science/minc2: Unbreak, Upgrade version 2.0.18 => 2.2.00 and stage

PR:		187764
Submitted by:	Ports Fury

7 files changed, 99 insertions, 64 deletions

diff --git a/science/minc2/Makefile b/science/minc2/Makefile
index 5dc1459eec09..ca729d91dec7 100644
--- a/science/minc2/Makefile
+++ b/science/minc2/Makefile
@@ -1,22 +1,11 @@
 # Created by: jbacon
 # $FreeBSD$
 
-############################################################################
-# http://www.bic.mni.mcgill.ca/software/minc/
-# is the ultimate source for MINC, and will always contain the latest
-# source release.  If this port is not up to date enough for you,
-# you can download the latest sources and build manually.  On FreeBSD,
-# you must configure with the environment variable LDFLAGS set to
-# ${LOCALBASE}/lib so that the configure script will find libnetcdf.
-# Of course, the netcdf port must be installed first.
-
 PORTNAME=	minc
-PORTVERSION=	2.0.18
-PORTREVISION=	2
+PORTVERSION=	2.2.00
 PORTEPOCH=	1
 CATEGORIES=	science biology
-MASTER_SITES=	http://packages.bic.mni.mcgill.ca/tgz/ \
-		http://www.nitrc.org/frs/download.php/801/
+MASTER_SITES=	GH
 PKGNAMESUFFIX=	2
 
 MAINTAINER=	ports@FreeBSD.org
@@ -24,18 +13,35 @@ COMMENT=	Medical Imaging NetCDF
 
 LICENSE=	BSD
 
-BROKEN=		Fails to build
-
-LIB_DEPENDS=	libnetcdf.so:${PORTSDIR}/science/netcdf \
-		libhdf5.so:${PORTSDIR}/science/hdf5
-
-USES=		libtool
-USE_LDCONFIG=	yes
-CPPFLAGS+=	${PTHREAD_CFLAGS} -I${LOCALBASE}/include -DH5_USE_16_API
-LDFLAGS+=	-L${LOCALBASE}/lib ${PTHREAD_LIBS}
+LIB_DEPENDS=	libhdf5.so:${PORTSDIR}/science/hdf5 \
+		libnetcdf.so:${PORTSDIR}/science/netcdf
+RUN_DEPENDS=	bash:${PORTSDIR}/shells/bash
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	BIC-MNI
+GH_TAGNAME=	release-${PORTVERSION}
+GH_COMMIT=	6f2f5b9
+
+USES=		bison gmake libtool perl5 shebangfix
+SHEBANG_FILES=	progs/mincview/mincview
+USE_PERL5=	build
+USE_AUTOTOOLS=	libtoolize aclocal autoheader automake autoconf
+LIBTOOLIZE_ARGS=--copy --force
+ACLOCAL_ARGS=	-I m4 --automake-acdir=${ACLOCAL_DIR}
+AUTOMAKE_ARGS=	--add-missing --copy --force-missing
 CONFIGURE_ARGS=	--enable-shared=yes --enable-static=yes
+INSTALL_TARGET=	install-strip
+USE_LDCONFIG=	yes
+
+CFLAGS+=	-Wno-error=return-type
+CPPFLAGS+=	-I${LOCALBASE}/include
+LDFLAGS+=	-L${LOCALBASE}/lib
 
 CONFLICTS=	minc-1* zh-tk-[0-9]*
-LATEST_LINK=	minc2
+
+pre-patch:
+	@${RM} -f ${WRKSRC}/ac_config_aux/*
+	@${RM} -f ${WRKSRC}/progs/minccalc/gram.[ch]
+	@${RM} -f ${WRKSRC}/progs/mincgen/ncgentab.[ch]
 
 .include <bsd.port.mk>
diff --git a/science/minc2/distinfo b/science/minc2/distinfo
index c471ce509e14..7af7cd3aacf8 100644
--- a/science/minc2/distinfo
+++ b/science/minc2/distinfo
@@ -1,2 +1,2 @@
-SHA256 (minc-2.0.18.tar.gz) = 674cc89c43edfdb1957251c0124ea83252740c667cf3c4d9fc6183dcdb10f3e5
-SIZE (minc-2.0.18.tar.gz) = 1628038
+SHA256 (minc-2.2.00.tar.gz) = 0a719564fd27775e08913e1ab7faeb96964c035ec2abfef85677b6965579cbfd
+SIZE (minc-2.2.00.tar.gz) = 3906835
diff --git a/science/minc2/files/patch-Makefile.am b/science/minc2/files/patch-Makefile.am
new file mode 100644
index 000000000000..e38283aec741
--- /dev/null
+++ b/science/minc2/files/patch-Makefile.am
@@ -0,0 +1,53 @@
+--- Makefile.am.orig
++++ Makefile.am
+@@ -274,28 +274,28 @@
+ 	m4/smr_WITH_BUILD_PATH.m4
+ 
+ ezMINC_files = \
+-	ezminc/examples/volume_msq_dist.cpp
+-	ezminc/examples/CMakeLists.txt
+-	ezminc/examples/fuzzy_volume_similarity.cpp
+-	ezminc/examples/trilinear_resample.cpp
+-	ezminc/examples/volume_avg.cpp
+-	ezminc/examples/volume_gtc_similarity.cpp
+-	ezminc/examples/volume_similarity.cpp
+-	ezminc/minc_1_simple_rw.cpp
+-	ezminc/minc_1_simple_rw.h
+-	ezminc/minc_io_4d_volume.h
+-	ezminc/minc_io_fixed_vector.h
+-	ezminc/minc_io_simple_volume.h
+-	ezminc/tests/minc_rw_test2.cpp
+-	ezminc/tests/minc_rw_test_4d.cpp
+-	ezminc/tests/minc_rw_test_simple.cpp
+-	ezminc/tests/CMakeLists.txt
+-	ezminc/tests/ezminc_rw_test.cpp
+-	ezminc/tests/ezminc_stats.cpp
+-	ezminc/minc_1_simple.h
+-	ezminc/CMakeLists.txt
+-	ezminc/minc_1_rw.cpp
+-	ezminc/minc_1_rw.h
++	ezminc/examples/volume_msq_dist.cpp \
++	ezminc/examples/CMakeLists.txt \
++	ezminc/examples/fuzzy_volume_similarity.cpp \
++	ezminc/examples/trilinear_resample.cpp \
++	ezminc/examples/volume_avg.cpp \
++	ezminc/examples/volume_gtc_similarity.cpp \
++	ezminc/examples/volume_similarity.cpp \
++	ezminc/minc_1_simple_rw.cpp \
++	ezminc/minc_1_simple_rw.h \
++	ezminc/minc_io_4d_volume.h \
++	ezminc/minc_io_fixed_vector.h \
++	ezminc/minc_io_simple_volume.h \
++	ezminc/tests/minc_rw_test2.cpp \
++	ezminc/tests/minc_rw_test_4d.cpp \
++	ezminc/tests/minc_rw_test_simple.cpp \
++	ezminc/tests/CMakeLists.txt \
++	ezminc/tests/ezminc_rw_test.cpp \
++	ezminc/tests/ezminc_stats.cpp \
++	ezminc/minc_1_simple.h \
++	ezminc/CMakeLists.txt \
++	ezminc/minc_1_rw.cpp \
++	ezminc/minc_1_rw.h \
+ 	ezminc/minc_io_exceptions.h
+ 	
+ voxeltoworld_SOURCES = progs/coordinates/voxeltoworld.c
diff --git a/science/minc2/files/patch-conversion_minctoecat_machine_indep.c b/science/minc2/files/patch-conversion_minctoecat_machine_indep.c
deleted file mode 100644
index 556375778be4..000000000000
--- a/science/minc2/files/patch-conversion_minctoecat_machine_indep.c
+++ /dev/null
@@ -1,20 +0,0 @@
---- conversion/minctoecat/machine_indep.c.orig	2007-03-29 07:08:46.000000000 +0200
-+++ conversion/minctoecat/machine_indep.c	2014-01-28 22:55:57.000000000 +0100
-@@ -61,7 +61,7 @@
- }
- 
- #if defined(__alpha) || defined(_WIN32) /* LITTLE_ENDIAN : alpha, intel */
--ftovaxf(f, bufr)
-+void ftovaxf(f, bufr)
- float f;
- unsigned short *bufr;
- {
-@@ -84,7 +84,7 @@
- 	bufr[1] =  ret >>16;
- }
- #else  /* BIG ENDIAN : sun hp sgi*/
--ftovaxf(orig,number)
-+void ftovaxf(orig,number)
-   unsigned short number[2];
-   float orig;
- {
diff --git a/science/minc2/pkg-descr b/science/minc2/pkg-descr
index 0730d1b37440..159e38789ec9 100644
--- a/science/minc2/pkg-descr
+++ b/science/minc2/pkg-descr
@@ -1,10 +1,4 @@
 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.
+associated set of tools and libraries.
 
 WWW: http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC  
-
-Port maintainer: Jason W. Bacon
-		 jwbacon@tds.net
diff --git a/science/minc2/pkg-message b/science/minc2/pkg-message
deleted file mode 100644
index cc3dd854da2b..000000000000
--- a/science/minc2/pkg-message
+++ /dev/null
@@ -1,8 +0,0 @@
-=============================================================================
-For questions or comments regarding this port, please contact the
-port maintainer: jwbacon@tds.net
-
-For MINC usage, please visit the MINC WEB site at
-
-http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC
-=============================================================================
diff --git a/science/minc2/pkg-plist b/science/minc2/pkg-plist
index 9b950ca353f3..a5308acb29a2 100644
--- a/science/minc2/pkg-plist
+++ b/science/minc2/pkg-plist
@@ -3,7 +3,10 @@ bin/ecattominc
 bin/invert_raw_image
 bin/minc_modify_header
 bin/mincaverage
+bin/mincblob
 bin/minccalc
+bin/minccmp
+bin/minccomplete
 bin/mincconcat
 bin/mincconvert
 bin/minccopy
@@ -20,9 +23,11 @@ bin/minclookup
 bin/mincmakescalar
 bin/mincmakevector
 bin/mincmath
+bin/mincmorph
 bin/mincpik
 bin/mincresample
 bin/mincreshape
+bin/mincsample
 bin/mincstats
 bin/minctoecat
 bin/minctoraw
@@ -36,6 +41,7 @@ bin/upet2mnc
 bin/vff2mnc
 bin/voxeltoworld
 bin/worldtovoxel
+bin/xfm2def
 bin/xfmconcat
 bin/xfmflip
 bin/xfminvert
@@ -66,18 +72,21 @@ include/volume_io/volume_cache.h
 include/voxel_loop.h
 lib/libminc2.a
 lib/libminc2.so
-lib/libminc2.so.1
-lib/libminc2.so.1.1.2
+lib/libminc2.so.3
+lib/libminc2.so.3.0.0
 lib/libvolume_io2.a
 lib/libvolume_io2.so
-lib/libvolume_io2.so.1
-lib/libvolume_io2.so.1.1.2
+lib/libvolume_io2.so.3
+lib/libvolume_io2.so.3.0.0
 man/man1/dcm2mnc.1.gz
 man/man1/ecattominc.1.gz
 man/man1/invert_raw_image.1.gz
 man/man1/minc_modify_header.1.gz
 man/man1/mincaverage.1.gz
+man/man1/mincblob.1.gz
 man/man1/minccalc.1.gz
+man/man1/minccmp.1.gz
+man/man1/minccomplete.1.gz
 man/man1/mincconcat.1.gz
 man/man1/mincconvert.1.gz
 man/man1/minccopy.1.gz
@@ -108,6 +117,7 @@ man/man1/transformtags.1.gz
 man/man1/upet2mnc.1.gz
 man/man1/vff2mnc.1.gz
 man/man1/voxeltoworld.1.gz
+man/man1/xfm2def.1.gz
 man/man1/xfmconcat.1.gz
 man/man1/xfmflip.1.gz
 man/man1/xfminvert.1.gz