From owner-freebsd-ports-bugs@FreeBSD.ORG Tue Oct 29 17:20:02 2013 Return-Path: Delivered-To: freebsd-ports-bugs@smarthost.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTP id 22ED491E for ; Tue, 29 Oct 2013 17:20:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) 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 F350526AA for ; Tue, 29 Oct 2013 17:20:01 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.7/8.14.7) with ESMTP id r9THK1ZI012384 for ; Tue, 29 Oct 2013 17:20:01 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.7/8.14.7/Submit) id r9THK1MM012383; Tue, 29 Oct 2013 17:20:01 GMT (envelope-from gnats) Date: Tue, 29 Oct 2013 17:20:01 GMT Message-Id: <201310291720.r9THK1MM012383@freefall.freebsd.org> To: freebsd-ports-bugs@FreeBSD.org Cc: From: Jason Bacon Subject: Re: ports/182077: maintainer update: science/minc2 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.14 Precedence: list Reply-To: Jason Bacon List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 29 Oct 2013 17:20:02 -0000 The following reply was made to PR ports/182077; it has been noted by GNATS. From: Jason Bacon To: bug-followup@FreeBSD.org, jwbacon@tds.net Cc: Subject: Re: ports/182077: maintainer update: science/minc2 Date: Tue, 29 Oct 2013 12:19:30 -0500 This is a multi-part message in MIME format. --------------080405020108030109000806 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Attached is a patch reverting to MINC 2.0.18. Note also that I'm giving up the port for adoption. I have not worked in the medical imaging field for years and I need to narrow my focus to my current work. There is a working 2.2.0 port at http://sourceforge.net/projects/freebsdwip/, but I would not recommend using it. According to the website (http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC), 2.0.18 is the latest stable release. The developers informed me that development of this branch has ceased and they are planning an official release of the new, separate libminc and minctools ASAP. -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jason W. Bacon jwbacon@tds.net Circumstances don't make a man: They reveal him. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --------------080405020108030109000806 Content-Type: text/plain; name="minc2-diff.txt" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="minc2-diff.txt" diff -ruN --exclude=CVS /usr/ports/science/minc2/Makefile /usr/wip/science/minc2/Makefile --- /usr/ports/science/minc2/Makefile 2013-10-26 08:41:31.000000000 -0500 +++ /usr/wip/science/minc2/Makefile 2013-10-29 12:00:41.000000000 -0500 @@ -11,13 +11,14 @@ # Of course, the netcdf port must be installed first. PORTNAME= minc -PORTVERSION= 2.2.00 -PORTREVISION= 1 +PORTVERSION= 2.0.18 +PORTEPOCH= 1 CATEGORIES= science biology -MASTER_SITES= http://packages.bic.mni.mcgill.ca/tgz/ +MASTER_SITES= http://packages.bic.mni.mcgill.ca/tgz/ \ + http://www.nitrc.org/frs/download.php/801/ PKGNAMESUFFIX= 2 -MAINTAINER= jwbacon@tds.net +MAINTAINER= ports@FreeBSD.org COMMENT= Medical Imaging NetCDF LICENSE= BSD @@ -25,13 +26,56 @@ LIB_DEPENDS= netcdf.4:${PORTSDIR}/science/netcdf \ hdf5:${PORTSDIR}/science/hdf5 +USE_AUTOTOOLS= libtool USE_LDCONFIG= yes -USES= cmake:outsource bison:build CPPFLAGS+= ${PTHREAD_CFLAGS} -I${LOCALBASE}/include -DH5_USE_16_API LDFLAGS+= -L${LOCALBASE}/lib ${PTHREAD_LIBS} -CMAKE_ARGS= -DMINC2_BUILD_SHARED_LIBS:BOOL=YES +CONFIGURE_ARGS= --enable-shared=yes --enable-static=yes CONFLICTS= minc-1* zh-tk-[0-9]* +LATEST_LINK= minc2 + +MAN1= dcm2mnc.1 \ + ecattominc.1 \ + invert_raw_image.1 \ + minc_modify_header.1 \ + mincaverage.1 \ + minccalc.1 \ + mincconcat.1 \ + mincconvert.1 \ + minccopy.1 \ + mincdiff.1 \ + mincedit.1 \ + mincexpand.1 \ + mincextract.1 \ + mincgen.1 \ + mincheader.1 \ + minchistory.1 \ + mincinfo.1 \ + minclookup.1 \ + mincmakescalar.1 \ + mincmakevector.1 \ + mincmath.1 \ + mincpik.1 \ + mincresample.1 \ + mincreshape.1 \ + mincstats.1 \ + minctoecat.1 \ + minctoraw.1 \ + mincview.1 \ + mincwindow.1 \ + mnc2nii.1 \ + nii2mnc.1 \ + rawtominc.1 \ + transformtags.1 \ + upet2mnc.1 \ + vff2mnc.1 \ + voxeltoworld.1 \ + xfmconcat.1 \ + xfmflip.1 \ + xfminvert.1 + +MAN3= ParseArgv.3 NO_STAGE= yes diff -ruN --exclude=CVS /usr/ports/science/minc2/distinfo /usr/wip/science/minc2/distinfo --- /usr/ports/science/minc2/distinfo 2013-07-10 08:59:11.000000000 -0500 +++ /usr/wip/science/minc2/distinfo 2013-10-24 10:43:46.000000000 -0500 @@ -1,2 +1,2 @@ -SHA256 (minc-2.2.00.tar.gz) = e689d3612db6241125e3155d5a5c109d4da6f4bd774cc00a7e6729f2a790a174 -SIZE (minc-2.2.00.tar.gz) = 1665189 +SHA256 (minc-2.0.18.tar.gz) = 674cc89c43edfdb1957251c0124ea83252740c667cf3c4d9fc6183dcdb10f3e5 +SIZE (minc-2.0.18.tar.gz) = 1628038 diff -ruN --exclude=CVS /usr/ports/science/minc2/files/patch-conversion__minctoecat__machine_indep.c /usr/wip/science/minc2/files/patch-conversion__minctoecat__machine_indep.c --- /usr/ports/science/minc2/files/patch-conversion__minctoecat__machine_indep.c 1969-12-31 18:00:00.000000000 -0600 +++ /usr/wip/science/minc2/files/patch-conversion__minctoecat__machine_indep.c 2013-10-24 10:43:46.000000000 -0500 @@ -0,0 +1,11 @@ +--- conversion/minctoecat/machine_indep.c.orig 2012-07-20 17:16:13.000000000 +0200 ++++ conversion/minctoecat/machine_indep.c 2012-07-20 17:17:48.000000000 +0200 +@@ -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 -ruN --exclude=CVS /usr/ports/science/minc2/pkg-plist /usr/wip/science/minc2/pkg-plist --- /usr/ports/science/minc2/pkg-plist 2013-07-10 08:59:11.000000000 -0500 +++ /usr/wip/science/minc2/pkg-plist 2013-10-24 10:43:46.000000000 -0500 @@ -3,7 +3,6 @@ bin/invert_raw_image bin/minc_modify_header bin/mincaverage -bin/mincblob bin/minccalc bin/mincconcat bin/mincconvert @@ -21,11 +20,9 @@ bin/mincmakescalar bin/mincmakevector bin/mincmath -bin/mincmorph bin/mincpik bin/mincresample bin/mincreshape -bin/mincsample bin/mincstats bin/minctoecat bin/minctoraw @@ -36,9 +33,11 @@ bin/rawtominc bin/transformtags bin/upet2mnc +bin/vff2mnc bin/voxeltoworld bin/worldtovoxel bin/xfmconcat +bin/xfmflip bin/xfminvert include/ParseArgv.h include/minc.h @@ -65,12 +64,12 @@ include/volume_io/volume.h include/volume_io/volume_cache.h include/voxel_loop.h -lib/MINC2Config.cmake -lib/UseMINC2.cmake +lib/libminc2.a +lib/libminc2.la lib/libminc2.so lib/libminc2.so.2 -lib/libminc2.so.2.2.00 +lib/libvolume_io2.a +lib/libvolume_io2.la lib/libvolume_io2.so lib/libvolume_io2.so.2 -lib/libvolume_io2.so.2.2.00 @dirrm include/volume_io --------------080405020108030109000806--