Error creating examples (C++)

[HaoZeke]

Bug Report

• No similar issues exist
• Replicated on similar systems

Description

I am not able to build shogun with the examples. Without the examples it builds alright.

Configuration

-- dir='/home/haozeke/Git/Github/machineLearning/shogun/src'
-- dir='/home/haozeke/Git/Github/machineLearning/shogun/build/src'
-- dir='/home/haozeke/Git/Github/machineLearning/shogun/src/gpl'
-- Using system's malloc
-- Could NOT find ViennaCL (missing: VIENNACL_INCLUDE_DIR VIENNACL_ENCODED_VERSION) (Required is at least version "1.5.0")
-- Could NOT find TFLogger (missing: TFLogger_DIR)
-- Could NOT find CPLEX (missing: CPLEX_LIBRARY CPLEX_INCLUDE_DIR) 
-- Found Arpack : /usr/lib/libarpack.so
-- Could NOT find MOSEK (missing: MOSEK_DIR MOSEK_INCLUDE_DIR MOSEK_LIBRARY MOSEK_LIBRARIES) 
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Lzo Library /usr/lib/liblzo2.so
-- Lzo Include Found in /usr/include
-- Could NOT find ColPack (missing: COLPACK_LIBRARIES COLPACK_LIBRARY_DIR COLPACK_INCLUDE_DIR) 
-- Could NOT find ARPREC (missing: ARPREC_LIBRARIES ARPREC_INCLUDE_DIR) 
-- Linker: GNU gold
-- ===================================================================================================================
-- Summary of Configuration Variables
-- The following OPTIONAL packages have been found:

 * CCache
 * GDB
 * Doxygen (required version >= 1.8.6)
 * OpenMP
 * CxaDemangle
 * rxcpp
 * BLAS
 * GLPK
 * ARPACK
 * Threads
 * Protobuf
 * JSON (required version >= 0.11)
 * LibXml2
 * HDF5
 * CURL
 * ZLIB
 * BZip2
 * LibLZMA
 * SNAPPY
 * LZO
 * NLopt
 * LpSolve
 * Sphinx
 * Pandoc

-- The following REQUIRED packages have been found:

 * PythonInterp

-- The following OPTIONAL packages have not been found:

 * ViennaCL (required version >= 1.5.0)
 * TFLogger (required version >= 0.1.0)
 * CPLEX
 * Mosek
 * ColPack
 * ARPREC

-- ===================================================================================================================
-- Integrations
--   OpenCV Integration is OFF 	 enable with -DOpenCV=ON
-- ===================================================================================================================
-- Interfaces
--   Python is OFF 		 enable with -DINTERFACE_PYTHON=ON
--   Octave is OFF 		 enable with -DINTERFACE_OCTAVE=ON
--   Java is OFF 		 enable with -DINTERFACE_JAVA=ON
--   Perl is OFF 		 enable with -DINTERFACE_PERL=ON
--   Ruby is OFF 		 enable with -DINTERFACE_RUBY=ON
--   C# is OFF 			 enable with -DINTERFACE_CSHARP=ON
--   R is OFF 			 enable with -DINTERFACE_R=ON
--   Lua is OFF 		 enable with -DINTERFACE_LUA=ON
--   Scala is OFF 		 enable with -DINTERFACE_SCALA=ON
--   CoreML is OFF 		 enable with -DINTERFACE_COREML=ON
-- ===================================================================================================================
-- To compile shogun type
--   make
-- 
-- To install shogun to /usr/local type
--   make install
-- 
-- or to install to a custom directory
--   make install DESTDIR=/my/special/path
--   (or rerun cmake with -DCMAKE_INSTALL_PREFIX=/my/special/path) to just change the prefix
-- ===================================================================================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/haozeke/Git/Github/machineLearning/shogun/build

Error

Scanning dependencies of target cpp-evaluation-cross_validation_support_vector_machine
[ 83%] Building CXX object examples/meta/cpp/CMakeFiles/cpp-evaluation-cross_validation_support_vector_machine.dir/evaluation/cross_validation_support_vector_machine.cpp.o
[ 83%] Linking CXX executable evaluation/cpp-evaluation-cross_validation_support_vector_machine
/usr/bin/ld: ../../../src/shogun/libshogun.so.18.0: undefined reference to `void shogun::LinalgBackendEigen::eigen_solver_symmetric_impl<double>(shogun::SGMatrix<double> const&, shogun::SGVector<double>&, shogun::SGMatrix<double>&, int) const'
/usr/bin/ld: ../../../src/shogun/libshogun.so.18.0: undefined reference to `void shogun::LinalgBackendEigen::eigen_solver_symmetric_impl<float>(shogun::SGMatrix<float> const&, shogun::SGVector<float>&, shogun::SGMatrix<float>&, int) const'
/usr/bin/ld: ../../../src/shogun/libshogun.so.18.0: undefined reference to `void shogun::LinalgBackendEigen::eigen_solver_symmetric_impl<long double>(shogun::SGMatrix<long double> const&, shogun::SGVector<long double>&, shogun::SGMatrix<long double>&, int) const'
/usr/bin/ld: ../../../src/shogun/libshogun.so.18.0: undefined reference to `void shogun::LinalgBackendEigen::eigen_solver_symmetric_impl<std::complex<double> >(shogun::SGMatrix<std::complex<double> > const&, shogun::SGVector<std::complex<double> >&, shogun::SGMatrix<std::complex<double> >&, int) const'
collect2: error: ld returned 1 exit status
make[2]: *** [examples/meta/cpp/CMakeFiles/cpp-evaluation-cross_validation_support_vector_machine.dir/build.make:93: examples/meta/cpp/evaluation/cpp-evaluation-cross_validation_support_vector_machine] Error 1
make[1]: *** [CMakeFiles/Makefile2:3816: examples/meta/cpp/CMakeFiles/cpp-evaluation-cross_validation_support_vector_machine.dir/all] Error 2
make: *** [Makefile:152: all] Error 2

System Details

Architecture and OS

Shogun

Git version at:

 * b5345f577 (HEAD -> develop, origin/develop, origin/HEAD) SG_ADD refactor (#4417)

Eigen

Strangely I already have eigen installed as well...

[gf712]

Hey, I think I have seen that error before in a build when compiling with gcc 8. Which compiler are you using?

[gf712]

From your other issue you seem to be using gcc-8. Could you try compiling with gcc-7 or lower? I am not sure what causes this issue though..

[karlnapf]

I saw this error before with an outdated build folder. If you start form scratch, it still happens?

[HaoZeke]

@gf712, I am indeed using gcc8

gcc -v          
Using built-in specs.                 COLLECT_GCC=gcc                       COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.1/lto-wrapper      Target: x86_64-pc-linux-gnu           Configured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared --enable-threads=posix --enable-libmpx --with-system-zlib --with-isl --enableConfigured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared --enable-threads=posix --enable-libmpx --with-system-zlib --with-isl --enable-__cxa_atexit --disable-libunwind-exceptions --enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp --enable-gnu-unique-object --enable-linker-build-id --enable-lto --enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu --enable-gnu-indirect-function --enable-multilib --disable-werror --enable-checking=release --enable-default-pie --enable-default-ssp --enable-cet=auto                       Thread model: posix
gcc version 8.2.1 20180831 (GCC)

I will test with a lower version.

@karlnapf, unfortunately I have replicated this on 2 machines (one shown here and the other described in #4420) with clean builds (deleting the whole folder)

[karlnapf]

We would have to dig a bit to replicate this error. I remember seeing it on some of our builds, but I dont know how or whether it was resolved. I think @vigsterkr might know more

[avramidis]

Please see #4506 and let me know what you think.

[avramidis]

@karlnapf I believe this issue was solved with #4506

[karlnapf]

@HaoZeke can you confirm?

[karlnapf]

@avramidis awesome! :)

[HaoZeke]

Yup this is now fixed! Thanks @karlnapf and @avramidis!