ports/180411: science/minc2: upgrade to 2.2.00

[Thierry Thomas]

>Number:         180411
>Category:       ports
>Synopsis:       science/minc2: upgrade to 2.2.00
>Confidential:   no
>Severity:       non-critical
>Priority:       medium
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Tue Jul 09 11:50:00 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator:     Thierry Thomas
>Release:        FreeBSD 9.1-STABLE i386
>Organization:
Kabbale Eros
>Environment:
System: N/A


	
>Description:
	Upgrade science/minc2 to the latest stable release.

	I switched from autotools to cmake, and man pages are no more installed.

>How-To-Repeat:
	N/A

>Fix:
	Please apply the hereunder patch.

--- minc2.diff begins here ---
diff -urN science/minc2.orig/Makefile science/minc2/Makefile
--- science/minc2.orig/Makefile	2013-01-27 21:27:29.000000000 +0100
+++ science/minc2/Makefile	2013-07-09 11:22:09.000000000 +0200
@@ -1,10 +1,5 @@
-############################################################################
-# New ports collection Makefile for:   minc 1.x (Medical Imaging NetCDF)
-# Date created:        21 Dec 2005
-# Whom:                jbacon
-#
+# Created by: jbacon
 # $FreeBSD: head/science/minc2/Makefile 301234 2012-07-20 16:33:32Z zeising $
-#
 
 ############################################################################
 # http://www.bic.mni.mcgill.ca/software/minc/
@@ -16,67 +11,30 @@
 # Of course, the netcdf port must be installed first.
 
 PORTNAME=	minc
-PORTVERSION=	2.0.18
+PORTVERSION=	2.2.00
 CATEGORIES=	science biology
-MASTER_SITES=	http://www.nitrc.org/frs/download.php/801/
+MASTER_SITES=	http://packages.bic.mni.mcgill.ca/tgz/
 
 MAINTAINER=	jwbacon at tds.net
 COMMENT=	Medical Imaging NetCDF
 
+LICENSE=	AS-IS
+LICENSE_NAME=	AS-IS
+LICENSE_FILE=	${WRKSRC}/COPYING
+LICENSE_PERMS=	dist-mirror pkg-mirror
+
 LIB_DEPENDS=	netcdf.4:${PORTSDIR}/science/netcdf \
 		hdf5:${PORTSDIR}/science/hdf5
 
-USE_AUTOTOOLS=	libtool
 USE_LDCONFIG=	yes
+USES=		cmake:outsource bison:build
 CPPFLAGS+=	${PTHREAD_CFLAGS} -I${LOCALBASE}/include -DH5_USE_16_API
 LDFLAGS+=	-L${LOCALBASE}/lib ${PTHREAD_LIBS}
-CONFIGURE_ARGS=	--enable-shared=yes --enable-static=yes
+CMAKE_ARGS=	-DMINC2_BUILD_SHARED_LIBS:BOOL=YES
 
 CONFLICTS=	minc-1* zh-tk-[0-9]*
 LATEST_LINK=	minc2
 
-MAN1=	dcm2mnc.1 \
-	ecattominc.1 \
-	invert_raw_image.1 \
-	minc_modify_header.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 \
-	mincmakevector.1 \
-	mincmath.1 \
-	mincpik.1 \
-	mincresample.1 \
-	mincreshape.1 \
-	mincstats.1 \
-	minctoecat.1 \
-	minctoraw.1 \
-	mincview.1 \
-	mincwindow.1 \
-	mnc2nii.1 \
-	nii2mnc.1 \
-	rawtominc.1 \
-	transformtags.1 \
-	upet2mnc.1 \
-	vff2mnc.1 \
-	voxeltoworld.1 \
-	xfmconcat.1 \
-	xfmflip.1 \
-	xfminvert.1
-
-MAN3=	ParseArgv.3
-
 post-install:
 	${CAT} ${PKGMESSAGE}
 
diff -urN science/minc2.orig/distinfo science/minc2/distinfo
--- science/minc2.orig/distinfo	2013-01-27 21:27:29.000000000 +0100
+++ science/minc2/distinfo	2013-07-09 10:01:04.000000000 +0200
@@ -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) = e689d3612db6241125e3155d5a5c109d4da6f4bd774cc00a7e6729f2a790a174
+SIZE (minc-2.2.00.tar.gz) = 1665189
diff -urN science/minc2.orig/files/patch-conversion__minctoecat__machine_indep.c science/minc2/files/patch-conversion__minctoecat__machine_indep.c
--- science/minc2.orig/files/patch-conversion__minctoecat__machine_indep.c	2013-01-27 21:27:29.000000000 +0100
+++ science/minc2/files/patch-conversion__minctoecat__machine_indep.c	1970-01-01 01:00:00.000000000 +0100
@@ -1,11 +0,0 @@
---- conversion/minctoecat/machine_indep.c.orig	2012-07-20 17:16:13.000000000 +0200
-+++ conversion/minctoecat/machine_indep.c	2012-07-20 17:17:48.000000000 +0200
-@@ -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 -urN science/minc2.orig/pkg-plist science/minc2/pkg-plist
--- science/minc2.orig/pkg-plist	2013-01-27 21:27:29.000000000 +0100
+++ science/minc2/pkg-plist	2013-07-09 11:26:56.000000000 +0200
@@ -3,6 +3,7 @@
 bin/invert_raw_image
 bin/minc_modify_header
 bin/mincaverage
+bin/mincblob
 bin/minccalc
 bin/mincconcat
 bin/mincconvert
@@ -20,9 +21,11 @@
 bin/mincmakescalar
 bin/mincmakevector
 bin/mincmath
+bin/mincmorph
 bin/mincpik
 bin/mincresample
 bin/mincreshape
+bin/mincsample
 bin/mincstats
 bin/minctoecat
 bin/minctoraw
@@ -33,11 +36,9 @@
 bin/rawtominc
 bin/transformtags
 bin/upet2mnc
-bin/vff2mnc
 bin/voxeltoworld
 bin/worldtovoxel
 bin/xfmconcat
-bin/xfmflip
 bin/xfminvert
 include/ParseArgv.h
 include/minc.h
@@ -64,12 +65,12 @@
 include/volume_io/volume.h
 include/volume_io/volume_cache.h
 include/voxel_loop.h
-lib/libminc2.a
-lib/libminc2.la
+lib/MINC2Config.cmake
+lib/UseMINC2.cmake
 lib/libminc2.so
 lib/libminc2.so.2
-lib/libvolume_io2.a
-lib/libvolume_io2.la
+lib/libminc2.so.2.2.00
 lib/libvolume_io2.so
 lib/libvolume_io2.so.2
+lib/libvolume_io2.so.2.2.00
 @dirrm include/volume_io
--- minc2.diff ends here ---

>Release-Note:
>Audit-Trail:
>Unformatted: