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

Browse Source 
PR:		187764
Submitted by:	Ports Fury
This commit is contained in:
John Marino 2014-07-29 21:33:51 +00:00
parent cefa532781
commit 549b6db417
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=363398
7 changed files with 97 additions and 62 deletions
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48
science/minc2/Makefile
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@ -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
# ${LOCALBASE}/lib so that the configure script will find libnetcdf.
# Of course, the netcdf port must be installed first.
PORTNAME= minc
PORTVERSION= 2.0.18
PORTREVISION= 2
PORTVERSION= 2.2.00
PORTEPOCH= 1
CATEGORIES= science biology
MASTER_SITES= http://packages.bic.mni.mcgill.ca/tgz/ \
http://www.nitrc.org/frs/download.php/801/
MASTER_SITES= GH
PKGNAMESUFFIX= 2
MAINTAINER= ports@FreeBSD.org
@ -24,18 +13,35 @@ COMMENT= Medical Imaging NetCDF
LICENSE= BSD
BROKEN= Fails to build
LIB_DEPENDS= libhdf5.so:${PORTSDIR}/science/hdf5 \
libnetcdf.so:${PORTSDIR}/science/netcdf
RUN_DEPENDS= bash:${PORTSDIR}/shells/bash
LIB_DEPENDS= libnetcdf.so:${PORTSDIR}/science/netcdf \
libhdf5.so:${PORTSDIR}/science/hdf5
USE_GITHUB= yes
GH_ACCOUNT= BIC-MNI
GH_TAGNAME= release-${PORTVERSION}
GH_COMMIT= 6f2f5b9
USES= libtool
USE_LDCONFIG= yes
CPPFLAGS+= ${PTHREAD_CFLAGS} -I${LOCALBASE}/include -DH5_USE_16_API
LDFLAGS+= -L${LOCALBASE}/lib ${PTHREAD_LIBS}
USES= bison gmake libtool perl5 shebangfix
SHEBANG_FILES= progs/mincview/mincview
USE_PERL5= build
USE_AUTOTOOLS= libtoolize aclocal autoheader automake autoconf
LIBTOOLIZE_ARGS=--copy --force
ACLOCAL_ARGS= -I m4 --automake-acdir=${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>

4
science/minc2/distinfo
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@ -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

53
science/minc2/files/patch-Makefile.am Normal file
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@ -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

20
science/minc2/files/patch-conversion_minctoecat_machine_indep.c
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@ -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;
{

8
science/minc2/pkg-descr
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@ -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

8
science/minc2/pkg-message
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@ -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
=============================================================================

18
science/minc2/pkg-plist
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@ -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