[med-svn] [Git][med-team/beads][master] 14 commits: Update OdsStream CMake dialect variable name.
Filippo Rusconi
gitlab at salsa.debian.org
Wed May 6 08:07:27 BST 2020
Filippo Rusconi pushed to branch master at Debian Med / beads
Commits:
621b9019 by Filippo Rusconi at 2020-05-05T20:01:00+02:00
Update OdsStream CMake dialect variable name.
- - - - -
0c422bd8 by Filippo Rusconi at 2020-05-05T20:02:22+02:00
Add VERSION variable to ease packaging.
- - - - -
4c75426c by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T21:24:42+02:00
New upstream 1.1.19 version packaging.
- - - - -
94d050a1 by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T21:32:18+02:00
Converted files from DOS to UNIX using the dos2unix program.
- - - - -
09e6858b by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T21:38:25+02:00
Fix spelling error. Removes the need for a patch.
- - - - -
5a562fa0 by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T21:38:57+02:00
Remove patches no more useful.
- - - - -
98a5239f by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T21:46:53+02:00
Remove Olivier Langella from Uploaders field and added Filippo Rusconi.
- - - - -
eea98688 by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T21:53:09+02:00
Add keywords.
- - - - -
0f4f9723 by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T22:01:03+02:00
Fix spelling errors (lintian).
- - - - -
8371df7e by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T22:01:20+02:00
Going on with packaging.
- - - - -
427388ea by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T23:42:13+02:00
Fix formatting.
- - - - -
67d56ddc by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T23:58:41+02:00
Initial upstream branch.
- - - - -
56fd188d by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T23:59:01+02:00
New upstream version 1.1.19+dfsg
- - - - -
098901c4 by Filippo Rusconi (Uploading Debian Developer) at 2020-05-05T23:59:01+02:00
Update upstream source from tag 'upstream/1.1.19+dfsg'
Update to upstream version '1.1.19+dfsg'
with Debian dir d3f2024bbcf2d780b37a9edb61fd93b336f78db0
- - - - -
11 changed files:
- CMakeLists.txt
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/series
- − debian/patches/spelling.patch
- − debian/patches/use_debian_packaged_cimg.h
- share/applications/beads.desktop
- src/CMakeLists.txt
- src/images/imageDeNovo.cpp
- src/qtbeads/main_window.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -1,216 +1,218 @@
-
-# cmake helps to compile "beads"
-# please install the cmake package depending on your linux distribution
-# and type in the beads root directory :
-# cmake .
-# make
-# make install
-cmake_minimum_required(VERSION 2.6)
-
-
-# The name of our project is "beads". CMakeLists files in this project can
-# refer to the root source directory of the project as ${beads_SOURCE_DIR} and
-# to the root binary directory of the project as ${beads_BINARY_DIR}.
-PROJECT(beads CXX C)
-
-
-#message ("compiler : ${CMAKE_CXX_COMPILER} ")
-
-SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-
-#IF ( CMAKE_BASE_NAME MATCHES "cl")
-# message ("on est sous Windows")
-# SET( WIN32 "true")
-#ENDIF(CMAKE_BASE_NAME MATCHES "cl")
-
-if (NOT CMAKE_BUILD_TYPE)
- SET( CMAKE_BUILD_TYPE "Release")
-ENDIF(NOT CMAKE_BUILD_TYPE)
-
-if (NOT CMAKE_INSTALL_PREFIX)
- SET (CMAKE_INSTALL_PREFIX /usr/local)
-ENDIF(NOT CMAKE_INSTALL_PREFIX)
-
-
-IF ( CMAKE_BUILD_TYPE MATCHES "Release")
- MESSAGE("compiling as release version")
- ADD_DEFINITIONS("-DQT_NO_DEBUG_OUTPUT")
-ELSE ( CMAKE_BUILD_TYPE MATCHES "Release" )
- MESSAGE("compiling as debug version")
-ENDIF( CMAKE_BUILD_TYPE MATCHES "Release" )
-
-
-
-#SET(WIN32 "true")
-#SET(MINGW "true")
-
-#set(CMAKE_MODULE_PATH ${beads_SOURCE_DIR}/cmake_modules)
-
-#IF ( PTHREADS_FOUND )
-# INCLUDE_DIRECTORIES ( ${PTHREADS_INCLUDE_DIR} )
-#ELSE ( PTHREADS_FOUND )
-# MESSAGE( FATAL_ERROR "No pthread installed" )
-#ENDIF( PTHREADS_FOUND )
-
-
-
-SET ( EXTRA_CIMG_LIBRARY "")
-
-SET ( CIMG_OS 0)
-IF(WIN32)
- SET ( CIMG_OS 2)
- #-O2 -lgdi32
- #SET ( EXTRA_CIMG_LIBRARY "gdi32")
- #SET(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG")
-# FIND_PACKAGE(FindMagick REQUIRED)
-ELSE(WIN32)
- #FIND_PACKAGE(Pthreads REQUIRED)
- SET(CMAKE_CXX_FLAGS_RELEASE "-s -O3 -DNDEBUG")
- SET ( CIMG_OS 1)
-ENDIF(WIN32)
-
-#
-#CMAKE_CXX_FLAGS
-SET(CMAKE_CXX_FLAGS_DEBUG "-g -s")
-SET(CMAKE_CXX_FLAGS_MINSIZEREL "-Os -DNDEBUG")
-SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -g")
-
-SET (BEADS_VERSION "1.1.18")
-
-SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
-SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
-#SET(CPACK_INSTALL_CMAKE_PROJECTS "/tmp;beads;src;/src")
-#SET(CPACK_NSIS_DISPLAY_NAME "CMake 2.5")
-SET(CPACK_OUTPUT_CONFIG_FILE "./CPackConfig.cmake")
-SET(CPACK_PACKAGE_DESCRIPTION_FILE ${beads_SOURCE_DIR}/COPYING)
-SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "beads is a detection software")
-SET(CPACK_PACKAGE_EXECUTABLES "beads")
-SET(CPACK_SOURCE_PACKAGE_FILE_NAME "beads-${BEADS_VERSION}")
-SET(CPACK_PACKAGE_FILE_NAME "beads-${BEADS_VERSION}-Linux-i686")
-SET(CPACK_PACKAGE_INSTALL_DIRECTORY "beads ${BEADS_VERSION}")
-SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "beads ${BEADS_VERSION}")
-SET(CPACK_PACKAGE_NAME "beads")
-SET(CPACK_PACKAGE_VENDOR "CNRS")
-
-IF ( CMAKE_BUILD_TYPE MATCHES "Debug")
- SET (BEADS_VERSION "${BEADS_VERSION}d")
-ENDIF( CMAKE_BUILD_TYPE MATCHES "Debug")
-SET(CPACK_PACKAGE_VERSION ${BEADS_VERSION})
-SET(CPACK_PACKAGE_VERSION_MAJOR "1")
-SET(CPACK_PACKAGE_VERSION_MINOR "1")
-SET(CPACK_PACKAGE_VERSION_PATCH "15")
-SET(CPACK_RESOURCE_FILE_LICENSE ${beads_SOURCE_DIR}/COPYING)
-SET(CPACK_RESOURCE_FILE_README ${beads_SOURCE_DIR}/README)
-SET(CPACK_RESOURCE_FILE_WELCOME ${beads_SOURCE_DIR}/INSTALL)
-SET(CPACK_SOURCE_GENERATOR "TGZ;TZ")
-SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "./CPackSourceConfig.cmake")
-SET(CPACK_SYSTEM_NAME "Linux-i686")
-SET(CPACK_TOPLEVEL_TAG "Linux-i686")
-
-SET(CPACK_SOURCE_IGNORE_FILES
- "moc_.*cxx"
- "/devel_archives/"
- "/build/"
+
+# cmake helps to compile "beads"
+# please install the cmake package depending on your linux distribution
+# and type in the beads root directory :
+# cmake .
+# make
+# make install
+cmake_minimum_required(VERSION 2.6)
+
+
+# The name of our project is "beads". CMakeLists files in this project can
+# refer to the root source directory of the project as ${beads_SOURCE_DIR} and
+# to the root binary directory of the project as ${beads_BINARY_DIR}.
+PROJECT(beads CXX C)
+
+
+#message ("compiler : ${CMAKE_CXX_COMPILER} ")
+
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+
+#IF ( CMAKE_BASE_NAME MATCHES "cl")
+# message ("on est sous Windows")
+# SET( WIN32 "true")
+#ENDIF(CMAKE_BASE_NAME MATCHES "cl")
+
+if (NOT CMAKE_BUILD_TYPE)
+ SET( CMAKE_BUILD_TYPE "Release")
+ENDIF(NOT CMAKE_BUILD_TYPE)
+
+if (NOT CMAKE_INSTALL_PREFIX)
+ SET (CMAKE_INSTALL_PREFIX /usr/local)
+ENDIF(NOT CMAKE_INSTALL_PREFIX)
+
+
+IF ( CMAKE_BUILD_TYPE MATCHES "Release")
+ MESSAGE("compiling as release version")
+ ADD_DEFINITIONS("-DQT_NO_DEBUG_OUTPUT")
+ELSE ( CMAKE_BUILD_TYPE MATCHES "Release" )
+ MESSAGE("compiling as debug version")
+ENDIF( CMAKE_BUILD_TYPE MATCHES "Release" )
+
+
+
+#SET(WIN32 "true")
+#SET(MINGW "true")
+
+#set(CMAKE_MODULE_PATH ${beads_SOURCE_DIR}/cmake_modules)
+
+#IF ( PTHREADS_FOUND )
+# INCLUDE_DIRECTORIES ( ${PTHREADS_INCLUDE_DIR} )
+#ELSE ( PTHREADS_FOUND )
+# MESSAGE( FATAL_ERROR "No pthread installed" )
+#ENDIF( PTHREADS_FOUND )
+
+
+
+SET ( EXTRA_CIMG_LIBRARY "")
+
+SET ( CIMG_OS 0)
+IF(WIN32)
+ SET ( CIMG_OS 2)
+ #-O2 -lgdi32
+ #SET ( EXTRA_CIMG_LIBRARY "gdi32")
+ #SET(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG")
+# FIND_PACKAGE(FindMagick REQUIRED)
+ELSE(WIN32)
+ #FIND_PACKAGE(Pthreads REQUIRED)
+ SET(CMAKE_CXX_FLAGS_RELEASE "-s -O3 -DNDEBUG")
+ SET ( CIMG_OS 1)
+ SET(EXTRA_CIMG_LIBRARY "X11")
+ENDIF(WIN32)
+
+#
+#CMAKE_CXX_FLAGS
+SET(CMAKE_CXX_FLAGS_DEBUG "-g -s")
+SET(CMAKE_CXX_FLAGS_MINSIZEREL "-Os -DNDEBUG")
+SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -g")
+
+SET (BEADS_VERSION "1.1.19")
+set(VERSION 1.1.19)
+
+SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
+SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
+#SET(CPACK_INSTALL_CMAKE_PROJECTS "/tmp;beads;src;/src")
+#SET(CPACK_NSIS_DISPLAY_NAME "CMake 2.5")
+SET(CPACK_OUTPUT_CONFIG_FILE "./CPackConfig.cmake")
+SET(CPACK_PACKAGE_DESCRIPTION_FILE ${beads_SOURCE_DIR}/COPYING)
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "beads is a detection software")
+SET(CPACK_PACKAGE_EXECUTABLES "beads")
+SET(CPACK_SOURCE_PACKAGE_FILE_NAME "beads-${BEADS_VERSION}")
+SET(CPACK_PACKAGE_FILE_NAME "beads-${BEADS_VERSION}-Linux-i686")
+SET(CPACK_PACKAGE_INSTALL_DIRECTORY "beads ${BEADS_VERSION}")
+SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "beads ${BEADS_VERSION}")
+SET(CPACK_PACKAGE_NAME "beads")
+SET(CPACK_PACKAGE_VENDOR "CNRS")
+
+IF ( CMAKE_BUILD_TYPE MATCHES "Debug")
+ SET (BEADS_VERSION "${BEADS_VERSION}d")
+ENDIF( CMAKE_BUILD_TYPE MATCHES "Debug")
+SET(CPACK_PACKAGE_VERSION ${BEADS_VERSION})
+SET(CPACK_PACKAGE_VERSION_MAJOR "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "1")
+SET(CPACK_PACKAGE_VERSION_PATCH "15")
+SET(CPACK_RESOURCE_FILE_LICENSE ${beads_SOURCE_DIR}/COPYING)
+SET(CPACK_RESOURCE_FILE_README ${beads_SOURCE_DIR}/README)
+SET(CPACK_RESOURCE_FILE_WELCOME ${beads_SOURCE_DIR}/INSTALL)
+SET(CPACK_SOURCE_GENERATOR "TGZ;TZ")
+SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "./CPackSourceConfig.cmake")
+SET(CPACK_SYSTEM_NAME "Linux-i686")
+SET(CPACK_TOPLEVEL_TAG "Linux-i686")
+
+SET(CPACK_SOURCE_IGNORE_FILES
+ "moc_.*cxx"
+ "/devel_archives/"
+ "/build/"
"/buildw64/"
- "/cbuild/"
- "/figures/"
- ".*\\\\.so"
- ".*\\\\.a"
- "/Soumis/"
- "/samples/"
- "/win32/"
- "/tests/"
- "Makefile"
- "install_manifest.txt"
- "cmake_install.cmake"
- "cmake_install.cmake"
- "CMakeCache.txt"
- "CPackConfig.cmake"
- "CPackSourceConfig.cmake"
- "install_manifest.txt"
+ "/cbuild/"
+ "/figures/"
+ ".*\\\\.so"
+ ".*\\\\.a"
+ "/Soumis/"
+ "/samples/"
+ "/win32/"
+ "/tests/"
+ "Makefile"
+ "install_manifest.txt"
+ "cmake_install.cmake"
+ "cmake_install.cmake"
+ "CMakeCache.txt"
+ "CPackConfig.cmake"
+ "CPackSourceConfig.cmake"
+ "install_manifest.txt"
".gitignore"
- "/CMakeFiles/"
- "/_CPack_Packages/"
- "/Debug/"
- "/Release/"
- "/\\\\.externalToolBuilders/"
- "/\\\\.git/"
- "/\\\\.settings/"
- "Makefile"
- "\\\\.cdtbuild"
- "\\\\.cdtproject"
- "\\\\.project"
- "\\\\.cproject"
- "beads$"
- ".*\\\\.tar\\\\.gz"
-)
-# cpack -G TGZ --config CPackSourceConfig.cmake
-# dpkg-buildpackage -rfakeroot
-
-#.dput.cf
-#[olivier-langella]
-#fqdn = ppa.launchpad.net
-#method = ftp
-#incoming = ~olivier-langella/ubuntu/
-#login = olivier-langella
-#allow_unsigned_uploads = 0
-#
-# debuild -S -sa
-# dput -f olivier-langella *changes
-
-
-
-
-
-#dch -Djessie "message"
-#cmake ..
-#make deb
-# scp beads* proteus.moulon.inra.fr:/var/www/apt/incoming
-# reprepro -Vb /var/www/apt processincoming default
-
-
-configure_file (${beads_SOURCE_DIR}/src/config.h.cmake ${beads_SOURCE_DIR}/src/config.h)
-
-
-SET(CPACK_PACKAGE_EXECUTABLES "beads" "beads")
-
-
-INCLUDE(CPack)
-
-
-#INCLUDE(CPack)
-
-
-
-
-# Recurse into the "src" subdirectories. This does not actually
-# cause another cmake executable to run. The same process will walk through
-# the project's entire directory structure.
-#ADD_DEFINITIONS( -lpthread)
-add_subdirectory (src)
-
-#SET(CPACK_STRIP_FILES "src/beads;src/qtbeads/qtbeads")
-
-INSTALL(PROGRAMS ${CMAKE_BINARY_DIR}/src/beads DESTINATION bin)
-INSTALL(PROGRAMS ${CMAKE_BINARY_DIR}/src/qtbeads/qtbeads DESTINATION bin)
-#INSTALL(DIRECTORY doc/man1 DESTINATION share/man/man1)
-INSTALL(FILES doc/man1/beads.1 DESTINATION share/man/man1)
-INSTALL(FILES share/applications/beads.desktop DESTINATION share/applications)
-INSTALL(FILES share/beads/beads_blue.conf DESTINATION share/beads)
-INSTALL(FILES share/beads/beads_silver.conf DESTINATION share/beads)
-INSTALL(FILES share/beads/beads_silver_small.conf DESTINATION share/beads)
-INSTALL(FILES share/beads/beads_icon.svg DESTINATION share/beads)
-
-add_custom_target(targz
- cpack -G TGZ --config CPackSourceConfig.cmake && tar xvfz beads-${BEADS_VERSION}.tar.gz
- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
- COMMENT "Creating .tar.gz" VERBATIM
-)
-
-
-add_custom_target(deb
- cd beads-${BEADS_VERSION} && dpkg-buildpackage
- DEPENDS targz
- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
- COMMENT "Creating Debian package" VERBATIM
-)
+ "/CMakeFiles/"
+ "/_CPack_Packages/"
+ "/Debug/"
+ "/Release/"
+ "/\\\\.externalToolBuilders/"
+ "/\\\\.git/"
+ "/\\\\.settings/"
+ "Makefile"
+ "\\\\.cdtbuild"
+ "\\\\.cdtproject"
+ "\\\\.project"
+ "\\\\.cproject"
+ "beads$"
+ ".*\\\\.tar\\\\.gz"
+)
+# cpack -G TGZ --config CPackSourceConfig.cmake
+# dpkg-buildpackage -rfakeroot
+
+#.dput.cf
+#[olivier-langella]
+#fqdn = ppa.launchpad.net
+#method = ftp
+#incoming = ~olivier-langella/ubuntu/
+#login = olivier-langella
+#allow_unsigned_uploads = 0
+#
+# debuild -S -sa
+# dput -f olivier-langella *changes
+
+
+
+
+
+#dch -Djessie "message"
+#cmake ..
+#make deb
+# scp beads* proteus.moulon.inra.fr:/var/www/apt/incoming
+# reprepro -Vb /var/www/apt processincoming default
+
+
+configure_file (${beads_SOURCE_DIR}/src/config.h.cmake ${beads_SOURCE_DIR}/src/config.h)
+
+
+SET(CPACK_PACKAGE_EXECUTABLES "beads" "beads")
+
+
+INCLUDE(CPack)
+
+
+#INCLUDE(CPack)
+
+
+
+
+# Recurse into the "src" subdirectories. This does not actually
+# cause another cmake executable to run. The same process will walk through
+# the project's entire directory structure.
+#ADD_DEFINITIONS( -lpthread)
+add_subdirectory (src)
+
+#SET(CPACK_STRIP_FILES "src/beads;src/qtbeads/qtbeads")
+
+INSTALL(PROGRAMS ${CMAKE_BINARY_DIR}/src/beads DESTINATION bin)
+INSTALL(PROGRAMS ${CMAKE_BINARY_DIR}/src/qtbeads/qtbeads DESTINATION bin)
+#INSTALL(DIRECTORY doc/man1 DESTINATION share/man/man1)
+INSTALL(FILES doc/man1/beads.1 DESTINATION share/man/man1)
+INSTALL(FILES share/applications/beads.desktop DESTINATION share/applications)
+INSTALL(FILES share/beads/beads_blue.conf DESTINATION share/beads)
+INSTALL(FILES share/beads/beads_silver.conf DESTINATION share/beads)
+INSTALL(FILES share/beads/beads_silver_small.conf DESTINATION share/beads)
+INSTALL(FILES share/beads/beads_icon.svg DESTINATION share/beads)
+
+add_custom_target(targz
+ cpack -G TGZ --config CPackSourceConfig.cmake && tar xvfz beads-${BEADS_VERSION}.tar.gz
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+ COMMENT "Creating .tar.gz" VERBATIM
+)
+
+
+add_custom_target(deb
+ cd beads-${BEADS_VERSION} && dpkg-buildpackage
+ DEPENDS targz
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+ COMMENT "Creating Debian package" VERBATIM
+)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+beads (1.1.19+dfsg-1) unstable; urgency=low
+
+ * New version updating the CMake build system to match
+ the changes operated in the libodsstream package
+ (closes: #959637) and the name of the libodsstream-dev
+ package name. Thanks a lot to Lucas Nussbaum
+ <lucas at debian.org> and Andreas Tille
+ <andreas at an3as.eu> for reporting the problem.
+
+ * Standards-Version: 4.5.0 (no changes needed).
+
+ * Changed the inra.fr to inrae.fr domain name of the home page.
+
+ -- Filippo Rusconi <lopippo at debian.org> Tue, 05 May 2020 20:08:31 +0200
+
beads (1.1.18+dfsg-4) unstable; urgency=medium
* Drop unneeded Build-Depends on libquazip5-headers
=====================================
debian/control
=====================================
@@ -1,19 +1,19 @@
Source: beads
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>,
- Olivier Langella <olivier.langella at moulon.inra.fr>
+ Filippo Rusconi <lopippo at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
cmake,
qtbase5-dev,
qttools5-dev,
- libodsstream-qt5-dev,
+ libodsstream-dev,
cimg-dev
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/beads
Vcs-Git: https://salsa.debian.org/med-team/beads.git
-Homepage: http://moulon.inra.fr/beads/beads.html
+Homepage: http://moulon.inrae.fr/beads/beads.html
Package: beads
Architecture: any
=====================================
debian/copyright
=====================================
@@ -31,6 +31,7 @@ License: MIT
Files: debian/*
Copyright: Andreas Tille <tille at debian.org>
+ Filippo Rusconi <lopippo at debian.org>
License: CeCILL
License: CeCILL
=====================================
debian/patches/series deleted
=====================================
@@ -1,3 +0,0 @@
-# qt5.patch
-use_debian_packaged_cimg.h
-spelling.patch
=====================================
debian/patches/spelling.patch deleted
=====================================
@@ -1,18 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 19 Oct 2017 14:58:04 +0200
-Description: Fix spelling issue
- Remark: There are two further issues reported by lintian but I hesitated to
- fix one that exports a defined DTD format (biology softwares) and I did not
- found the string "assignement" inside the codebase of beads
-
---- a/src/images/imageDeNovo.cpp
-+++ b/src/images/imageDeNovo.cpp
-@@ -123,7 +123,7 @@ bool imageDeNovo::build_image_with_spot_
- ifs >> temp;
-
- if (!ifs.good()) {
-- cerr << "denovo spot file not well formated" << endl;
-+ cerr << "denovo spot file not well formatted" << endl;
- }
-
- while (ifs.good()) {
=====================================
debian/patches/use_debian_packaged_cimg.h deleted
=====================================
@@ -1,16 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 19 Oct 2017 14:58:04 +0200
-Description: Use Debian packaged CImg.h from cimg-dev package since
- the code copy shipped together with upstream is outdated and does not
- build with recent gcc
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -67,6 +67,7 @@ ELSE(WIN32)
- #FIND_PACKAGE(Pthreads REQUIRED)
- SET(CMAKE_CXX_FLAGS_RELEASE "-s -O3 -DNDEBUG")
- SET ( CIMG_OS 1)
-+ SET(EXTRA_CIMG_LIBRARY "X11")
- ENDIF(WIN32)
-
- #
=====================================
share/applications/beads.desktop
=====================================
@@ -9,3 +9,4 @@ Terminal=false
Type=Application
StartupNotify=true
X-Ubuntu-Gettext-Domain=beads
+Keywords=Chemistry;Biology;Electrophoresis
=====================================
src/CMakeLists.txt
=====================================
@@ -1,114 +1,114 @@
-
-FIND_PACKAGE( Qt5 COMPONENTS Core Gui Xml REQUIRED )
-
-list( APPEND CMAKE_MODULE_PATH
- ${PROJECT_SOURCE_DIR}/cmake_modules
-)
-
-set (CImg_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/src/cimg")
-
-if (DEBIAN_PACKAGE)
-# CImg_FOUND - system has CImg lib
- set (CImg_FOUND 1)
-# CImg_INCLUDE_DIRS - the CImg include directory
- set (CImg_INCLUDE_DIR "/usr/include")
-# CImg_SYSTEM_LIBS - external libraries that CImg uses
- set (CImg_SYSTEM_LIBS "/usr/lib${LIB_SUFFIX}/libz.so"
- "/usr/lib${LIB_SUFFIX}/libpng16.so"
- "/usr/lib${LIB_SUFFIX}/libjpeg.so"
- "/usr/lib${LIB_SUFFIX}/libtiff.so")
-# CImg_SYSTEM_LIBS_DIR - external library directories
- set (CImg_SYSTEM_LIBS_DIR "")
-# CImg_CFLAGS - compilation flags
- set (CImg_CFLAGS "pthread" "-Dcimg_use_png" "-Dcimg_use_jpeg" "-Dcimg_use_tiff" "-Dcimg_use_zlib")
-
-else (DEBIAN_PACKAGE)
- find_package( CImg REQUIRED )
-endif (DEBIAN_PACKAGE)
-
-# Add CIMG Flags to Compilation Flags
-SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CIMG_CFLAGS}")
-
-#INCLUDE_DIRECTORIES(${ODSSTREAM_INCLUDE_DIR})
-
-if (MINGW32)
- INCLUDE_DIRECTORIES( ${QUAZIP_INCLUDE_DIR} )
-ELSE (MINGW32)
- FIND_PACKAGE( Odsstream REQUIRED )
-ENDIF (MINGW32)
-
-
-
-SET( BEADS_FOR_QT_CPP
- ConfigFile/ConfigFile
- parameters
- encode/base64
- images/imageIntensity.cpp
- images/imageDirect.cpp
- images/imageCode
- images/imageCoule
- images/imagePaths
- images/imageConfluent
- images/imageProb
- images/parameterProb
- parameterDetection
- images/parameterConfluent
- detection
- images/imageDetection
- images/imageNumber
- images/parameterNumber
- images/imageContours
- spotPROTICdbDocument
- spot
- spotDocument
- spotSvgDocument
- images/imageDeNovo
-)
-
-IF(WIN32)
-ELSE(WIN32)
- #FIND_PACKAGE(X11 REQUIRED)
-
- #INCLUDE_DIRECTORIES(X11_INCLUDE_DIR)
- # X11_FOUND is true if X11 is available.
- # * X11_INCLUDE_DIR contains the include directories to use X11.
- # * X11_LIBRARIES points to the libraries to link against to use X11..
- # Make sure the compiler can find include files from our Hello library.
- #include_directories (${X11_INCLUDE_DIR})
-
- #ADD_DEFINITIONS(${PTHREADS_DEFINITIONS})
- # -m -pthread FindThreads
-
- # Make sure the linker can find the Hello library once it is built.
- #link_directories (${X11_INCLUDE_DIR})
-ENDIF(WIN32)
-
-
-add_executable (beads beads.cpp )
-target_include_directories (beads PUBLIC ${ODSSTREAM_INCLUDE_DIR} ${CImg_INCLUDE_DIRS} ${CImg_SYSTEM_LIBS_DIR})
-SET_TARGET_PROPERTIES(beads
- PROPERTIES OUTPUT_NAME beads
- CLEAN_DIRECT_OUTPUT 1
- CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CImg_CFLAGS}"
- )
-
-target_link_libraries (beads cppbeads
- ${ODSSTREAM_QT5_LIBRARY} ${CImg_SYSTEM_LIBS} ${CImg_CFLAGS} Qt5::Core Qt5::Gui Qt5::Xml)
-
-
-add_library ( cppbeads STATIC
- ${BEADS_FOR_QT_CPP}
-)
-
-target_include_directories (cppbeads PUBLIC ${ODSSTREAM_INCLUDE_DIR}
- ${CImg_INCLUDE_DIRS} ${CImg_SYSTEM_LIBS_DIR})
-SET_TARGET_PROPERTIES(cppbeads
- PROPERTIES OUTPUT_NAME cppbeads-qt5
- CLEAN_DIRECT_OUTPUT 1
- CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CImg_CFLAGS}"
-)
-target_link_libraries (cppbeads
- ${ODSSTREAM_QT5_LIBRARY} ${CImg_SYSTEM_LIBS} ${CImg_CFLAGS} Qt5::Core Qt5::Gui Qt5::Xml)
-
-
-SUBDIRS (qtbeads)
+
+FIND_PACKAGE( Qt5 COMPONENTS Core Gui Xml REQUIRED )
+
+list( APPEND CMAKE_MODULE_PATH
+ ${PROJECT_SOURCE_DIR}/cmake_modules
+)
+
+set (CImg_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/src/cimg")
+
+if (DEBIAN_PACKAGE)
+# CImg_FOUND - system has CImg lib
+ set (CImg_FOUND 1)
+# CImg_INCLUDE_DIRS - the CImg include directory
+ set (CImg_INCLUDE_DIR "/usr/include")
+# CImg_SYSTEM_LIBS - external libraries that CImg uses
+ set (CImg_SYSTEM_LIBS "/usr/lib${LIB_SUFFIX}/libz.so"
+ "/usr/lib${LIB_SUFFIX}/libpng16.so"
+ "/usr/lib${LIB_SUFFIX}/libjpeg.so"
+ "/usr/lib${LIB_SUFFIX}/libtiff.so")
+# CImg_SYSTEM_LIBS_DIR - external library directories
+ set (CImg_SYSTEM_LIBS_DIR "")
+# CImg_CFLAGS - compilation flags
+ set (CImg_CFLAGS "pthread" "-Dcimg_use_png" "-Dcimg_use_jpeg" "-Dcimg_use_tiff" "-Dcimg_use_zlib")
+
+else (DEBIAN_PACKAGE)
+ find_package( CImg REQUIRED )
+endif (DEBIAN_PACKAGE)
+
+# Add CIMG Flags to Compilation Flags
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CIMG_CFLAGS}")
+
+#INCLUDE_DIRECTORIES(${OdsStream_INCLUDE_DIRS})
+
+if (MINGW32)
+ INCLUDE_DIRECTORIES( ${QUAZIP_INCLUDE_DIR} )
+ELSE (MINGW32)
+ FIND_PACKAGE(OdsStream REQUIRED )
+ENDIF (MINGW32)
+
+
+
+SET( BEADS_FOR_QT_CPP
+ ConfigFile/ConfigFile
+ parameters
+ encode/base64
+ images/imageIntensity.cpp
+ images/imageDirect.cpp
+ images/imageCode
+ images/imageCoule
+ images/imagePaths
+ images/imageConfluent
+ images/imageProb
+ images/parameterProb
+ parameterDetection
+ images/parameterConfluent
+ detection
+ images/imageDetection
+ images/imageNumber
+ images/parameterNumber
+ images/imageContours
+ spotPROTICdbDocument
+ spot
+ spotDocument
+ spotSvgDocument
+ images/imageDeNovo
+)
+
+IF(WIN32)
+ELSE(WIN32)
+ #FIND_PACKAGE(X11 REQUIRED)
+
+ #INCLUDE_DIRECTORIES(X11_INCLUDE_DIR)
+ # X11_FOUND is true if X11 is available.
+ # * X11_INCLUDE_DIR contains the include directories to use X11.
+ # * X11_LIBRARIES points to the libraries to link against to use X11..
+ # Make sure the compiler can find include files from our Hello library.
+ #include_directories (${X11_INCLUDE_DIR})
+
+ #ADD_DEFINITIONS(${PTHREADS_DEFINITIONS})
+ # -m -pthread FindThreads
+
+ # Make sure the linker can find the Hello library once it is built.
+ #link_directories (${X11_INCLUDE_DIR})
+ENDIF(WIN32)
+
+
+add_executable (beads beads.cpp )
+target_include_directories (beads PUBLIC ${OdsStream_INCLUDE_DIRS} ${CImg_INCLUDE_DIRS} ${CImg_SYSTEM_LIBS_DIR})
+SET_TARGET_PROPERTIES(beads
+ PROPERTIES OUTPUT_NAME beads
+ CLEAN_DIRECT_OUTPUT 1
+ CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CImg_CFLAGS}"
+ )
+
+target_link_libraries (beads cppbeads
+ OdsStream::Core ${CImg_SYSTEM_LIBS} ${CImg_CFLAGS} Qt5::Core Qt5::Gui Qt5::Xml)
+
+
+add_library ( cppbeads STATIC
+ ${BEADS_FOR_QT_CPP}
+)
+
+target_include_directories (cppbeads PUBLIC ${ODSSTREAM_INCLUDE_DIR}
+ ${CImg_INCLUDE_DIRS} ${CImg_SYSTEM_LIBS_DIR})
+SET_TARGET_PROPERTIES(cppbeads
+ PROPERTIES OUTPUT_NAME cppbeads-qt5
+ CLEAN_DIRECT_OUTPUT 1
+ CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CImg_CFLAGS}"
+)
+target_link_libraries (cppbeads
+ OdsStream::Core ${CImg_SYSTEM_LIBS} ${CImg_CFLAGS} Qt5::Core Qt5::Gui Qt5::Xml)
+
+
+SUBDIRS (qtbeads)
=====================================
src/images/imageDeNovo.cpp
=====================================
@@ -123,7 +123,7 @@ bool imageDeNovo::build_image_with_spot_file(const QString & filename) {
ifs >> temp;
if (!ifs.good()) {
- cerr << "denovo spot file not well formated" << endl;
+ cerr << "denovo spot file not well formatted" << endl;
}
while (ifs.good()) {
=====================================
src/qtbeads/main_window.cpp
=====================================
@@ -286,7 +286,7 @@ void MainWindow::about() {
this,
tr("About QTbeads %1").arg(BEADS_VERSION),
tr(
- "<div><a href=\"http://pappso.inra.fr/bioinfo/beads/index.php\">QTbeads</a> %1 is a 2-DE electrophoresis gel image spot detection software developped by <a href=\"http://pappso.inra.fr/\">PAPPSO</a></div><div>beads is freely available under the terms of the <a href=\"http://www.cecill.info/licences/Licence_CeCILL_V1.1-US.html\">CeCILL</a> licence</div>").arg(
+ "<div><a href=\"http://pappso.inra.fr/bioinfo/beads/index.php\">QTbeads</a> %1 is a 2-DE electrophoresis gel image spot detection software developed by <a href=\"http://pappso.inra.fr/\">PAPPSO</a></div><div>beads is freely available under the terms of the <a href=\"http://www.cecill.info/licences/Licence_CeCILL_V1.1-US.html\">CeCILL</a> licence</div>").arg(
BEADS_VERSION));
}
@@ -605,7 +605,7 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
this->setCursor(Qt::ArrowCursor);
} catch (qtbeadsError& e) {
- qDebug() << "an error occured " << e.getMessage();
+ qDebug() << "an error occurred " << e.getMessage();
QMessageBox::critical(this, tr("qtbeads"),
tr("Detection aborted : ").append(e.getMessage()));
/*
View it on GitLab: https://salsa.debian.org/med-team/beads/-/compare/7758e0997e2e8301f360a1b7b8184281d83f1096...098901c4943a657a1a0f9055d8f7004e59bad1fa
--
View it on GitLab: https://salsa.debian.org/med-team/beads/-/compare/7758e0997e2e8301f360a1b7b8184281d83f1096...098901c4943a657a1a0f9055d8f7004e59bad1fa
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