[med-svn] r19563 - in trunk/packages/hyphy/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-07-08 07:35:21 +0000 (Wed, 08 Jul 2015)
New Revision: 19563

Added:
   trunk/packages/hyphy/trunk/debian/patches/use_debian_sqlite.patch
Modified:
   trunk/packages/hyphy/trunk/debian/control
   trunk/packages/hyphy/trunk/debian/patches/series
Log:
Try to use Debian packaged sqlite


Modified: trunk/packages/hyphy/trunk/debian/control
===================================================================
--- trunk/packages/hyphy/trunk/debian/control	2015-07-08 06:46:01 UTC (rev 19562)
+++ trunk/packages/hyphy/trunk/debian/control	2015-07-08 07:35:21 UTC (rev 19563)
@@ -9,7 +9,8 @@
                libcurl4-gnutls-dev | libcurl4-dev,
                python,
                libgtk2.0-dev,
-               libssl-dev
+               libssl-dev,
+               libsqlite3-dev
 Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/hyphy/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/hyphy/trunk/

Modified: trunk/packages/hyphy/trunk/debian/patches/series
===================================================================
--- trunk/packages/hyphy/trunk/debian/patches/series	2015-07-08 06:46:01 UTC (rev 19562)
+++ trunk/packages/hyphy/trunk/debian/patches/series	2015-07-08 07:35:21 UTC (rev 19563)
@@ -1 +1,2 @@
 # arch_all_files_to_usr_share.patch
+use_debian_sqlite.patch

Added: trunk/packages/hyphy/trunk/debian/patches/use_debian_sqlite.patch
===================================================================
--- trunk/packages/hyphy/trunk/debian/patches/use_debian_sqlite.patch	                        (rev 0)
+++ trunk/packages/hyphy/trunk/debian/patches/use_debian_sqlite.patch	2015-07-08 07:35:21 UTC (rev 19563)
@@ -0,0 +1,103 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -211,13 +211,12 @@ file(GLOB SRC_NEW src/new/*.cpp)
+ 
+ set(SRC_LINK src/lib/Link/THyPhy.cpp)
+ set(SRC_PREFS src/gui/preferences.cpp)
+-set(SRC_SQLITE3 contrib/SQLite-3.8.2/sqlite3.c)
+ set(SRC_UNIXMAIN src/mains/unix.cpp)
+ set(SRC_GTKMAIN src/mains/gtk.cpp)
+ set(SRC_MACMAIN src/mains/mac.cpp)
+ set(SRC_UTILS src/utils/hyphyunixutils.cpp)
+ 
+-set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_SQLITE3} ${SRC_UTILS})
++set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_UTILS})
+ 
+ 
+ #-------------------------------------------------------------------------------
+@@ -229,11 +228,6 @@ set_property(
+ )
+ 
+ set_property(
+-    SOURCE ${SRC_SQLITE3}
+-    PROPERTY COMPILE_FLAGS "-Wno-int-to-pointer-cast -Wno-pointer-to-int-cast"
+-)
+-
+-set_property(
+     SOURCE src/core/calcnode2.cpp
+     PROPERTY COMPILE_FLAGS "-fstrict-aliasing -funroll-loops"
+ )
+@@ -250,7 +244,6 @@ endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
+ include_directories(
+     src/core/include
+     src/lib/Link src/new/include
+-    contrib/SQLite-3.8.2 # SQLite
+     src/gui/include
+     src/gui/include/Components
+     src/gui/include/WindowClasses
+@@ -438,11 +431,38 @@ set_target_properties(
+     LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
+ )
+ 
++# check for Debian packaged sqlite
++# stolen from https://sources.debian.net/src/u1db/13.10-6/debian/patches/fix_linking/?hl=103
++find_package(PkgConfig)
++pkg_check_modules(PC_SQLITE3 sqlite3)
++
++find_path(SQLITE3_INCLUDE_DIR sqlite3.h
++  HINTS
++  ${PC_SQLITE3_INCLUDE_DIRS}
++  /usr/include
++  /usr/local/include
++  /opt/local/include
++)
++
++find_library(SQLITE3_LIBRARY
++  NAMES ${SQLITE3_NAMES} libsqlite3.so libsqlite3.a
++  HINTS ${PC_SQLITE3_LIBRARY_DIRS}
++  /usr/lib /usr/local/lib /opt/local/lib
++)
++
++include(FindPackageHandleStandardArgs)
++find_package_handle_standard_args(SQLITE3 DEFAULT_MSG SQLITE3_LIBRARY SQLITE3_INCLUDE_DIR)
++
++if(SQLITE3_FOUND)
++  set(SQLITE3_LIBRARIES ${SQLITE3_LIBRARY})
++  set(SQLITE3_INCLUDE_DIRS ${SQLITE3_INCLUDE_DIR})
++endif()
++
++
+ #-------------------------------------------------------------------------------
+ # hyphy gtk+ target
+ #-------------------------------------------------------------------------------
+ 
+-
+ find_package(GTK2 2.6)
+ 
+ if((${GTK2_FOUND}))
+@@ -454,6 +474,7 @@ if((${GTK2_FOUND}))
+     )
+ 	include_directories(
+         ${GTK2_INCLUDE_DIRS}
++        ${SQLITE3_INCLUDE_DIRS}
+         src/gui/gtk/include
+         src/gui/gtk/include/Components
+         /Developer/Headers/FlatCarbon
+@@ -463,7 +484,7 @@ if((${GTK2_FOUND}))
+         EXCLUDE_FROM_ALL
+         ${SRC_GUI_GTK} ${SRC_GTKMAIN} ${SRC_GUI} ${SRC_COMMON}
+     )
+-    target_link_libraries(HYPHYGTK ${DEFAULT_LIBRARIES} ${GTK2_LIBRARIES})
++    target_link_libraries(HYPHYGTK ${DEFAULT_LIBRARIES} ${GTK2_LIBRARIES} ${SQLITE3_LIBRARIES})
+ 
+ 	add_custom_target(GTK DEPENDS HYPHYGTK)
+ 
+@@ -544,7 +565,7 @@ if(APPLE AND NOT ${MACOSX_GT_LION})
+     add_executable(HyPhy
+         MACOSX_BUNDLE
+ 		    EXCLUDE_FROM_ALL
+-        ${SRC_CORE} ${SRC_NEW} ${SRC_SQLITE3} ${SRC_GUI} ${SRC_MACGUI} ${SRC_MACMAIN}
++        ${SRC_CORE} ${SRC_NEW} ${SRC_GUI} ${SRC_MACGUI} ${SRC_MACMAIN}
+         ${RES_MACGUI}
+     )
+