shogun-toolbox/shogun — pull request #824 by ptizoom (2012-11-14 15:18:43+00:00)
Title: perl_modular: fixed string_from_pdl<char> conversion.

also added SGStringList typemaps in/out interface.

cd /usr/src/shogun
cd src
./configure --interfaces=perl_modular
make all run-testsuite

____result even better: now the DNA stuff is working (minor exceptions).

*** Testing in ../data/classifier/*.m
../data/classifier/LibLinear_0017_1en05_1_True.m	OK
../data/classifier/LibLinear_023_1en05_1_True.m	OK
../data/classifier/LibLinear_15_1en05_1_True.m	OK
../data/classifier/LibLinear_30_1en05_16_True.m	OK
../data/classifier/LibLinear_30_1en05_1_True.m	OK
../data/classifier/SubGradientSVM_0017_1en05_1_05_False.m	OK
../data/classifier/SubGradientSVM_023_1en05_1_05_False.m	OK
../data/classifier/SubGradientSVM_15_1en05_1_05_False.m	ERROR
[INFO] done. [INFO] converged after 12904 iterations [INFO] objective: 17.635402 alpha: 0.000000 dir_deriv: 0.000017 num_bound: 9 num_active: 11 [INFO] solver time:119.272302 s classified: 2.902479e-01 <--- accuracy: 1.000000e-04
../data/classifier/SubGradientSVM_30_1en05_1_05_False.m	OK
../data/classifier/SubGradientSVM_30_1en05_16_05_False.m	OK
../data/classifier/SVMLin_0017_1en05_1_True.m	OK
../data/classifier/SVMLin_023_1en05_1_True.m	OK
../data/classifier/SVMLin_15_1en05_1_True.m	OK
../data/classifier/SVMLin_30_1en05_16_True.m	OK
../data/classifier/SVMLin_30_1en05_1_True.m	OK
../data/classifier/SVMOcas_0017_1en05_1_05_False.m	OK
../data/classifier/SVMOcas_023_1en05_1_05_False.m	OK
../data/classifier/SVMOcas_15_1en05_1_05_False.m	ERROR
[INFO] Ocas Converged after 12 iterations ================================== timing statistics: output_time: 0.005435 s sort_time: 0.000041 s add_time: 0.000327 s w_time: 0.000060 s solver_time 0.002080 s ocas_time 0.008205 s classified: 2.720155e-01 <--- accuracy: 1.000000e-04
../data/classifier/SVMOcas_30_1en05_1_05_False.m	ERROR
[INFO] Ocas Converged after 23 iterations ================================== timing statistics: output_time: 0.099012 s sort_time: 0.000071 s add_time: 0.000763 s w_time: 0.000184 s solver_time 0.058570 s ocas_time 0.159052 s classified: 1.694003e+00 <--- accuracy: 1.000000e-04
../data/classifier/SVMOcas_30_1en05_16_05_False.m	ERROR
[INFO] Ocas Converged after 23 iterations ================================== timing statistics: output_time: 0.003772 s sort_time: 0.000050 s add_time: 0.000523 s w_time: 0.000129 s solver_time 0.055538 s ocas_time 0.060425 s classified: 1.694003e+00 <--- accuracy: 1.000000e-04
../data/classifier/SVMSGD_0017_1en05_1_True.m	Can't locate object method "set_epsilon" via package "modshogun::SVMSGD" at classifier.pm line 180.
$VAR1 = bless( {}, 'modshogun::SVMSGD' );
ERROR
[INFO] lambda=2.673797, epochs=5, eta0=0.782020 [INFO] Estimating sparsity and bscale num_vec=22 num_feat=11. [INFO] using 22 examples. skip=16 bscale=0.282615 [INFO] Training on 22 vectors [INFO] Norm: 0.084089, Bias: -0.215520 classified: 1.606063e-01, bias: 1.887768e-01 <--- accuracy: 1.000000e-04
../data/classifier/SVMSGD_023_1en05_1_True.m	Can't locate object method "set_epsilon" via package "modshogun::SVMSGD" at classifier.pm line 180.
$VAR1 = bless( {}, 'modshogun::SVMSGD' );
ERROR
[INFO] lambda=0.197628, epochs=5, eta0=1.499815 [INFO] Estimating sparsity and bscale num_vec=22 num_feat=11. [INFO] using 22 examples. skip=16 bscale=0.282615 [INFO] Training on 22 vectors [INFO] Norm: 0.708958, Bias: -0.131405 classified: 8.379712e-02, bias: 1.135324e-01 <--- accuracy: 1.000000e-04
../data/classifier/SVMSGD_15_1en05_1_True.m	Can't locate object method "set_epsilon" via package "modshogun::SVMSGD" at classifier.pm line 180.
$VAR1 = bless( {}, 'modshogun::SVMSGD' );
ERROR
[INFO] lambda=0.030303, epochs=5, eta0=2.396782 [INFO] Estimating sparsity and bscale num_vec=22 num_feat=11. [INFO] using 22 examples. skip=16 bscale=0.282615 [INFO] Training on 22 vectors [INFO] Norm: 11.914167, Bias: 0.167660 classified: 7.895516e-01, bias: 3.042243e-01 <--- accuracy: 1.000000e-04
../data/classifier/SVMSGD_30_1en05_16_True.m	Can't locate object method "set_epsilon" via package "modshogun::SVMSGD" at classifier.pm line 180.
$VAR1 = bless( {}, 'modshogun::SVMSGD' );
ERROR
[INFO] lambda=0.001515, epochs=5, eta0=5.068576 [INFO] Estimating sparsity and bscale num_vec=22 num_feat=11. [INFO] using 22 examples. skip=16 bscale=0.282615 [INFO] Training on 22 vectors [INFO] Norm: 473.630873, Bias: 1.745407 classified: 4.640132e+00, bias: 1.126473e-02 <--- accuracy: 1.000000e-04
../data/classifier/SVMSGD_30_1en05_1_True.m	Can't locate object method "set_epsilon" via package "modshogun::SVMSGD" at classifier.pm line 180.
$VAR1 = bless( {}, 'modshogun::SVMSGD' );
ERROR
[INFO] lambda=0.001515, epochs=5, eta0=5.068576 [INFO] Estimating sparsity and bscale num_vec=22 num_feat=11. [INFO] using 22 examples. skip=16 bscale=0.282615 [INFO] Training on 22 vectors [INFO] Norm: 473.630873, Bias: 1.745407 classified: 4.640132e+00, bias: 1.126473e-02 <--- accuracy: 1.000000e-04

*** Testing in ../data/clustering/*.m
../data/clustering/Hierarchical_EuclidianDistance_3.m	OK
../data/clustering/KMeans_EuclidianDistance_3.m	OK

*** Testing in ../data/distance/*.m
../data/distance/BrayCurtisDistance_fnord.m	OK
../data/distance/CanberraMetric_fnord.m	OK
../data/distance/CanberraWordDistance_DNA_False_60_3_0.m	OK
../data/distance/ChebyshewMetric_fnord.m	OK
../data/distance/ChiSquareDistance_fnord.m	OK
../data/distance/CosineDistance_fnord.m	OK
../data/distance/EuclidianDistance_fnord.m	OK
../data/distance/GeodesicMetric_fnord.m	OK
../data/distance/HammingWordDistance_False_DNA_False_60_3_0.m	OK
../data/distance/HammingWordDistance_True_DNA_False_60_3_0.m	OK
../data/distance/JensenMetric_fnord.m	OK
../data/distance/ManhattanMetric_fnord.m	OK
../data/distance/ManhattanWordDistance_DNA_False_60_3_0.m	OK
../data/distance/MinkowskiMetric_13.m	OK
../data/distance/SparseEuclidianDistance_fnord.m	OK
../data/distance/TanimotoDistance_fnord.m	OK

*** Testing in ../data/distribution/*.m
../data/distribution/Histogram_60_3_0_False_DNA.m	ERROR
derivatives: inf, likelihood: 1.648175e-10 <--- accuracy: 1.000000e-07
../data/distribution/HMM_1en10_60_4_1_0_6_3_False_CUBE.m	ERROR
best_path: 5.902874e+02, derivatives: 1.937667e+04, likelihood: 1.475719e+02 <--- accuracy: 1.000000e-06
../data/distribution/LinearHMM_60_3_0_False_DNA.m	OK

*** Testing in ../data/kernel/*.m
../data/kernel/Chi2_10_12.m	OK
../data/kernel/Combined_True_3_10_3_LocalAlignmentString_60_FixedDegreeString_10_60_PolyMatchString_DNA_10_DNA_DNA_60.m	ERROR

../data/kernel/CommUlongString_DNA_10_0_False_3_60_False.m	OK
../data/kernel/CommWordString_DNA_10_0_False_3_60_False.m	OK
../data/kernel/Const_230.m	OK
../data/kernel/Custom_7.m	ERROR
fulltriangle: 4.836426e-09, fullfull: 8.154925e-01, triangletriangle: 4.836426e-09 <--- accuracy: 1.000000e-07
../data/kernel/Diag_10_230.m	OK
../data/kernel/Distance_10_CanberraMetric_17.m	OK
../data/kernel/FixedDegreeString_3_DNA_10_60.m	OK
../data/kernel/Gaussian_10_13.m	OK
../data/kernel/GaussianShift_10_1_13_2.m	OK
../data/kernel/HistogramWordString_DNA_0_3_60_False.m	Can't locate object method "get_confidences" via package "modshogun::Labels" at kernel.pm line 235.
ERROR

../data/kernel/LinearByte_RAWBYTE_60.m	OK
../data/kernel/Linear_fnord.m	OK
../data/kernel/LinearString_DNA_60.m	OK
../data/kernel/LinearWord_fnord.m	OK
../data/kernel/LocalAlignmentString_DNA_10_60.m	at /usr/src/shogun/src/interfaces/perl_modular/modshogun.pm line 17641.
ERROR

../data/kernel/MatchWordString_3_DNA_10_0_3_60_False.m	OK
../data/kernel/OligoString_DNA_10_3_60_12.m	at /usr/src/shogun/src/interfaces/perl_modular/modshogun.pm line 17752.
ERROR

../data/kernel/OligoString_DNA_10_4_60_17.m	at /usr/src/shogun/src/interfaces/perl_modular/modshogun.pm line 17752.
ERROR

../data/kernel/Poly_1_0_10_3_6_01_False_False_CUBE_1_FK.m	ERROR
km_train: inf, km_test: inf <--- accuracy: 1.000000e-06
../data/kernel/Poly_1_0_10_3_6_01_False_False_CUBE_1_TOP.m	ERROR
km_train: inf, km_test: inf <--- accuracy: 1.000000e-06
../data/kernel/Poly_3_10_False.m	OK
../data/kernel/Poly_3_10_True.m	OK
../data/kernel/PolyMatchString_3_DNA_10_60_False.m	OK
../data/kernel/PolyMatchString_3_DNA_10_60_True.m	OK
../data/kernel/PolyMatchWordString_3_DNA_10_0_3_60_False_False.m	OK
../data/kernel/PolyMatchWordString_3_DNA_10_0_3_60_True_False.m	OK
../data/kernel/SalzbergWordString_DNA_0_3_60_False.m	Can't locate object method "get_confidences" via package "modshogun::Labels" at kernel.pm line 235.
ERROR

../data/kernel/Sigmoid_10_05_07.m	OK
../data/kernel/Sigmoid_10_11_13.m	OK
../data/kernel/SimpleLocalityImprovedString_DNA_10_5_60_5_7.m	at /usr/src/shogun/src/interfaces/perl_modular/modshogun.pm line 18173.
ERROR

../data/kernel/SparseGaussian_10_17.m	OK
../data/kernel/SparseLinear_fnord.m	OK
../data/kernel/SparsePoly_3_10_False.m	OK
../data/kernel/SparsePoly_3_10_True.m	OK
../data/kernel/WeightedCommWordString_DNA_10_0_False_3_60_False.m	OK
../data/kernel/WeightedDegreePositionString_1_DNA_10_60.m	OK
../data/kernel/WeightedDegreePositionString_20_DNA_10_60.m	OK
../data/kernel/WeightedDegreeString_DNA_1_60.m	OK
../data/kernel/WeightedDegreeString_DNA_20_60.m	OK

*** Testing in ../data/preprocessor/*.m
../data/preprocessor/LogPlusOne_12_Gaussian.m	OK
../data/preprocessor/NormOne_12_Gaussian.m	OK
../data/preprocessor/PruneVarSubMean_False_12_Gaussian.m	OK
../data/preprocessor/PruneVarSubMean_True_12_Gaussian.m	OK
../data/preprocessor/SortUlongString_DNA_0_CommUlongString_3_60_False.m	OK
../data/preprocessor/SortWordString_DNA_0_CommWordString_3_60_False.m	OK

*** Testing in ../data/regression/*.m
../data/regression/KRR_1_15_Gaussian_1en05.m	Can't locate object method "new" via package "modshogun::KERNELRIDGEREGRESSION" (perhaps you forgot to load "modshogun::KERNELRIDGEREGRESSION"?) at regression.pm line 27.
ERROR

../data/regression/KRR_1_15_Gaussian_1en06.m	Can't locate object method "new" via package "modshogun::KERNELRIDGEREGRESSION" (perhaps you forgot to load "modshogun::KERNELRIDGEREGRESSION"?) at regression.pm line 27.
ERROR

../data/regression/KRR_16_15_Gaussian_1en05.m	Can't locate object method "new" via package "modshogun::KERNELRIDGEREGRESSION" (perhaps you forgot to load "modshogun::KERNELRIDGEREGRESSION"?) at regression.pm line 27.
ERROR

../data/regression/LibSVR_0017_1_15_Gaussian_1en05_001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/LibSVR_023_1_15_Gaussian_1en05_001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/LibSVR_15_1_15_Gaussian_1en05_001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/LibSVR_30_1_15_Gaussian_00001_0001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/LibSVR_30_1_15_Gaussian_00001_001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/LibSVR_30_1_15_Gaussian_1en05_001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/LibSVR_30_16_15_Gaussian_00001_0001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/SVRLight_0017_1_15_Gaussian_1en05_001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/SVRLight_023_1_15_Gaussian_1en05_001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/SVRLight_15_1_15_Gaussian_1en05_001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/SVRLight_30_1_15_Gaussian_00001_0001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/SVRLight_30_1_15_Gaussian_00001_001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR

../data/regression/SVRLight_30_1_15_Gaussian_1en05_001.m	Can't locate object method "get_labels" via package "modshogun::Labels" at regression.pm line 56.
ERROR