--- minc-2.1.00.orig/debian/watch +++ minc-2.1.00/debian/watch @@ -0,0 +1,2 @@ +version=3 +http://packages.bic.mni.mcgill.ca/tgz/ minc-(.*)\.tar\.gz --- minc-2.1.00.orig/debian/compat +++ minc-2.1.00/debian/compat @@ -0,0 +1 @@ +5 --- minc-2.1.00.orig/debian/copyright +++ minc-2.1.00/debian/copyright @@ -0,0 +1,17 @@ +This package was debianized by Steven Robbins in August 2001 +It was downloaded from ftp://ftp.bic.mni.mcgill.ca/pub/minc/ + +Download site as of 2006-02-05 is +http://packages.bic.mni.mcgill.ca/tgz/ + +Copyright 1993-2000 Peter Neelin and David MacDonald, McConnell Brain +Imaging Centre, Montreal Neurological Institute, McGill University. +Permission to use, copy, modify, and distribute this software and its +documentation for any purpose and without fee is hereby granted, +provided that the above copyright notice appear in all copies. The +author and McGill University make no representations about the +suitability of this software for any purpose. It is provided "as is" +without express or implied warranty. + +Current upstream maintenance is done on the minc-development mailing list. +http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development --- minc-2.1.00.orig/debian/control +++ minc-2.1.00/debian/control @@ -0,0 +1,70 @@ +Source: minc +Homepage: http://www.bic.mni.mcgill.ca/ServicesSoftware/HomePage +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team +Uploaders: Steve M. Robbins +Build-Depends: cdbs, debhelper (>= 5), csh, libnetcdf-dev, zlib1g-dev, texlive-latex-base, + libhdf5-mpi-dev +Standards-Version: 3.8.0.0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/minc/trunk/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/minc/trunk/?rev=0&sc=0 + +Package: minc-tools +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, csh | c-shell, netcdf-bin, libgetopt-tabular-perl, libtext-format-perl, imagemagick +Description: MNI medical image format tools + This package contains tools to manipulate MINC files. + . + The Minc file format is a highly flexible medical image file format + built on top of the NetCDF generalized data format. The format is + simple, self-describing, extensible, portable and N-dimensional, with + programming interfaces for both low-level data access and high-level + volume manipulation. On top of the libraries is a suite of generic + image-file manipulation tools. The format, libraries and tools are + designed for use in a medical-imaging research environment: they are + simple and powerful and make no attempt to provide a pretty interface + to users. + +Package: libminc2-1 +Section: libs +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: MNI medical image format library + This package contains the libraries libminc2 and libvolume_io2. + . + The Minc file format is a highly flexible medical image file format. + Minc version 1 is built on top of the NetCDF generalized data format. + Minc version 2 is built on top of the HDF data format. This library + handles both formats. In each case the format is + simple, self-describing, extensible, portable and N-dimensional, with + programming interfaces for both low-level data access and high-level + volume manipulation. On top of the libraries is a suite of generic + image-file manipulation tools. The format, libraries and tools are + designed for use in a medical-imaging research environment : they are + simple and powerful and make no attempt to provide a pretty interface + to users. + +Package: libminc-dev +Conflicts: libminc0-dev +Replaces: libminc0-dev +Section: libdevel +Architecture: any +Depends: ${misc:Depends}, libminc2-1 (= ${binary:Version}), libnetcdf-dev, + libhdf5-openmpi-dev [!arm !armel !hppa !mips !mipsel !s390], + libhdf5-lam-dev [ arm armel hppa mips mipsel s390] +Description: MNI medical image format development environment + This package contains the library and headers for libminc2 and + libvolume_io2. + . + The Minc file format is a highly flexible medical image file format. + Minc version 1 is built on top of the NetCDF generalized data format. + Minc version 2 is built on top of the HDF data format. This library + handles both formats. In each case the format is + simple, self-describing, extensible, portable and N-dimensional, with + programming interfaces for both low-level data access and high-level + volume manipulation. On top of the libraries is a suite of generic + image-file manipulation tools. The format, libraries and tools are + designed for use in a medical-imaging research environment : they are + simple and powerful and make no attempt to provide a pretty interface + to users. --- minc-2.1.00.orig/debian/changelog +++ minc-2.1.00/debian/changelog @@ -0,0 +1,287 @@ +minc (2.1.00-2) unstable; urgency=low + + * patches/decompress-whole-file.diff: New. Always decompress entire + file to support compressed MINC2 files. Closes: #585676. + + -- Steve M. Robbins Sun, 18 Dec 2011 20:47:03 -0600 + +minc (2.1.00-1) unstable; urgency=low + + * New upstream. + + -- Steve M. Robbins Tue, 17 Aug 2010 22:26:16 -0500 + +minc (2.0.18+cvs20100518-1) unstable; urgency=low + + * Pull upstream CVS, contains fixes for netcdf 4. Closes: #577060, + #581296. + + * control: replace libhdf5-*-dev (differing by architecture) by + libhdf5-mpi-dev. + + -- Steve M. Robbins Tue, 18 May 2010 22:53:30 -0500 + +minc (2.0.18-1) unstable; urgency=low + + * New upstream version. + + -- Steve M. Robbins Mon, 20 Jul 2009 05:24:57 -0500 + +minc (2.0.17-1) unstable; urgency=low + + * New upstream version. + + * patches/04_manpages.diff: + * debian/patches/05_parseargv.diff: Remove; applied upstream. + + -- Steve M. Robbins Tue, 20 Jan 2009 19:37:41 -0600 + +minc (2.0.16-4) unstable; urgency=low + + * debian/patches/05_parseargv.diff: New. Patch from upstream to fix arg + parsing on 64bits. Closes: #510629. This was also the root cause of + mincheader and mincdiff failing. Closes: #506276. + + * debian/control: Add ${misc:Depends}, since we use debhelper. + + * debian/rules: Do not install test code acr_test, dicom_test. + + -- Steve M. Robbins Sat, 03 Jan 2009 16:29:06 -0600 + +minc (2.0.16-3) unstable; urgency=low + + * debian/control: Extend previous fix from build-depends to libminc-dev + depends; i.e. use OpenMPI, except for certain architectures that it + doesn't support; in the latter case, use LAM. + + -- Steve M. Robbins Thu, 30 Oct 2008 01:10:55 -0500 + +minc (2.0.16-2) unstable; urgency=low + + * debian/control: Use OpenMPI, except for certain architectures that it + doesn't support; in the latter case, use LAM. + + -- Steve M. Robbins Mon, 27 Oct 2008 01:11:21 -0500 + +minc (2.0.16-1) unstable; urgency=low + + * New upstream release. + - debian/patches/02_mincedit-no-escape-chars: Remove. Applied upstream. + + * debian/control: Switch dependencies from libhdf5-serial-dev to + libhdf5-openmpi-dev. + * debian/rules: Add CFLAGS=-I/usr/include/mpi to configure step so that + mpi.h is found. + + * debian/control: Remove tetex-bin from build-depends (was alternative + to texlive-latex-base). Update Standards-Version to 3.8.0 (no + changes). + + * debian/patches/04_manpages.diff: Fix errors in manpages, mainly + removal of trailing TAB characters. + + * debian/rules: Adhere to parallel keyword in DEB_BUILD_OPTIONS. + + -- Steve M. Robbins Sat, 11 Oct 2008 23:55:42 -0500 + +minc (2.0.15-3) unstable; urgency=low + + [ Charles Plessy ] + * debian/copyright: added upstream contact information. + + [ Steve M. Robbins ] + * debian/patches/02_mincedit-no-escape-chars.diff: New. Patch mincedit + to remove extraneous \n strings. Closes: 486048. + * debian/control: Replace depends on netcdfg-dev by libnetcdf-dev. + + -- Steve M. Robbins Thu, 19 Jun 2008 07:40:18 -0500 + +minc (2.0.15-2) unstable; urgency=low + + [ David Paleino ] + * debian/rules: + - conditionally add -mieee on Alpha (Closes: #368263) + + [ Steve M. Robbins ] + * debian/rules: Do not run the tests, since they are broken in many + ways; e.g. int functions without a return statement, checking + floating-point values without a tolerance, and some that require a + list of files on the command line but are given none. + Closes: #475808. + + -- Steve M. Robbins Thu, 05 Jun 2008 09:24:59 -0500 + +minc (2.0.15-1) unstable; urgency=low + + [ Charles Plessy ] + * Changed the doc-base section according to the new policy. + + [ David Paleino ] + * New upstream release + * debian/patches/: + - 01_mincedit-sensible-viewer.diff updated + - 02_testdir-runtests.diff removed, it has been merged upstream + + -- Steve M. Robbins Sat, 31 May 2008 05:53:26 -0500 + +minc (2.0.14-2) unstable; urgency=low + + * rules: Don't install byte_swap or extract; can use "dd" instead of + these tools. Closes: #459834. + + * control: Package minc-tools depends on libgetopt-tabular-perl. + * rules: Don't install Tabular.pm. + * Getopt-Tabular-0.3/Tabular.pm: Remove. + * patches/04_progs-use-lib.diff: Remove. + * copyright: Remove Getopt-Tabular license text. + + -- Steve M. Robbins Fri, 11 Jan 2008 00:30:23 -0600 + +minc (2.0.14-1) unstable; urgency=low + + * New upstream version. Closes: #450922. + + * control: Set Maintainer to debian-med-packaging. + Add build-depends for libhdf5-serial-dev, texlive-latex-base. + Rename package libminc0 --> libminc2-1. + Rename package libminc0-dev --> libminc-dev. + Package libminc-dev depends on libhdf5-serial-dev. + Package minc-tools depends on imagemagick. + + * rules: Configure with --enable-minc2 and --enable-acr-nema. + + * Getopt-Tabular-0.3/Tabular.pm: New. Perl module required + for mincpik and xfmflip. Closes: #457074. + + * patches/02_testdir-runtests.diff: New. Fix test scripts. + + * patches/03_mincview.diff: New. Use 'display' from ImageMagick rather + than 'xv' to view images. Closes: #457072. + + * patches/04_progs-use-lib.diff: New. Add "use lib" declaration to find + the private Getopt::Tabular. + + -- Steve M. Robbins Sun, 06 Jan 2008 20:40:29 -0600 + +minc (1.5-2) NEVER UPLOADED; urgency=low + + * Rewrite build system using cdbs. + - patches/01_mincedit-sensible-viewer.diff: New. Obtained from + existing Debian diff. + + * control: Build-depend on texlive-latex-base | tetex-bin, rather + than just tetex-bin. Update to Standards-Version 3.7.3 (no change + required). Use ${binary:Version} rather than ${Source-Version} + for libminc0-dev dependency on libminc0. Add Homepage and Vcs-Svn + header fields. + + -- Steve M. Robbins Sat, 29 Dec 2007 15:10:53 -0600 + +minc (1.5-1) unstable; urgency=low + + * New upstream. + + -- Steve M. Robbins Mon, 13 Nov 2006 23:26:13 -0600 + +minc (1.4.1-1) unstable; urgency=low + + * New upstream. + + -- Steve M. Robbins Sat, 11 Nov 2006 22:14:54 -0600 + +minc (1.4-4) unstable; urgency=low + + * testdir/create_grid_xfm.c: initialize minc_input_options properly. + Closes: #352183. + + -- Steve M. Robbins Sat, 18 Feb 2006 17:33:37 -0500 + +minc (1.4-3) unstable; urgency=low + + * Build-depend on csh. Closes: #351826. + + -- Steve M. Robbins Tue, 7 Feb 2006 20:02:56 -0500 + +minc (1.4-2) unstable; urgency=low + + * Rebuild to pick up new netcdf library, which changed due to + C++ ABI transition (#346312). + + -- Steve M. Robbins Sun, 5 Feb 2006 13:45:22 -0500 + +minc (1.4-1) unstable; urgency=low + + * New upstream version. + + * Omit dependency on essential package debianutils (for sensible-editor). + Closes: #316425. + + -- Steve M. Robbins Sun, 3 Jul 2005 20:31:25 -0400 + +minc (1.3-3) unstable; urgency=low + + * progs/mincedit/mincedit: use "sensible-editor" rather than "emacs". + Closes: #292194. + + -- Steve M. Robbins Thu, 27 Jan 2005 22:21:22 -0500 + +minc (1.3-2) unstable; urgency=low + + * debian/rules: package minc-tools depends on libtext-format-perl + Closes: #278840. + + -- Steve M. Robbins Sun, 28 Nov 2004 14:33:06 -0500 + +minc (1.3-1) unstable; urgency=low + + * New upstream version. + Re-ran all auto*-tools machinery, as upstream used fairly old versions. + + * configure.in: Don't use AC_CONFIG_LINKS to generate link + volume_io/Include/volume_io to directory volume_io/Include as + autoconf 2.59 chokes on it. Use shell commands instead. + + * volume_io/Include/internal_volume_io.h: Do not include "config.h". + * volume_io/Prog_utils/files.c: Do include "config.h". + * volume_io/Prog_utils/time.c: Restore call to sysconf( _SC_CLK_TCK ), + wrapped in #if HAVE_SYSCONF. + + -- Steve M. Robbins Sun, 28 Nov 2004 14:22:03 -0500 + +minc (1.2-1) unstable; urgency=low + + * New upstream version. + + * debian/control: minc-tools depend on netcdf-bin (for ncdump). + + -- Steve M. Robbins Sat, 20 Dec 2003 11:22:09 -0500 + +minc (1.1-1) unstable; urgency=low + + * New upstream. + - build shared lib package + - rename devel package to libminc0-dev + + -- Steve M. Robbins Sat, 25 Jan 2003 18:25:04 -0500 + +minc (1.0-2) unstable; urgency=low + + * libminc-dev: Depend on netcdfg-dev. + + * minc-tools: Use "csh|c-shell" in dependency line, remove dependency + on "awk" on advice from lintian. + + * Update from upstream CVS. + + -- Steve M. Robbins Wed, 11 Dec 2002 12:27:36 -0500 + +minc (1.0-1) unstable; urgency=low + + * Initial Debian package. Closes: #153629. + + * Patches from upstream CVS: + - libsrc/ParseArgv.h: declare as "extern C" + - progs/mincstats/mincstats.c: fix segfault + + -- Steve M. Robbins Mon, 29 Jul 2002 16:06:56 -0400 + --- minc-2.1.00.orig/debian/index.html +++ minc-2.1.00/debian/index.html @@ -0,0 +1,38 @@ + + +MINC Documentation + + + + +

MINC Library Documentation

+ +The MINC library is used to deal with large files typically encountered +in medical imaging. A +programmer's guide +and a +programmer's reference manual +are available. + +

The volume_io library, also included +in the MINC package, provides a simpler programming interface to MINC. +

+ +

Additional Links

+ +

For other tools that work well with MINC, check +out the MNI Brain +Imaging Centre software toolbox. +

+ +

There are two mailing lists for MINC: minc +users and minc +development. +

+ +
+
+Last modified: Sat Dec 20 09:27:53 EST 2003 + --- minc-2.1.00.orig/debian/rules +++ minc-2.1.00/debian/rules @@ -0,0 +1,53 @@ +#! /usr/bin/make -f + +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/class/autotools.mk +include /usr/share/cdbs/1/rules/simple-patchsys.mk + +CFLAGS = -I/usr/include/mpi + +# This should fix #368263 +ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH) +ifeq ($(CPU),alpha) + CFLAGS += -mieee +endif + +ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) + NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) + MAKEFLAGS += -j$(NUMJOBS) +endif + +DEB_CONFIGURE_EXTRA_FLAGS = --enable-shared --enable-minc2 --enable-acr-nema CFLAGS="$(CFLAGS)" +DEB_MAKE_BUILD_TARGET = all +#DEB_MAKE_CHECK_TARGET = check + +ps_docs = doc/prog_ref.ps doc/prog_guide.ps volume_io/Documentation/volume_io.ps + +build/libminc-dev:: $(ps_docs) + +doc/prog_ref.ps doc/prog_guide.ps: + $(MAKE) -C doc docs + +volume_io/Documentation/volume_io.ps: + $(MAKE) -C volume_io/Documentation docs + +install/minc-tools:: + rm -f debian/tmp/usr/bin/mincexample? + rm -f debian/tmp/usr/bin/byte_swap + rm -f debian/tmp/usr/bin/extract + rm -f debian/tmp/usr/bin/acr_test + rm -f debian/tmp/usr/bin/dicom_test + dh_install -pminc-tools --autodest debian/tmp/usr/bin + dh_install -pminc-tools --autodest debian/tmp/usr/share/man + dh_link -pminc-tools \ + /usr/share/man/man1/voxeltoworld.1 \ + /usr/share/man/man1/worldtovoxel.1 + +install/libminc2-1:: + dh_install -plibminc2-1 --autodest debian/tmp/usr/lib/lib*.so.* + +install/libminc-dev:: + dh_install -plibminc-dev --autodest debian/tmp/usr/lib/lib*.so + dh_install -plibminc-dev --autodest debian/tmp/usr/lib/lib*.a + dh_install -plibminc-dev --autodest debian/tmp/usr/include + dh_installdocs -plibminc-dev $(ps_docs) debian/index.html --- minc-2.1.00.orig/debian/libminc-dev.doc-base +++ minc-2.1.00/debian/libminc-dev.doc-base @@ -0,0 +1,15 @@ +Document: minc +Title: MINC Medical Image Format Library Reference +Author: Peter Neelin +Abstract: The Minc file format is a highly flexible medical image file format. + Minc version 1 is built on top of the NetCDF generalized data format. + Minc version 2 is built on top of the HDF data format. This library + handles both formats. In each case the format is + simple, self-describing, extensible, portable and N-dimensional, with + programming interfaces for both low-level data access and high-level + volume manipulation. +Section: Science/Biology + +Format: HTML +Index: /usr/share/doc/libminc-dev/index.html +Files: /usr/share/doc/libminc-dev/index.html --- minc-2.1.00.orig/debian/patches/decompress-whole-file.diff +++ minc-2.1.00/debian/patches/decompress-whole-file.diff @@ -0,0 +1,22 @@ +Description: Decompress entire externally-compressed file + MINC 1 files were often compressed using gzip or similar. There is code in + the library that decompresses only the initial portion of the file when only + the header is required (e.g. for "mincinfo"). This code is broken for MINC 2 + files, so we work around this by forcing a decompression of the entire file. +Author: Steve Robbins +Bug: 585676 +Forwarded: http://www.bic.mni.mcgill.ca/pipermail/minc-development/2011-December/000938.html + + +--- libsrc/netcdf_convenience.c.orig 2011-12-18 17:17:20.222227060 -0600 ++++ libsrc/netcdf_convenience.c 2011-12-18 17:45:40.734965898 -0600 +@@ -264,7 +264,8 @@ + #else /* Unix */ + + +- if (!header_only) { /* Decompress the whole file */ ++ /* Force whole file decompression always. */ ++ if (1) { /* Decompress the whole file */ + + (void) sprintf(whole_command, "exec %s %s > %s 2> /dev/null", + command, infile, outfile); --- minc-2.1.00.orig/debian/patches/03_mincview.diff +++ minc-2.1.00/debian/patches/03_mincview.diff @@ -0,0 +1,14 @@ +--- progs/mincview/mincview.old 2007-03-29 00:08:53.000000000 -0500 ++++ progs/mincview/mincview 2008-01-02 21:10:36.000000000 -0600 +@@ -6,9 +6,8 @@ + # Displays images with patient left on left side of the screen. + + # Constants +-set xv_visual = `xdpyinfo | awk '($1=="class:"){visual=$2};(($1=="depth:") && (visual=="TrueColor") && ($2==24)) {found=1}; END {if (found) print "-visual TrueColor"}'` +-set VIEWER = "xv" # Any pnm display program that handles a list of files +-set VIEWER_OPTIONS = "-geometry 512x512 -fixed -cmap -raw $xv_visual" ++set VIEWER = "display" # Any pnm display program that handles a list of files ++set VIEWER_OPTIONS = "-geometry 512x512" + set PGM_CODE = "P5" + set PPM_CODE = "P6" + set usage = "Usage: $0 []" --- minc-2.1.00.orig/debian/patches/01_mincedit-sensible-viewer.diff +++ minc-2.1.00/debian/patches/01_mincedit-sensible-viewer.diff @@ -0,0 +1,11 @@ +--- minc-2.0.15.orig/progs/mincedit/mincedit ++++ minc-2.0.15/progs/mincedit/mincedit +@@ -109,7 +109,7 @@ + then + editor=${EDITOR} + else +- editor="emacs" ++ editor="sensible-editor" + fi + fi + ;;