Hi, Here is the the cmake output and other details.
Below is the cmake command issued. aref@aref-Inspiron-N5010:~/shogun-develop/release$ cmake -DCMAKE_INSTALL_PREFIX="/usr/local" -DPythonModular=ON -DRModular=ON -DBUNDLE_EIGEN=ON .. >>cmake_out.txt 2>&1 aref@aref-Inspiron-N5010:~/shogun-develop/release$ _______________________________________________________________________________________________________________ This is the build drectory after cmake aref@aref-Inspiron-N5010:~/shogun-develop/release$ ls CMakeCache.txt cmake_out.txt doc Makefile CMakeFiles CPackConfig.cmake Eigen3 src cmake_install.cmake CPackSourceConfig.cmake examples aref@aref-Inspiron-N5010:~/shogun-develop/release$ ________________________________________________________________________________________________________________ This is the output of cmake written to file. -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Found CCache: /usr/bin/ccache -- Found SWIG: /usr/bin/swig2.0 (found suitable version "2.0.11", minimum required is "2.0.5") -- Performing Test _HAS_CXX11_FLAG -- Performing Test _HAS_CXX11_FLAG - Success -- Checking C++11 support for "__func__" -- Checking C++11 support for "__func__": works -- Checking C++11 support for "atomic" -- Checking C++11 support for "atomic": works -- Checking C++11 support for "auto" -- Checking C++11 support for "auto": works -- Checking C++11 support for "auto_ret_type" -- Checking C++11 support for "auto_ret_type": works -- Checking C++11 support for "class_override_final" -- Checking C++11 support for "class_override_final": not supported -- Checking C++11 support for "constexpr" -- Checking C++11 support for "constexpr": works -- Checking C++11 support for "cstdint" -- Checking C++11 support for "cstdint": works -- Checking C++11 support for "decltype" -- Checking C++11 support for "decltype": works -- Checking C++11 support for "initializer_list" -- Checking C++11 support for "initializer_list": works -- Checking C++11 support for "lambda" -- Checking C++11 support for "lambda": works -- Checking C++11 support for "long_long" -- Checking C++11 support for "long_long": works -- Checking C++11 support for "nullptr" -- Checking C++11 support for "nullptr": works -- Checking C++11 support for "regex" -- Checking C++11 support for "regex": not supported -- Checking C++11 support for "rvalue-references" -- Checking C++11 support for "rvalue-references": works -- Checking C++11 support for "sizeof_member" -- Checking C++11 support for "sizeof_member": works -- Checking C++11 support for "static_assert" -- Checking C++11 support for "static_assert": works -- Checking C++11 support for "variadic_templates" -- Checking C++11 support for "variadic_templates": works -- Looking for C++ include unordered_map -- Looking for C++ include unordered_map - found -- Using system's malloc -- Looking for isfinite -- Looking for isfinite - not found -- Looking for isinf -- Looking for isinf - found -- Looking for isnan -- Looking for isnan - found -- Looking for signgam -- Looking for signgam - found -- Looking for fdopen -- Looking for fdopen - found -- Looking for log2 -- Looking for log2 - found -- Looking for powl -- Looking for powl - found -- Looking for lgammal -- Looking for lgammal - found -- Looking for sqrtl -- Looking for sqrtl - found -- Looking for finite -- Looking for finite - found -- Looking for isfinite -- Looking for isfinite - not found -- Looking for isinf -- Looking for isinf - found -- Looking for isnan -- Looking for isnan - found -- Performing Test HAVE_STD_ISINF -- Performing Test HAVE_STD_ISINF - Success -- Performing Test HAVE_STD_ISFINITE -- Performing Test HAVE_STD_ISFINITE - Success -- Performing Test HAVE_STD_ISNAN -- Performing Test HAVE_STD_ISNAN - Success -- Looking for xmmintrin.h -- Looking for xmmintrin.h - found -- Looking for emmintrin.h -- Looking for emmintrin.h - found -- Looking for arc4random -- Looking for arc4random - not found -- Found GDB: /usr/bin/gdb -- Could NOT find MOSEK (missing: MOSEK_DIR MOSEK_INCLUDE_DIR MOSEK_LIBRARY) -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- Found PkgConfig: /usr/bin/pkg-config (found version "0.26") -- Looking for dgemm_ -- Looking for dgemm_ - found -- A library with BLAS API found. -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Looking for clapack_dpotrf in /usr/lib/atlas-base/liblapack_atlas.so.3 -- Looking for clapack_dpotrf in /usr/lib/atlas-base/liblapack_atlas.so.3 - found -- Could NOT find ATLAS (missing: ATLAS_INCLUDES) -- Found CBLAS: /usr/lib/libcblas.so.3 -- Looking for cblas_dsyrk in /usr/lib/libcblas.so.3 -- Looking for cblas_dsyrk in /usr/lib/libcblas.so.3 - found -- Found GLPK: /usr/lib/x86_64-linux-gnu/libglpk.so -- Could NOT find CPLEX (missing: CPLEX_LIBRARY CPLEX_INCLUDE_DIR) -- Found Arpack : /usr/lib/libarpack.so -- Could NOT find OPENCL (missing: OPENCL_INCLUDE_DIR) -- Could NOT find ViennaCL (missing: VIENNACL_INCLUDE_DIR OPENCL_INCLUDE_DIRS OPENCL_LIBRARIES) (Required is at least version "1.5.0") -- checking for one of the modules 'libColPack>=1.0.9;ColPack>=1.0.9' -- Could NOT find NLOPT (missing: NLOPT_LIBRARY NLOPT_INCLUDE_DIR) -- Could NOT find LPSOLVE (missing: LPSOLVE_LIBRARIES LPSOLVE_INCLUDE_DIR) -- Could NOT find ColPack (missing: COLPACK_LIBRARIES COLPACK_LIBRARY_DIR COLPACK_INCLUDE_DIR) -- Could NOT find ARPREC (missing: ARPREC_LIBRARIES ARPREC_INCLUDE_DIR) -- Found Doxygen: /usr/bin/doxygen (found suitable version "1.8.6", minimum required is "1.8.6") -- Found PythonInterp: /usr/bin/python (found version "2.7.6") -- checking for one of the modules 'libjson>=0.11;json>=0.11;json-c>=0.11' -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.1") -- Found HDF5: /usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.35.0") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6") -- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - found -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so - found -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so - found -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so - found -- Found LibLZMA: /usr/include (found version "5.1.0") -- Could NOT find SNAPPY (missing: SNAPPY_LIBRARIES SNAPPY_INCLUDE_DIR) -- Lzo includes and libraries NOT found. -- Spinlock support found -- Found PROTOBUF: /usr/lib/x86_64-linux-gnu/libprotobuf.so -- Supported backend(s) for linear algebra NOT FOUND/NOT ENABLED -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found version "2.7.6") -- Found NumPy: version "1.8.2" /usr/lib/python2.7/dist-packages/numpy/core/include -- Found R: /usr/bin/R -- =================================================================================================================== -- Summary of Configuration Variables -- -- The following OPTIONAL packages have been found: * CCache * GDB * OpenMP * BLAS * LAPACK * CBLAS * GLPK * ARPACK * Doxygen (required version >= 1.8.6) * LibXml2 * HDF5 * CURL * ZLIB * BZip2 * LibLZMA * Spinlock * Threads * Protobuf -- The following REQUIRED packages have been found: * SWIG (required version >= 2.0.5) * PythonLibs * PythonInterp * NumPy * R -- The following OPTIONAL packages have not been found: * Mosek * Atlas * CPLEX * ViennaCL (required version >= 1.5.0) * NLopt * LpSolve * ColPack * ARPREC * SNAPPY * LZO -- The following REQUIRED packages have not been found: * OpenCL -- =================================================================================================================== -- Enabled Integration -- OpenCV Integration is OFF - enable with -DOpenCV=ON -- =================================================================================================================== -- Enabled Interfaces -- libshogun is ON -- python modular is ON -- octave modular is OFF - enable with -DOctaveModular=ON -- java modular is OFF - enable with -DJavaModular=ON -- perl modular is OFF - enable with -DPerlModular=ON -- ruby modular is OFF - enable with -DRubyModular=ON -- csharp modular is OFF - enable with -DCSharpModular=ON -- R modular is ON -- lua modular is OFF - enable with -DLuaModular=ON -- -- Enabled legacy interfaces -- cmdline static is OFF - enable with -DCmdLineStatic=ON -- python static is OFF - enable with -DPythonStatic=ON -- octave static is OFF - enable with -DOctaveStatic=ON -- matlab static is OFF - enable with -DMatlabStatic=ON -- R static is OFF - enable with -DRStatic=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/aref/shogun-develop/release On Sun, Jan 24, 2016 at 6:07 AM, Aref Nammari <[email protected]> wrote: > I am not sure what do you mean by "cake output". I removed the > LaplacianInferenceMethod from the import statement (it wasn't even used in > the rest of the script) and everything works. I tried all the examples in > the modular_python graphical including eigenfaces.py and everything seems > to work--I had to modify some things because some of the examples used > functions that were changed or renamed and LaplacianInferenceMethod could > be one of those. Am I right to believe that there is not an issue with > Eigen but rather the issue us with the examples not following recent > changes in shogun 4.0.0? > > On Sun, Jan 24, 2016 at 3:31 AM, Heiko Strathmann < > [email protected]> wrote: > >> Hi >> >> Ok, that's one down. Can you post your cake output? Seems like Eigen >> wasn't detected >> >> H >> >> >> On Saturday, 23 January 2016, Aref Nammari <[email protected]> wrote: >> >>> Hi Heiko, >>> >>> I downloaded and built the latest git develop branch and got the same >>> results. It is the "from modshogun import LaplacianInferenceMethod " that >>> is the source of the error--cannot import error. >>> >>> Aref >>> >>> On Fri, Jan 22, 2016 at 8:42 AM, Aref Nammari <[email protected]> >>> wrote: >>> >>>> Hello Heiko, >>>> >>>> Thank you for the reply. >>>> I believe the problem is not related to Eigen3. I took a look at the >>>> script I was trying to run and tried to see where the error was. I narrowed >>>> it down to an import statement " from modshogun import >>>> LaplacianInferenceMethod ". This import causes a not found error. The >>>> exception in the script returns 'Eigen3 needed for Gaussian Processes' >>>> which led me to believe that there was a problem in the build. I think the >>>> build is OK. However, I am not quite sure why the import does not work. The >>>> example I was trying to run is in >>>> examples/undocumented/python_modular/graphical/classifier_gaussian_process_binary_classification.py >>>> I will try the latest version in git and see if the problem persists. >>>> >>>> >>>> Thanks, >>>> Aref >>>> >>>> On Fri, Jan 22, 2016 at 3:52 AM, Heiko Strathmann < >>>> [email protected]> wrote: >>>> >>>>> Hi Aref, >>>>> >>>>> This is weird, can you post a gist with the cmake output somewhere? >>>>> >>>>> Also, could you try to do the same thing again with the latest git >>>>> version of shogun? >>>>> >>>>> H >>>>> >>>>> 2016-01-21 20:14 GMT+00:00 Aref Nammari <[email protected]>: >>>>> >>>>>> Hello, >>>>>> >>>>>> >>>>>> >>>>>> I have installed shogun-toolbox version 4.0.0 downloaded from >>>>>> shogun-toolbox.org. I installed python –modular and RModular. No >>>>>> errors were reported during the build process. I tried several examples >>>>>> and >>>>>> they seem to work with the exception of examples requiring Eigen3. During >>>>>> the build process I have turned BUNDLE_EIGEN ON and the package appears >>>>>> to >>>>>> have been downloaded but when I try some of the examples requiring Eigen3 >>>>>> (such Gaussian_processe examples) I get an error “Gaussian processes >>>>>> require Eigen3 be installed). I am not sure what the problem is or how to >>>>>> solve it. Any help in this area is appreciated. I am running python 2.7.6 >>>>>> and also have Anaconda installed. The OS is Ubuntu 14.04 LTS. >>>>>> >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Aref >>>>>> >>>>> >>>>> >>>> >>> >
