ports/187764: science/minc2: Update to version 2.2.00
KATO Tsuguru
tkato432 at yahoo.com
Wed Mar 19 18:40:09 UTC 2014
>Number: 187764
>Category: ports
>Synopsis: science/minc2: Update to version 2.2.00
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Wed Mar 19 18:40:08 UTC 2014
>Closed-Date:
>Last-Modified:
>Originator: KATO Tsuguru
>Release: FreeBSD 8.4-RELEASE-p7 i386
>Organization:
>Environment:
>Description:
- Update to version 2.2.00
New file:
files/patch-Makefile.am
Remove file:
files/patch-conversion_minctoecat_machine_indep.c
pkg-message
>How-To-Repeat:
>Fix:
diff -urN /usr/ports/science/minc2/Makefile science/minc2/Makefile
--- /usr/ports/science/minc2/Makefile 2014-01-30 04:14:24.000000000 +0900
+++ science/minc2/Makefile 2014-03-20 00:00:00.000000000 +0900
@@ -1,21 +1,11 @@
# 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
-# ${LOCALBASE}/lib so that the configure script will find libnetcdf.
-# Of course, the netcdf port must be installed first.
-
PORTNAME= minc
-PORTVERSION= 2.0.18
+PORTVERSION= 2.2.00
PORTEPOCH= 1
CATEGORIES= science biology
-MASTER_SITES= http://packages.bic.mni.mcgill.ca/tgz/ \
- http://www.nitrc.org/frs/download.php/801/
+MASTER_SITES= GH
PKGNAMESUFFIX= 2
MAINTAINER= ports at FreeBSD.org
@@ -23,16 +13,45 @@
LICENSE= BSD
-LIB_DEPENDS= libnetcdf.so.4:${PORTSDIR}/science/netcdf \
- libhdf5.so.0:${PORTSDIR}/science/hdf5
-
-USE_AUTOTOOLS= libtool
-USE_LDCONFIG= yes
-CPPFLAGS+= ${PTHREAD_CFLAGS} -I${LOCALBASE}/include -DH5_USE_16_API
-LDFLAGS+= -L${LOCALBASE}/lib ${PTHREAD_LIBS}
+LIB_DEPENDS= libhdf5.so.7:${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]*
-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 2014-03-20 00:00:00.000000000 +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 2014-03-20 00:00:00.000000000 +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 2014-03-20 00:00:00.000000000 +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 at 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 at 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 2014-03-20 00:00:00.000000000 +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
>Release-Note:
>Audit-Trail:
>Unformatted:
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