-fonts/freefont-ttf
 #		${LOCALBASE}/lib/parmetis/libmetis.a:${PORTSDIR}/math/parmetis
 LIB_DEPENDS=	execinfo:${PORTSDIR}/devel/libexecinfo	\
 		readline.5:${PORTSDIR}/devel/readline
@@ -201,7 +201,7 @@ pre-configure:
 		-e "s|\$$LAMHOME/platforms/\$$WM_OPTIONS|${LOCALBASE}|"		\
 		-e "s|^SOURCE |source |"					\
 		${BATCHRC:S|^|${WRKSRC}/|}
-	${REINPLACE_CMD} -e "s|-lGL|-L${X11BASE}/lib -lGL|"	\
+	${REINPLACE_CMD} -e "s|-lGL|-L${LOCALBASE}/lib -lGL|"	\
 		${GL2FIX:S|^|${WRKSRC}/|}
 	${REINPLACE_CMD} -e "s|GCC_VERSION=4.1.1|GCC_VERSION=${GCC_VER:S/_//}|"	\
 		-e "s|JAVA_VERSION=1.4.2+|JAVA_VERSION=${JAVA_PORT_VERSION}|"	\
@@ -218,7 +218,7 @@ pre-configure:
 		-e "s|-lpthread|${PTHREAD_LIBS}|"		\
 		${WRKSRC}/wmake/rules/${OPSYS}/${f}
 .endfor
-	${REINPLACE_CMD} -e "s|/usr/X11R6|${X11BASE}|"		\
+	${REINPLACE_CMD} -e "s|/usr/X11R6|${LOCALBASE}|"		\
 		${WRKSRC}/wmake/rules/${OPSYS}/X
 .for f in ${VER2FIX}
 	${REINPLACE_CMD} -e "s|%%ARCH%%|${ARCH}|"	\
diff --git a/science/paraview/Makefile b/science/paraview/Makefile
index 8926a7ac5943..e91faf12a1e9 100644
--- a/science/paraview/Makefile
+++ b/science/paraview/Makefile
@@ -40,7 +40,7 @@ pre-patch:
 		${WRKDIR}/paraview-${PORTVERSION}/GUI/Widgets/CMakeLists.txt
 
 post-patch:
-	@${REINPLACE_CMD} -e 's,/usr/X11R6,${X11BASE},g' \
+	@${REINPLACE_CMD} -e 's,/usr/X11R6,${LOCALBASE},g' \
 		${WRKDIR}/paraview-${PORTVERSION}/Utilities/TclTk/tk*/unix/configure
 
 do-configure:
@@ -48,8 +48,8 @@ do-configure:
 	cd ${WRKSRC} && \
 	${LOCALBASE}/bin/cmake ../${DISTNAME} \
 		-DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} \
-		-DCMAKE_C_FLAGS="${CFLAGS} -I${X11BASE}/include -I${LOCALBASE}/include" \
-		-DCMAKE_CXX_FLAGS="${CXXFLAGS} -I${X11BASE}/include -I${LOCALBASE}/include" \
+		-DCMAKE_C_FLAGS="${CFLAGS} -I${LOCALBASE}/include" \
+		-DCMAKE_CXX_FLAGS="${CXXFLAGS} -I${LOCALBASE}/include" \
 		-DPARAVIEW_USE_SYSTEM_HDF5=1 \
 		-DBUILD_SHARED_LIBS="ON" \
 		-DVTK_USE_SYSTEM_PNG="ON" \
diff --git a/science/ruby-dcl/Makefile b/science/ruby-dcl/Makefile
index b6c1fe894b54..614419d85eea 100644
--- a/science/ruby-dcl/Makefile
+++ b/science/ruby-dcl/Makefile
@@ -16,7 +16,7 @@ MAINTAINER=	murakami@ahs.scitec.kobe-u.ac.jp
 COMMENT=	A Ruby interface to the scientific graphic library DCL
 
 BUILD_DEPENDS=	${RUBY_SITEARCHLIBDIR}/narray.so:${PORTSDIR}/math/ruby-narray \
-		${X11BASE}/lib/libcdcl.a:${PORTSDIR}/science/cdcl
+		${LOCALBASE}/lib/libcdcl.a:${PORTSDIR}/science/cdcl
 RUN_DEPENDS=	${RUBY_SITEARCHLIBDIR}/narray.so:${PORTSDIR}/math/ruby-narray
 
 .if defined(WITHOUT_GTK)
diff --git a/science/szip/Makefile b/science/szip/Makefile
index cec796895e95..b6e959d86a2b 100644
--- a/science/szip/Makefile
+++ b/science/szip/Makefile
@@ -20,7 +20,7 @@ COMMENT=	Lossless compression library for scientific data
 
 USE_AUTOTOOLS=	libtool:15
 GNU_CONFIGURE=	yes
-INSTALLS_SHLIB=	yes
+USE_LDCONFIG=	yes
 DOCFILE=	Release_notes_2_0.pdf
 
 post-install:
diff --git a/science/v_sim/Makefile b/science/v_sim/Makefile
index 854adcdfc0f0..e0c9f6fbc470 100644
--- a/science/v_sim/Makefile
+++ b/science/v_sim/Makefile
@@ -18,7 +18,7 @@ USE_GL=		yes
 USE_GMAKE=	yes
 GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--disable-gtk-doc
-CONFIGURE_ENV=	CPPFLAGS="${CFLAGS} -I${X11BASE}/include -I${LOCALBASE}/include"	\
+CONFIGURE_ENV=	CPPFLAGS="${CFLAGS} -I${LOCALBASE}/include"	\
 		LDFLAGS="${LDFLAGS} -L${LOCALBASE}/lib"
 
 MAN1=		v_sim.1
diff --git a/science/vis5d+/Makefile b/science/vis5d+/Makefile
index f0ce912f8d71..a156076130c3 100644
--- a/science/vis5d+/Makefile
+++ b/science/vis5d+/Makefile
@@ -33,8 +33,8 @@ CONFIGURE_ARGS=	--enable-gtk --enable-threads --with-netcdf \
 		--with-mixkit=${LOCALBASE}/lib/libmix.a --with-x
 USE_LDCONFIG=	yes
 
-CPPFLAGS=	-I${LOCALBASE}/include -I${X11BASE}/include ${PTHREAD_CFLAGS}
-LDFLAGS=	-L${LOCALBASE}/lib -L${X11BASE}/lib ${PTHREAD_LIBS}
+CPPFLAGS=	-I${LOCALBASE}/include ${PTHREAD_CFLAGS}
+LDFLAGS=	-L${LOCALBASE}/lib ${PTHREAD_LIBS}
 
 CFLAGS+=	-DMIX_ANSI_IOSTREAMS -fpermissive
 
diff --git a/science/vmd/Makefile b/science/vmd/Makefile
index 2ebc6e378aab..aadc89825068 100644
--- a/science/vmd/Makefile
+++ b/science/vmd/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=		vmd
 PORTVERSION=		1.8.3
-PORTREVISION=		1
+PORTREVISION=		2
 CATEGORIES=		science graphics python tcl tk
 MASTER_SITES=		http://jedi.ks.uiuc.edu/~johns/raytracer/files/0.97/:tachyon \
 			ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src/:stride
@@ -18,7 +18,7 @@ DISTFILES=		${VMD_DIST} \
 MAINTAINER=		sangwoos@gmail.com
 COMMENT=		A molecular visualization program
 
-BUILD_DEPENDS=		makedepend:${X_IMAKE_PORT} \
+BUILD_DEPENDS=		makedepend:${PORTSDIR}/devel/makedepend \
 			${PYNUMERIC}
 LIB_DEPENDS=		tcl84:${PORTSDIR}/lang/tcl84 \
 			tk84:${PORTSDIR}/x11-toolkits/tk84 \
@@ -27,7 +27,7 @@ RUN_DEPENDS=		${PYNUMERIC}
 
 USE_PERL5_BUILD=	yes
 USE_GMAKE=		yes
-USE_GL=			yes
+USE_GL=			glu
 USE_PYTHON=		yes
 
 RESTRICTED=		"License has restrictions"