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Linking problem with boost during build #295

Closed rcurtin closed 9 years ago

rcurtin commented 9 years ago

Reported by Madda on 9 Jul 43830007 18:54 UTC Hi, I am trying to build mlpack-1.0.7, but I am getting linking errors with boost. There was already a ticket on this topic and the suggestion was to add -D BOOST_ROOT=/usr/include/ which I did, but I am still getting problems.

These are the command:

$ sudo cmake -D BOOST_ROOT=/usr/local/ -D ARMADILLO_INCLUDE_DIR=/usr/local/armadillo-3.920.2/include/ -D ARMADILLO_LIBRARY=/usr/local/armadillo-3.920.2/libarmadillo.so ../ CMake Warning at CMakeLists.txt:81 (message): This is a 64-bit system, but Armadillo was compiled without 64-bit index support. Consider recompiling Armadillo with ARMA_64BIT_WORD to enable 64-bit indices (large matrix support). MLPACK will still work without ARMA_64BIT_WORD defined, but will not scale to matrices with more than 4 billion elements.

-- Boost version: 1.54.0 -- Found the following Boost libraries: -- program_options -- unit_test_framework -- Boost version: 1.54.0 -- Found the following Boost libraries: -- random -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) CMake Warning at CMakeLists.txt:270 (message): txt2man not found; man pages will not be generated.

-- Configuring done -- Generating done -- Build files have been written to: /usr/local/mlpack/mlpack-1.0.7/build

$ sudo make Scanning dependencies of target mlpack [ 1%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/dists/discrete_distribution.cpp.o [ 2%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/dists/gaussian_distribution.cpp.o [ 3%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/kernels/epanechnikov_kernel.cpp.o [ 4%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/kernels/pspectrum_string_kernel.cpp.o [ 5%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/math/lin_alg.cpp.o [ 6%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/math/random.cpp.o [ 7%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/optimizers/aug_lagrangian/aug_lagrangian_test_functions.cpp.o [ 8%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/optimizers/lbfgs/test_functions.cpp.o [ 9%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/optimizers/sgd/test_function.cpp.o [ 10%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/tree/mrkd_statistic.cpp.o [ 11%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/util/cli.cpp.o [ 12%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/util/cli_deleter.cpp.o [ 13%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/util/log.cpp.o [ 14%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/util/option.cpp.o [ 15%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/util/prefixedoutstream.cpp.o [ 17%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/util/save_restore_utility.cpp.o [ 18%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/util/string_util.cpp.o [ 19%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/core/util/timers.cpp.o [ 20%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/methods/cf/cf.cpp.o In file included from /usr/local/mlpack/mlpack-1.0.7/src/mlpack/../mlpack/methods/neighbor_search/neighbor_search.hpp:254:0, from /usr/local/mlpack/mlpack-1.0.7/src/mlpack/methods/cf/cf.hpp:29, from /usr/local/mlpack/mlpack-1.0.7/src/mlpack/methods/cf/cf.cpp:26: /usr/local/mlpack/mlpack-1.0.7/src/mlpack/../mlpack/methods/neighbor_search/neighbor_search_impl.hpp: In member function void mlpack::neighbor::NeighborSearch<SortPolicy, MetricType, TreeType>::Search(size_t, arma::Mat&, arma::mat&) SortPolicy = mlpack::neighbor::NearestNeighborSort, MetricType = mlpack::metric::LMetric<2, true>, TreeType = mlpack::tree::BinarySpaceTreemlpack::bound::HRectBound<2, mlpack::neighbor::NeighborSearchStatmlpack::neighbor::NearestNeighborSort, arma::Mat >, size_t = long unsigned int, arma::mat = arma::Mat: /usr/local/mlpack/mlpack-1.0.7/src/mlpack/methods/cf/cf.cpp:144:67: instantiated from here /usr/local/mlpack/mlpack-1.0.7/src/mlpack/../mlpack/methods/neighbor_search/neighbor_search_impl.hpp:205:10: warning: unused variable numPrunes 21% Building CXX object src/mlpack/CMakeFiles/mlpack.dir/methods/det/dtree.cpp.o /usr/local/mlpack/mlpack-1.0.7/src/mlpack/methods/det/dtree.cpp:143:6: warning: unused parameter maxLeafSize 22% Building CXX object src/mlpack/CMakeFiles/mlpack.dir/methods/det/dt_utils.cpp.o [ 23%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/methods/lars/lars.cpp.o [ 24%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/methods/linear_regression/linear_regression.cpp.o [ 25%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/methods/neighbor_search/sort_policies/nearest_neighbor_sort.cpp.o [ 26%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/methods/neighbor_search/sort_policies/furthest_neighbor_sort.cpp.o [ 27%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/methods/neighbor_search/unmap.cpp.o [ 28%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/methods/pca/pca.cpp.o [ 29%] Building CXX object src/mlpack/CMakeFiles/mlpack.dir/methods/radical/radical.cpp.o Linking CXX shared library ../../lib/libmlpack.so Moving header files to include/mlpack/ [ 29%] Built target mlpack Scanning dependencies of target cf [ 30%] Building CXX object src/mlpack/methods/cf/CMakeFiles/cf.dir/cf_main.cpp.o Linking CXX executable ../../../../bin/cf CMakeFiles/cf.dir/cf_main.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)': cf_main.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKSsS4_i[undefined reference toboost::program_options::validation_error::get_template(boost::program_options::validation_error::kind_t)' cf_main.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKSsS4_i_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKSsS4_i:)+0x44): 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)' CMakeFiles/cf.dir/cf_main.cpp.o: In functionboost::program_options::error_with_option_name::~error_with_option_name()': cf_main.cpp:(.text._ZN5boost15program_options22error_with_option_nameD2Ev[undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/cf.dir/cf_main.cpp.o: In functionboost::program_options::validation_error::~validation_error()': cf_main.cpp:(.text._ZN5boost15program_options16validation_errorD2Ev_ZN5boost15program_options16validation_errorD5Ev:)+0x7): undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/cf.dir/cf_main.cpp.o: In functionboost::program_options::error_with_option_name::~error_with_option_name()': cf_main.cpp:(.text._ZN5boost15program_options22error_with_option_nameD0Ev[undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/cf.dir/cf_main.cpp.o: In functionboost::program_options::invalid_option_value::~invalid_option_value()': cf_main.cpp:(.text._ZN5boost15program_options20invalid_option_valueD0Ev_ZN5boost15program_options20invalid_option_valueD5Ev:)+0x7): undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/cf.dir/cf_main.cpp.o: In functionboost::program_options::invalid_option_value::~invalid_option_value()': cf_main.cpp:(.text._ZN5boost15program_options20invalid_option_valueD2Ev[undefined reference to vtable for boost::program_options::error_with_option_name' CMakeFiles/cf.dir/cf_main.cpp.o:cf_main.cpp:(.text._ZN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEED2Ev[_ZN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEED5Ev](_ZN5boost15program_options20invalid_option_valueD5Ev]+0x7):)+0x2c): more undefined references tovtable for boost::program_options::error_with_option_name' follow CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorEfor boost::program_options::validation_error+0x20): undefined reference to boost::program_options::error_with_option_name::what() const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[for boost::program_options::validation_error](vtable)+0x30): undefined reference toboost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEEfor boost::exception_detail::error_info_injectorboost::program_options::validation_error+0x20): undefined reference to boost::program_options::error_with_option_name::what() const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[for boost::exception_detail::error_info_injector<boost::program_options::validation_error>](vtable)+0x30): undefined reference toboost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEEfor boost::exception_detail::clone_implboost::exception_detail::error_info_injector+0x28): undefined reference to boost::program_options::error_with_option_name::what() const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >](vtable)+0x38): undefined reference toboost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueEfor boost::program_options::invalid_option_value+0x20): undefined reference to boost::program_options::error_with_option_name::what() const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[for boost::program_options::invalid_option_value](vtable)+0x30): undefined reference toboost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEEfor boost::exception_detail::error_info_injectorboost::program_options::invalid_option_value+0x20): undefined reference to boost::program_options::error_with_option_name::what() const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>](vtable)+0x30): undefined reference toboost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEEfor boost::exception_detail::clone_implboost::exception_detail::error_info_injector+0x28): undefined reference to boost::program_options::error_with_option_name::what() const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >](vtable)+0x38): undefined reference toboost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/cf.dir/cf_main.cpp.o:(.rodata._ZTIN5boost15program_options16validation_errorEfor boost::program_options::validation_error+0x10): undefined reference to typeinfo for boost::program_options::error_with_option_name' ../../../../lib/libmlpack.so.1.0: undefined reference toboost::program_options::detail::cmdline::get_canonical_option_prefix()' collect2: ld returned 1 exit status make[* bin/cf Error 1 make[* src/mlpack/methods/cf/CMakeFiles/cf.dir/all Error 2 make: *\ [all] Error 2

I hope ypu can help me. Best, Madda

rcurtin commented 9 years ago

Commented by rcurtin on 22 Jun 43830035 01:41 UTC Adding BOOST_ROOT would only be necessary if the configuration step (cmake) failed. Are you on RHEL6? If so, try adding -D Boost_NO_BOOST_CMAKE=1 to the cmake command. If that doesn't help, can you tell me more about your system? i.e. what distribution, what version of Boost is installed, what version of CMake, and a copy of the CMakeCache.txt that CMake generated in your build directory.

rcurtin commented 9 years ago

Commented by Madda on 8 Dec 43831377 07:43 UTC Hello,

I have Ubuntu 12.04; I installed the boost libraries with the ubuntu packages and the version is 1.48.0.2; Cmake version is 2.8.10.1

I tried adding -D Boost_NO_BOOST_CMAKE=1 but I still get the same errors.

This is the CMakeChace.txt generated

This is the CMakeCache file.

For build in directory: /usr/local/mlpack/mlpack-1.0.7/build

It was generated by CMake: /usr/local/bin/cmake

You can edit this file to change values found and used by cmake.

If you do not want to change any of the values, simply exit the editor.

If you do want to change a value, simply edit, save, and exit the editor.

The syntax for the file is as follows:

KEY:TYPE=VALUE

KEY is the name of a variable in the cache.

TYPE is a hint to GUI's for the type of VALUE, DO NOT EDIT TYPE!.

VALUE is the current value for the KEY.

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//The Boost RANDOM library Boost_RANDOM_LIBRARY:FILEPATH=/usr/lib/libboost_random-mt.so

//Boost random library (debug) Boost_RANDOM_LIBRARY_DEBUG:FILEPATH=/usr/lib/libboost_random-mt.so

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//The Boost UNIT_TEST_FRAMEWORK library Boost_UNIT_TEST_FRAMEWORK_LIBRARY:FILEPATH=/usr/lib/libboost_unit_test_framework-mt.so

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Thanks a lot for your help, Madda

rcurtin commented 9 years ago

Commented by rcurtin on 8 Jun 43838969 16:16 UTC Hi there,

I'm sorry for the slow response. I have spent some time investigating the issue but I don't have a solution yet. I am attempting to set up an Ubuntu 12.04 system so that I can reproduce the problem.

Can you give me the output of the following command?

VERBOSE=1 make

This should give a lot of output and might help me figure out why the linker isn't actually linking against the boost program_options library.

Also, does the file /usr/lib/libboost_program_options-mt.so exist on your filesystem?

Thanks,

Ryan

rcurtin commented 9 years ago

Commented by Madda on 31 Aug 43839753 18:46 UTC Hi,

I manages to solve the problem, but in a very unclean way. The file /usr/lib/libboost_program_options-mt.so is existing.

What I did is to remove the boost installed with the ubuntu packages, and to install from scratch boost-1.54. I installed them in /usr/local/boost/ , so in /usr/local/include/boost/ I have the headers and in /usr/local/lib the .so files.

I tried to compile the mlpack with: ccmake -D BOOST_ROOT=/ust/local/boost ,but I still had the same problems.

So I went into CMakeCache.txt and saw that: Boost_LIBRARY_DIRS:FILEPATH=/usr/lib Boost_PROGRAM_OPTIONS_LIBRARY:FILEPATH=/usr/lib/libboost_program_options-mt.so Boost_PROGRAM_OPTIONS_LIBRARY_DEBUG:FILEPATH=/usr/lib/libboost_program_options-mt.so Boost_PROGRAM_OPTIONS_LIBRARY_RELEASE:FILEPATH=/usr/lib/libboost_program_options-mt.so

I modified these lines: Boost_LIBRARY_DIRS:FILEPATH=/usr/local/lib Boost_PROGRAM_OPTIONS_LIBRARY:FILEPATH=/usr/local/lib/libboost_program_options.so
Boost_PROGRAM_OPTIONS_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_program_options.so Boost_PROGRAM_OPTIONS_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_program_options.so

(In /usr/local/lib/ there is no libboost_program_options-mt.so but only libboost_program_options.so)

And then it compiles without errors. I think this is not the appropriate way!!!!

Do you have any suggestion on how to do it in the correct way?

Thanks a lot! Madda

rcurtin commented 9 years ago

Commented by birm on 23 Sep 44186418 00:19 UTC It seems that, from other projects, using the BOOST_ROOT variable has helped; do you want me to conditionally set this depending on the installation environment in CMakeLists, or would that not be of any help here?

rcurtin commented 9 years ago

Commented by rcurtin on 19 May 44196307 10:29 UTC Hello Madda,

I'm sorry for the very slow response to this ticket.

I think that when you specified 'ccmake -D BOOST_ROOT=/ust/local/boost', that was incorrect, and you should have specified BOOST_ROOT=/usr/local/ because the libraries are in /usr/local/lib/ and the headers in /usr/local/include/, not /usr/local/boost/lib/ and /usr/local/boost/include/.

Even so, I am not sure what happened in your situation. I think that maybe on your system, you had only partially uninstalled the Boost libraries, causing the FindBoost script to find Boost headers in /usr/include/ and assume the libraries were in /usr/lib/.

If specifying BOOST_ROOT=/usr/local/ does not work, you can try adding additional options that are documented in the FindBoost.cmake script:

If none of these work, feel free to reopen the ticket, but I am fairly sure that one of these things should resolve the issue.

Thanks for the patience, and sorry for the slow response.

Ryan