2019-10-16T00:35:58 Created temporary directory: /tmp/pip-ephem-wheel-cache-7yy45ahb 2019-10-16T00:35:58 Created temporary directory: /tmp/pip-req-tracker-f2yqyqig 2019-10-16T00:35:58 Created requirements tracker '/tmp/pip-req-tracker-f2yqyqig' 2019-10-16T00:35:58 Created temporary directory: /tmp/pip-wheel-c_1uscf2 2019-10-16T00:35:58 Collecting amlearn==0.1.0 2019-10-16T00:35:58 1 location(s) to search for versions of amlearn: 2019-10-16T00:35:58 * https://pypi.org/simple/amlearn/ 2019-10-16T00:35:58 Getting page https://pypi.org/simple/amlearn/ 2019-10-16T00:35:58 Analyzing links from page https://pypi.org/simple/amlearn/ 2019-10-16T00:35:58 Found link https://files.pythonhosted.org/packages/5b/37/b16f0e09d837e63766331f1e212eccd32b46da07fa38269be86c0908c613/amlearn-0.0.1rc1.tar.gz#sha256=3feb0259f07d515171eb3f5dbcd60a40a90a2c04b9114be537d617d1df4addee (from https://pypi.org/simple/amlearn/), version: 0.0.1rc1 2019-10-16T00:35:58 Found link https://files.pythonhosted.org/packages/c9/69/69f3bd8acf04b6af467a52a212de838bf9cc412724b0197b1523b8703808/amlearn-0.1.0.tar.gz#sha256=20a099bc7da2324c247c1f5bd4c61cbf207ad59248a0c161fac0a08d11112f36 (from https://pypi.org/simple/amlearn/), version: 0.1.0 2019-10-16T00:35:58 Found link https://files.pythonhosted.org/packages/d8/26/d78c59d9be85d65e5fae532c317c98f8dc8184831f66a0ae50fc6099e23d/amlearn-0.2.0.tar.gz#sha256=02a6393944cbf8a784db0d554708f37a035c9203518531e46e870bc1453cef7f (from https://pypi.org/simple/amlearn/), version: 0.2.0 2019-10-16T00:35:58 Found link https://files.pythonhosted.org/packages/bb/91/5d7bc08da68c418d6a61ba40238d065acafeff63ecd5c802d6bff7790aba/amlearn-0.2.1.tar.gz#sha256=036b1f5f9152145124dc681a3345d518f374c1a8785f602addf4bc27494917f3 (from https://pypi.org/simple/amlearn/), version: 0.2.1 2019-10-16T00:35:58 Using version 0.1.0 (newest of versions: 0.1.0) 2019-10-16T00:35:58 Created temporary directory: /tmp/pip-unpack-niaojy9p 2019-10-16T00:35:59 Downloading https://files.pythonhosted.org/packages/c9/69/69f3bd8acf04b6af467a52a212de838bf9cc412724b0197b1523b8703808/amlearn-0.1.0.tar.gz (82kB) 2019-10-16T00:35:59 Downloading from URL https://files.pythonhosted.org/packages/c9/69/69f3bd8acf04b6af467a52a212de838bf9cc412724b0197b1523b8703808/amlearn-0.1.0.tar.gz#sha256=20a099bc7da2324c247c1f5bd4c61cbf207ad59248a0c161fac0a08d11112f36 (from https://pypi.org/simple/amlearn/) 2019-10-16T00:35:59 Added amlearn==0.1.0 from https://files.pythonhosted.org/packages/c9/69/69f3bd8acf04b6af467a52a212de838bf9cc412724b0197b1523b8703808/amlearn-0.1.0.tar.gz#sha256=20a099bc7da2324c247c1f5bd4c61cbf207ad59248a0c161fac0a08d11112f36 to build tracker '/tmp/pip-req-tracker-f2yqyqig' 2019-10-16T00:35:59 Running setup.py (path:/tmp/pip-wheel-c_1uscf2/amlearn/setup.py) egg_info for package amlearn 2019-10-16T00:35:59 Running command python setup.py egg_info 2019-10-16T00:36:01 running egg_info 2019-10-16T00:36:01 running build_src 2019-10-16T00:36:01 build_src 2019-10-16T00:36:01 building extension "amlearn.fmodules" sources 2019-10-16T00:36:01 f2py options: [] 2019-10-16T00:36:01 f2py:> build/src.linux-armv7l-3.7/amlearn/fmodulesmodule.c 2019-10-16T00:36:01 creating build 2019-10-16T00:36:01 creating build/src.linux-armv7l-3.7 2019-10-16T00:36:01 creating build/src.linux-armv7l-3.7/amlearn 2019-10-16T00:36:05 Reading fortran codes... 2019-10-16T00:36:05 Reading file 'amlearn/featurize/src/utils.f90' (format:free) 2019-10-16T00:36:05 Reading file 'amlearn/featurize/src/voronoi_nn.f90' (format:free) 2019-10-16T00:36:05 {'before': '', 'this': 'use', 'after': ':: distance '} 2019-10-16T00:36:05 Line #49 in amlearn/featurize/src/voronoi_nn.f90:" use :: distance " 2019-10-16T00:36:05 analyzeline: Could not crack the use statement. 2019-10-16T00:36:05 Reading file 'amlearn/featurize/src/voronoi_stats.f90' (format:free) 2019-10-16T00:36:05 {'before': '', 'this': 'use', 'after': ':: a_stats, only: all_stats '} 2019-10-16T00:36:05 Line #205 in amlearn/featurize/src/voronoi_stats.f90:" use :: a_stats, only: all_stats " 2019-10-16T00:36:05 analyzeline: Could not crack the use statement. 2019-10-16T00:36:05 {'before': '', 'this': 'use', 'after': ':: a_stats, only: all_stats '} 2019-10-16T00:36:05 Line #230 in amlearn/featurize/src/voronoi_stats.f90:" use :: a_stats, only: all_stats " 2019-10-16T00:36:05 analyzeline: Could not crack the use statement. 2019-10-16T00:36:05 {'before': '', 'this': 'use', 'after': ':: a_stats, only : all_stats '} 2019-10-16T00:36:05 Line #318 in amlearn/featurize/src/voronoi_stats.f90:" use :: a_stats, only : all_stats " 2019-10-16T00:36:05 analyzeline: Could not crack the use statement. 2019-10-16T00:36:05 {'before': '', 'this': 'use', 'after': ':: c_stats, only : customize_stats '} 2019-10-16T00:36:05 Line #320 in amlearn/featurize/src/voronoi_stats.f90:" use :: c_stats, only : customize_stats " 2019-10-16T00:36:05 analyzeline: Could not crack the use statement. 2019-10-16T00:36:05 Reading file 'amlearn/featurize/src/boop.f90' (format:free) 2019-10-16T00:36:05 {'before': '', 'this': 'use', 'after': ':: angle '} 2019-10-16T00:36:05 Line #9 in amlearn/featurize/src/boop.f90:" use :: angle " 2019-10-16T00:36:05 analyzeline: Could not crack the use statement. 2019-10-16T00:36:05 Reading file 'amlearn/featurize/src/mro_stats.f90' (format:free) 2019-10-16T00:36:05 {'before': '', 'this': 'use', 'after': ':: c_stats '} 2019-10-16T00:36:05 Line #5 in amlearn/featurize/src/mro_stats.f90:" use :: c_stats " 2019-10-16T00:36:05 analyzeline: Could not crack the use statement. 2019-10-16T00:36:05 Reading file 'amlearn/featurize/src/neighbor_data.f90' (format:free) 2019-10-16T00:36:05 Reading file 'amlearn/featurize/src/distance_stats.f90' (format:free) 2019-10-16T00:36:05 {'before': '', 'this': 'use', 'after': ':: a_stats '} 2019-10-16T00:36:05 Line #17 in amlearn/featurize/src/distance_stats.f90:" use :: a_stats " 2019-10-16T00:36:05 analyzeline: Could not crack the use statement. 2019-10-16T00:36:05 Reading file 'amlearn/featurize/src/distance_nn.f90' (format:free) 2019-10-16T00:36:05 {'before': '', 'this': 'use', 'after': ':: distance '} 2019-10-16T00:36:05 Line #29 in amlearn/featurize/src/distance_nn.f90:" use :: distance " 2019-10-16T00:36:05 analyzeline: Could not crack the use statement. 2019-10-16T00:36:05 {'before': '', 'this': 'use', 'after': ':: quicksort '} 2019-10-16T00:36:05 Line #31 in amlearn/featurize/src/distance_nn.f90:" use :: quicksort " 2019-10-16T00:36:05 analyzeline: Could not crack the use statement. 2019-10-16T00:36:05 Post-processing... 2019-10-16T00:36:05 Block: fmodules 2019-10-16T00:36:05 Block: determinant_func 2019-10-16T00:36:05 Block: determinant 2019-10-16T00:36:05 Block: distance 2019-10-16T00:36:05 Block: distance_info 2019-10-16T00:36:05 Block: quicksort 2019-10-16T00:36:05 Block: quick_sort 2019-10-16T00:36:05 Block: cg_function 2019-10-16T00:36:05 Block: calculate_cg 2019-10-16T00:36:05 Block: angle 2019-10-16T00:36:05 Block: angle_info 2019-10-16T00:36:05 Block: c_stats 2019-10-16T00:36:05 Block: customize_stats 2019-10-16T00:36:05 Block: a_stats 2019-10-16T00:36:05 Block: all_stats 2019-10-16T00:36:05 Block: determinant 2019-10-16T00:36:05 Block: voronoi 2019-10-16T00:36:05 Block: voronoi_index 2019-10-16T00:36:05 Block: i_fold_symmetry 2019-10-16T00:36:05 Block: line_percent 2019-10-16T00:36:05 {} 2019-10-16T00:36:05 In: :fmodules:amlearn/featurize/src/voronoi_stats.f90:character_motif 2019-10-16T00:36:05 vars2fortran: No typespec for argument "n_voro". 2019-10-16T00:36:05 {} 2019-10-16T00:36:05 In: :fmodules:amlearn/featurize/src/voronoi_stats.f90:character_motif 2019-10-16T00:36:05 vars2fortran: No typespec for argument "n_target". 2019-10-16T00:36:05 Block: character_motif 2019-10-16T00:36:05 Block: area_wt_i_fold_symmetry 2019-10-16T00:36:05 Block: vol_wt_i_fold_symmetry 2019-10-16T00:36:05 Block: voronoi_area_stats 2019-10-16T00:36:05 Block: voronoi_area_stats_separate 2019-10-16T00:36:05 Block: voronoi_vol_stats 2019-10-16T00:36:05 Block: voronoi_vol_stats_separate 2019-10-16T00:36:05 Block: voronoi_distance_stats 2019-10-16T00:36:05 Block: calculate_boop 2019-10-16T00:36:05 {'attrspec': ['intent(in)']} 2019-10-16T00:36:05 In: :fmodules:amlearn/featurize/src/mro_stats.f90:sro_to_mro 2019-10-16T00:36:05 vars2fortran: No typespec for argument "n_neighbor_limit". 2019-10-16T00:36:05 Block: sro_to_mro 2019-10-16T00:36:05 Block: add_neighbor_features 2019-10-16T00:36:05 Block: cn_dist 2019-10-16T00:36:05 Block: cutoff_distance_stats 2019-10-16T00:36:05 Block: distance_neighbor 2019-10-16T00:36:05 Post-processing (stage 2)... 2019-10-16T00:36:05 Block: fmodules 2019-10-16T00:36:05 Block: unknown_interface 2019-10-16T00:36:05 Block: determinant_func 2019-10-16T00:36:05 Block: determinant 2019-10-16T00:36:05 Block: distance 2019-10-16T00:36:05 Block: distance_info 2019-10-16T00:36:05 Block: quicksort 2019-10-16T00:36:05 Block: quick_sort 2019-10-16T00:36:05 Block: cg_function 2019-10-16T00:36:05 Block: calculate_cg 2019-10-16T00:36:05 Block: angle 2019-10-16T00:36:05 Block: angle_info 2019-10-16T00:36:05 Block: c_stats 2019-10-16T00:36:05 Block: customize_stats 2019-10-16T00:36:05 Block: a_stats 2019-10-16T00:36:05 Block: all_stats 2019-10-16T00:36:05 Block: determinant 2019-10-16T00:36:05 Block: voronoi 2019-10-16T00:36:05 Block: voronoi_index 2019-10-16T00:36:05 Block: i_fold_symmetry 2019-10-16T00:36:05 Block: line_percent 2019-10-16T00:36:05 Block: character_motif 2019-10-16T00:36:05 Block: area_wt_i_fold_symmetry 2019-10-16T00:36:05 Block: vol_wt_i_fold_symmetry 2019-10-16T00:36:05 Block: voronoi_area_stats 2019-10-16T00:36:05 Block: voronoi_area_stats_separate 2019-10-16T00:36:05 Block: voronoi_vol_stats 2019-10-16T00:36:05 Block: voronoi_vol_stats_separate 2019-10-16T00:36:05 Block: voronoi_distance_stats 2019-10-16T00:36:05 Block: calculate_boop 2019-10-16T00:36:05 Block: sro_to_mro 2019-10-16T00:36:05 Block: add_neighbor_features 2019-10-16T00:36:05 Block: cn_dist 2019-10-16T00:36:05 Block: cutoff_distance_stats 2019-10-16T00:36:05 Block: distance_neighbor 2019-10-16T00:36:05 Building modules... 2019-10-16T00:36:05 Building module "fmodules"... 2019-10-16T00:36:05 Constructing wrapper function "determinant"... 2019-10-16T00:36:05 deter_value = determinant(face) 2019-10-16T00:36:05 Constructing wrapper function "voronoi"... 2019-10-16T00:36:05 n_neighbor_list,neighbor_lists,neighbor_area_lists,neighbor_vol_lists,neighbor_distance_lists,neighbor_edge_lists,n_neighbor_max,n_edge_max = voronoi(atom_type,atom_coords,cutoff,allow_neighbor_limit,small_face_thres,pbc,bds,n_neighbor_list,neighbor_lists,neighbor_area_lists,neighbor_vol_lists,neighbor_distance_lists,neighbor_edge_lists,n_neighbor_max,n_edge_max,[n_atoms,n_neighbor_limit]) 2019-10-16T00:36:05 Constructing wrapper function "voronoi_index"... 2019-10-16T00:36:05 voronoi_index_list = voronoi_index(voronoi_index_list,n_neighbor_list,neighbor_edge_lists,edge_min,edge_max,include_beyond_edge_max,[n_atoms,neighbor_num_limit]) 2019-10-16T00:36:05 Constructing wrapper function "i_fold_symmetry"... 2019-10-16T00:36:05 i_symm_list = i_fold_symmetry(i_symm_list,n_neighbor_list,neighbor_edge_lists,edge_min,edge_max,include_beyond_edge_max,[n_atoms,neighbor_num_limit]) 2019-10-16T00:36:05 Constructing wrapper function "line_percent"... 2019-10-16T00:36:05 percent_list = line_percent(percent_list,value_list,[n_atoms,n_values]) 2019-10-16T00:36:05 Constructing wrapper function "character_motif"... 2019-10-16T00:36:05 motif_one_hot = character_motif(motif_one_hot,voronoi_index_list,edge_min,target_voro_idx,frank_kasper,[n_atoms,n_voro,n_target]) 2019-10-16T00:36:05 Constructing wrapper function "area_wt_i_fold_symmetry"... 2019-10-16T00:36:05 area_wt_i_symm_list = area_wt_i_fold_symmetry(area_wt_i_symm_list,n_neighbor_list,neighbor_edge_lists,neighbor_area_lists,edge_min,edge_max,include_beyond_edge_max,[n_atoms,neighbor_num_limit]) 2019-10-16T00:36:05 Constructing wrapper function "vol_wt_i_fold_symmetry"... 2019-10-16T00:36:05 vol_wt_i_symm_list = vol_wt_i_fold_symmetry(vol_wt_i_symm_list,n_neighbor_list,neighbor_edge_lists,neighbor_vol_lists,edge_min,edge_max,include_beyond_edge_max,[n_atoms,neighbor_num_limit]) 2019-10-16T00:36:05 Constructing wrapper function "voronoi_area_stats"... 2019-10-16T00:36:05 area_stats = voronoi_area_stats(area_stats,n_neighbor_list,neighbor_area_lists,[n_atoms,neighbor_num_limit]) 2019-10-16T00:36:05 Constructing wrapper function "voronoi_area_stats_separate"... 2019-10-16T00:36:05 area_stats_separate = voronoi_area_stats_separate(area_stats_separate,n_neighbor_list,neighbor_edge_lists,neighbor_area_lists,edge_min,edge_max,include_beyond_edge_max,[n_atoms,neighbor_num_limit]) 2019-10-16T00:36:05 Constructing wrapper function "voronoi_vol_stats"... 2019-10-16T00:36:05 vol_stats = voronoi_vol_stats(vol_stats,n_neighbor_list,neighbor_vol_lists,[n_atoms,neighbor_num_limit]) 2019-10-16T00:36:05 Constructing wrapper function "voronoi_vol_stats_separate"... 2019-10-16T00:36:05 vol_stats_separate = voronoi_vol_stats_separate(vol_stats_separate,n_neighbor_list,neighbor_edge_lists,neighbor_vol_lists,edge_min,edge_max,include_beyond_edge_max,[n_atoms,neighbor_num_limit]) 2019-10-16T00:36:05 Constructing wrapper function "voronoi_distance_stats"... 2019-10-16T00:36:05 distance_stats = voronoi_distance_stats(distance_stats,n_neighbor_list,neighbor_distance_lists,[n_atoms,neighbor_num_limit]) 2019-10-16T00:36:05 Constructing wrapper function "calculate_boop"... 2019-10-16T00:36:05 ql,wlbar,coarse_ql,coarse_wlbar = calculate_boop(atom_coords,pbc,bds,n_neighbor_list,neighbor_lists,low_order,higher_order,coarse_lower_order,coarse_higher_order,ql,wlbar,coarse_ql,coarse_wlbar,[n_atoms,n_neighbor_limit]) 2019-10-16T00:36:05 Constructing wrapper function "sro_to_mro"... 2019-10-16T00:36:05 mro_feature = sro_to_mro(sro_feature,n_neighbor_list,neighbor_lists,stats_types,mro_feature,[n_atoms,n_neighbor_limit,sum_stats_types]) 2019-10-16T00:36:05 Constructing wrapper function "add_neighbor_features"... 2019-10-16T00:36:05 features_new = add_neighbor_features(pred_last,neigh_voro,probs,features_new,[n_atoms,n_neighs,n_probs,n_features]) 2019-10-16T00:36:05 Constructing wrapper function "cn_dist"... 2019-10-16T00:36:06 cn = cn_dist(n_neighbor_list) 2019-10-16T00:36:06 Constructing wrapper function "cutoff_distance_stats"... 2019-10-16T00:36:06 cutoff_distance_stats(distance_stats,n_neighbor_list,neighbor_distance_lists,[n_atoms,n_neighbor_limit]) 2019-10-16T00:36:06 Constructing wrapper function "distance_neighbor"... 2019-10-16T00:36:06 n_neighbor_max,n_neighbor_list,neighbor_lists,neighbor_distance_lists = distance_neighbor(atom_type,atom_coords,distance_cutoff,allow_neighbor_limit,pbc,bds,n_neighbor_max,n_neighbor_list,neighbor_lists,neighbor_distance_lists,[n_atoms,n_neighbor_limit]) 2019-10-16T00:36:06 Constructing F90 module support for "determinant_func"... 2019-10-16T00:36:06 Constructing wrapper function "determinant_func.determinant"... 2019-10-16T00:36:06 deter_value = determinant(matrix) 2019-10-16T00:36:06 Constructing F90 module support for "distance"... 2019-10-16T00:36:06 Constructing wrapper function "distance.distance_info"... 2019-10-16T00:36:06 r,d = distance_info(atom_coords_i,atom_coords_j,bds,pbc) 2019-10-16T00:36:06 Constructing F90 module support for "quicksort"... 2019-10-16T00:36:06 Creating wrapper for Fortran subroutine "quick_sort"("quick_sort")... 2019-10-16T00:36:06 Constructing wrapper function "quicksort.quick_sort"... 2019-10-16T00:36:06 quick_sort(array,sort_col,sort_index_min,sort_index_max) 2019-10-16T00:36:06 Constructing F90 module support for "cg_function"... 2019-10-16T00:36:06 Creating wrapper for Fortran function "calculate_cg"("calculate_cg")... 2019-10-16T00:36:06 Constructing wrapper function "cg_function.calculate_cg"... 2019-10-16T00:36:06 cg = calculate_cg(half_l_min,half_l_max) 2019-10-16T00:36:06 Constructing F90 module support for "angle"... 2019-10-16T00:36:06 Constructing wrapper function "angle.angle_info"... 2019-10-16T00:36:06 ksai,theta = angle_info(atom_coords_i,atom_coords_j,bds,pbc) 2019-10-16T00:36:06 Constructing F90 module support for "c_stats"... 2019-10-16T00:36:06 Creating wrapper for Fortran function "customize_stats"("customize_stats")... 2019-10-16T00:36:06 Constructing wrapper function "c_stats.customize_stats"... 2019-10-16T00:36:06 stats = customize_stats(list,stats_types,stats_types_sum,self_prop) 2019-10-16T00:36:06 Constructing F90 module support for "a_stats"... 2019-10-16T00:36:06 Creating wrapper for Fortran function "all_stats"("all_stats")... 2019-10-16T00:36:06 Constructing wrapper function "a_stats.all_stats"... 2019-10-16T00:36:06 stats = all_stats(list,[len_bn]) 2019-10-16T00:36:06 Wrote C/API module "fmodules" to file "build/src.linux-armv7l-3.7/amlearn/fmodulesmodule.c" 2019-10-16T00:36:06 Fortran 90 wrappers are saved to "build/src.linux-armv7l-3.7/amlearn/fmodules-f2pywrappers2.f90" 2019-10-16T00:36:06 adding 'build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn/fortranobject.c' to sources. 2019-10-16T00:36:06 adding 'build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn' to include_dirs. 2019-10-16T00:36:06 creating build/src.linux-armv7l-3.7/build 2019-10-16T00:36:06 creating build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7 2019-10-16T00:36:06 creating build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn 2019-10-16T00:36:06 copying /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn 2019-10-16T00:36:06 copying /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn 2019-10-16T00:36:06 adding 'build/src.linux-armv7l-3.7/amlearn/fmodules-f2pywrappers2.f90' to sources. 2019-10-16T00:36:06 build_src: building npy-pkg config files 2019-10-16T00:36:06 creating pip-egg-info/amlearn.egg-info 2019-10-16T00:36:06 writing pip-egg-info/amlearn.egg-info/PKG-INFO 2019-10-16T00:36:06 writing dependency_links to pip-egg-info/amlearn.egg-info/dependency_links.txt 2019-10-16T00:36:06 writing requirements to pip-egg-info/amlearn.egg-info/requires.txt 2019-10-16T00:36:06 writing top-level names to pip-egg-info/amlearn.egg-info/top_level.txt 2019-10-16T00:36:06 writing manifest file 'pip-egg-info/amlearn.egg-info/SOURCES.txt' 2019-10-16T00:36:06 reading manifest file 'pip-egg-info/amlearn.egg-info/SOURCES.txt' 2019-10-16T00:36:06 writing manifest file 'pip-egg-info/amlearn.egg-info/SOURCES.txt' 2019-10-16T00:36:06 rmbadname1: Replacing "len" with "len_bn". 2019-10-16T00:36:06 rmbadname1: Replacing "len" with "len_bn". 2019-10-16T00:36:06 rmbadname1: Replacing "min" with "min_bn". 2019-10-16T00:36:06 rmbadname1: Replacing "max" with "max_bn". 2019-10-16T00:36:06 appenddecl: "dimension" not implemented. 2019-10-16T00:36:06 appenddecl: "dimension" not implemented. 2019-10-16T00:36:06 rmbadname1: Replacing "len" with "len_bn". 2019-10-16T00:36:06 "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) 2019-10-16T00:36:06 appenddecl: "dimension" not implemented. 2019-10-16T00:36:06 sortvarnames: failed to compute dependencies because of cyclic dependencies between target_voro_idx, voronoi_index_list, motif_one_hot, n_voro, n_target, n_atoms 2019-10-16T00:36:06 Source in /tmp/pip-wheel-c_1uscf2/amlearn has version 0.1.0, which satisfies requirement amlearn==0.1.0 from https://files.pythonhosted.org/packages/c9/69/69f3bd8acf04b6af467a52a212de838bf9cc412724b0197b1523b8703808/amlearn-0.1.0.tar.gz#sha256=20a099bc7da2324c247c1f5bd4c61cbf207ad59248a0c161fac0a08d11112f36 2019-10-16T00:36:06 Removed amlearn==0.1.0 from https://files.pythonhosted.org/packages/c9/69/69f3bd8acf04b6af467a52a212de838bf9cc412724b0197b1523b8703808/amlearn-0.1.0.tar.gz#sha256=20a099bc7da2324c247c1f5bd4c61cbf207ad59248a0c161fac0a08d11112f36 from build tracker '/tmp/pip-req-tracker-f2yqyqig' 2019-10-16T00:36:06 Building wheels for collected packages: amlearn 2019-10-16T00:36:06 Created temporary directory: /tmp/pip-wheel-sr8ab_wl 2019-10-16T00:36:06 Building wheel for amlearn (setup.py): started 2019-10-16T00:36:06 Destination directory: /tmp/pip-wheel-sr8ab_wl 2019-10-16T00:36:06 Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-c_1uscf2/amlearn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-sr8ab_wl 2019-10-16T00:36:08 running bdist_wheel 2019-10-16T00:36:08 running build 2019-10-16T00:36:08 running config_cc 2019-10-16T00:36:08 unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2019-10-16T00:36:08 running config_fc 2019-10-16T00:36:08 unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2019-10-16T00:36:08 running build_src 2019-10-16T00:36:08 build_src 2019-10-16T00:36:08 building extension "amlearn.fmodules" sources 2019-10-16T00:36:08 f2py options: [] 2019-10-16T00:36:08 adding 'build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn/fortranobject.c' to sources. 2019-10-16T00:36:08 adding 'build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn' to include_dirs. 2019-10-16T00:36:08 adding 'build/src.linux-armv7l-3.7/amlearn/fmodules-f2pywrappers2.f90' to sources. 2019-10-16T00:36:08 build_src: building npy-pkg config files 2019-10-16T00:36:08 running build_py 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7/scripts 2019-10-16T00:36:08 copying scripts/feature_violinplot.py -> build/lib.linux-armv7l-3.7/scripts 2019-10-16T00:36:08 copying scripts/distribution.py -> build/lib.linux-armv7l-3.7/scripts 2019-10-16T00:36:08 copying scripts/featurize_bp_symmfunc.py -> build/lib.linux-armv7l-3.7/scripts 2019-10-16T00:36:08 copying scripts/pdp_plot.py -> build/lib.linux-armv7l-3.7/scripts 2019-10-16T00:36:08 copying scripts/fractal_analysis.py -> build/lib.linux-armv7l-3.7/scripts 2019-10-16T00:36:08 copying scripts/__init__.py -> build/lib.linux-armv7l-3.7/scripts 2019-10-16T00:36:08 copying scripts/featurize_interstice.py -> build/lib.linux-armv7l-3.7/scripts 2019-10-16T00:36:08 copying scripts/generalization.py -> build/lib.linux-armv7l-3.7/scripts 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7/amlearn 2019-10-16T00:36:08 copying amlearn/_version.py -> build/lib.linux-armv7l-3.7/amlearn 2019-10-16T00:36:08 copying amlearn/__init__.py -> build/lib.linux-armv7l-3.7/amlearn 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7/amlearn/featurize 2019-10-16T00:36:08 copying amlearn/featurize/pipeline.py -> build/lib.linux-armv7l-3.7/amlearn/featurize 2019-10-16T00:36:08 copying amlearn/featurize/nearest_neighbor.py -> build/lib.linux-armv7l-3.7/amlearn/featurize 2019-10-16T00:36:08 copying amlearn/featurize/__init__.py -> build/lib.linux-armv7l-3.7/amlearn/featurize 2019-10-16T00:36:08 copying amlearn/featurize/symmetry_function.py -> build/lib.linux-armv7l-3.7/amlearn/featurize 2019-10-16T00:36:08 copying amlearn/featurize/medium_range_order.py -> build/lib.linux-armv7l-3.7/amlearn/featurize 2019-10-16T00:36:08 copying amlearn/featurize/base.py -> build/lib.linux-armv7l-3.7/amlearn/featurize 2019-10-16T00:36:08 copying amlearn/featurize/short_range_order.py -> build/lib.linux-armv7l-3.7/amlearn/featurize 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/logging.py -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/backend.py -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/__init__.py -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/packing.py -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/verbose.py -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/check.py -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/basetest.py -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/directory.py -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/data.py -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7/amlearn/learn 2019-10-16T00:36:08 copying amlearn/learn/regressor.py -> build/lib.linux-armv7l-3.7/amlearn/learn 2019-10-16T00:36:08 copying amlearn/learn/__init__.py -> build/lib.linux-armv7l-3.7/amlearn/learn 2019-10-16T00:36:08 copying amlearn/learn/preprocessor.py -> build/lib.linux-armv7l-3.7/amlearn/learn 2019-10-16T00:36:08 copying amlearn/learn/base.py -> build/lib.linux-armv7l-3.7/amlearn/learn 2019-10-16T00:36:08 copying amlearn/learn/classifier.py -> build/lib.linux-armv7l-3.7/amlearn/learn 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7/amlearn/featurize/tests 2019-10-16T00:36:08 copying amlearn/featurize/tests/test_short_range_order.py -> build/lib.linux-armv7l-3.7/amlearn/featurize/tests 2019-10-16T00:36:08 copying amlearn/featurize/tests/test_nearest_neighbor.py -> build/lib.linux-armv7l-3.7/amlearn/featurize/tests 2019-10-16T00:36:08 copying amlearn/featurize/tests/test_featurizer_pipeline.py -> build/lib.linux-armv7l-3.7/amlearn/featurize/tests 2019-10-16T00:36:08 copying amlearn/featurize/tests/__init__.py -> build/lib.linux-armv7l-3.7/amlearn/featurize/tests 2019-10-16T00:36:08 copying amlearn/featurize/tests/test_medium_range_order.py -> build/lib.linux-armv7l-3.7/amlearn/featurize/tests 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7/amlearn/featurize/src 2019-10-16T00:36:08 copying amlearn/featurize/src/__init__.py -> build/lib.linux-armv7l-3.7/amlearn/featurize/src 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7/amlearn/utils/tests 2019-10-16T00:36:08 copying amlearn/utils/tests/test_backend.py -> build/lib.linux-armv7l-3.7/amlearn/utils/tests 2019-10-16T00:36:08 copying amlearn/utils/tests/__init__.py -> build/lib.linux-armv7l-3.7/amlearn/utils/tests 2019-10-16T00:36:08 copying amlearn/utils/tests/test_data.py -> build/lib.linux-armv7l-3.7/amlearn/utils/tests 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7/amlearn/learn/tests 2019-10-16T00:36:08 copying amlearn/learn/tests/__init__.py -> build/lib.linux-armv7l-3.7/amlearn/learn/tests 2019-10-16T00:36:08 copying amlearn/learn/tests/test_classifier.py -> build/lib.linux-armv7l-3.7/amlearn/learn/tests 2019-10-16T00:36:08 creating build/lib.linux-armv7l-3.7/amlearn/learn/sklearn_patch 2019-10-16T00:36:08 copying amlearn/learn/sklearn_patch/_split.py -> build/lib.linux-armv7l-3.7/amlearn/learn/sklearn_patch 2019-10-16T00:36:08 copying amlearn/learn/sklearn_patch/_validation.py -> build/lib.linux-armv7l-3.7/amlearn/learn/sklearn_patch 2019-10-16T00:36:08 copying amlearn/learn/sklearn_patch/__init__.py -> build/lib.linux-armv7l-3.7/amlearn/learn/sklearn_patch 2019-10-16T00:36:08 copying amlearn/utils/default_environment.yaml -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/amlearn_logging.yaml -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 copying amlearn/utils/PTE.json -> build/lib.linux-armv7l-3.7/amlearn/utils 2019-10-16T00:36:08 running build_ext 2019-10-16T00:36:09 customize UnixCCompiler 2019-10-16T00:36:09 customize UnixCCompiler using build_ext 2019-10-16T00:36:09 get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' 2019-10-16T00:36:09 customize Gnu95FCompiler 2019-10-16T00:36:09 Found executable /usr/bin/gfortran 2019-10-16T00:36:09 customize Gnu95FCompiler 2019-10-16T00:36:09 customize Gnu95FCompiler using build_ext 2019-10-16T00:36:09 building 'amlearn.fmodules' extension 2019-10-16T00:36:09 compiling C sources 2019-10-16T00:36:09 C compiler: arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 2019-10-16T00:36:09 creating build/temp.linux-armv7l-3.7/build 2019-10-16T00:36:09 creating build/temp.linux-armv7l-3.7/build/src.linux-armv7l-3.7 2019-10-16T00:36:09 creating build/temp.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn 2019-10-16T00:36:09 creating build/temp.linux-armv7l-3.7/build/src.linux-armv7l-3.7/build 2019-10-16T00:36:09 creating build/temp.linux-armv7l-3.7/build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7 2019-10-16T00:36:09 creating build/temp.linux-armv7l-3.7/build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn 2019-10-16T00:36:09 compile options: '-Ibuild/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c' 2019-10-16T00:36:09 arm-linux-gnueabihf-gcc: build/src.linux-armv7l-3.7/amlearn/fmodulesmodule.carm-linux-gnueabihf-gcc: build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn/fortranobject.c 2019-10-16T00:36:10 In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2019-10-16T00:36:10 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2019-10-16T00:36:10 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2019-10-16T00:36:10 from build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn/fortranobject.h:13, 2019-10-16T00:36:10 from build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn/fortranobject.c:2: 2019-10-16T00:36:10 /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2019-10-16T00:36:10 #warning "Using deprecated NumPy API, disable it with " \ 2019-10-16T00:36:10 ^~~~~~~ 2019-10-16T00:36:10 In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2019-10-16T00:36:10 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2019-10-16T00:36:10 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2019-10-16T00:36:10 from build/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn/fortranobject.h:13, 2019-10-16T00:36:10 from build/src.linux-armv7l-3.7/amlearn/fmodulesmodule.c:16: 2019-10-16T00:36:10 /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2019-10-16T00:36:10 #warning "Using deprecated NumPy API, disable it with " \ 2019-10-16T00:36:10 ^~~~~~~ 2019-10-16T00:36:10 build/src.linux-armv7l-3.7/amlearn/fmodulesmodule.c:112:12: warning: ‘f2py_size’ defined but not used [-Wunused-function] 2019-10-16T00:36:10 static int f2py_size(PyArrayObject* var, ...) 2019-10-16T00:36:10 ^~~~~~~~~ 2019-10-16T00:36:15 compiling Fortran 90 module sources 2019-10-16T00:36:15 creating build/temp.linux-armv7l-3.7/amlearn 2019-10-16T00:36:15 Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops 2019-10-16T00:36:15 Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops 2019-10-16T00:36:15 Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops 2019-10-16T00:36:15 creating build/temp.linux-armv7l-3.7/amlearn/featurize 2019-10-16T00:36:15 creating build/temp.linux-armv7l-3.7/amlearn/featurize/src 2019-10-16T00:36:15 compile options: '-Ibuild/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c' 2019-10-16T00:36:15 extra options: '-Jbuild/temp.linux-armv7l-3.7/amlearn -Ibuild/temp.linux-armv7l-3.7/amlearn' 2019-10-16T00:36:15 gfortran:f90: amlearn/featurize/src/utils.f90 2019-10-16T00:36:17 amlearn/featurize/src/utils.f90:259:15: 2019-10-16T00:36:17 REAL(16) :: std 2019-10-16T00:36:17 1 2019-10-16T00:36:17 Error: Kind 16 not supported for type REAL at (1) 2019-10-16T00:36:17 amlearn/featurize/src/utils.f90:285:18: 2019-10-16T00:36:17 std = std + (list(atom) - mean)**2 2019-10-16T00:36:17 1 2019-10-16T00:36:17 Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion] 2019-10-16T00:36:18 error: Command "/usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops -Ibuild/src.linux-armv7l-3.7/build/src.linux-armv7l-3.7/amlearn -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c -c amlearn/featurize/src/utils.f90 -o build/temp.linux-armv7l-3.7/amlearn/featurize/src/utils.o -Jbuild/temp.linux-armv7l-3.7/amlearn -Ibuild/temp.linux-armv7l-3.7/amlearn" failed with exit status 1 2019-10-16T00:36:18 Building wheel for amlearn (setup.py): finished with status 'error' 2019-10-16T00:36:18 ERROR: Failed building wheel for amlearn 2019-10-16T00:36:18 Running setup.py clean for amlearn 2019-10-16T00:36:18 Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-c_1uscf2/amlearn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2019-10-16T00:36:20 running clean 2019-10-16T00:36:20 removing 'build/temp.linux-armv7l-3.7' (and everything under it) 2019-10-16T00:36:20 removing 'build/lib.linux-armv7l-3.7' (and everything under it) 2019-10-16T00:36:20 'build/bdist.linux-armv7l' does not exist -- can't clean it 2019-10-16T00:36:20 'build/scripts.linux-armv7l-3.7' does not exist -- can't clean it 2019-10-16T00:36:20 Failed to build amlearn 2019-10-16T00:36:20 Cleaning up... 2019-10-16T00:36:20 Removing source in /tmp/pip-wheel-c_1uscf2/amlearn 2019-10-16T00:36:20 Removed build tracker '/tmp/pip-req-tracker-f2yqyqig' 2019-10-16T00:36:20 ERROR: Failed to build one or more wheels 2019-10-16T00:36:20 Exception information: 2019-10-16T00:36:20 Traceback (most recent call last): 2019-10-16T00:36:20 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 178, in main 2019-10-16T00:36:20 status = self.run(options, args) 2019-10-16T00:36:20 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 178, in run 2019-10-16T00:36:20 "Failed to build one or more wheels" 2019-10-16T00:36:20 pip._internal.exceptions.CommandError: Failed to build one or more wheels