IRC logs of #shogun for Thursday, 2019-02-07

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--- Log opened Thu Feb 07 00:00:00 2019
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-shogun-buildbot:#shogun- Build deb4 - python3 #495 is complete: Success [build successful] - http://buildbot.shogun-toolbox.org:8080/#builders/28/builds/49504:32
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glitchHi !04:59
glitchi have successfully build shogun , was going through05:00
glitchrunning the interfaces05:00
glitchas mentioned in http://shogun.ml/examples/latest/quickstart/interfaces.html05:00
glitchbut cant get native_example.cpp in the dirs or subdirs of shogun05:03
glitch:/05:03
wuwei[m]glitch: hi05:07
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glitchwuwei : hey !05:08
wuwei[m]you can set BUILD_META_EXAMPLES=ON in cmake and you will find generated cpp files in build/example/meta05:09
glitchokay05:09
glitchbut last time while building05:09
glitchi had turned it off05:09
glitchdue to a tons on dependencies05:10
glitchshould i rerun BUILD_META_EXMPLE=on ?05:10
wuwei[m]yes05:10
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glitchjust  rerunned cmake BUILD_META_EXAMPLES=ON ..05:13
glitchgives a tons of errors as previousley encountered05:14
wuwei[m]what errors?05:15
glitch-- Configuring incomplete, errors occurred!05:16
glitchCould NOT find rxcpp (missing: rxcpp_INCLUDE_DIR)  -- Could NOT find TFLogger (missing: TFLogger_DIR)05:16
glitchCould NOT find GLPK (missing: GLPK_LIBRARY GLPK_INCLUDE_DIR GLPK_PROPER_VERSION_FOUND)  -- Could NOT find CPLEX (missing: CPLEX_LIBRARY CPLEX_INCLUDE_DIR)  -- Could NOT find MOSEK (missing: MOSEK_DIR MOSEK_INCLUDE_DIR MOSEK_LIBRARY MOSEK_LIBRARIES)05:16
glitchCould NOT find Protobuf (missing: Protobuf_INCLUDE_DIR)  -- Could NOT find JSON (missing: JSON_INCLUDE_DIR JSON_LIBRARY) (Required is at least version "0.11")05:16
glitchCould NOT find CURL (missing: CURL_LIBRARY CURL_INCLUDE_DIR)  -- Could NOT find SNAPPY (missing: SNAPPY_LIBRARIES SNAPPY_INCLUDE_DIR)  -- Lzo includes and libraries NOT found.05:16
glitchCould 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)05:16
wuwei[m]I think most of these are optional05:17
wuwei[m]do you know exactly which error made the configuration fail?05:19
glitchi wish i knew it05:24
glitchbut this is all i get out of the terminal05:24
glitchencountering the 1st error05:25
glitchdir='/home/saphire/shogun/src/gpl' -- Using system's malloc -- Could NOT find rxcpp (missing: rxcpp_INCLUDE_DIR)05:25
wuwei[m]could u paste the full output on pastebin?05:28
glitchhttps://pastebin.com/MBq8Dkm105:32
wuwei[m]okay i see05:33
wuwei[m]ctags is missing05:33
glitchoh! yes ! now it works05:37
glitch:D05:37
glitchthank you !05:37
wuwei[m]:)05:37
glitchgetting started for the 1st PR :D05:38
glitchbut i cant find the file native_example.cpp05:43
wuwei[m]i think it means whatever file in examples/meta/cpp :)05:43
glitchthe only file i am seeing in shogun/examples/meta/cpp05:45
glitchis CMakeLists.txt05:45
glitch:/05:45
wuwei[m]build/examples/meta/cpp05:45
wuwei[m]haha05:45
glitchoh ! they are all there05:46
glitchbut !05:47
glitch~/shogun/build/examples/meta/cpp$ ls base_api             converter         Makefile     regression binary               distance          meta_api     statistical_testing clustering           evaluation        multiclass CMakeFiles           gaussian_process  neural_nets cmake_install.cmake  kernel            pipeline05:47
glitchall are empty05:47
glitchsaphire@saphire-GL553VE:~/shogun/build/examples/meta/cpp$ cd neural_nets/ saphire@saphire-GL553VE:~/shogun/build/examples/meta/cpp/neural_nets$ ls05:47
glitch:/05:47
wuwei[m]that's weird05:47
glitch:/05:48
glitchyes05:48
wuwei[m]did u see any error / warning when u ran make05:48
wuwei[m]you should see something like "Generating example ..."05:50
glitchnothing except the the missing packages already encountered05:50
glitchyou it showed 'genereating examples'05:51
glitchi am posting on pastebin05:51
glitchhttps://pastebin.com/HEk1RUhe05:52
wuwei[m]did u run "make"05:53
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glitchyup i did run make after it05:53
wuwei[m]can u also paste the output of make05:54
glitchsure thing05:54
glitchhttps://pastebin.com/DeJXrznj05:57
wuwei[m]it looks okay :)05:58
glitchya , it goes through bulding all .cxx files05:59
glitchbut i dont see any built05:59
glitchshould i check the permissions to write ?05:59
glitchfor the directory ?05:59
wuwei[m]i think they should have been generated, can u search in the build dir06:00
glitchyup i did search for native_example.cpp06:01
glitchbut none found06:01
wuwei[m]i saw this "/home/saphire/shogun/build/examples/meta/cpp/statistical_testing/linear_time_maximum_mean_discrepancy.cpp:17:53:  "06:01
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wuwei[m]does this file exist?06:01
glitchyup06:02
glitchit exists !!06:02
glitch:D06:02
glitchthere was a permission issue in the directory06:03
glitchi got contents in those dirs now06:04
glitchbut still no sigh of native_example.cpp06:04
glitch:/06:04
glitch~/shogun/build/examples/meta/cpp/clustering$ ls cpp-clustering-gaussian_mixture_models  gaussian_mixture_models.cpp cpp-clustering-hierarchical             hierarchical.cpp cpp-clustering-kmeans                   kmeans.cpp06:05
glitchls cpp-regression-kernel_ridge_regression cpp-regression-kernel_ridge_regression_nystrom cpp-regression-least_angle_regression cpp-regression-linear_ridge_regression cpp-regression-multiple_kernel_learning cpp-regression-random_forest_regression cpp-regression-support_vector_regression kernel_ridge_regression.cpp kernel_ridge_regression_nystrom.cpp least_angle_regression.cpp linear_ridge_regression.cpp multiple_kernel_learning.cpp rand06:05
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wuwei[m]cool06:05
glitch:D06:05
glitchi guess i am good to go without native_example06:06
glitchthank you !! @wuwei06:09
wuwei[m]:D06:09
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glitchhey one more thing06:22
glitchi was trying to enable interface for python06:22
glitchusing cmake BUILD_META_EXAMPLES=ON -DINTERFACE_PYTHON=ON ..06:23
glitchhttps://pastebin.com/vNp8L6dn06:26
glitchencountered 2 errors while running make06:26
wuwei[m]output of cmake looks fine06:27
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glitchhttps://pastebin.com/WEUbXSF206:31
glitchonly after make06:31
glitchshogun_doxygen.i:612: Error: Syntax error in input(1). src/interfaces/python/CMakeFiles/_interface_python.dir/build.make:61: recipe for target 'src/interfaces/python/shogunPYTHON_wrap.cxx' failed make[2]: *** [src/interfaces/python/shogunPYTHON_wrap.cxx] Error 1 CMakeFiles/Makefile2:370: recipe for target 'src/interfaces/python/CMakeFiles/_interface_python.dir/all' failed make[1]: *** [src/interfaces/python/CMakeFiles/_interface_python06:31
wuwei[m]hmm i don't know, maybe gf712 has idea06:33
glitch:/06:33
glitchso for the time being is there any way to include shogun.py to the path ?06:34
wuwei[m]since it's doxygen error, you can exclude it from the build06:35
wuwei[m]edit doc/CmakeLists.txt and remove the doxygen target06:36
glitchaye aye captain !06:36
glitchyou mean i should delete the doxygen dir ?06:39
glitch~/shogun/build/doc$ ls CMakeFiles  cmake_install.cmake  cookbook  doxygen  Makefile06:39
wuwei[m]you can explicitly set DOXYGEN_FOUND to 006:39
glitchbecause there is no such file CmakeLists.txt06:39
wuwei[m]in shogun/doc06:40
glitchIF(DOXYGEN_FOUND)     add_subdirectory(doxygen)     LIST(APPEND DOC_DEPENDENCIES doxygen) ENDIF()06:42
glitchdoes commenting help to than setting to 006:42
wuwei[m]yes it should work06:42
glitchyup , commenting out didnt give an error of missing dependency06:47
glitchbut still06:47
glitchon make06:47
glitch[ 73%] Generating shogun_doxygen.i06:47
glitchthe error persists06:47
glitch[ 73%] Built target python_doxy2swig [ 73%] copying SWIG files [ 73%] Built target interface_python_src [ 73%] Swig source shogun_doxygen.i:612: Error: Syntax error in input(1). src/interfaces/python/CMakeFiles/_interface_python.dir/build.make:61: recipe for target 'src/interfaces/python/shogunPYTHON_wrap.cxx' failed make[2]: *** [src/interfaces/python/shogunPYTHON_wrap.cxx] Error 1 CMakeFiles/Makefile2:370: recipe for target 'src/inte06:47
wuwei[m]try removing entire build/examples and build again06:48
glitchi removed build/example , but the error persisted06:57
glitchso i removed build06:57
glitchand rebuild06:57
glitchit works showing no errors06:58
glitchScanning dependencies of target build_cpp_meta_examples [100%] Compiled generated cpp examples [100%] Built target build_cpp_meta_examples06:58
glitchbut still on searching for shogun.py06:58
glitchno reasults found06:58
glitch:/06:58
glitchi made sure of BUILD_META_EXAMPLES=ON DINTERFACE_PYTHON=ON06:58
wuwei[m]just found that there is another thing need to change in shogun/cmake/ShogunInterface.cmake06:59
glitchokay , whats the patch ?07:00
wuwei[m]there is IF(DOXYGEN_FOUND)07:00
glitchcommented out the whole block07:04
glitchhave rerun the whole process of rebuilding and make07:08
glitchbut still no shugun.py07:09
wuwei[m]what do you have in build/src/interfaces/python07:10
glitchthere is no subdir interfaces here07:11
glitch~/shogun/build/src$ ls shogun saphire@saphire-GL553VE:~/shogun/build/src$07:11
glitchonly a dir named shogun07:12
wuwei[m]when u retun cmake, have u set INTERFACE_PYTHON=ON ?07:12
glitchyup , was it supposed to be INTERFACE_PYTHON=ON coz the documentation said DINTERFACE_PYTHON=ON07:13
wuwei[m]-DINTERFACE_PYTHON=ON07:13
glitchya :/ i did add that as a parameter including BUILD_META_EXAMPLES=ON07:14
wuwei[m]when u ran make, did u find "_shogun.so" being built?07:19
glitchmm it went too fast to be noticable07:21
glitch:/07:21
glitchcan you take remote control of my pc ?07:22
wuwei[m]U can redirect the output, make > output.log07:23
glitchhttps://pastebin.com/SXCUbc5107:29
wuwei[m]'src/interfaces/python/shogunPYTHON_wrap.cxx' failed07:29
wuwei[m]but why?07:30
glitch:( i have no idea07:30
wuwei[m]check your output in stderr07:31
wuwei[m](you can redirect it using make 2>err.log)07:31
glitch /home/saphire/shogun/build/src/interfaces/python/shogun.i:49: Error: Unable to find 'shogun_doxygen.i' make[2]: *** [src/interfaces/python/shogunPYTHON_wrap.cxx] Error 1 make[1]: *** [src/interfaces/python/CMakeFiles/_interface_python.dir/all] Error 2 make: *** [all] Error 207:33
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wuwei[m]okay in shogun.i there's another HAVE_DOXYGEN07:35
glitchshould i remove both the lines ?07:37
glitchsame err.log07:39
glitchhttps://pastebin.com/SZKsdwnQ07:40
glitchbut there are more popping07:40
wuwei[m]yes07:40
glitchhave just rerun the build , check the err.log07:40
glitchhave just commented the preprocessor07:41
glitch /*#ifdef HAVE_DOXYGEN*/07:41
wuwei[m]i think an easier way is, in shogun/CmakeLists.txt, set HAVE_DOXYGEN and FOUND_DOXYGEN to 007:41
wuwei[m]so that you don;t need to change other things07:42
glitchbut setting FOUND_DOXYGEN to zero gives an error  while running cmake07:42
wuwei[m]what error07:46
glitch'DOXYGEN' not found07:47
wuwei[m]does set(FOUND_DOXYGEN 0) work?07:48
glitchi guess it checks for the status of dependencies and pops a message when its set to zero , when its not found07:48
wuwei[m]btw 'DOXYGEN' not found is not error07:49
glitch  if given arguments:      "DOXYGEN_FOUND" "0"    Unknown arguments specified   -- Configuring incomplete, errors occurred!07:50
glitch~/shogun/build$ cmake BUILD_META_EXAMPLES=ON -DINTERFACE_PYTHON=ON .. CMake Error at CMakeLists.txt:348 (IF):   if given arguments:      "DOXYGEN_FOUND" "0"    Unknown arguments specified   -- Configuring incomplete, errors occurred! See also "/home/saphire/shogun/build/CMakeFiles/CMakeOutput.log". See also "/home/saphire/shogun/build/CMakeFiles/CMakeError.log".07:50
wuwei[m]try removing that if block, just set the two variables you need07:51
glitch#IF(DOXYGEN_FOUND) #SET(HAVE_DOXYGEN 1) #ENDIF()07:52
glitchhave commented out07:53
glitch-- Generating done -- Build files have been written to: /home/saphire/shogun/build07:53
wuwei[m]yes and add set(DOXYGEN_FOUND 0) SET(HAVE_DOXYGEN 0)07:53
glitchseems to work07:53
glitchsame error.log07:56
glitch:/07:56
wuwei[m]okay lets try editing shogun.i07:57
wuwei[m]:)07:57
glitch%include "shogun_doxygen.i"07:59
glitchi found it containiing ....should this line be removed ?07:59
wuwei[m]yes07:59
glitchdidnt find it helpful after commenting out08:02
glitchsame error08:02
wuwei[m]maybe you need remove the interface dir08:02
glitch /*#ifdef HAVE_DOXYGEN #ifndef SWIGRUBY %include "shogun_doxygen.i" #endif #endif */08:03
glitchi have done this to the shogun.i08:03
glitch[ 74%] copying SWIG files [ 74%] Built target interface_python_src [ 74%] Swig source Scanning dependencies of target _interface_python08:06
glitchsome noticable difference08:06
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glichhey :wuweii !08:29
wuwei[m]glich: hey08:29
glichfinally after a long build08:29
glichshogun.py08:29
glichappears under src/interfaces/python08:29
glich:D08:29
wuwei[m]great08:29
glichI am really fortunate to get your help08:30
glichcant thank you more for your patience !!08:30
glich:D I mean it , !!08:30
wuwei[m]no problem :)08:30
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heytitleHi!, I've just created a PR addressing #4512. Could you please review it and give me feedback?14:53
heytitlehttps://github.com/shogun-toolbox/shogun/pull/451614:53
gf712heytitle thank you for your PR. Someone will have a look at it soon, but give it a couple of days!15:45
heytitlenp!15:53
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--- Log closed Fri Feb 08 00:00:02 2019
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