masschroq (2.2.25-1~buster+1) buster

CMakeLists.txt

@@ -137,7 +137,7 @@ message(STATUS "${BoldYellow}CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}.${ColourReset
 
 SET (MASSCHROQ_MAJOR_VERSION 2)
 SET (MASSCHROQ_MINOR_VERSION 2)
-SET (MASSCHROQ_PATCH_LEVEL   24)
+SET (MASSCHROQ_PATCH_LEVEL   25)
 SET (MASSCHROQ_VERSION
   "${MASSCHROQ_MAJOR_VERSION}.${MASSCHROQ_MINOR_VERSION}.${MASSCHROQ_PATCH_LEVEL}")
 SET (MASSCHROQ_LIB_NAME "masschroq")
@@ -146,7 +146,7 @@ SET (MASSCHROQ_LIB_SOVERSION ${MASSCHROQ_MAJOR_VERSION})
 
 SET (MASSCHROQ_SCHEMA_VERSION "${MASSCHROQ_MAJOR_VERSION}.2")
 #SET (masschroq_BINARY_DIR "bin")
-SET(VERSION 2.2.24)
+SET(VERSION 2.2.25)
 
 
 # We want C++17

CMakeStuff/modules/AlglibConfig.cmake

-#sudo apt install libalglib-dev
- 
-# Look for the necessary header
-set(Alglib_INCLUDE_DIR /usr/include/libalglib)
-mark_as_advanced(Alglib_INCLUDE_DIR)
-
-# Look for the necessary library
-set(Alglib_LIBRARY /usr/lib/x86_64-linux-gnu/libalglib.so)
-mark_as_advanced(Alglib_LIBRARY)
-
-set(Alglib_FOUND 1)
-
-
-    set(Alglib_INCLUDE_DIRS ${Alglib_INCLUDE_DIR})
-    set(Alglib_LIBRARIES ${Alglib_LIBRARY})
-    if(NOT TARGET Alglib::Alglib)
-        add_library(Alglib::Alglib UNKNOWN IMPORTED)
-        set_target_properties(Alglib::Alglib PROPERTIES
-            IMPORTED_LOCATION             "${Alglib_LIBRARY}"
-            INTERFACE_INCLUDE_DIRECTORIES "${Alglib_INCLUDE_DIR}")
-    endif()

debian/changelog

+masschroq (2.2.25-1~buster+1) buster; urgency=medium
+
+  * fix shared library location path
+
+ -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 18 Dec 2020 09:52:10 +0100
+
 masschroq (2.2.24-1~buster+1) buster; urgency=medium
 
   * trying a fix for https://forgemia.inra.fr/pappso/masschroq/-/issues/5

debian/masschroq-cli.install

 /usr/bin/masschroq
-/usr/lib/*/masschroq/libmasschroq.*
+/usr/lib/*/libmasschroq.*
 /usr/share/masschroq/masschroq.svg

debian/rules

 #!/usr/bin/make -f
 # -*- makefile -*-
 
+include /usr/share/dpkg/pkg-info.mk
+
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 export DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
 
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
+
 %:
 	dh $@ --buildsystem=cmake
 
 override_dh_auto_configure:
-	dh_auto_configure -- -DLIB_SUFFIX="/$(DEB_HOST_MULTIARCH)" -DCMAKE_INSTALL_PREFIX=/usr -DGO_LATEX=true -DCMAKE_BUILD_TYPE=Release
-
+	dh_auto_configure -- \
+		-DCMAKE_INSTALL_PREFIX=/usr \
+		-DCMAKE_BUILD_TYPE=Release \
+		-DGO_LATEX=true \
+		-DCMAKE_SKIP_RPATH=1
+		
 override_dh_auto_build:
-	dh_auto_build
+	dh_auto_build --no-parallel
 	dh_auto_build -- pdf
+

src/CMakeLists.txt

@@ -181,7 +181,7 @@ endif (NOGUI)
 
 
 add_library(${MASSCHROQ_LIB_NAME} SHARED ${MASSCHROQ_LIB_SRCS}  ${MASSCHROQ_LIB_MOC_SRCS}
-        ${SAXLIB_SRCS} ${OBIWARP_SRCS} ${MASSCHROQ_RCC_SRCS_QT5})
+        ${SAXLIB_SRCS} ${MASSCHROQ_RCC_SRCS_QT5})
 target_link_libraries(${MASSCHROQ_LIB_NAME}
     PappsoMSpp::Core
     PappsoMSpp::Widget
@@ -191,10 +191,12 @@ target_link_libraries(${MASSCHROQ_LIB_NAME}
     Qt5::Xml
     Qt5::XmlPatterns
     Qt5::Concurrent
+    ${QCustomPlot_LIBRARIES}
+    ${Quazip5_LIBRARY}
 )
 target_include_directories (${MASSCHROQ_LIB_NAME} PUBLIC
-    ${QCustomPlot_INCLUDES}
-    ${QUAZIP_INCLUDE_DIR}
+    ${QCustomPlot_INCLUDE_DIR}
+    ${Quazip5_INCLUDE_DIRS}
 )
 set_target_properties(${MASSCHROQ_LIB_NAME} PROPERTIES
         VERSION ${MASSCHROQ_LIB_VERSION}
@@ -211,7 +213,7 @@ target_link_libraries(masschroq_main ${MASSCHROQ_LIB_NAME}
 set_target_properties(masschroq_main PROPERTIES OUTPUT_NAME masschroq)
 
 target_include_directories (masschroq_main PUBLIC 
-    ${QUAZIP_INCLUDE_DIR}
+    ${Quazip5_INCLUDE_DIRS}
 )
 
 if (NOGUI)
@@ -258,7 +260,13 @@ else (MXE)
   #ADD_EXECUTABLE(new_parseur parseur.cpp)
   #TARGET_LINK_LIBRARIES(new_parseur ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES})
 
-  install(TARGETS ${MASSCHROQ_LIB_NAME} LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  install(TARGETS ${MASSCHROQ_LIB_NAME} 
+        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}/
+        # This one is for WIN32
+        RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}/
+        ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}/
+        COMPONENT library
+  )
 
 endif(MXE)
 

src/config.h

@@ -2,7 +2,7 @@
 #define _CONFIG_H
 
 #define SOFTWARE_NAME "MassChroQ"
-#define MASSCHROQ_VERSION "2.2.24"
+#define MASSCHROQ_VERSION "2.2.25"
 #define MASSCHROQ_XSD "masschroq-2.2.xsd"
 #define MASSCHROQ_SCHEMA_VERSION "2.2"
 #define MASSCHROQ_SCHEMA_FILE \

src/lib/alignments/alignment_ms2.cpp

@@ -89,8 +89,7 @@ AlignmentMs2::setSharedPeptides(const Msrun *p_msrun_ref,
 {
 
   const PeptideList &pep_list_ref = p_msrun_ref->getPeptideList();
-  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
-           << " pep_list_ref.size()=" << pep_list_ref.size();
+  qDebug() << " pep_list_ref.size()=" << pep_list_ref.size();
 
   for(auto &&p_petide : pep_list_ref)
     {

templates/share/applications/masschroq-gui.desktop

 [Desktop Entry]
-Name=MassChroQ GUI 2.2.24
+Name=MassChroQ GUI 2.2.25
 Categories=Education;Science;Math;
 Comment=MassChroQ GUI launcher
 Exec=masschroq_gui %U

templates/share/applications/masschroq-studio.desktop

 [Desktop Entry]
-Name=MassChroQ Studio 2.2.24
+Name=MassChroQ Studio 2.2.25
 Categories=Education;Science;Math;
 Comment=MassChroQ parameters editor
 Exec=masschroq_studio %U