Attachment 141052 Details for Bug 187764 – science_minc2.diff

[patch] science_minc2.diff

science_minc2.diff (text/x-diff), 8.74 KB, created by tkato432 on 2014-05-03 12:57:50 UTC

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Creator: tkato432

Created: 2014-05-03 12:57:50 UTC

Size: 8.74 KB

patch

obsolete

>diff -urN /usr/ports/science/minc2/Makefile science/minc2/Makefile
>--- /usr/ports/science/minc2/Makefile	2014-05-03 16:49:01.000000000 +0900
>+++ science/minc2/Makefile	2014-05-03 20:00:00.000000000 +0900
>@@ -1,22 +1,11 @@
> # Created by: jbacon
> # $FreeBSD: head/science/minc2/Makefile 352855 2014-05-03 03:17:19Z sunpoet $
> 
>-############################################################################
>-# 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
>-# ${LOCALBASE}/lib so that the configure script will find libnetcdf.
>-# Of course, the netcdf port must be installed first.
>-
> PORTNAME=	minc
>-PORTVERSION=	2.0.18
>-PORTREVISION=	2
>+PORTVERSION=	2.2.00
> PORTEPOCH=	1
> CATEGORIES=	science biology
>-MASTER_SITES=	http://packages.bic.mni.mcgill.ca/tgz/ \
>-		http://www.nitrc.org/frs/download.php/801/
>+MASTER_SITES=	GH
> PKGNAMESUFFIX=	2
> 
> MAINTAINER=	ports@FreeBSD.org
>@@ -24,16 +13,45 @@
> 
> LICENSE=	BSD
> 
>-LIB_DEPENDS=	libnetcdf.so:${PORTSDIR}/science/netcdf \
>-		libhdf5.so:${PORTSDIR}/science/hdf5
>-
>-USE_AUTOTOOLS=	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-${PORTVERSION}
>+GH_COMMIT=	6f2f5b9
>+
>+USES=		bison gmake perl5 shebangfix
>+SHEBANG_FILES=	progs/mincview/mincview
>+USE_PERL5=	build
>+USE_AUTOTOOLS=	libtoolize aclocal autoheader automake autoconf
>+LIBTOOLIZE_ARGS=--copy --force
>+ACLOCAL_ARGS=	-I m4 --automake-acdir=${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]*
>-LATEST_LINK=	minc2
>+
>+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>
>diff -urN /usr/ports/science/minc2/distinfo science/minc2/distinfo
>--- /usr/ports/science/minc2/distinfo	2014-01-30 04:14:24.000000000 +0900
>+++ science/minc2/distinfo	2014-05-03 20:00:00.000000000 +0900
>@@ -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 -urN /usr/ports/science/minc2/files/patch-Makefile.am science/minc2/files/patch-Makefile.am
>--- /usr/ports/science/minc2/files/patch-Makefile.am	1970-01-01 09:00:00.000000000 +0900
>+++ science/minc2/files/patch-Makefile.am	2014-05-03 20:00:00.000000000 +0900
>@@ -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 -urN /usr/ports/science/minc2/files/patch-conversion_minctoecat_machine_indep.c science/minc2/files/patch-conversion_minctoecat_machine_indep.c
>--- /usr/ports/science/minc2/files/patch-conversion_minctoecat_machine_indep.c	2014-01-30 04:14:24.000000000 +0900
>+++ science/minc2/files/patch-conversion_minctoecat_machine_indep.c	1970-01-01 09:00:00.000000000 +0900
>@@ -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 -urN /usr/ports/science/minc2/pkg-descr science/minc2/pkg-descr
>--- /usr/ports/science/minc2/pkg-descr	2014-01-23 03:07:19.000000000 +0900
>+++ science/minc2/pkg-descr	2014-05-03 20:00:00.000000000 +0900
>@@ -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 -urN /usr/ports/science/minc2/pkg-message science/minc2/pkg-message
>--- /usr/ports/science/minc2/pkg-message	2014-01-23 03:07:19.000000000 +0900
>+++ science/minc2/pkg-message	1970-01-01 09:00:00.000000000 +0900
>@@ -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 -urN /usr/ports/science/minc2/pkg-plist science/minc2/pkg-plist
>--- /usr/ports/science/minc2/pkg-plist	2014-01-30 04:14:24.000000000 +0900
>+++ science/minc2/pkg-plist	2014-05-03 20:00:00.000000000 +0900
>@@ -3,7 +3,10 @@
> 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/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/vff2mnc
> bin/voxeltoworld
> bin/worldtovoxel
>+bin/xfm2def
> bin/xfmconcat
> bin/xfmflip
> bin/xfminvert
>@@ -67,17 +73,20 @@
> lib/libminc2.a
> lib/libminc2.la
> lib/libminc2.so
>-lib/libminc2.so.2
>+lib/libminc2.so.3
> lib/libvolume_io2.a
> lib/libvolume_io2.la
> lib/libvolume_io2.so
>-lib/libvolume_io2.so.2
>+lib/libvolume_io2.so.3
> 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/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

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Attachments on bug 187764: 141051 | 141052 | 141053 | 141054 | 143446 | 144520