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-rw-r--r--biology/L-Breeder/Makefile6
-rw-r--r--biology/L-Breeder/files/patch-Unix-Makefile4
-rw-r--r--biology/garlic/Makefile3
-rw-r--r--biology/garlic/files/patch-Makefile4
-rw-r--r--biology/gperiodic/Makefile2
-rw-r--r--biology/kinemage/files/patch-Makefile4
-rw-r--r--biology/molden/Makefile7
-rw-r--r--biology/molden/distinfo6
-rw-r--r--biology/molden/files/patch-aa8
-rw-r--r--biology/ncbi-toolkit/Makefile2
-rw-r--r--biology/ortep3/Makefile2
-rw-r--r--biology/phylip/Makefile8
-rw-r--r--biology/platon/Makefile6
-rw-r--r--biology/platon/files/Makefile4
-rw-r--r--biology/protomol/Makefile4
-rw-r--r--biology/rasmol/Makefile3
-rw-r--r--biology/seaview/files/patch-Makefile4
-rw-r--r--biology/tinker/Makefile7
-rw-r--r--biology/xdrawchem/Makefile9
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}"
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-13 00:19:40 +0000