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 >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>> >>>> >>> >> >
