From 97498410e1fc5c39eac0282a6620b8fcb0f02ff3 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Mon, 18 Oct 2010 15:47:53 -0700 Subject: [PATCH] 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. --- CMakeLists.txt | 2 +- alg/CMakeLists.txt | 2 +- alg/test/CMakeLists.txt | 4 ++-- alg/test/test_alphabet.cpp | 7 ++++--- alg/test/test_annotation_color.cpp | 5 +++-- alg/test/test_annotations.cpp | 5 +++-- alg/test/test_color.cpp | 6 ++++-- alg/test/test_conserved_path.cpp | 6 ++++-- alg/test/test_drawable.cpp | 7 ++++--- alg/test/test_flp.cpp | 6 ++++-- alg/test/test_glseqbrowser.cpp | 8 +++++--- alg/test/test_glsequence.cpp | 7 ++++--- alg/test/test_mussa.cpp | 6 ++++-- alg/test/test_nway.cpp | 6 ++++-- alg/test/test_seq.cpp | 7 ++++--- alg/test/test_seq_span.cpp | 5 +++-- alg/test/test_sequence.cpp | 6 ++++-- alg/test/test_sequence_location.cpp | 5 +++-- alg/tsf/CMakeLists.txt | 4 ++-- alg/tsf/test_tsf.cpp | 5 +++-- py/CMakeLists.txt | 4 ++-- py/test/CMakeLists.txt | 4 ++-- py/test/test_python.cpp | 5 +++-- qui/CMakeLists.txt | 2 +- 24 files changed, 74 insertions(+), 50 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 6db7a97..59fba73 100644 --- 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 a9308d0..83315dc 100644 --- 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 c13a90a..8530993 100644 --- 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 854c1b3..c854530 100644 --- a/alg/test/test_alphabet.cpp +++ b/alg/test/test_alphabet.cpp @@ -1,5 +1,6 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_alphabet +#include #include #include @@ -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 aa06060..15373d8 100644 --- a/alg/test/test_annotation_color.cpp +++ b/alg/test/test_annotation_color.cpp @@ -1,5 +1,6 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_annotation_color +#include #include "alg/annotation_colors.hpp" #include "alg/color.hpp" diff --git a/alg/test/test_annotations.cpp b/alg/test/test_annotations.cpp index 2e4cb50..5a92f09 100644 --- a/alg/test/test_annotations.cpp +++ b/alg/test/test_annotations.cpp @@ -1,5 +1,6 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_annotations +#include #include #include "annotations.hpp" diff --git a/alg/test/test_color.cpp b/alg/test/test_color.cpp index 351a54a..1c19ed9 100644 --- a/alg/test/test_color.cpp +++ b/alg/test/test_color.cpp @@ -1,6 +1,8 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_color +#include #include + #include #include diff --git a/alg/test/test_conserved_path.cpp b/alg/test/test_conserved_path.cpp index ed772b6..2ccea3b 100644 --- a/alg/test/test_conserved_path.cpp +++ b/alg/test/test_conserved_path.cpp @@ -1,5 +1,7 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_conserved_path +#include + #include using namespace boost::assign; diff --git a/alg/test/test_drawable.cpp b/alg/test/test_drawable.cpp index 8319984..3914276 100644 --- a/alg/test/test_drawable.cpp +++ b/alg/test/test_drawable.cpp @@ -1,5 +1,6 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_drawable +#include #include @@ -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 e606f98..54aa76a 100644 --- 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 + #include #include -#include #include #include namespace fs = boost::filesystem; diff --git a/alg/test/test_glseqbrowser.cpp b/alg/test/test_glseqbrowser.cpp index acd450e..9587472 100644 --- a/alg/test/test_glseqbrowser.cpp +++ b/alg/test/test_glseqbrowser.cpp @@ -1,5 +1,7 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_glseqbrowser +#include + #include 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 47621af..29bbf34 100644 --- a/alg/test/test_glsequence.cpp +++ b/alg/test/test_glsequence.cpp @@ -1,5 +1,6 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_glsequence +#include #include #include @@ -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 9f11a5e..5255fe2 100644 --- a/alg/test/test_mussa.cpp +++ b/alg/test/test_mussa.cpp @@ -1,5 +1,7 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_mussa +#include + #include #include namespace fs = boost::filesystem; diff --git a/alg/test/test_nway.cpp b/alg/test/test_nway.cpp index 9bd8b64..9c7d342 100644 --- a/alg/test/test_nway.cpp +++ b/alg/test/test_nway.cpp @@ -1,5 +1,7 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_nway +#include + #include namespace fs = boost::filesystem; diff --git a/alg/test/test_seq.cpp b/alg/test/test_seq.cpp index 767bc5d..bdbe60b 100644 --- a/alg/test/test_seq.cpp +++ b/alg/test/test_seq.cpp @@ -1,5 +1,6 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_seq +#include #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 c71382e..9e22f3c 100644 --- a/alg/test/test_seq_span.cpp +++ b/alg/test/test_seq_span.cpp @@ -1,5 +1,6 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_seq_span +#include #include "seq_span.hpp" #include "mussa_exceptions.hpp" diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp index ae03cdb..aefa6ac 100644 --- a/alg/test/test_sequence.cpp +++ b/alg/test/test_sequence.cpp @@ -1,5 +1,7 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE +#include + #include #include namespace fs=boost::filesystem; diff --git a/alg/test/test_sequence_location.cpp b/alg/test/test_sequence_location.cpp index dd97d08..e05c0c8 100644 --- a/alg/test/test_sequence_location.cpp +++ b/alg/test/test_sequence_location.cpp @@ -1,5 +1,6 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE +#include #include "alg/sequence_location.hpp" #include "alg/sequence.hpp" diff --git a/alg/tsf/CMakeLists.txt b/alg/tsf/CMakeLists.txt index 237d473..d135567 100644 --- 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 1e2efe2..e7f1ffd 100644 --- a/alg/tsf/test_tsf.cpp +++ b/alg/tsf/test_tsf.cpp @@ -1,5 +1,6 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_tsf +#include #include "trivial_filter.hpp" diff --git a/py/CMakeLists.txt b/py/CMakeLists.txt index 0e08488..dbfdb2d 100644 --- 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 50e18b0..bbaf0a2 100644 --- 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 c33b7ad..2ed991f 100644 --- a/py/test/test_python.cpp +++ b/py/test/test_python.cpp @@ -1,5 +1,6 @@ -#define BOOST_AUTO_TEST_MAIN -#include +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE test_python +#include #include "py/python.hpp" #include diff --git a/qui/CMakeLists.txt b/qui/CMakeLists.txt index 23adbc5..1ae54fd 100644 --- 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) -- 2.30.2