Attachment #141051 for bug #187764




# Created by: jbacon
# $FreeBSD: head/science/minc2/Makefile 341763 2014-01-29 17:31:04Z thierry $

############################################################################
# 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=	2.2.00
PORTEPOCH=	1
CATEGORIES=	science biology
MASTER_SITES=	GH
		http://www.nitrc.org/frs/download.php/801/
PKGNAMESUFFIX=	2

MAINTAINER=	ports@FreeBSD.org


LICENSE=	BSD

LIB_DEPENDS=	libhdf5.so.7:${PORTSDIR}/science/hdf5-18 \
		libnetcdf.so.7:${PORTSDIR}/science/netcdf4
RUN_DEPENDS=	bash:${PORTSDIR}/shells/bash

USE_GITHUB=	yes
GH_ACCOUNT=	BIC-MNI
GH_TAGNAME=	release-${PORTVERSION}
GH_COMMIT=	6f2f5b9

USES=		bison gmake 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
CONFIGURE_ARGS=	--enable-shared=yes --enable-static=yes
USE_LDCONFIG=	yes

CFLAGS+=	-Wno-return-type
CPPFLAGS+=	-I${LOCALBASE}/include
LDFLAGS+=	-L${LOCALBASE}/lib

CONFLICTS=	minc-1* zh-tk-[0-9]*

STRIP_FILES=	dcm2mnc ecattominc invert_raw_image minc_modify_header \
		mincaverage mincblob minccalc minccmp \
		mincconcat mincconvert minccopy mincdump \
		mincexpand mincextract mincgen mincinfo \
		minclookup mincmakescalar mincmakevector mincmath \
		mincmorph mincresample mincreshape mincsample \
		mincstats minctoecat minctoraw mincwindow \
		mnc2nii nii2mnc rawtominc transformtags \
		upet2mnc vff2mnc voxeltoworld worldtovoxel \
		xfm2def xfmconcat xfminvert

post-install:
.for i in ${STRIP_FILES}
	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/${i}
.endfor

.include <bsd.port.mk>

Lines 1-2 Link Here

(-)science/minc2/distinfo (-2 / +2 lines)
1	SHA256 (minc-2.0.18.tar.gz) = 674cc89c43edfdb1957251c0124ea83252740c667cf3c4d9fc6183dcdb10f3e5	1	SHA256 (minc-2.2.00.tar.gz) = 0a719564fd27775e08913e1ab7faeb96964c035ec2abfef85677b6965579cbfd
2	SIZE (minc-2.0.18.tar.gz) = 1628038	2	SIZE (minc-2.2.00.tar.gz) = 3906835




--- 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




--- 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;
 {

Lines 1-10 Link Here

(-)science/minc2/pkg-descr (-7 / +1 lines)
1	MINC (Medical Imaging NetCDF) is a medical imaging data format and an	1	MINC (Medical Imaging NetCDF) is a medical imaging data format and an
2	associated set of tools and libraries. MINC was created in 1993 by Peter	2	associated set of tools and libraries.
3	Neelin at the McConnell Brain Imaging Centre of the Montreal Neurological
4	Institute. Many others have contributed to the design and implementation
5	MINC over the years.
6		3
7	WWW: http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC	4	WWW: http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC
8
9	Port maintainer: Jason W. Bacon
10	jwbacon@tds.net

Lines 1-8 Link Here

(-)science/minc2/pkg-message (-8 lines)
1	=============================================================================
2	For questions or comments regarding this port, please contact the
3	port maintainer: jwbacon@tds.net
4
5	For MINC usage, please visit the MINC WEB site at
6
7	http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC
8	=============================================================================

Lines 3-9 Link Here

(-)science/minc2/pkg-plist (-2 / +12 lines)
3	bin/invert_raw_image	3	bin/invert_raw_image
4	bin/minc_modify_header	4	bin/minc_modify_header
5	bin/mincaverage	5	bin/mincaverage
		6	bin/mincblob
6	bin/minccalc	7	bin/minccalc
		8	bin/minccmp
		9	bin/minccomplete
7	bin/mincconcat	10	bin/mincconcat
8	bin/mincconvert	11	bin/mincconvert
9	bin/minccopy	12	bin/minccopy
Lines 20-28 Link Here
20	bin/mincmakescalar	23	bin/mincmakescalar
21	bin/mincmakevector	24	bin/mincmakevector
22	bin/mincmath	25	bin/mincmath
		26	bin/mincmorph
23	bin/mincpik	27	bin/mincpik
24	bin/mincresample	28	bin/mincresample
25	bin/mincreshape	29	bin/mincreshape
		30	bin/mincsample
26	bin/mincstats	31	bin/mincstats
27	bin/minctoecat	32	bin/minctoecat
28	bin/minctoraw	33	bin/minctoraw
Lines 36-41 Link Here
36	bin/vff2mnc	41	bin/vff2mnc
37	bin/voxeltoworld	42	bin/voxeltoworld
38	bin/worldtovoxel	43	bin/worldtovoxel
		44	bin/xfm2def
39	bin/xfmconcat	45	bin/xfmconcat
40	bin/xfmflip	46	bin/xfmflip
41	bin/xfminvert	47	bin/xfminvert
Lines 67-83 Link Here
67	lib/libminc2.a	73	lib/libminc2.a
68	lib/libminc2.la	74	lib/libminc2.la
69	lib/libminc2.so	75	lib/libminc2.so
70	lib/libminc2.so.2	76	lib/libminc2.so.3
71	lib/libvolume_io2.a	77	lib/libvolume_io2.a
72	lib/libvolume_io2.la	78	lib/libvolume_io2.la
73	lib/libvolume_io2.so	79	lib/libvolume_io2.so
74	lib/libvolume_io2.so.2	80	lib/libvolume_io2.so.3
75	man/man1/dcm2mnc.1.gz	81	man/man1/dcm2mnc.1.gz
76	man/man1/ecattominc.1.gz	82	man/man1/ecattominc.1.gz
77	man/man1/invert_raw_image.1.gz	83	man/man1/invert_raw_image.1.gz
78	man/man1/minc_modify_header.1.gz	84	man/man1/minc_modify_header.1.gz
79	man/man1/mincaverage.1.gz	85	man/man1/mincaverage.1.gz
		86	man/man1/mincblob.1.gz
80	man/man1/minccalc.1.gz	87	man/man1/minccalc.1.gz
		88	man/man1/minccmp.1.gz
		89	man/man1/minccomplete.1.gz
81	man/man1/mincconcat.1.gz	90	man/man1/mincconcat.1.gz
82	man/man1/mincconvert.1.gz	91	man/man1/mincconvert.1.gz
83	man/man1/minccopy.1.gz	92	man/man1/minccopy.1.gz
Lines 108-113 Link Here
108	man/man1/upet2mnc.1.gz	117	man/man1/upet2mnc.1.gz
109	man/man1/vff2mnc.1.gz	118	man/man1/vff2mnc.1.gz
110	man/man1/voxeltoworld.1.gz	119	man/man1/voxeltoworld.1.gz
		120	man/man1/xfm2def.1.gz
111	man/man1/xfmconcat.1.gz	121	man/man1/xfmconcat.1.gz
112	man/man1/xfmflip.1.gz	122	man/man1/xfmflip.1.gz
113	man/man1/xfminvert.1.gz	123	man/man1/xfminvert.1.gz

Return to bug 187764

Lines 1-21 Link Here

(-)science/minc2/Makefile (-20 / +39 lines)
1	# Created by: jbacon	1	# Created by: jbacon
2	# $FreeBSD: head/science/minc2/Makefile 341763 2014-01-29 17:31:04Z thierry $	2	# $FreeBSD: head/science/minc2/Makefile 341763 2014-01-29 17:31:04Z thierry $
3		3
4	############################################################################
5	# http://www.bic.mni.mcgill.ca/software/minc/
6	# is the ultimate source for MINC, and will always contain the latest
7	# source release. If this port is not up to date enough for you,
8	# you can download the latest sources and build manually. On FreeBSD,
9	# you must configure with the environment variable LDFLAGS set to
10	# ${LOCALBASE}/lib so that the configure script will find libnetcdf.
11	# Of course, the netcdf port must be installed first.
12
13	PORTNAME= minc	4	PORTNAME= minc
14	PORTVERSION= 2.0.18	5	PORTVERSION= 2.2.00
15	PORTEPOCH= 1	6	PORTEPOCH= 1
16	CATEGORIES= science biology	7	CATEGORIES= science biology
17	MASTER_SITES= http://packages.bic.mni.mcgill.ca/tgz/ \	8	MASTER_SITES= GH
18	http://www.nitrc.org/frs/download.php/801/
19	PKGNAMESUFFIX= 2	9	PKGNAMESUFFIX= 2
20		10
21	MAINTAINER= ports@FreeBSD.org	11	MAINTAINER= ports@FreeBSD.org
Lines 23-38 Link Here
23		13
24	LICENSE= BSD	14	LICENSE= BSD
25		15
26	LIB_DEPENDS= libnetcdf.so.4:${PORTSDIR}/science/netcdf \	16	LIB_DEPENDS= libhdf5.so.7:${PORTSDIR}/science/hdf5-18 \
27	libhdf5.so.0:${PORTSDIR}/science/hdf5	17	libnetcdf.so.7:${PORTSDIR}/science/netcdf4
28		18	RUN_DEPENDS= bash:${PORTSDIR}/shells/bash
29	USE_AUTOTOOLS= libtool	19
30	USE_LDCONFIG= yes	20	USE_GITHUB= yes
31	CPPFLAGS+= ${PTHREAD_CFLAGS} -I${LOCALBASE}/include -DH5_USE_16_API	21	GH_ACCOUNT= BIC-MNI
32	LDFLAGS+= -L${LOCALBASE}/lib ${PTHREAD_LIBS}	22	GH_TAGNAME= release-${PORTVERSION}
		23	GH_COMMIT= 6f2f5b9
		24
		25	USES= bison gmake perl5 shebangfix
		26	SHEBANG_FILES= progs/mincview/mincview
		27	USE_PERL5= build
		28	USE_AUTOTOOLS= libtoolize aclocal autoheader automake autoconf
		29	LIBTOOLIZE_ARGS=--copy --force
		30	ACLOCAL_ARGS= -I m4 --automake-acdir=${ACLOCAL_DIR}
		31	AUTOMAKE_ARGS= --add-missing
33	CONFIGURE_ARGS= --enable-shared=yes --enable-static=yes	32	CONFIGURE_ARGS= --enable-shared=yes --enable-static=yes
		33	USE_LDCONFIG= yes
		34
		35	CFLAGS+= -Wno-return-type
		36	CPPFLAGS+= -I${LOCALBASE}/include
		37	LDFLAGS+= -L${LOCALBASE}/lib
34		38
35	CONFLICTS= minc-1* zh-tk-[0-9]*	39	CONFLICTS= minc-1* zh-tk-[0-9]*
36	LATEST_LINK= minc2	40
		41	STRIP_FILES= dcm2mnc ecattominc invert_raw_image minc_modify_header \
		42	mincaverage mincblob minccalc minccmp \
		43	mincconcat mincconvert minccopy mincdump \
		44	mincexpand mincextract mincgen mincinfo \
		45	minclookup mincmakescalar mincmakevector mincmath \
		46	mincmorph mincresample mincreshape mincsample \
		47	mincstats minctoecat minctoraw mincwindow \
		48	mnc2nii nii2mnc rawtominc transformtags \
		49	upet2mnc vff2mnc voxeltoworld worldtovoxel \
		50	xfm2def xfmconcat xfminvert
		51
		52	post-install:
		53	.for i in ${STRIP_FILES}
		54	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/${i}
		55	.endfor
37		56
38	.include <bsd.port.mk>	57	.include <bsd.port.mk>

Line 0 Link Here

(-)science/minc2/files/patch-Makefile.am (+53 lines)
	1	--- Makefile.am.orig
	2	+++ Makefile.am
	3	@@ -274,28 +274,28 @@
	4	m4/smr_WITH_BUILD_PATH.m4
	5
	6	ezMINC_files = \
	7	- ezminc/examples/volume_msq_dist.cpp
	8	- ezminc/examples/CMakeLists.txt
	9	- ezminc/examples/fuzzy_volume_similarity.cpp
	10	- ezminc/examples/trilinear_resample.cpp
	11	- ezminc/examples/volume_avg.cpp
	12	- ezminc/examples/volume_gtc_similarity.cpp
	13	- ezminc/examples/volume_similarity.cpp
	14	- ezminc/minc_1_simple_rw.cpp
	15	- ezminc/minc_1_simple_rw.h
	16	- ezminc/minc_io_4d_volume.h
	17	- ezminc/minc_io_fixed_vector.h
	18	- ezminc/minc_io_simple_volume.h
	19	- ezminc/tests/minc_rw_test2.cpp
	20	- ezminc/tests/minc_rw_test_4d.cpp
	21	- ezminc/tests/minc_rw_test_simple.cpp
	22	- ezminc/tests/CMakeLists.txt
	23	- ezminc/tests/ezminc_rw_test.cpp
	24	- ezminc/tests/ezminc_stats.cpp
	25	- ezminc/minc_1_simple.h
	26	- ezminc/CMakeLists.txt
	27	- ezminc/minc_1_rw.cpp
	28	- ezminc/minc_1_rw.h
	29	+ ezminc/examples/volume_msq_dist.cpp \
	30	+ ezminc/examples/CMakeLists.txt \
	31	+ ezminc/examples/fuzzy_volume_similarity.cpp \
	32	+ ezminc/examples/trilinear_resample.cpp \
	33	+ ezminc/examples/volume_avg.cpp \
	34	+ ezminc/examples/volume_gtc_similarity.cpp \
	35	+ ezminc/examples/volume_similarity.cpp \
	36	+ ezminc/minc_1_simple_rw.cpp \
	37	+ ezminc/minc_1_simple_rw.h \
	38	+ ezminc/minc_io_4d_volume.h \
	39	+ ezminc/minc_io_fixed_vector.h \
	40	+ ezminc/minc_io_simple_volume.h \
	41	+ ezminc/tests/minc_rw_test2.cpp \
	42	+ ezminc/tests/minc_rw_test_4d.cpp \
	43	+ ezminc/tests/minc_rw_test_simple.cpp \
	44	+ ezminc/tests/CMakeLists.txt \
	45	+ ezminc/tests/ezminc_rw_test.cpp \
	46	+ ezminc/tests/ezminc_stats.cpp \
	47	+ ezminc/minc_1_simple.h \
	48	+ ezminc/CMakeLists.txt \
	49	+ ezminc/minc_1_rw.cpp \
	50	+ ezminc/minc_1_rw.h \
	51	ezminc/minc_io_exceptions.h
	52
	53	voxeltoworld_SOURCES = progs/coordinates/voxeltoworld.c

Lines 1-20 Link Here

(-)science/minc2/files/patch-conversion_minctoecat_machine_indep.c (-20 lines)
1	--- conversion/minctoecat/machine_indep.c.orig 2007-03-29 07:08:46.000000000 +0200
2	+++ conversion/minctoecat/machine_indep.c 2014-01-28 22:55:57.000000000 +0100
3	@@ -61,7 +61,7 @@
4	}
5
6	#if defined(__alpha) \|\| defined(_WIN32) /* LITTLE_ENDIAN : alpha, intel */
7	-ftovaxf(f, bufr)
8	+void ftovaxf(f, bufr)
9	float f;
10	unsigned short *bufr;
11	{
12	@@ -84,7 +84,7 @@
13	bufr[1] = ret >>16;
14	}
15	#else /* BIG ENDIAN : sun hp sgi*/
16	-ftovaxf(orig,number)
17	+void ftovaxf(orig,number)
18	unsigned short number[2];
19	float orig;
20	{