Update mussa to build on ubuntu 10.04 with qt 4.6.2 +boost 1.40.0.1

I needed to turn off linking against static libraries as I was getting
linker errors in the python components.

Additionally I updated the Boost.Test code to compile with the the
newer boost library. After looking through the documentation, it looks
like the BOOST_TEST_MODULE feature was added in 1.36, though I'm not
fully sure.

So although I adjusted the FindBoost required version, I might've
gotten it wrong.

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6db7a979a88404c026e86ff262d7ff37509cea35..59fba73805356ac8808ab569f7d3e18e60f224f9 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -21,7 +21,7 @@ IF(QT_QTASSISTANT_FOUND)
 ENDIF(QT_QTASSISTANT_FOUND)
 INCLUDE( ${QT_USE_FILE} )
 FIND_PACKAGE(OpenGL)
-set(Boost_USE_STATIC_LIBS   ON)
+set(Boost_USE_STATIC_LIBS   OFF)
 set(Boost_USE_MULTITHREADED ON)
 FIND_PACKAGE(Boost 1.40 REQUIRED filesystem serialization system program_options )
 FIND_PACKAGE(Boost 1.40 COMPONENTS python)

diff --git a/alg/CMakeLists.txt b/alg/CMakeLists.txt
index a9308d0589d4db20627414f234b2a7a5e503c225..83315dca6333bf4438a4e672f2e7b5d2ca1cb517 100644 (file)
--- a/alg/CMakeLists.txt
+++ b/alg/CMakeLists.txt
@@ -1,6 +1,6 @@
 FIND_PACKAGE(OpenGL )
 
-set(Boost_USE_STATIC_LIBS   ON)
+set(Boost_USE_STATIC_LIBS   OFF)
 set(Boost_USE_MULTITHREADED ON)
 FIND_PACKAGE(Boost 1.34.1 REQUIRED filesystem unit_test_framework
                                                                serialization system program_options )

diff --git a/alg/test/CMakeLists.txt b/alg/test/CMakeLists.txt
index c13a90a74ee3d512e14eab41866e71c5b632eefa..8530993a21dc44decaec05da987a7ca33b05235d 100644 (file)
--- a/alg/test/CMakeLists.txt
+++ b/alg/test/CMakeLists.txt
@@ -1,8 +1,8 @@
 FIND_PACKAGE(OpenGL)
 
-set(Boost_USE_STATIC_LIBS   ON)
+set(Boost_USE_STATIC_LIBS   OFF)
 set(Boost_USE_MULTITHREADED ON)
-FIND_PACKAGE(Boost 1.34.1 REQUIRED filesystem unit_test_framework serialization system)
+FIND_PACKAGE(Boost 1.36.0 REQUIRED filesystem unit_test_framework serialization system)
 FIND_PACKAGE(Qt4)
 INCLUDE( ${QT_USE_FILE} )
 INCLUDE(Platform)

diff --git a/alg/test/test_alphabet.cpp b/alg/test/test_alphabet.cpp
index 854c1b3b24c01f189a5ea0326bec63b12c6f9728..c854530554aa85055854cbc3f59300b046eea393 100644 (file)
--- a/alg/test/test_alphabet.cpp
+++ b/alg/test/test_alphabet.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_alphabet
+#include <boost/test/unit_test.hpp>
 
 #include <boost/archive/text_oarchive.hpp>
 #include <boost/archive/text_iarchive.hpp>
@@ -172,4 +173,4 @@ BOOST_AUTO_TEST_CASE( alphabet_reverse_complement )
   
   BOOST_CHECK_EQUAL(*new_seq, known_rc_seq);
   
-}
\ No newline at end of file
+}

diff --git a/alg/test/test_annotation_color.cpp b/alg/test/test_annotation_color.cpp
index aa06060c37deb49b2bb2356d035b3a7679297e27..15373d89243ee2a4238b08ee4a0d3e1f603d8404 100644 (file)
--- a/alg/test/test_annotation_color.cpp
+++ b/alg/test/test_annotation_color.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_annotation_color
+#include <boost/test/unit_test.hpp>
 
 #include "alg/annotation_colors.hpp"
 #include "alg/color.hpp"

diff --git a/alg/test/test_annotations.cpp b/alg/test/test_annotations.cpp
index 2e4cb50642e6871858df209ea8234952332ebcbd..5a92f096fd317cfe0e26fcf0f05b63ff49a2fa7f 100644 (file)
--- a/alg/test/test_annotations.cpp
+++ b/alg/test/test_annotations.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_annotations
+#include <boost/test/unit_test.hpp>
 
 #include <boost/shared_ptr.hpp>
 #include "annotations.hpp"

diff --git a/alg/test/test_color.cpp b/alg/test/test_color.cpp
index 351a54a06021e5c324ee21dc5afd185e0747a7d9..1c19ed9cfc240c1213e95b0e1b1eb1a03e212723 100644 (file)
--- a/alg/test/test_color.cpp
+++ b/alg/test/test_color.cpp
@@ -1,6 +1,8 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_color
+#include <boost/test/unit_test.hpp>
 #include <boost/test/floating_point_comparison.hpp>
+
 #include <string>
 #include <sstream>
 

diff --git a/alg/test/test_conserved_path.cpp b/alg/test/test_conserved_path.cpp
index ed772b6995ecc3e268cd9f9d6900a0e8ed01730b..2ccea3bbfba5b4fd0bb8da3a4baa4562e7ea5a52 100644 (file)
--- a/alg/test/test_conserved_path.cpp
+++ b/alg/test/test_conserved_path.cpp
@@ -1,5 +1,7 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_conserved_path
+#include <boost/test/unit_test.hpp>
+
 #include <boost/assign/std/vector.hpp>
 using namespace boost::assign;
 

diff --git a/alg/test/test_drawable.cpp b/alg/test/test_drawable.cpp
index 8319984a9b57ec42f7af9c85b401258574bd8156..391427670985dfebdcef97a2c138795eaf514eca 100644 (file)
--- a/alg/test/test_drawable.cpp
+++ b/alg/test/test_drawable.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_drawable
+#include <boost/test/unit_test.hpp>
 
 #include <boost/shared_ptr.hpp>
 
@@ -97,4 +98,4 @@ BOOST_AUTO_TEST_CASE( test_drawable_find_drawable )
      
   BOOST_CHECK_EQUAL(drawsp->drawFunction(), test_draw_func_find_drawable);
   ssp->drawable()->drawFunction();
-}
\ No newline at end of file
+}

diff --git a/alg/test/test_flp.cpp b/alg/test/test_flp.cpp
index e606f98e82df1cd2050b88d424cb29df5e966290..54aa76a9ad18d6495ae01c77cf328f4a2c4cc05f 100644 (file)
--- a/alg/test/test_flp.cpp
+++ b/alg/test/test_flp.cpp
@@ -1,8 +1,10 @@
-#define BOOST_AUTO_TEST_MAIN
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_flp
+#include <boost/test/auto_unit_test.hpp>
+
 #include <iostream>
 #include <list>
 
-#include <boost/test/auto_unit_test.hpp>
 #include <boost/filesystem/operations.hpp>
 #include <boost/filesystem/path.hpp>
 namespace fs = boost::filesystem;

diff --git a/alg/test/test_glseqbrowser.cpp b/alg/test/test_glseqbrowser.cpp
index acd450eef09d4d72aed63b89dc0bdb05fbe83008..9587472ae5ab73bbbea1ae6780d5e70a3f0230ae 100644 (file)
--- a/alg/test/test_glseqbrowser.cpp
+++ b/alg/test/test_glseqbrowser.cpp
@@ -1,5 +1,7 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_glseqbrowser
+#include <boost/test/unit_test.hpp>
+
 #include <boost/assign/std/vector.hpp>
 using namespace boost::assign;
 
@@ -218,4 +220,4 @@ BOOST_AUTO_TEST_CASE( setSelectedTracks )
   BOOST_CHECK_EQUAL(seq_locs.front().getSequence(), seq0);
   BOOST_CHECK_EQUAL(seq_locs.front().getLeft(), 0);
   BOOST_CHECK_EQUAL(seq_locs.front().getRight(), 2);
-}
\ No newline at end of file
+}

diff --git a/alg/test/test_glsequence.cpp b/alg/test/test_glsequence.cpp
index 47621af4eac63fe11154339bdb39aaa69fd1bfd8..29bbf34839a171bfeeb5bd9312d0681ec210297a 100644 (file)
--- a/alg/test/test_glsequence.cpp
+++ b/alg/test/test_glsequence.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_glsequence
+#include <boost/test/unit_test.hpp>
 #include <boost/test/floating_point_comparison.hpp>
 #include <boost/shared_ptr.hpp>
 
@@ -274,4 +275,4 @@ BOOST_AUTO_TEST_CASE ( shared_ptr_test )
   BOOST_CHECK_EQUAL(seq0.use_count(), 1);
   BOOST_CHECK_EQUAL(seq1.use_count(), 1);
 }
-*/
\ No newline at end of file
+*/

diff --git a/alg/test/test_mussa.cpp b/alg/test/test_mussa.cpp
index 9f11a5e117e199a19b9adaf0b5ed49299720cf3a..5255fe26d7a309130c99b0369bbb8749fba7298a 100644 (file)
--- a/alg/test/test_mussa.cpp
+++ b/alg/test/test_mussa.cpp
@@ -1,5 +1,7 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_mussa
+#include <boost/test/unit_test.hpp>
+
 #include <boost/filesystem/path.hpp>
 #include <boost/filesystem/operations.hpp>
 namespace fs = boost::filesystem;

diff --git a/alg/test/test_nway.cpp b/alg/test/test_nway.cpp
index 9bd8b6432d7e218883da1e13a0aee58e67638fb2..9c7d34233ffae87ff562ecdf35d7bef3f817586b 100644 (file)
--- a/alg/test/test_nway.cpp
+++ b/alg/test/test_nway.cpp
@@ -1,5 +1,7 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_nway
+#include <boost/test/unit_test.hpp>
+
 #include <boost/filesystem/path.hpp>
 namespace fs = boost::filesystem;
 

diff --git a/alg/test/test_seq.cpp b/alg/test/test_seq.cpp
index 767bc5dd344bd3beaf908464af3784f1fdca8175..bdbe60b4e53cdc5a0b477048d833dd5009b187e5 100644 (file)
--- a/alg/test/test_seq.cpp
+++ b/alg/test/test_seq.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_seq
+#include <boost/test/unit_test.hpp>
 
 #include "seq.hpp"
 
@@ -38,4 +39,4 @@ BOOST_AUTO_TEST_CASE( seqstring_string_dna_alphabet )
   BOOST_CHECK_EQUAL(s.get_alphabet_ref(), dna_alphabet);
   BOOST_CHECK_EQUAL(s.get_alphabet(), Alphabet::dna_alphabet());
   BOOST_CHECK_EQUAL(s.size(), 4);  
-}
\ No newline at end of file
+}

diff --git a/alg/test/test_seq_span.cpp b/alg/test/test_seq_span.cpp
index c71382ece05f53f13aa98f76a43f49e9d494780b..9e22f3cb3f93fed3425d9a6106c6c12c8660dddb 100644 (file)
--- a/alg/test/test_seq_span.cpp
+++ b/alg/test/test_seq_span.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_seq_span
+#include <boost/test/unit_test.hpp>
 
 #include "seq_span.hpp"
 #include "mussa_exceptions.hpp"

diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index ae03cdbe8206d206c5843bde03dbdb57d8805f35..aefa6ac6c7aa6ec2b68285d674622d89d82ee127 100644 (file)
--- a/alg/test/test_sequence.cpp
+++ b/alg/test/test_sequence.cpp
@@ -1,5 +1,7 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE
+#include <boost/test/unit_test.hpp>
+
 #include <boost/filesystem/path.hpp>
 #include <boost/filesystem/operations.hpp>
 namespace fs=boost::filesystem;

diff --git a/alg/test/test_sequence_location.cpp b/alg/test/test_sequence_location.cpp
index dd97d08597eb6297047ad0979530965ee8d9650e..e05c0c8c8102ecbeeafebc910454f862bede59e8 100644 (file)
--- a/alg/test/test_sequence_location.cpp
+++ b/alg/test/test_sequence_location.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE
+#include <boost/test/unit_test.hpp>
 
 #include "alg/sequence_location.hpp"
 #include "alg/sequence.hpp"

diff --git a/alg/tsf/CMakeLists.txt b/alg/tsf/CMakeLists.txt
index 237d473d118944fa9b12197ee34dc846be381384..d135567a13a3eb48318bebfe5e6ebf050e234000 100644 (file)
--- a/alg/tsf/CMakeLists.txt
+++ b/alg/tsf/CMakeLists.txt
@@ -1,6 +1,6 @@
-set(Boost_USE_STATIC_LIBS   ON)
+set(Boost_USE_STATIC_LIBS   OFF)
 set(Boost_USE_MULTITHREADED ON)
-FIND_PACKAGE(Boost 1.34.1 REQUIRED unit_test_framework)
+FIND_PACKAGE(Boost 1.36.0 REQUIRED unit_test_framework)
 INCLUDE(Platform)
 
 SET(SOURCES trivial_filter.cpp)

diff --git a/alg/tsf/test_tsf.cpp b/alg/tsf/test_tsf.cpp
index 1e2efe24276a90b130e7819e0d6466bf8365cdc7..e7f1ffda4b844cba8ac97908cf6a554f95b542d0 100644 (file)
--- a/alg/tsf/test_tsf.cpp
+++ b/alg/tsf/test_tsf.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_tsf
+#include <boost/test/unit_test.hpp>
 
 #include "trivial_filter.hpp"
 

diff --git a/py/CMakeLists.txt b/py/CMakeLists.txt
index 0e0848816cfeecd013ca8d276654595fb04e8a93..dbfdb2d3c4e3ae0974b6063dcbe6e443c532425e 100644 (file)
--- a/py/CMakeLists.txt
+++ b/py/CMakeLists.txt
@@ -1,4 +1,4 @@
-set(Boost_USE_STATIC_LIBS   ON)
+set(Boost_USE_STATIC_LIBS   OFF)
 set(Boost_USE_MULTITHREADED ON)
 FIND_PACKAGE(Boost 1.34.1 COMPONENTS python filesystem serialization)
 FIND_PACKAGE(OpenGL)
@@ -38,7 +38,7 @@ IF(Boost_PYTHON_LIBRARY)
   SET(MUSSA_LIBRARIES
         mussa_core
         ${Boost_PYTHON_LIBRARY}
-       ${Boost_SYSTEM_LIBRARY}
+        ${Boost_SYSTEM_LIBRARY}
         ${Boost_FILESYSTEM_LIBRARY}
         ${Boost_SERIALIZATION_LIBRARY}
         ${OPENGL_gl_LIBRARY}

diff --git a/py/test/CMakeLists.txt b/py/test/CMakeLists.txt
index 50e18b008ccab14895ca34d3073fa40c1764bf8b..bbaf0a25af58c2569c1e4268a751c08c1dc6a8fc 100644 (file)
--- a/py/test/CMakeLists.txt
+++ b/py/test/CMakeLists.txt
@@ -1,8 +1,8 @@
 FIND_PACKAGE(PythonLibs)
 
-set(Boost_USE_STATIC_LIBS   ON)
+set(Boost_USE_STATIC_LIBS   OFF)
 set(Boost_USE_MULTITHREADED ON)
-FIND_PACKAGE(Boost 1.34.1 COMPONENTS program_options filesystem serialization python unit_test_framework )
+FIND_PACKAGE(Boost 1.36.0 COMPONENTS program_options filesystem serialization python unit_test_framework )
 INCLUDE(Platform)
 
 IF(Boost_PYTHON_FOUND)

diff --git a/py/test/test_python.cpp b/py/test/test_python.cpp
index c33b7ad8278e0038769fd8eead8b97ec70a0bd49..2ed991f1cba1cd26dcb40b84f05a4c19e1c65701 100644 (file)
--- a/py/test/test_python.cpp
+++ b/py/test/test_python.cpp
@@ -1,5 +1,6 @@
-#define BOOST_AUTO_TEST_MAIN
-#include <boost/test/auto_unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE test_python
+#include <boost/test/unit_test.hpp>
 
 #include "py/python.hpp"
 #include <string>

diff --git a/qui/CMakeLists.txt b/qui/CMakeLists.txt
index 23adbc5fe44b1deb851523db6b32bd83c7a3be4e..1ae54fd01c741dfb00c164502f82c36b476cf89e 100644 (file)
--- a/qui/CMakeLists.txt
+++ b/qui/CMakeLists.txt
@@ -10,7 +10,7 @@ IF(QT_QTASSISTANT_FOUND)
 ENDIF(QT_QTASSISTANT_FOUND)
 INCLUDE( ${QT_USE_FILE} )
 FIND_PACKAGE(OpenGL)
-set(Boost_USE_STATIC_LIBS   ON)
+set(Boost_USE_STATIC_LIBS   OFF)
 set(Boost_USE_MULTITHREADED ON)
 FIND_PACKAGE(Boost 1.34.1)
 FIND_PACKAGE(PythonLibs)