Hey Aref and Roman, I've updated that in https://github.com/shogun-toolbox/shogun/commit/40db9eb6ab357ccb59b75bf8556f5b7dfd2d29a9
Thanks, Sergey On Tue, Jan 26, 2016 at 8:43 PM, Aref Nammari <[email protected]> wrote: > Thank you Roman. I suspected that something like that happened since I > found other instances were functions were renamed. I will certainly try it. > > I appreciate your input and help. > > Cheers > > On Tue, Jan 26, 2016 at 10:31 AM, Roman Votyakov <[email protected]> > wrote: > >> Hi Aref, >> >> in this version of Shogun LaplacianInferenceMethod class was renamed to >> SingleLaplacianInferenceMethod, >> but it was not renamed in this script. So you could try to rename this >> import statement to SingleLaplacianInferenceMethod in the script to use >> Laplace's approximation method. >> >> Best, >> Roman >> >> On Tue, Jan 26, 2016 at 8:07 PM, Aref Nammari <[email protected]> >> wrote: >> >>> Hi Sergey, >>> >>> Importing modshogun in python works without any errors. I do believe >>> that the issue I was having is not really related to Eigen3 which as you >>> mention is downloaded and used. The error I had was due to not finding >>> LaplacianInferenceMethod in modshogun when I was trying to run an example >>> script was trying to import it. I removed the the import statement and >>> everything works fine (LaplacianInferenceMethod was not even used in the >>> script). At this point I think that this issue could be closed although I >>> am not sure why I was getting the error or why LaplacianInferenceMethod was >>> not found. >>> Thanks for taking the time to look into this issue. >>> >>> Aref >>> >>> On Tue, Jan 26, 2016 at 9:39 AM, Sergey Lisitsyn <[email protected] >>> > wrote: >>> >>>> Hey Aref, >>>> >>>> it seems that eigen3 is downloaded and used. >>>> >>>> What happens when you just 'import modshogun' within your python? >>>> >>>> Sergey >>>> >>>> On Sun, Jan 24, 2016 at 5:00 PM, Aref Nammari <[email protected]> >>>> wrote: >>>> >>>>> 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 >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>> >>>>> >>>> >>> >> >
