debian/0000775000000000000000000000000012236042231007163 5ustar debian/README.Debian0000664000000000000000000000030411313514236011225 0ustar amide for Debian ---------------- This package comes without libfame support because of the non-free license. -- Dominique Belhachemi Sun, 16 Dec 2007 21:32:15 +0200 debian/dirs0000664000000000000000000000003511313514236010051 0ustar usr/bin var/lib/scrollkeeper debian/source/0000775000000000000000000000000012120616025010463 5ustar debian/source/format0000664000000000000000000000001411301174376011701 0ustar 3.0 (quilt) debian/copyright0000664000000000000000000000617111313514236011127 0ustar Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat Debianized-By: Dominique Belhachemi Debianized-Date: Fri, 20 Apr 2007 21:32:15 +0200 Original-Source: http://amide.sourceforge.net/ Files: debian/* Copyright: 2008, Dominique Belhachemi License: GPL-2+ The Debian packaging is licensed under the GPL-2 or any later version, see `/usr/share/common-licenses/GPL-2' Files: * Copyright: Copyright (©) 2007 by Andy Loening License: GPL-2+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License, version 2 can be found in `/usr/share/common-licenses/GPL-2'. Files: ./src/amitk_xif_sel.h ./src/amitk_xif_sel.c ./src/amitk_dial.h ./src/amitk_dial.c Copyright: Copyright (©) 2007 by Andy Loening License: LGPL-2+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. . On Debian systems, the complete text of the GNU Lesser General Public License, version 2.0 can be found in `/usr/share/common-licenses/LGPL-2'. Files: Documentation Copyright: Copyright (©) 2007 by Andy Loening License: GFDL-1.1 Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.1 or any later version published by the Free Software Foundation with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. You may obtain a copy of the GNU Free Documentation License from the Free Software Foundation by visiting their Web site (http://www.fsf.org) or by writing to: Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. . On Debian systems, the complete text of the GNU Free Documentation License can be found in `/usr/share/common-licenses/GFDL` debian/amide.menu0000664000000000000000000000024511313514236011135 0ustar ?package(amide):command="/usr/bin/amide" icon="/usr/share/pixmaps/amide_logo_small.xpm" needs="X11" \ section="Applications/Science/Medicine" title="AMIDE" debian/changelog0000664000000000000000000001342212236042231011037 0ustar amide (1.0.4-1build1) trusty; urgency=low * No change rebuild against libav 9. -- Dmitrijs Ledkovs Tue, 05 Nov 2013 01:06:33 +0000 amide (1.0.4-1) unstable; urgency=low * New upstream version (adapted patch) Closes: #653365 * debian/gcc-4.8_format-securit.patch: Make sure package builds even with --format-security enabled (hardening flags) * debian/control: - cme fix dpkg-control - debhelper 9 - anonscm in Vcs fields * Make use of dh-autoreconf Closes: #653366 * debian/patches/deprecated-libav.patch: recent libavcodec removed some more deprecated functions (thanks for the patch to Andreas Moog ) Closes: #720779 * deactivate doc creation because it breaks the build process. Any help to get this running again is appreciated (see debian/rules) * debian/rules: Propagate hardening options -- Andreas Tille Mon, 26 Aug 2013 14:53:06 +0200 amide (1.0.1-1) unstable; urgency=low * debian/README.source: removed because it is redundant * debian/control: - Fixed Vcs-Svn - Removed quilt from Build-Depends * debian/install: Make use of dh_install * debian/rules: - Remove unknown option --enable-rpm-install from configure arguments - rewritten to make use of dh --with autotools_dev * debian/deletable.files: Removed. There is no need to hack around broken upstream tarballs. Upstream contains some *.bak files which are cleaned up in upstream clean target * debian/autogen.sh: Not needed when properly using autotools-dev -- Andreas Tille Mon, 09 Jan 2012 13:28:04 +0100 amide (1.0.0-1) unstable; urgency=low * New upstream release * update watch file to scan 1.x branch * fix vcs field -- Dominique Belhachemi Sat, 17 Sep 2011 21:07:29 -0400 amide (0.9.3-1) unstable; urgency=low * New upstream version * Removed debian/get-orig-source which is not needed because uscan works perfectly and thus use uscan in debian/rules * debian/control: - Standards-Version: 3.9.1 (no changes needed) - Debhelper 8 - Build-Depends: libdcmtk2-dev (instead of libdcmtk1-dev) * debian/source/format: 3.0 (quilt) * debian/rules: Deleted some useless comments * debian/patches/20_fix_add_needed.diff: Removed because applied upstream * debian/patches/10_all.diff: Make sure -lavcodec and -lavutil is propagated to the linker -- Andreas Tille Thu, 24 Mar 2011 15:02:45 +0100 amide (0.9.2-1.1) unstable; urgency=low * Non-maintainer upload. * Bug fix: "FTBFS with --no-add-needed, missing -lavutil", thanks to Julien Cristau (Closes: #614725). -- Reinhard Tartler Fri, 25 Feb 2011 15:54:15 +0100 amide (0.9.2-1) unstable; urgency=low * New upstream release * put amide under Debian Med team maintenance * changed patch system: using quilt instead of dpatch * added dependency: libavcodec-dev for fly through video generation -- Dominique Belhachemi Sun, 20 Dec 2009 13:38:23 -0500 amide (0.9.1-5) unstable; urgency=low * debian/control: removed build dependency to libglib1.2-dev and libglib1.2-dev (Closes: #523561) * debian/control: Standards-Version: 3.8.1 * debian/changelog: updated references to GPL-2 and LGPL-2 -- Dominique Belhachemi Sun, 12 Apr 2009 13:01:46 -0400 amide (0.9.1-4) unstable; urgency=low * debian/compat: bumped up to 7 * debian/rules: uses "dh_prep" now instead of "dh_clean -k" * desktop category is now: Categories=Graphics;MedicalSoftware; * Add var/lib/scrollkeeper to debian/dirs to so that scrollkeeper-update can use it when run by the build system. * debugging symbols disabled * debian/copyright: is now machine-interpretable -- Dominique Belhachemi Wed, 19 Feb 2009 09:21:05 -0500 amide (0.9.1-3) unstable; urgency=low * fixed lintian warning: doc-base-uses-applications-section * debian/control: Standards-Version: 3.8.0 * debian/control: DM-Upload-Allowed: yes -- Dominique Belhachemi Fri, 14 Nov 2008 17:10:08 +0100 amide (0.9.1-2) unstable; urgency=low * debian/control: removed builddep libniftiio1-dev (Closes: #460358) * fixed implicit pointer conversion (Closes: #457987) -- Dominique Belhachemi Sun, 13 Jan 2008 10:53:11 +0200 amide (0.9.1-1) unstable; urgency=low * New upstream release * debian-policy 3.7.3 ready -- Dominique Belhachemi Thu, 20 Dec 2007 22:33:35 +0200 amide (0.8.22-2) unstable; urgency=low * debian/control: libvolpack1-dev added -- Dominique Belhachemi Sun, 16 Dec 2007 23:13:12 +0200 amide (0.8.22-1) unstable; urgency=low * New upstream release * make use of autoconf in debian/rules file * small bug-fixes * Back to menu-1 format * all changes can be found in debian/patches folder -- Dominique Belhachemi Sat, 23 Nov 2007 19:13:12 +0200 amide (0.8.21-4) unstable; urgency=low * debian/control: libniftiio1-dev dependency is updated -- Dominique Belhachemi Mon, 16 Sep 2007 22:10:46 +0200 amide (0.8.21-3) unstable; urgency=low * debian/copyright : Add documentation license (GFDL) without optional features. -- Dominique Belhachemi Sat, 28 Jul 2007 02:54:46 +0200 amide (0.8.21-2) unstable; urgency=low * Add missing libglib1.2-dev dependency. -- Dominique Belhachemi Wed, 18 Jul 2007 01:42:45 +0200 amide (0.8.21-1) unstable; urgency=low * Initial release (Closes: #409913) -- Dominique Belhachemi Sun, 15 Jul 2007 21:32:15 +0200 debian/control0000664000000000000000000000302712236042231010570 0ustar Source: amide Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Dominique Belhachemi , Andreas Tille Section: graphics Priority: optional Build-Depends: gnome-doc-utils, gtk-doc-tools, libtool, debhelper (>= 9), autotools-dev, dh-autoreconf, scrollkeeper, libxml-parser-perl, libgtk2.0-dev, libxml2-dev, libgnomecanvas2-dev, libgnomeui-dev, libgsl0-dev, libmdc2-dev, libdcmtk2-dev, libvolpack1-dev, libavcodec-dev, libavformat-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/amide/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/amide/trunk/ Homepage: http://amide.sourceforge.net/ Package: amide Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: software for Medical Imaging AMIDE: (Amide's a Medical Imaging Data Examiner) AMIDE is a tool for viewing and analyzing medical image data sets. It's capabilities include the simultaneous handling of multiple data sets imported from a variety of file formats, image fusion, 3D region of interest drawing and analysis, volume rendering, and rigid body alignments. debian/rules0000775000000000000000000000133312207321070010242 0ustar #!/usr/bin/make -f export ACLOCAL = aclocal -I m4 %: dh $@ --with autotools_dev --with autoreconf override_dh_autoreconf: dh_autoreconf --as-needed debian/configure_helper.sh override_dh_auto_configure: dh_auto_configure -- \ --disable-amide-debug \ --config-cache \ --disable-dependency-tracking \ --prefix=/usr \ --localstatedir=/var/lib/amide \ --mandir=\$${prefix}/share/man \ --infodir=\$${prefix}/share/info \ --localstatedir=/var/lib/amide \ LDFLAGS="-Wl,-z,defs $(LDFLAGS)" # To create the docs this option would be needed but it causes build problems # see doc/README # --enable-gtk-doc \ override_dh_auto_test: echo "Do not run autotest" get-orig-source: uscan --verbose --force-download debian/watch0000664000000000000000000000016711636037203010226 0ustar # See uscan(1) for format # Compulsory line, this is a version 3 file version=3 http://sf.net/amide/amide-(1.*)\.tgz debian/install0000664000000000000000000000005711702557454010575 0ustar debian/amide_logo_small.xpm usr/share/pixmaps/ debian/patches/0000775000000000000000000000000012207323540010615 5ustar debian/patches/10_all.patch0000664000000000000000000000675712206650036012727 0ustar Author: Andreas Tille Date: Thu, 24 Mar 2011 15:02:45 +0100 LastChanged: Mon, 26 Aug 2013 14:53:06 +0200 Description: debian/patches/10_all.diff: Make sure -lavcodec and -lavutil is propagated to the linker --- a/configure.in +++ b/configure.in @@ -69,7 +69,7 @@ if test $CC = "gcc"; then read continue_with_bad_gcc if test $continue_with_bad_gcc = "y"; then echo "removing optimizations to reduce potential of compiler error" - CFLAGS="-g -O0" + CFLAGS="-O0" else exit 1 fi @@ -92,8 +92,8 @@ fi dnl check for various libraries and programs that we might need AM_PATH_GSL(1.1.1, FOUND_LIBGSL=yes, FOUND_LIBGSL=no) -AC_CHECK_LIB(ecat, matrix_open, FOUND_LIBECAT=yes, FOUND_LIBECAT=no, -L/sw/lib) -AC_CHECK_LIB(volpack, vpGetErrorString, FOUND_VOLPACK=yes, FOUND_VOLPACK=no, -lm -L/sw/lib -L/usr/local/lib) +AC_CHECK_LIB(ecat, matrix_open, FOUND_LIBECAT=yes, FOUND_LIBECAT=no) +AC_CHECK_LIB(volpack, vpGetErrorString, FOUND_VOLPACK=yes, FOUND_VOLPACK=no, -lm) AM_PATH_XMEDCON(0.10.0, FOUND_XMEDCON=yes, FOUND_XMEDCON=no) @@ -101,8 +101,8 @@ AM_PATH_XMEDCON(0.10.0, FOUND_XMEDCON=ye dnl switch to C++ for DCMTK library stuff - also, if pthread is on the platform, probably need that dnl autoconf doesn't have a nice macro for checking for c++ libraries, therefore the below: AC_CHECK_LIB(pthread, pthread_mutex_init, THREAD_LIBS="-lpthread", THREAD_LIBS="") -AMIDE_LIBDCMDATA_LIBS="-L/usr/local/dicom/lib -L/usr/lib64/dcmtk -L/usr/lib/dcmtk -ldcmdata -loflog -lofstd -lz $THREAD_LIBS" -AMIDE_LIBDCMDATA_CFLAGS="-I/usr/local/dicom/include" +AMIDE_LIBDCMDATA_LIBS="-ldcmdata -lofstd -loflog -lavcodec -lavutil -lz $THREAD_LIBS" +AMIDE_LIBDCMDATA_CFLAGS="-I/usr/include/dcmtk/dcmdata" dnl 2010.02.20 AMIDE_LIBDCMDATA_CFLAGS="-I/usr/local/dicom/include/dcmtk/dcmdata -I/usr/local/dicom/include/dcmtk/ofstd -I/usr/local/dicom/include -I/usr/include/dcmtk/dcmdata -I/usr/local/include/dcmtk/ofstd -I/sw/include/dcmtk/dcmdata -I/sw/include/dcmtk/ofstd -I/sw/include/dcmtk" saved_libs="${LIBS}" LIBS="${LIBS} ${AMIDE_LIBDCMDATA_LIBS}" @@ -249,7 +249,7 @@ if (test $enable_libmdc = yes) && (test AC_DEFINE(AMIDE_LIBMDC_SUPPORT, 1, Define to compile with (X)MedCon) dnl 2007.10.28 - new xmedcon's should be using glib2/gtk2, dont' have to overwrite XMEDCON_LIBS - dnl XMEDCON_LIBS="-L/usr/local/lib -L/usr/local/xmedcon/lib -lmdc" + dnl XMEDCON_LIBS="-lmdc" AC_SUBST(XMEDCON_LIBS) else echo "compiling without xmedcon/libmdc file support" @@ -453,6 +453,3 @@ AC_OUTPUT dnl help/C/Makefile dnl help/es/Makefile -dnl Move the spec file so it won't get eaten by make distclean -echo "Moving SPEC file to base directory" -mv etc/amide.spec ./ --- a/src/Makefile.am +++ b/src/Makefile.am @@ -23,12 +23,11 @@ AM_CFLAGS = \ $(GSL_CFLAGS) \ $(LIBFAME_CFLAGS) \ $(AMIDE_GTK_CFLAGS) \ - $(AMIDE_DEBUG_CFLAGS) \ $(AMIDE_CHECK_OBSOLETE_CFLAGS) \ $(AMIDE_LIBDCMDATA_CFLAGS) \ - -I/usr/local/include \ $(XMEDCON_CFLAGS) \ - $(FFMPEG_CFLAGS) + $(LIBAVCODEC_CFLAGS) \ + -DG_DISABLE_DEPRECATED @@ -41,12 +40,11 @@ bin_PROGRAMS = amide # to be behind the DCMTK stuff amide_LDADD = \ $(GSL_LIBS) \ - $(LIBFAME_LIBS) \ $(AMIDE_LIBECAT_LIBS) \ $(AMIDE_LIBVOLPACK_LIBS) \ $(AMIDE_GTK_LIBS) \ $(XMEDCON_LIBS) \ - $(FFMPEG_LIBS) \ + $(LIBAVCODEC_LIBS) \ $(AMIDE_LIBDCMDATA_LIBS) \ $(AMIDE_LDADD_WIN32) --- a/etc/amide.desktop.in +++ b/etc/amide.desktop.in @@ -1,5 +1,4 @@ [Desktop Entry] -Encoding=UTF-8 _GenericName=Medical Image Examiner _Name=Amide _Comment=analysis tool for medical images debian/patches/deprecated-libav.patch0000664000000000000000000000160212207132566015036 0ustar Author: Andreas Moog LastChanged: Tue, 27 Aug 2013 13:34:56 +0200 BugsDebian: http://bugs.debian.org/720779 Description: recent libavcodec removed some more deprecated functions and your source code needs some adaptation. --- amide-1.0.4.orig/src/mpeg_encode.c +++ amide-1.0.4/src/mpeg_encode.c @@ -261,7 +261,7 @@ return NULL; } - encode->context = avcodec_alloc_context(); + encode->context = avcodec_alloc_context3(NULL); if (!encode->context) { g_warning("couldn't allocate memory for encode->context"); encode_free(encode); @@ -299,7 +299,7 @@ encode->context->trellis=2; /* turn trellis quantization on */ /* open it */ - if (avcodec_open(encode->context, encode->codec) < 0) { + if (avcodec_open2(encode->context, encode->codec, NULL) < 0) { g_warning("could not open codec"); encode_free(encode); return NULL; debian/patches/series0000664000000000000000000000010212207132302012015 0ustar 10_all.patch gcc-4.8_format-security.patch deprecated-libav.patch debian/patches/gcc-4.8_format-security.patch0000664000000000000000000000255412206735634016136 0ustar Author: Andreas Tille LastChanged: Mon, 26 Aug 2013 14:53:06 +0200 Description: Make sure package builds even with --format-security enabled (build using hardening flags) --- amide-1.0.4.orig/src/amide.c +++ amide-1.0.4/src/amide.c @@ -146,7 +146,7 @@ #endif NULL); - g_warning(comments); + g_warning("%s", comments); g_free(comments); amide_gconf_set_string("MISSING_FUNCTIONALITY", "AlreadyWarned", VERSION); --- amide-1.0.4.orig/src/amide_gnome.c +++ amide-1.0.4/src/amide_gnome.c @@ -166,7 +166,7 @@ g_set_error (error, AMIDE_GNOME_URL_ERROR, AMIDE_GNOME_URL_ERROR_VFS, - gnome_vfs_result_to_string (result)); + "%s", gnome_vfs_result_to_string (result)); } return FALSE; --- amide-1.0.4.orig/src/amitk_space_edit.c +++ amide-1.0.4/src/amitk_space_edit.c @@ -335,7 +335,7 @@ GTK_DIALOG_DESTROY_WITH_PARENT, GTK_MESSAGE_QUESTION, GTK_BUTTONS_OK_CANCEL, - message); + "%s", message); return_val = gtk_dialog_run(GTK_DIALOG(question)); gtk_widget_destroy(question); --- amide-1.0.4.orig/src/tb_profile.c +++ amide-1.0.4/src/tb_profile.c @@ -368,7 +368,7 @@ } results = results_as_string(tb_profile); - fprintf(file_pointer, results); + fprintf(file_pointer, "%s", results); g_free(results); fclose(file_pointer); debian/docs0000664000000000000000000000000611313514236010036 0ustar todo debian/amide.doc-base_deactivated0000664000000000000000000000056412207320350014202 0ustar ## See debian/rules and doc/README for problems creating the docs Document: amide Title: Debian amide Manual Author: Andy Loening Abstract: This manual describes what amide is and how it can be used to analyze medical imaging data sets. Section: Science/Medicine Format: HTML Index: /usr/share/gtk-doc/html/amitk/index.html Files: /usr/share/gtk-doc/html/amitk/*.html debian/compat0000664000000000000000000000000212206650162010366 0ustar 9 debian/amide_logo_small.xpm0000664000000000000000000001660011313514236013207 0ustar /* XPM */ static char * amide_logo_small_xpm[] = { "32 32 332 2", " c None", ". c #3230B9", "+ c #2F2DA9", "@ c #2F2DA4", "# c #2F2DA3", "$ c #302E9A", "% c #323067", "& c #343396", "* c #2F2D8C", "= c #2F2D84", "- c #2F2D87", "; c #2F2D8A", "> c #2F2D8D", ", c #2F2D8E", "' c #2F2D89", ") c #2F2D85", "! c #2F2D82", "~ c #2E2D61", "{ c #33317E", "] c #2F2D93", "^ c #2F2D98", "/ c #2F2D9B", "( c #2F2D9C", "_ c #2F2D9A", ": c #2F2D96", "< c #2F2D91", "[ c #2F2D83", "} c #2F2D81", "| c #2F2D73", "1 c #1B1A25", "2 c #2F2D4D", "3 c #2E2C69", "4 c #2F2D8B", "5 c #2F2D97", "6 c #2F2DA7", "7 c #2F2DAA", "8 c #2F2DA8", "9 c #2F2DA2", "0 c #2F2D94", "a c #2F2D7E", "b c #272644", "c c #0F0F11", "d c #0C0C12", "e c 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