From owner-freebsd-ports-bugs@FreeBSD.ORG Wed Mar 19 18:40:09 2014 Return-Path: Delivered-To: freebsd-ports-bugs@smarthost.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 43A2973B for ; Wed, 19 Mar 2014 18:40:09 +0000 (UTC) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:1900:2254:206c::16:87]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id 23C8CC89 for ; Wed, 19 Mar 2014 18:40:09 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.8/8.14.8) with ESMTP id s2JIe9gS002664 for ; Wed, 19 Mar 2014 18:40:09 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.8/8.14.8/Submit) id s2JIe8L1002663; Wed, 19 Mar 2014 18:40:08 GMT (envelope-from gnats) Resent-Date: Wed, 19 Mar 2014 18:40:08 GMT Resent-Message-Id: <201403191840.s2JIe8L1002663@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, KATO Tsuguru Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id EBB9B4CD for ; Wed, 19 Mar 2014 18:32:00 +0000 (UTC) Received: from omta01.auone-net.jp (mail-or2-f145.auone-net.jp [111.87.219.145]) by mx1.freebsd.org (Postfix) with ESMTP id B05E0C06 for ; Wed, 19 Mar 2014 18:32:00 +0000 (UTC) Received: from coppermine.my.domain (ZT028161.ppp.dion.ne.jp [59.128.28.161]) by omta01.auone-net.jp (au one net mail) with ESMTP id 59AF298000A for ; Thu, 20 Mar 2014 03:31:54 +0900 (JST) Message-Id: <20140320032635.c255a6d9748efaf751c7d6af@yahoo.com> Date: Thu, 20 Mar 2014 03:26:35 +0900 From: KATO Tsuguru To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/187764: science/minc2: Update to version 2.2.00 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.17 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 19 Mar 2014 18:40:09 -0000 >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 -# ${LOCALBASE}/lib so that the configure script will find libnetcdf. -# Of course, the netcdf port must be installed first. - PORTNAME= minc -PORTVERSION= 2.0.18 +PORTVERSION= 2.2.00 PORTEPOCH= 1 CATEGORIES= science biology -MASTER_SITES= http://packages.bic.mni.mcgill.ca/tgz/ \ - http://www.nitrc.org/frs/download.php/801/ +MASTER_SITES= GH PKGNAMESUFFIX= 2 MAINTAINER= ports@FreeBSD.org @@ -23,16 +13,45 @@ LICENSE= BSD -LIB_DEPENDS= libnetcdf.so.4:${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 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@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 2014-03-20 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: