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| 1 | sudo cmake28 /path/to/bam-readcount | |
| 2 | -- The C compiler identification is GNU 4.4.7 | |
| 3 | -- The CXX compiler identification is GNU 4.4.7 | |
| 4 | -- Check for working C compiler: /usr/bin/cc | |
| 5 | -- Check for working C compiler: /usr/bin/cc -- works | |
| 6 | -- Detecting C compiler ABI info | |
| 7 | -- Detecting C compiler ABI info - done | |
| 8 | -- Check for working CXX compiler: /usr/bin/c++ | |
| 9 | -- Check for working CXX compiler: /usr/bin/c++ -- works | |
| 10 | -- Detecting CXX compiler ABI info | |
| 11 | -- Detecting CXX compiler ABI info - done | |
| 12 | -- Looking for include file pthread.h | |
| 13 | -- Looking for include file pthread.h - found | |
| 14 | -- Looking for pthread_create | |
| 15 | -- Looking for pthread_create - not found | |
| 16 | -- Looking for pthread_create in pthreads | |
| 17 | -- Looking for pthread_create in pthreads - not found | |
| 18 | -- Looking for pthread_create in pthread | |
| 19 | -- Looking for pthread_create in pthread - found | |
| 20 | -- Found Threads: TRUE | |
| 21 | No CMAKE_BUILD_TYPE specified, defaulting to release | |
| 22 | -- Boost version: 1.54.0 | |
| 23 | -- Found the following Boost libraries: | |
| 24 | -- program_options | |
| 25 | -- Found ZLIB: /usr/local/lib/libz.so (found version "1.2.3") | |
| 26 | -- Boost version: 1.54.0 | |
| 27 | -- Could NOT find GTest (missing: GTEST_INCLUDE_DIR) | |
| 28 | Google Test framework not found, no tests will be built | |
| 29 | GTest is available at http://code.google.com/p/googletest/ | |
| 30 | Ubuntu users can likely sudo apt-get install gtest | |
| 31 | -- Configuring done | |
| 32 | -- Generating done | |
| 33 | - | -- Build files have been written to: /home/stud-jta/Downloads/bam-readcount/build |
| 33 | + | -- Build files have been written to: /path/to/bam-readcount/build |
| 34 | - | [stud-jta@johnbosco build]$ sudo make deps |
| 34 | + | [build]$ sudo make deps |
| 35 | Scanning dependencies of target samtools-lib | |
| 36 | [ 12%] Creating directories for 'samtools-lib' | |
| 37 | [ 25%] Performing download step (verify and extract) for 'samtools-lib' | |
| 38 | -- verifying file... | |
| 39 | - | file='/home/stud-jta/Downloads/bam-readcount/vendor/samtools-0.1.19.tar.gz' |
| 39 | + | file='/path/to/bam-readcount/vendor/samtools-0.1.19.tar.gz' |
| 40 | -- verifying file... warning: did not verify file - no URL_HASH specified? | |
| 41 | -- extracting... | |
| 42 | - | src='/home/stud-jta/Downloads/bam-readcount/vendor/samtools-0.1.19.tar.gz' |
| 42 | + | src='/path/to/bam-readcount/vendor/samtools-0.1.19.tar.gz' |
| 43 | - | dst='/home/stud-jta/Downloads/bam-readcount/build/vendor/samtools' |
| 43 | + | dst='/path/to/bam-readcount/build/vendor/samtools' |
| 44 | -- extracting... [tar xfz] | |
| 45 | -- extracting... [analysis] | |
| 46 | -- extracting... [rename] | |
| 47 | -- extracting... [clean up] | |
| 48 | -- extracting... done | |
| 49 | [ 37%] No patch step for 'samtools-lib' | |
| 50 | [ 50%] No update step for 'samtools-lib' | |
| 51 | [ 62%] Performing configure step for 'samtools-lib' | |
| 52 | - | Building samtools, build log at /home/stud-jta/Downloads/bam-readcount/build/vendor/samtools/build.log |
| 52 | + | Building samtools, build log at /path/to/bam-readcount/build/vendor/samtools/build.log |
| 53 | [ 75%] Performing build step for 'samtools-lib' | |
| 54 | [ 87%] No install step for 'samtools-lib' | |
| 55 | [100%] Completed 'samtools-lib' | |
| 56 | [100%] Built target samtools-lib | |
| 57 | Scanning dependencies of target deps | |
| 58 | [100%] Built target deps | |
| 59 | - | [stud-jta@johnbosco build]$ sudo make |
| 59 | + | [build]$ sudo make |
| 60 | [ 44%] Built target samtools-lib | |
| 61 | [ 44%] Built target deps | |
| 62 | Scanning dependencies of target gtest160 | |
| 63 | [ 50%] Creating directories for 'gtest160' | |
| 64 | [ 55%] Performing download step (verify and extract) for 'gtest160' | |
| 65 | -- verifying file... | |
| 66 | - | file='/home/stud-jta/Downloads/bam-readcount/build-common/vendor/gtest-1.6.0.tar.gz' |
| 66 | + | file='/path/to/bam-readcount/build-common/vendor/gtest-1.6.0.tar.gz' |
| 67 | -- verifying file... warning: did not verify file - no URL_HASH specified? | |
| 68 | -- extracting... | |
| 69 | - | src='/home/stud-jta/Downloads/bam-readcount/build-common/vendor/gtest-1.6.0.tar.gz' |
| 69 | + | src='/path/to/bam-readcount/build-common/vendor/gtest-1.6.0.tar.gz' |
| 70 | - | dst='/home/stud-jta/Downloads/bam-readcount/build/vendor/src/gtest160' |
| 70 | + | dst='/path/to/bam-readcount/build/vendor/src/gtest160' |
| 71 | -- extracting... [tar xfz] | |
| 72 | -- extracting... [analysis] | |
| 73 | -- extracting... [rename] | |
| 74 | -- extracting... [clean up] | |
| 75 | -- extracting... done | |
| 76 | [ 61%] No patch step for 'gtest160' | |
| 77 | [ 66%] No update step for 'gtest160' | |
| 78 | [ 72%] Performing configure step for 'gtest160' | |
| 79 | -- The CXX compiler identification is GNU 4.4.7 | |
| 80 | -- The C compiler identification is GNU 4.4.7 | |
| 81 | -- Check for working CXX compiler: /usr/bin/c++ | |
| 82 | -- Check for working CXX compiler: /usr/bin/c++ -- works | |
| 83 | -- Detecting CXX compiler ABI info | |
| 84 | -- Detecting CXX compiler ABI info - done | |
| 85 | -- Check for working C compiler: /usr/bin/cc | |
| 86 | -- Check for working C compiler: /usr/bin/cc -- works | |
| 87 | -- Detecting C compiler ABI info | |
| 88 | -- Detecting C compiler ABI info - done | |
| 89 | -- Found PythonInterp: /usr/bin/python (found version "2.6.6") | |
| 90 | -- Looking for include file pthread.h | |
| 91 | -- Looking for include file pthread.h - found | |
| 92 | -- Looking for pthread_create | |
| 93 | -- Looking for pthread_create - not found | |
| 94 | -- Looking for pthread_create in pthreads | |
| 95 | -- Looking for pthread_create in pthreads - not found | |
| 96 | -- Looking for pthread_create in pthread | |
| 97 | -- Looking for pthread_create in pthread - found | |
| 98 | -- Found Threads: TRUE | |
| 99 | -- Configuring done | |
| 100 | -- Generating done | |
| 101 | -- Build files have been written to: /path/to/bam-readcount/build/vendor/gtest160-build | |
| 102 | [ 77%] Performing build step for 'gtest160' | |
| 103 | Scanning dependencies of target gtest | |
| 104 | [ 50%] Building CXX object CMakeFiles/gtest.dir/src/gtest-all.cc.o | |
| 105 | Linking CXX static library libgtest.a | |
| 106 | [ 50%] Built target gtest | |
| 107 | Scanning dependencies of target gtest_main | |
| 108 | [100%] Building CXX object CMakeFiles/gtest_main.dir/src/gtest_main.cc.o | |
| 109 | Linking CXX static library libgtest_main.a | |
| 110 | [100%] Built target gtest_main | |
| 111 | [ 83%] No install step for 'gtest160' | |
| 112 | [ 88%] Completed 'gtest160' | |
| 113 | [ 88%] Built target gtest160 | |
| 114 | Scanning dependencies of target bamrc | |
| 115 | [ 94%] Building CXX object build/src/lib/bamrc/CMakeFiles/bamrc.dir/BasicStat.cpp.o | |
| 116 | Linking CXX static library libbamrc.a | |
| 117 | [ 94%] Built target bamrc | |
| 118 | Scanning dependencies of target bam-readcount | |
| 119 | [100%] Building CXX object build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o | |
| 120 | Linking CXX executable ../../../../bin/bam-readcount | |
| 121 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `main': | |
| 122 | bamreadcount.cpp:(.text+0x665): undefined reference to `boost::program_options::options_description::m_default_line_length' | |
| 123 | bamreadcount.cpp:(.text+0x6b1): undefined reference to `boost::program_options::options_description::options_description(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| 124 | bamreadcount.cpp:(.text+0x6e0): undefined reference to `boost::program_options::bool_switch(bool*)' | |
| 125 | bamreadcount.cpp:(.text+0x795): undefined reference to `boost::program_options::bool_switch(bool*)' | |
| 126 | bamreadcount.cpp:(.text+0xada): undefined reference to `boost::program_options::options_description::add_options()' | |
| 127 | bamreadcount.cpp:(.text+0xaf9): undefined reference to `boost::program_options::options_description_easy_init::operator()(char const*, char const*)' | |
| 128 | bamreadcount.cpp:(.text+0xb10): undefined reference to `boost::program_options::options_description_easy_init::operator()(char const*, boost::program_options::value_semantic const*, char const*)' | |
| 129 | bamreadcount.cpp:(.text+0xb27): undefined reference to `boost::program_options::options_description_easy_init::operator()(char const*, boost::program_options::value_semantic const*, char const*)' | |
| 130 | bamreadcount.cpp:(.text+0xb3e): undefined reference to `boost::program_options::options_description_easy_init::operator()(char const*, boost::program_options::value_semantic const*, char const*)' | |
| 131 | bamreadcount.cpp:(.text+0xb53): undefined reference to `boost::program_options::options_description_easy_init::operator()(char const*, boost::program_options::value_semantic const*, char const*)' | |
| 132 | bamreadcount.cpp:(.text+0xb68): undefined reference to `boost::program_options::options_description_easy_init::operator()(char const*, boost::program_options::value_semantic const*, char const*)' | |
| 133 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:bamreadcount.cpp:(.text+0xb7d): more undefined references to `boost::program_options::options_description_easy_init::operator()(char const*, boost::program_options::value_semantic const*, char const*)' follow | |
| 134 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `main': | |
| 135 | bamreadcount.cpp:(.text+0xbfa): undefined reference to `boost::program_options::options_description::options_description(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' | |
| 136 | bamreadcount.cpp:(.text+0xcd7): undefined reference to `boost::program_options::options_description::add_options()' | |
| 137 | bamreadcount.cpp:(.text+0xcf9): undefined reference to `boost::program_options::options_description_easy_init::operator()(char const*, boost::program_options::value_semantic const*, char const*)' | |
| 138 | bamreadcount.cpp:(.text+0xd0e): undefined reference to `boost::program_options::options_description_easy_init::operator()(char const*, boost::program_options::value_semantic const*, char const*)' | |
| 139 | bamreadcount.cpp:(.text+0xd23): undefined reference to `boost::program_options::options_description::options_description(unsigned int, unsigned int)' | |
| 140 | bamreadcount.cpp:(.text+0xd38): undefined reference to `boost::program_options::options_description::add(boost::program_options::options_description const&)' | |
| 141 | bamreadcount.cpp:(.text+0xd48): undefined reference to `boost::program_options::options_description::add(boost::program_options::options_description const&)' | |
| 142 | bamreadcount.cpp:(.text+0xd55): undefined reference to `boost::program_options::positional_options_description::positional_options_description()' | |
| 143 | bamreadcount.cpp:(.text+0xd6c): undefined reference to `boost::program_options::positional_options_description::add(char const*, int)' | |
| 144 | bamreadcount.cpp:(.text+0xd83): undefined reference to `boost::program_options::positional_options_description::add(char const*, int)' | |
| 145 | bamreadcount.cpp:(.text+0xd90): undefined reference to `boost::program_options::variables_map::variables_map()' | |
| 146 | bamreadcount.cpp:(.text+0xdbc): undefined reference to `boost::program_options::detail::cmdline::set_options_description(boost::program_options::options_description const&)' | |
| 147 | bamreadcount.cpp:(.text+0xddc): undefined reference to `boost::program_options::detail::cmdline::set_positional_options(boost::program_options::positional_options_description const&)' | |
| 148 | bamreadcount.cpp:(.text+0xe01): undefined reference to `boost::program_options::store(boost::program_options::basic_parsed_options<char> const&, boost::program_options::variables_map&, bool)' | |
| 149 | bamreadcount.cpp:(.text+0xe99): undefined reference to `boost::program_options::notify(boost::program_options::variables_map&)' | |
| 150 | bamreadcount.cpp:(.text+0xf67): undefined reference to `boost::program_options::operator<<(std::basic_ostream<char, std::char_traits<char> >&, boost::program_options::options_description const&)' | |
| 151 | bamreadcount.cpp:(.text+0xf95): undefined reference to `vtable for boost::program_options::variables_map' | |
| 152 | bamreadcount.cpp:(.text+0x129e): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 153 | bamreadcount.cpp:(.text+0x170d): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 154 | bamreadcount.cpp:(.text+0x1fe8): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 155 | bamreadcount.cpp:(.text+0x2041): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 156 | bamreadcount.cpp:(.text+0x21ed): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 157 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)': | |
| 158 | bamreadcount.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x34): undefined reference to `boost::program_options::validation_error::get_template(boost::program_options::validation_error::kind_t)' | |
| 159 | bamreadcount.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x4a): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)' | |
| 160 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > boost::program_options::to_internal<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)': | |
| 161 | bamreadcount.cpp:(.text._ZN5boost15program_options11to_internalISsEESt6vectorISsSaISsEERKS2_IT_SaIS5_EE[std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > boost::program_options::to_internal<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)]+0x7d): undefined reference to `boost::program_options::to_internal(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' | |
| 162 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)': | |
| 163 | bamreadcount.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x50): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)' | |
| 164 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::typed_value<long, char>::name() const': | |
| 165 | bamreadcount.cpp:(.text._ZNK5boost15program_options11typed_valueIlcE4nameEv[boost::program_options::typed_value<long, char>::name() const]+0x31): undefined reference to `boost::program_options::arg' | |
| 166 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::typed_value<bool, char>::name() const': | |
| 167 | bamreadcount.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[boost::program_options::typed_value<bool, char>::name() const]+0x31): undefined reference to `boost::program_options::arg' | |
| 168 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const': | |
| 169 | bamreadcount.cpp:(.text._ZNK5boost15program_options11typed_valueISscE4nameEv[boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const]+0x31): undefined reference to `boost::program_options::arg' | |
| 170 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::typed_value<int, char>::name() const': | |
| 171 | bamreadcount.cpp:(.text._ZNK5boost15program_options11typed_valueIicE4nameEv[boost::program_options::typed_value<int, char>::name() const]+0x31): undefined reference to `boost::program_options::arg' | |
| 172 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const': | |
| 173 | bamreadcount.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorISsSaISsEE[boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const]+0x1c): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)' | |
| 174 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const': | |
| 175 | bamreadcount.cpp:(.text._ZNK5boost15program_options11typed_valueISscE6xparseERNS_3anyERKSt6vectorISsSaISsEE[boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const]+0x1c): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)' | |
| 176 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::variables_map::~variables_map()': | |
| 177 | bamreadcount.cpp:(.text._ZN5boost15program_options13variables_mapD2Ev[_ZN5boost15program_options13variables_mapD5Ev]+0x13): undefined reference to `vtable for boost::program_options::variables_map' | |
| 178 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::error_with_option_name::~error_with_option_name()': | |
| 179 | bamreadcount.cpp:(.text._ZN5boost15program_options22error_with_option_nameD2Ev[_ZN5boost15program_options22error_with_option_nameD5Ev]+0x19): undefined reference to `vtable for boost::program_options::error_with_option_name' | |
| 180 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error const&)': | |
| 181 | bamreadcount.cpp:(.text._ZN5boost15program_options16validation_errorC2ERKS1_[_ZN5boost15program_options16validation_errorC5ERKS1_]+0x38): undefined reference to `vtable for boost::program_options::error_with_option_name' | |
| 182 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `std::basic_string<char, std::char_traits<char>, std::allocator<char> > const& boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool)': | |
| 183 | bamreadcount.cpp:(.text._ZN5boost15program_options10validators17get_single_stringIcEERKSbIT_St11char_traitsIS3_ESaIS3_EERKSt6vectorIS7_SaIS7_EEb[std::basic_string<char, std::char_traits<char>, std::allocator<char> > const& boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool)]+0xa0): undefined reference to `boost::program_options::validation_error::get_template(boost::program_options::validation_error::kind_t)' | |
| 184 | bamreadcount.cpp:(.text._ZN5boost15program_options10validators17get_single_stringIcEERKSbIT_St11char_traitsIS3_ESaIS3_EERKSt6vectorIS7_SaIS7_EEb[std::basic_string<char, std::char_traits<char>, std::allocator<char> > const& boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool)]+0xb4): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)' | |
| 185 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::variables_map::~variables_map()': | |
| 186 | bamreadcount.cpp:(.text._ZN5boost15program_options13variables_mapD0Ev[_ZN5boost15program_options13variables_mapD5Ev]+0x13): undefined reference to `vtable for boost::program_options::variables_map' | |
| 187 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::run()': | |
| 188 | bamreadcount.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE3runEv[boost::program_options::basic_command_line_parser<char>::run()]+0x22): undefined reference to `boost::program_options::detail::cmdline::get_canonical_option_prefix()' | |
| 189 | bamreadcount.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE3runEv[boost::program_options::basic_command_line_parser<char>::run()]+0x55): undefined reference to `boost::program_options::detail::cmdline::run()' | |
| 190 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `void boost::program_options::validate<long, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, long*, long)': | |
| 191 | bamreadcount.cpp:(.text._ZN5boost15program_options8validateIlcEEvRNS_3anyERKSt6vectorISbIT0_St11char_traitsIS5_ESaIS5_EESaIS9_EEPT_l[void boost::program_options::validate<long, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, long*, long)]+0x34): undefined reference to `boost::program_options::validators::check_first_occurrence(boost::any const&)' | |
| 192 | bamreadcount.cpp:(.text._ZN5boost15program_options8validateIlcEEvRNS_3anyERKSt6vectorISbIT0_St11char_traitsIS5_ESaIS5_EESaIS9_EEPT_l[void boost::program_options::validate<long, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, long*, long)]+0x514): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' | |
| 193 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long)': | |
| 194 | bamreadcount.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorISbIT0_St11char_traitsIS5_ESaIS5_EESaIS9_EEPT_l[void boost::program_options::validate<int, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long)]+0x34): undefined reference to `boost::program_options::validators::check_first_occurrence(boost::any const&)' | |
| 195 | bamreadcount.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorISbIT0_St11char_traitsIS5_ESaIS5_EESaIS9_EEPT_l[void boost::program_options::validate<int, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long)]+0x4f4): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' | |
| 196 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIlcEE[vtable for boost::program_options::typed_value<long, char>]+0x38): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| 197 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTIN5boost15program_options11typed_valueIlcEE[typeinfo for boost::program_options::typed_value<long, char>]+0x18): undefined reference to `typeinfo for boost::program_options::value_semantic_codecvt_helper<char>' | |
| 198 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[vtable for boost::program_options::validation_error]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const' | |
| 199 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[vtable for boost::program_options::validation_error]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 200 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTIN5boost15program_options16validation_errorE[typeinfo for boost::program_options::validation_error]+0x10): undefined reference to `typeinfo for boost::program_options::error_with_option_name' | |
| 201 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::validation_error>]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const' | |
| 202 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::validation_error>]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 203 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >]+0x28): undefined reference to `boost::program_options::error_with_option_name::what() const' | |
| 204 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 205 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const' | |
| 206 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 207 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[vtable for boost::program_options::invalid_option_value]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const' | |
| 208 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[vtable for boost::program_options::invalid_option_value]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 209 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >]+0x28): undefined reference to `boost::program_options::error_with_option_name::what() const' | |
| 210 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' | |
| 211 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[vtable for boost::program_options::typed_value<bool, char>]+0x38): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| 212 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTIN5boost15program_options11typed_valueIbcEE[typeinfo for boost::program_options::typed_value<bool, char>]+0x18): undefined reference to `typeinfo for boost::program_options::value_semantic_codecvt_helper<char>' | |
| 213 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISscEE[vtable for boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>]+0x38): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| 214 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTIN5boost15program_options11typed_valueISscEE[typeinfo for boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>]+0x18): undefined reference to `typeinfo for boost::program_options::value_semantic_codecvt_helper<char>' | |
| 215 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[vtable for boost::program_options::typed_value<int, char>]+0x38): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' | |
| 216 | CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o:(.rodata._ZTIN5boost15program_options11typed_valueIicEE[typeinfo for boost::program_options::typed_value<int, char>]+0x18): undefined reference to `typeinfo for boost::program_options::value_semantic_codecvt_helper<char>' | |
| 217 | collect2: ld returned 1 exit status | |
| 218 | make[2]: *** [bin/bam-readcount] Error 1 | |
| 219 | make[1]: *** [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/all] Error 2 | |
| 220 | make: *** [all] Error 2 |
