Add science/minc2.

MINC (Medical Imaging NetCDF) is a medical imaging data format and an
associated set of tools and libraries. MINC was created in 1993 by Peter
Neelin at the McConnell Brain Imaging Centre of the Montreal Neurological
Institute. Many others have contributed to the design and implementation
MINC over the years.

PR:		ports/93495
Submitted by:	Jason Bacon <bacon (at) smithers.neuro.mcw.edu>
Repocopied by:	marcus

3 files changed, 31 insertions, 21 deletions

diff --git a/science/minc2/Makefile b/science/minc2/Makefile
index ec961a33e97e..41ed616e2b81 100644
--- a/science/minc2/Makefile
+++ b/science/minc2/Makefile
@@ -16,24 +16,27 @@
 # Of course, the netcdf port must be installed first.
 
 PORTNAME=	minc
-PORTVERSION=	1.4
-PORTREVISION=	1
+PORTVERSION=	2.0.09
 CATEGORIES=	science biology
-MASTER_SITES=	http://www.bic.mni.mcgill.ca/software/distribution/packages/ \
+MASTER_SITES=	http://www.bic.mni.mcgill.ca/users/bert/ \
 		http://www.neuro.mcw.edu/~bacon/Ports/distfiles/
 
 MAINTAINER=	bacon@smithers.neuro.mcw.edu
 COMMENT=	Medical Imaging NetCDF
 
-LIB_DEPENDS=	netcdf.1:${PORTSDIR}/science/netcdf
+LIB_DEPENDS=	netcdf.1:${PORTSDIR}/science/netcdf \
+		hdf5.0:${PORTSDIR}/science/hdf5
 
 INSTALLS_SHLIB=	yes
 GNU_CONFIGURE=	yes
 USE_GCC=	3.2+
-CONFIGURE_ENV=	CPPFLAGS="-I${LOCALBASE}/include" \
-		LDFLAGS="${LDFLAGS} -L${LOCALBASE}/lib"
-CONFIGURE_ARGS=	--enable-static=yes --enable-shared=yes
-CONFIGURE_TARGET=	--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
+CONFIGURE_ENV=	CPPFLAGS="${CPPFLAGS} ${PTHREAD_CFLAGS} -I${LOCALBASE}/include" \
+		LDFLAGS="${LDFLAGS} -L${LOCALBASE}/lib ${PTHREAD_LIBS}"
+CONFIGURE_ARGS=	--enable-shared=yes --enable-static=yes
+CONFIGURE_TARGET=--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
+
+CONFLICTS=	minc-1*
+LATEST_LINK=	minc2
 
 MAN1=	dcm2mnc.1 \
 	ecattominc.1 \
@@ -42,12 +45,15 @@ MAN1=	dcm2mnc.1 \
 	mincaverage.1 \
 	minccalc.1 \
 	mincconcat.1 \
+	mincconvert.1 \
 	minccopy.1 \
 	mincdiff.1 \
 	mincedit.1 \
 	mincexpand.1 \
 	mincextract.1 \
+	mincgen.1 \
 	mincheader.1 \
+	minchistory.1 \
 	mincinfo.1 \
 	minclookup.1 \
 	mincmakescalar.1 \
@@ -69,10 +75,9 @@ MAN1=	dcm2mnc.1 \
 	voxeltoworld.1 \
 	xfmconcat.1 \
 	xfminvert.1
-
 MAN3=	ParseArgv.3
 
 post-install:
-	@${CAT} ${PKGMESSAGE}
+	${CAT} ${PKGMESSAGE}
 
 .include <bsd.port.mk>
diff --git a/science/minc2/distinfo b/science/minc2/distinfo
index c73ee7c2269b..59fb4e5c7afd 100644
--- a/science/minc2/distinfo
+++ b/science/minc2/distinfo
@@ -1,3 +1,3 @@
-MD5 (minc-1.4.tar.gz) = 873a6deed8109f95d29a197bad9f6070
-SHA256 (minc-1.4.tar.gz) = a07c9523f232c823f38275bc8bb23011e70a29a0a45071dad0dec81317a75c4f
-SIZE (minc-1.4.tar.gz) = 1213768
+MD5 (minc-2.0.09.tar.gz) = 8a8606163852f91d6dc66dbcc3fde4ee
+SHA256 (minc-2.0.09.tar.gz) = b55907a5dd26c1b98b39f6cb81133336d7c794d4f7d4ad38b02561a9cc489390
+SIZE (minc-2.0.09.tar.gz) = 1418085
diff --git a/science/minc2/pkg-plist b/science/minc2/pkg-plist
index 293bf89a7dff..c1d540edba89 100644
--- a/science/minc2/pkg-plist
+++ b/science/minc2/pkg-plist
@@ -5,11 +5,14 @@ bin/minc_modify_header
 bin/mincaverage
 bin/minccalc
 bin/mincconcat
+bin/mincconvert
 bin/minccopy
 bin/mincdiff
+bin/mincdump
 bin/mincedit
 bin/mincexpand
 bin/mincextract
+bin/mincgen
 bin/mincheader
 bin/minchistory
 bin/mincinfo
@@ -36,6 +39,8 @@ bin/xfmconcat
 bin/xfminvert
 include/ParseArgv.h
 include/minc.h
+include/minc2.h
+include/minc_compat.h
 include/minc_simple.h
 include/nd_loop.h
 include/time_stamp.h
@@ -57,12 +62,12 @@ include/volume_io/vol_io_prototypes.h
 include/volume_io/volume.h
 include/volume_io/volume_cache.h
 include/voxel_loop.h
-lib/libminc.a
-lib/libminc.la
-lib/libminc.so
-lib/libminc.so.1
-lib/libvolume_io.a
-lib/libvolume_io.la
-lib/libvolume_io.so
-lib/libvolume_io.so.0
+lib/libminc2.a
+lib/libminc2.la
+lib/libminc2.so
+lib/libminc2.so.2
+lib/libvolume_io2.a
+lib/libvolume_io2.la
+lib/libvolume_io2.so
+lib/libvolume_io2.so.2
 @dirrm include/volume_io