debian/0000775000000000000000000000000012211110533007155 5ustar debian/patches/0000775000000000000000000000000012031017334010611 5ustar debian/patches/series0000664000000000000000000000017312030551524012032 0ustar nonlinux_fixes no_undefineds ifdef_fixes missing_header version_suffix nuisance2advice compile_against_libglu qwt6-linking debian/patches/ifdef_fixes0000664000000000000000000000172511741350602013021 0ustar Author: Michael Hanke Description: Prevent compile failure when -DQT4_FILE_POS_BUG=1 --- a/caret_files/DeformationMapFile.cxx +++ b/caret_files/DeformationMapFile.cxx @@ -381,7 +381,7 @@ * Read the deformation map file's data. */ void -DeformationMapFile::readFileData(QFile& /*file*/, QTextStream& stream, QDataStream& binStream, +DeformationMapFile::readFileData(QFile& file, QTextStream& stream, QDataStream& binStream, QDomElement& /* rootElement */) throw (FileException) { --- a/caret_files/TopologyFile.cxx +++ b/caret_files/TopologyFile.cxx @@ -1694,7 +1694,7 @@ * Read topology file version 1. */ void -TopologyFile::readFileDataVersion1(QFile& /*file*/, +TopologyFile::readFileDataVersion1(QFile& file, QTextStream& stream, QDataStream& binStream) throw (FileException) { debian/patches/squeeze-dsc-patch-qtassistant0000777000000000000000000000000011741242110023717 2lenny-dsc-patch-qtassistantustar debian/patches/lenny-dsc-patch-qtassistant0000664000000000000000000000146511741552007016117 0ustar diff --git a/debian/control b/debian/control index bbd0e82..64a8670 100644 --- a/debian/control +++ b/debian/control @@ -3,7 +3,7 @@ Section: science Priority: optional Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko -Build-Depends: debhelper (>= 5), libqt4-dev (>= 4.3), libqt4-opengl-dev | libqt4-dev (<< 4.4.0), libqwt5-qt4-dev, libvtk5-dev, libminc-dev, libqtassistantclient-dev, libpng12-dev | libpng-dev +Build-Depends: debhelper (>= 5), libqt4-dev (>= 4.3), libqt4-opengl-dev | libqt4-dev (<< 4.4.0), libqwt5-qt4-dev, libvtk5-dev, libminc-dev, libpng12-dev | libpng-dev Standards-Version: 3.9.3 Homepage: http://brainvis.wustl.edu/wiki/index.php/Caret:About Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/caret.git debian/patches/version_suffix0000664000000000000000000000133411741350602013613 0ustar --- a/caret_common/CaretVersion.h +++ b/caret_common/CaretVersion.h @@ -29,12 +29,23 @@ #include +#ifdef CARET_BUILDID +# undef SHSH +# undef SHSHSH +# undef CARET_BUILDID_STRING +# define SHSH(x) #x +# define SHSHSH(x) SHSH(x) +# define CARET_BUILDID_STRING SHSHSH(CARET_BUILDID) /* now in "quotes" */ +#else +# undef CARET_BUILDID_STRING +#endif + /// class for caret version information class CaretVersion { public: /// Version 5.64, June 3, 2011 /// get the version of caret as a QString - static QString getCaretVersionAsString() { return "5.64"; } + static QString getCaretVersionAsString() { return "5.64" " " CARET_BUILDID_STRING; } }; #endif // __CARET_VERSION_H__ debian/patches/karmic-dsc-patch-qtassistant0000777000000000000000000000000011741242110023504 2lenny-dsc-patch-qtassistantustar debian/patches/qwt6-linking0000664000000000000000000000406212031017334013070 0ustar Description: Upstream changes introduced in version 5.6.4~dfsg.1-1ubuntu1 This patch has been created by dpkg-source during the package build. Here's the last changelog entry, hopefully it gives details on why those changes were made: . caret (5.6.4~dfsg.1-1ubuntu1) oneiric; urgency=low . * Build-depend on libqwt-dev instead of libqwt5-qt4-dev as part of qwt6 transition . The person named in the Author field signed this changelog entry. Author: Scott Kitterman --- The information above should follow the Patch Tagging Guidelines, please checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here are templates for supplementary fields that you might want to add: Origin: , Bug: Bug-Debian: http://bugs.debian.org/ Bug-Ubuntu: https://launchpad.net/bugs/ Forwarded: Reviewed-By: Last-Update: Index: caret-5.6.4~dfsg.1/caret_qmake_include.pro =================================================================== --- caret-5.6.4~dfsg.1.orig/caret_qmake_include.pro 2012-09-27 11:39:17.000000000 +0200 +++ caret-5.6.4~dfsg.1/caret_qmake_include.pro 2012-09-27 11:39:17.000000000 +0200 @@ -271,7 +271,7 @@ LIBS += -lpng -lGLU contains (DEFINES, HAVE_QWT) { - QWT_LIBS = -L$$(QWT_LIB_DIR) -lqwt-qt4 + QWT_LIBS = -L$$(QWT_LIB_DIR) -lqwt } DEFINES -= HAVE_MPEG VTK_LIBS -= -lvtkMPEG2Encode Index: caret-5.6.4~dfsg.1/caret/caret5.pro =================================================================== --- caret-5.6.4~dfsg.1.orig/caret/caret5.pro 2012-09-27 11:39:17.000000000 +0200 +++ caret-5.6.4~dfsg.1/caret/caret5.pro 2012-09-27 11:39:36.000000000 +0200 @@ -201,7 +201,7 @@ LIBS += $$VTK_LIBS LIBS -= -lvtkjpeg -lvtkpng -lvtkexpat -lvtkzlib - LIBS += -ldl -lz -lqwt-qt4 + LIBS += -ldl -lz -lqwt QTPLUGIN -= qgif qjpeg qtiff QMAKE_CXXFLAGS += -DUBUNTU debian/patches/nuisance2advice0000664000000000000000000000411411741350602013604 0ustar --- a/caret/main.cxx +++ b/caret/main.cxx @@ -613,11 +613,13 @@ #endif #ifdef UBUNTU + if (QDir("/usr/share/caret/data_files").exists() == false) { QtTextEditDialog* te = new QtTextEditDialog(theMainWindow, true, true); te->setWindowTitle("UBUNTU WARNING"); te->setMinimumSize(600, 600); te->setText(UbuntuMessage::getWarningMessage()); - te->exec(); + te->exec(); + } #endif UBUNTU if (initialSpecFiles.empty() == false) { --- a/caret_common/UbuntuMessage.h +++ b/caret_common/UbuntuMessage.h @@ -18,7 +18,7 @@ "Only versions of Caret downloaded from the above web site " "are supported by the Van Essen Laboratory." "\n\n" - "This version of Caret is an Ubuntu package and is neither " + "This version of Caret is a Debian package and is neither " "distributed, nor supported, by the Van Essen Laboratory." "\n\n" "Some functionality may be missing if Caret cannot locate " @@ -33,10 +33,15 @@ " - Surface-Based Registration\n" " - Surface Flattening\n" "\n" + "Please see /usr/share/doc/caret/README.Debian for information " + "on how to obtain the relevant resources as Debian package. " + "This message is shown, because the resource package (caret-data) " + "has not been found on this system.\n" + "\n" "The official Caret distribution contains specific versions " "of third party software known to function correctly with " - "Caret. However, this Ubuntu version of Caret relies on " - "separately installed Ubuntu packages that contain the third party " + "Caret. However, this Debian version of Caret relies on " + "separately installed Debian packages that contain the third party " "software and these third party packages may not be " "compatible with Caret. As a result, some functions in Caret " "may not operate correctly. Faulty surface drawing is one " @@ -45,4 +50,4 @@ return s; } }; -#endif // __UBUNTU_MESSAGE_H__ \ No newline at end of file +#endif // __UBUNTU_MESSAGE_H__ debian/patches/missing_header0000664000000000000000000000047311741242110013520 0ustar --- a/caret_statistics/StatisticRandomNumberOperator.h +++ b/caret_statistics/StatisticRandomNumberOperator.h @@ -28,6 +28,7 @@ /*LICENSE_END*/ #include +#include /// class for a random number generator object used with standard library algorithms class StatisticRandomNumberOperator { debian/patches/no_undefineds0000664000000000000000000000124611741350602013364 0ustar --- a/caret_brain_set/caret_brain_set.pro +++ b/caret_brain_set/caret_brain_set.pro @@ -5,12 +5,14 @@ TARGET = CaretBrainSet CONFIG += staticlib INCLUDEPATH += . +# need to include before ubuntu settings to get VTK_LIBS +include(../caret_qmake_include.pro) dll { CONFIG -= staticlib CONFIG += plugin + LIBS += $$VTK_LIBS } -include(../caret_qmake_include.pro) vs:TEMPLATE=vclib !vs:TEMPLATE=lib --- a/caret/caret5.pro +++ b/caret/caret5.pro @@ -201,7 +201,7 @@ LIBS += $$VTK_LIBS LIBS -= -lvtkjpeg -lvtkpng -lvtkexpat -lvtkzlib - LIBS += -ldl + LIBS += -ldl -lz -lqwt-qt4 QTPLUGIN -= qgif qjpeg qtiff QMAKE_CXXFLAGS += -DUBUNTU debian/patches/nonlinux_fixes0000664000000000000000000000047411741350626013624 0ustar --- a/caret_common/Basename.cxx +++ b/caret_common/Basename.cxx @@ -36,7 +36,7 @@ #include -#if defined(Q_OS_LINUX) || defined(Q_OS_GLIBC) +#if defined(Q_OS_LINUX) || defined(Q_OS_GLIBC) || defined(Q_OS_FREEBSD_KERNEL) || defined(Q_OS_HURD) static const char *period = "."; #endif #ifdef Q_OS_MAC debian/patches/jaunty-dsc-patch-qtassistant0000777000000000000000000000000011741242110023550 2lenny-dsc-patch-qtassistantustar debian/patches/lucid-dsc-patch-qtassistant0000777000000000000000000000000011741242110023336 2lenny-dsc-patch-qtassistantustar debian/patches/compile_against_libglu0000664000000000000000000000223311755431735015251 0ustar Description: Include and link with libGLU library Caret uses directly functions from libGLU without include GL/glu.h header neither linking against libGLU.so. The build process used to work luckily in the past because QtOpenGL depended it (not anymore). Author: Nicolas Bourdaud Origin: vendor Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=672020 Forwarded: no Last-Update: 2012-05-17 --- a/caret_files/BorderFile.cxx +++ b/caret_files/BorderFile.cxx @@ -34,6 +34,8 @@ #include #include +#include + #include "BorderFile.h" #include "ColorFile.h" #include "CoordinateFile.h" --- a/caret_brain_set/BrainModelOpenGL.h +++ b/caret_brain_set/BrainModelOpenGL.h @@ -30,6 +30,7 @@ #include // includes OpenGL includes ;) #include +#include #include "BorderFile.h" #include "BrainModel.h" --- a/caret_qmake_include.pro +++ b/caret_qmake_include.pro @@ -263,7 +263,7 @@ -lvtkCommon \ -lvtksys - LIBS += -lpng + LIBS += -lpng -lGLU contains (DEFINES, HAVE_QWT) { QWT_LIBS = -L$$(QWT_LIB_DIR) -lqwt-qt4 } debian/caret.manpages0000664000000000000000000000001711741242110011772 0ustar debian/caret.1 debian/TODO0000664000000000000000000000005711741277766007704 0ustar * introduce main config in /etc/caret/caret.sh debian/README.Debian-source0000664000000000000000000000110611741242110012516 0ustar README on source packaging of caret: -------------------------------------------------------------- The source tarball of the package was generated by dh_wraporig v.0.1.363 script which can be obtained from alioth's exppsy project repository: http://svn.debian.org/wsvn/pkg-exppsy/tools/dh_wraporig For this package dh_wraporig performed following actions: * Extracted files from md5:94ea24cced57512b0b5ac04d86298f7c ../caret_source.v5.61.zip * Removed following files/directories: caret_vtk4_classes * Additional parameters for tar on tarball creation were: --exclude *~ debian/README.Debian0000664000000000000000000000507111741242110011225 0ustar Caret for Debian ================ This document describes the differences between the Debian package of Caret and original Caret releases. But first a note from the Caret authors: | The official version of Caret software is produced by the Van Essen | Laboratory at Washington University and is available from: | http://brainvis.wustl.edu/wiki/index.php/Caret:About | | Only versions of Caret downloaded from the above web site are supported by | the Van Essen Laboratory. | | This version of Caret is an Debian package and is neither distributed, nor | supported, by the Van Essen Laboratory. | | Some functionality may be missing if Caret cannot locate resources that are | included in the official distribution. These functions include, but are not | limited to: | | - Help Menu Documentation | - Landmark Border Drawing | - Map Volumes to Surface via PALS Atlas | - Movie Making | - Multi-Resolution Morphing | - Projection of Foci via PALS Atlas | - Surface-Based Registration | - Surface Flattening | | The official Caret distribution contains specific versions of third party | software known to function correctly with Caret. However, this version | of Caret relies on separately installed packages that contain the third | party software and these third party packages may not be compatible with | Caret. As a result, some functions in Caret may not operate correctly. User interface -------------- The Caret package provides desktop integration via desktop files for the main Caret GUI application. Additionally, the package includes a manpage. Caret binaries are called via a simple wrapper script that configures an appropriate environment (browser selection and path settings) for using Caret on Debian systems. Missing Functionality --------------------- Due to patent issues Debian VTK comes without MPEG2 support. Therefore the MPEG support in CARET is disabled as well. CARET is build with MINC support, but at the moment without ITK support. The Debian maintainer has to figure out what kind of advantages ITK support really has. Unlike the source distribution, the binary distribution of Caret comes with a set of additional documentation and data files, e.g. for fMRI mapping data into several stereotaxic spaces. This package does not include them. Currently, all additional data packages are are available from the NeuroDebian repository at http://neuro.debian.net. However, the Debian maintainer is working on integrating this package in Debian as well. -- Michael Hanke Sat, 12 Mar 2011 14:49:15 -0500 debian/control0000664000000000000000000000351212030551535010573 0ustar Source: caret Section: science Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko Build-Depends: debhelper (>= 5), libqt4-dev (>= 4.3), libqt4-opengl-dev | libqt4-dev (<< 4.4.0), libqwt-dev, libvtk5-dev, libminc-dev, libqtassistantclient-dev, libpng12-dev | libpng-dev, libglu1-mesa-dev Standards-Version: 3.9.3 Homepage: http://brainvis.wustl.edu/wiki/index.php/Caret:About Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/caret.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/caret.git Package: caret Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: qt-assistant-compat Suggests: caret-data (>= 5.6.2~dfsg.1~) Description: Computerized Anatomical Reconstruction and Editing Toolkit This software allows for creating, viewing and manipulating surface reconstructions of the cerebral and cerebellar cortex, viewing volumes and for displaying experimental data on the surfaces and volumes. While Caret is primarily a GUI application with 'caret_command' there is also a versatile command line tool, that allows access to a substantial proportion of Caret's functionality. . Caret can download and use stereotaxic atlases (human, monkey, mouse and rat) from an open online database. . Some functionality of Caret is only available when additional data files, provided by the caret-data package, are available. This includes: . - Map volumes to surface via PALS atlas - Multi-resolution morphing - Projection of foci via PALS atlas - Surface-based registration - Surface flattening . Currently the caret-data package is only available from the NeuroDebian repository. Please see http://neuro.debian.net for more information. debian/caret.links0000664000000000000000000000043611741242110011324 0ustar /usr/lib/caret/bin/caret_app_wrapper /usr/bin/caret5 /usr/lib/caret/bin/caret_app_wrapper /usr/bin/caret_command /usr/lib/caret/bin /usr/share/caret/bin /usr/share/man/man1/caret.1.gz /usr/share/man/man1/caret5.1.gz /usr/share/man/man1/caret.1.gz /usr/share/man/man1/caret_command.1.gz debian/source/0000775000000000000000000000000011741242110010461 5ustar debian/source/format0000664000000000000000000000001411741242110011667 0ustar 3.0 (quilt) debian/caret.menu0000664000000000000000000000033511741242110011146 0ustar ?package(caret): \ needs="X11" \ section="Applications/Science/Medicine" \ title="Caret" \ longtitle="Computerized Anatomical Reconstruction and Editing Toolkit" \ command="/usr/bin/caret5" \ hints="MRI,fMRI" debian/caret_statistics/0000775000000000000000000000000011357366152012551 5ustar debian/caret.10000664000000000000000000000253511741242110010346 0ustar .TH "CARET" "1" "December 2007" "Michael Hanke" "" .SH "NAME" caret \- interactive viewing, manipulation and analysis of surface reconstructions of the cerebral and cerebellar cortex .SH "DESCRIPTION" Caret is a software application for viewing and manipulating surface reconstructions of the cerebral and cerebellar cortex, viewing volumes, for displaying experimental data on the surfaces and volumes and performing functional and structural analysis of the cerebral cortex. .PP Besides the main GUI application, the Caret software package provides a command line interface \fBcaret_command\fR that significantly improves the efficiency when analyzing a large number of datasets. .PP \fBcaret_command\fR provides an extensive help output when called with the \fI-help\fR option. .PP Questions regarding the usage of \fBCaret\fR or related theory can be posted on the \fBCaret mailing list\fR (see \fIhttp://brainvis.wustl.edu/caret/#Help\fR). .SH "SEE ALSO" The Caret homepage at .I http://brainvis.wustl.edu/caret which provides extensive documentation, including tutorials and demo datasets. .SH "AUTHOR" \fBCaret\fR was written by John Harwell, Heather Drury, Donna Hanlon and David Van Essen; Washington University School of Medicine .PP This manual page was written by Michael Hanke , for the Debian project (but may be used by others). debian/rules0000775000000000000000000000645611741350654010271 0ustar #!/usr/bin/make -f # -*- makefile -*- # build identifier BUILD_ID = $(shell cut -d ' ' -f 1,1 < /etc/issue.net)_$(shell dpkg-architecture -qDEB_BUILD_ARCH_CPU) # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 # caret build depends on some env vars export VTK_INC_DIR=$(shell dirname $$(find /usr/include/ -type f -name vtkConfigure.h | head -n1)) export VTK_LIB_DIR=/usr/lib export QWT_INC_DIR=/usr/include/qwt-qt4 export QWT_LIB_DIR=/usr/lib export NETCDF_INC_DIR=/usr/include export NETCDF_LIB_DIR=/usr/lib export QTDIR=/usr CARET_APPS="caret caret_command" CXXFLAGS = -Wall -g ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CXXFLAGS += -O0 else CXXFLAGS += -O2 endif caretcfg-%: @echo "Configuring: '$*'" cd $* && qmake-qt4 "CONFIG+=release ubuntu dll" \ "QMAKE_CXXFLAGS_RELEASE=$(CXXFLAGS) -DCARET_BUILDID=\"$(BUILD_ID)\"" \ "QMAKE_LFLAGS_RELEASE += -Wl,--as-needed" \ "CONFIG -= profile" caretbuild-%: @echo "Building: '$*'" cd $* && make caretclean-%: @echo "Cleaning: '$*'" # ignore when there is no Makefile -cd $* && make clean -cd $* && rm Makefile configure: configure-stamp configure-stamp: caretcfg-caret_statistics caretcfg-caret_common caretcfg-caret_brain_set \ caretcfg-caret_command_operations caretcfg-caret_files caretcfg-caret_cifti \ caretcfg-caret_uniformize caretcfg-caret_widgets caretcfg-caret \ caretcfg-caret_command dh_testdir touch $@ build: build-stamp build-stamp: configure \ caretbuild-caret_statistics caretbuild-caret_common \ caretbuild-caret_uniformize caretbuild-caret_widgets caretbuild-caret_files \ caretbuild-caret_brain_set caretbuild-caret_cifti caretbuild-caret_command_operations \ caretbuild-caret caretbuild-caret_command dh_testdir touch $@ clean: caretclean-caret_statistics caretclean-caret_common caretclean-caret_brain_set \ caretclean-caret_command_operations caretclean-caret_cifti caretclean-caret_files \ caretclean-caret_uniformize caretclean-caret_widgets caretclean-caret \ caretclean-caret_command dh_testdir dh_testroot -find . -name '*.so' -exec rm '{}' \; -rm caret/caret5 caret_command/caret_command rm -f build-stamp configure-stamp dh_clean install: build dh_testdir dh_testroot dh_prep dh_installdirs # install internal libs find $(CURDIR) -name '*.so' -exec cp \{\} $(CURDIR)/debian/caret/usr/lib/caret/lib \; # install binaries cp caret/caret5 caret_command/caret_command $(CURDIR)/debian/caret/usr/lib/caret/bin # ensure executable permissions for wrapper script chmod +x debian/caret_app_wrapper # Build architecture-independent files here. binary-indep: build install # We have nothing to do by default. # Build architecture-dependent files here. binary-arch: build install dh_testdir dh_testroot dh_installchangelogs dh_installdocs dh_install dh_installmenu dh_installman dh_desktop dh_link dh_strip dh_compress dh_fixperms dh_installdeb dh_shlibdeps -lcaret_brain_set:caret_command_operations:caret_uniformize:caret_widgets:caret_common:caret_files:caret_statistics:caret_cifti dh_gencontrol dh_md5sums dh_builddeb binary: binary-indep binary-arch .PHONY: build clean binary-indep binary-arch binary install configure debian/repack.sh0000775000000000000000000000211511741350602010772 0ustar #!/bin/bash # Repackage Caret upstream sources. Determine version, strip unnecessary # files, zip->tar.gz # # Usage: # repack.sh # set -e ORIGSRC=$1 if [ -z "$ORIGSRC" ]; then echo "No upstream sources given." exit 1 fi CURDIR=$(pwd) WDIR=$(mktemp -d) SUBDIR=caret5_source # put upstream sources into working dir ORIGSRC_PATH=$(readlink -f ${ORIGSRC}) cd $WDIR unzip -q $ORIGSRC_PATH UPSTREAM_VERSION_STRING=$(cat $WDIR/$SUBDIR/caret_common/CaretVersion.h | grep getCaretVersionAsString | cut -d '"' -f 2,2) UPSTREAM_VERSION=$(python -c "import re; a=str($UPSTREAM_VERSION_STRING); print re.sub(r'([0-9])', r'\1.', a.replace('.',''))[:-1]") ORIG_VERSION="$UPSTREAM_VERSION~dfsg.1" echo "Determined version: $UPSTREAM_VERSION" echo "Debian orig version: $ORIG_VERSION" # remove non-free pieces rm -rf $SUBDIR/caret_vtk4_classes mv $SUBDIR caret-$ORIG_VERSION.orig tar czf caret_$ORIG_VERSION.orig.tar.gz caret-$ORIG_VERSION.orig mv caret_$ORIG_VERSION.orig.tar.gz $CURDIR # clean working dir rm -rf $WDIR echo "Tarball is at: $CURDIR/caret_$ORIG_VERSION.orig.tar.gz" debian/caret.install0000664000000000000000000000017211741350713011660 0ustar debian/caret_app_wrapper usr/lib/caret/bin debian/caret.desktop usr/share/applications caret/caret5.png usr/share/pixmaps debian/gbp.conf0000664000000000000000000000006711741242110010603 0ustar [git-import-orig] # import filter: filter = ['debian'] debian/compat0000664000000000000000000000000211741242110010357 0ustar 5 debian/caret_command_operations/0000775000000000000000000000000011357366152014240 5ustar debian/changelog0000664000000000000000000002377412211110533011044 0ustar caret (5.6.4~dfsg.1-3ubuntu3) saucy; urgency=low * Rebuild for libminc2-1 -> libminc2-3 transition. -- Andreas Moog Mon, 02 Sep 2013 15:22:36 +0200 caret (5.6.4~dfsg.1-3ubuntu2) quantal; urgency=low * debian/patches/qwt6-linking: Also replace -lqwt-qt4 with -lqwt in caret/caret5.pro -- Michael Bienia Thu, 27 Sep 2012 11:42:13 +0200 caret (5.6.4~dfsg.1-3ubuntu1) quantal; urgency=low * Merge from Debian unstable. Remaining changes: - Build-depend on libqwt-dev instead of libqwt5-qt4-dev as part of qwt6 transition - Add debian/patches/qwt6-linking and update no_undefineds to fix link target for qwt6 -- Michael Bienia Wed, 26 Sep 2012 11:59:25 +0200 caret (5.6.4~dfsg.1-3) unstable; urgency=low * Add patch to properly link against libGLU. Thanks to Nicolas Bourdaud for the patch (Closes: #672020). -- Michael Hanke Fri, 18 May 2012 13:35:38 +0200 caret (5.6.4~dfsg.1-2) unstable; urgency=low * Add patch to support HURD as well. * Rename custom rules targets to avoid conflict with standard names, such as build-arch (Closes: #666376). * Added dummy targets build-arch and build-indep to debian/rules. * Bumped Standards-Version to 3.9.3, no changes necessary. * Removed DM-Upload flag, no longer necessary. * Install icon for Caret (Closes: #639973). * Remove backport patch for wheezy -- it has libqtassistantclient-dev now. -- Michael Hanke Wed, 11 Apr 2012 20:38:22 +0200 caret (5.6.4~dfsg.1-1ubuntu3) precise; urgency=low * Fix FTBFS, adding glu.h and -lGLU where necessary. -- Ilya Barygin Sun, 05 Feb 2012 09:46:16 +0400 caret (5.6.4~dfsg.1-1ubuntu2) precise; urgency=low * No change rebuild for vtk transition. -- Bhavani Shankar Wed, 21 Dec 2011 18:14:46 +0530 caret (5.6.4~dfsg.1-1ubuntu1) oneiric; urgency=low * Build-depend on libqwt-dev instead of libqwt5-qt4-dev as part of qwt6 transition * Add debian/patches/qwt6-linking and update no_undefineds to fix link target for qwt6 -- Scott Kitterman Fri, 26 Aug 2011 17:15:54 -0400 caret (5.6.4~dfsg.1-1build1) oneiric; urgency=low * No-change rebuild for VTK 5.6. -- Stefano Rivera Sun, 12 Jun 2011 13:45:12 +0200 caret (5.6.4~dfsg.1-1) unstable; urgency=low * New upstream release. * Adjusted packaging and patches for Cifti library addition. -- Michael Hanke Sat, 04 Jun 2011 19:15:58 -0400 caret (5.6.2~dfsg.1-3) unstable; urgency=low * Remove dysfunctional --no-undefined linker option. * Add patch to add header include required by GCC 4.6 (Closes: #625110). -- Michael Hanke Sat, 07 May 2011 12:47:02 -0400 caret (5.6.2~dfsg.1-2) unstable; urgency=low * Added patch to fix a FTBFS on kFreeBSD due to changes in the way Qt handles platform defines (i.e. Q_OS_GLIBC -> Q_OS_FREEBSD_KERNEL). Closes: #618645 * Move Caret into the "science" section of the menu (LP: #680495). -- Michael Hanke Fri, 15 Apr 2011 16:21:10 -0400 caret (5.6.2~dfsg.1-1) unstable; urgency=low * New upstream release. Merged most patches. Thanks to John Harwell and Jon Schindler. * Switch the source package format 3.0 (quilt). Moved remaining patch under quilt's arms. * Bumped Standards-Version to 3.9.1, no changes necessary. * Changed maintainer to NeuroDebian team. * Updated debian/copyright. * Improved package description to mention unavailable functionality when the caret-data package is missing. * Addressed upstream's concerns about support for the Debian package, by a) adding a patch that clearly identifies Caret as a Debian build and b) put explicit support information into README.Debian. * Patch upstream's "this is not a supported version" dialog on application startup to show information on missing functionality and how to obtain the missing pieces. Moreover, this dialog won't be displayed when all relevant data files are found on a particular system to keep the nuisance-level low. * Address removal of QAssistantClient() from Qt 4.7 by adjusting dependencies accordingly (Closes: #588977). Thanks to Alex Valavanis and for the report and patch. * Fix FTBFS due to underspecified linking for internal libraries (Closes: #554061). -- Michael Hanke Sun, 13 Mar 2011 13:32:13 -0400 caret (5.6.1.3~dfsg.1-2) unstable; urgency=low * Add slightly modified patch to address FTBFS on kFreeBSD originally provided by Cyril Brulebois -- Thanks (Closes: #575235). -- Michael Hanke Thu, 25 Mar 2010 09:08:10 -0400 caret (5.6.1.3~dfsg.1-1) unstable; urgency=low * New upstream release. Still no upstream support for VTK 5.2 (or later). * Applied patch for compatibility with GCC 4.4 (Closes: #525789). Thanks to Martin Michlmayr. * Add fixes for compatibility with VTK 5.2 (Closes: #520701, #520867). * Bumped Standards-Version to 3.8.4 -- no changes necessary. -- Michael Hanke Mon, 22 Mar 2010 20:46:27 -0400 caret (5.6.1~dfsg.1-4) unstable; urgency=low * Clarify copyright statement of the pieces of the Caret sources that have been derived from AFNI, after checking with ftp-masters (Closes: #518688). -- Michael Hanke Sat, 21 Mar 2009 19:02:39 +0100 caret (5.6.1~dfsg.1-3) unstable; urgency=low * Reverse the order of the build-dependency alternatives on libqt4 and libqt4-opengl-dev. The reason is that sbuild currently only considers the first alternative (see #403246), and hence the package FTBFS on the buildds. The alternative on libqt4-dev 4.3 is kept in the package as it allows to easily build backports on etch systems. (Closes: #519270). -- Michael Hanke Wed, 11 Mar 2009 18:42:13 +0100 caret (5.6.1~dfsg.1-2) unstable; urgency=low * Patched to build with VTK 5.2 (Closes: #518640). * Updated the upstream homepage field. Thanks to Francesco Poli for pointing this out. * Updated package description and added a reference to it. -- Michael Hanke Tue, 10 Mar 2009 15:20:06 +0100 caret (5.6.1~dfsg.1-1) unstable; urgency=low * New Upstream Version. * Added 'DM-Upload-Allowed: yes' to debian/control. * Minimized GCC compatibility-related Debian diff. Upstream applied slightly modified patch. * Fixed LD_LIBRARY_PATH setting in dh_shlibdeps call in debian/rules. -- Michael Hanke Mon, 12 Jan 2009 14:26:01 +0100 caret (5.6~dfsg.1-1) UNRELEASED; urgency=low * New upstream version. * Do not install link for caret_edit manpage, since the binary is not installed by the Debian package. * Use minc version 2 instead of old libminc0. * Bumped Standards-Version to 3.8.0 -- no changes necessary. * Several bugfixes (missing headers) for GCC 4.3 compatibility. * Adjust build-dependencies to account for the new libqt4-opengl-dev package, built by qt4-x11 (from 4.4.0-1 on). Done in a backport-friendly way, i.e. alternatively depend on libqt4-dev (>= 4.3) and (<< 4.4.0). * Added Yaroslav Halchenko to Uploaders. * caret-data is not recommended, but suggested dependency as the package is not yet in the Debian archive. Added relevant notes to README.Debian. * Converted debian/copyright into a machine readable format. * Include the AFNI licensing terms in debian/copyright as pieces of caret_uniformize were derived from AFNI. -- Michael Hanke Thu, 21 Aug 2008 09:40:25 +0200 caret (5.5.2~dfsg.1-1) UNRELEASED; urgency=low * New Upstream Version. Build-depends on Qt >= 4.3. Merged most commandline tools into 'caret_command'. * Package now honours DEB_BUILD_OPTIONS setting 'noopt'. * Build with debug symbols by default. * Debian packaging does not use upstream Makefile wrapper to qmake anymore, as it might hide build-failures. Calling qmake from debian/rules directly instead. * Simplified Debian diff to minimize conflicts between upstream changes and Debian packaging. * Set linker flags -Wl,--as-needed and --no-undefined to reduce the number of package dependencies and ensure proper internal shared libraries. * Do not build 'caret_edit' anymore as it caused problems with the internal shared libraries. This should be no problem, as it is a very simple editor and all of the 1000 editors in Debian should be able to do what 'caret_edit' does/did. -- Michael Hanke Mon, 30 Jun 2008 19:40:29 +0200 caret (5.5.1~dfsg.1-2) UNRELEASED; urgency=low * Added a manpage. * Fixed desktop and menu files to comply to the latest menu policy. -- Michael Hanke Tue, 11 Sep 2007 21:59:09 +0200 caret (5.5.1~dfsg.1-1) UNRELEASED; urgency=low * New Upstream Version. * Abandoned dpatch in favor of Git. -- Michael Hanke Sun, 8 Jul 2007 13:17:27 +0200 caret (5.5~dfsg.1-1) UNRELEASED; urgency=low [ Michael Hanke ] * Initial release. (Closes: #421703) * MPEG support is disabled as VTK in Debian does not provide the necessary library for patent reasons (see #408552). * The package builds internal libraries as shared libs instead of static linking to reduce the size of the distributed binaries. * A desktop and menu file for Caret5 was added. * Caret binaries are called via a wrapper script that sets an appropriate LD_LIBRARY_PATH for the necessary caret-internal libs and some Qt image format plugins. * Caret depends on the caret-data package that provides tutorials, online help and atlas datasets. While these files are part of the binary distribution of Caret they are not part of the sources. The Debian maintainer packaged them in a separate source package using the binary distribution as source (caret-data). [ Yaroslav Halchenko ] * Uses dh_wraporig to make source tarball DFSG-free -- Michael Hanke Tue, 22 May 2007 12:43:33 +0200 debian/caret_app_wrapper0000775000000000000000000000205411741242110012606 0ustar #! /bin/sh -e # Copyright (C) 2007 by # Michael Hanke michael.hanke@gmail.com # # This script 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. if [ "${0##*/}" = "caret_app_wrapper" ]; then echo 'caret_app_wrapper: This script should not be run like this, see caret(1) for details' 1>&2 exit 1 fi # setup library search path for carets internal libs and Qt4 plugins LD_LIBRARY_PATH=/usr/lib/caret/lib/:/usr/lib/qt4/plugins/imageformats \ CARET5_HOME=/usr/share/caret \ CARET_WEB_BROWSER=/etc/alternatives/x-www-browser \ CARET_ATLAS_DIRECTORIES=/usr/share/caret/data_files/fmri_mapping_files \ /usr/lib/caret/bin/${0##*/} "$@" debian/watch0000664000000000000000000000162711741242110010220 0ustar # Compulsory line, this is a version 3 file version=3 # download area is password protected so this will not work! # however, the password is known -- not listing it here to be polite # Following lines should at least check for the most recent available # release (for QA page) # Convert numeric portion of version after the '.' into a list of # numbers separated with a '.' since upstream seems to use string # comparisons for their versions, so line of versions like # 5.6 5.61 5.611 5.62 # is in increasing order opts="dversionmangle=s/~dfsg\.\d+$//,uversionmangle=s/(?!^)(\d)(?=[^\.])/$1./" \ http://brainvis.wustl.edu/wiki/index.php/Caret:Download \ http://brainmap.wustl.edu/pub/caret/caret_source.v(.*).zip # Actual sources could be downloaded from following link # but authorization is required ATM # http://brainvis.wustl.edu/pub/caret/index.html \ # caret_source\.v(.*)\.zip debian dh_wraporig debian/caret.desktop0000664000000000000000000000040311741350713011660 0ustar [Desktop Entry] Encoding=UTF-8 GenericName=Cortical Surface Reconstruction and Visualization Name=Caret Exec=caret5 TryExec=caret5 Type=Application Terminal=false Icon=caret5 Categories=Education;Graphics;Science;DataVisualization;MedicalSoftware;Qt;Viewer; debian/copyright0000664000000000000000000001227611741242110011124 0ustar Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat Name: Caret Maintainer: John Harwell Source: http://brainmap.wustl.edu/pub/caret References: @article{lipsia, author = "David C. Van Essen and Heather A. Drury and James Dickson and John Harwell and Donna Hanlon and Charles H. Anderson", title = "An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex", journal = "Journal of American Medical Informatics Association", volume = "8", pages = "443–459", year = "2001", url = "http://www.pubmedcentral.nih.gov/articlerender.fcgi?pubmedid=11522765" } Files: * Copyright: Copyright 1995-2010, John Harwell Heather Drury Donna Hanlon David Van Essen Copyright: Copyright 1995-2002, Washington University School of Medicine License: GPL-2+ On Debian systems the full text of the GNU General Public License can be found in the `/usr/share/common-licenses/GPL' file. Files: caret_common/MathUtilities.cxx Copyright: Copyright 1993-2002, Ken Martin Will Schroeder Bill Lorensen License: other Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . * Neither name of Ken Martin, Will Schroeder, or Bill Lorensen nor the names of any contributors may be used to endorse or promote products derived from this software without specific prior written permission. . * Modified source versions must be plainly marked as such, and must not be misrepresented as being the original software. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: caret_brain_set/BrainModelVolumeBiasCorrection.cxx Copyright: Copyright (c) 2002 Insight Consortium. All rights reserved. License: BSD This code adapted from the ITK Application "BiasCorrector.cxx" . Copyright (c) The Regents of the University of California. All rights reserved. . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: caret_uniformize/* Copyright: Copyright 1994-2000, Medical College of Wisconsin License: GPL-2+ This source code has been derived from parts of the AFNI package (http://afni.nimh.nih.gov). While AFNI's source code is (partially) covered by several different copyrights and licenses, the pieces included in the Caret sources are exclusively covered by the GNU General Public License. . On Debian systems the full text of the GNU General Public License can be found in the `/usr/share/common-licenses/GPL' file. Files: debian/* Copyright: Copyright 2007-2008, Michael Hanke License: GPL-2+ On Debian systems the full text of the GNU General Public License can be found in the `/usr/share/common-licenses/GPL' file. debian/dirs0000664000000000000000000000007411741242110010046 0ustar usr/bin usr/lib/caret/bin usr/lib/caret/lib usr/share/caret