2021-07-08T19:44:44,778 Created temporary directory: /tmp/pip-ephem-wheel-cache-orx1wrva 2021-07-08T19:44:44,781 Created temporary directory: /tmp/pip-req-tracker-i_p9s3se 2021-07-08T19:44:44,781 Initialized build tracking at /tmp/pip-req-tracker-i_p9s3se 2021-07-08T19:44:44,781 Created build tracker: /tmp/pip-req-tracker-i_p9s3se 2021-07-08T19:44:44,782 Entered build tracker: /tmp/pip-req-tracker-i_p9s3se 2021-07-08T19:44:44,782 Created temporary directory: /tmp/pip-wheel-dtxaxguy 2021-07-08T19:44:44,816 1 location(s) to search for versions of nwalign: 2021-07-08T19:44:44,816 * https://pypi.org/simple/nwalign/ 2021-07-08T19:44:44,816 Fetching project page and analyzing links: https://pypi.org/simple/nwalign/ 2021-07-08T19:44:44,817 Getting page https://pypi.org/simple/nwalign/ 2021-07-08T19:44:44,818 Found index url https://pypi.org/simple 2021-07-08T19:44:44,909 Found link https://files.pythonhosted.org/packages/c8/26/9ca7ef2ddd1680a8a56c8b9c04f0b97f6c5a4b1fdd32f4795022317823a8/nwalign-0.1.tar.gz#sha256=4faa5fa9e60b19bee52adbf0a511b970bd29ad01d91112088c468c0bd58085cd (from https://pypi.org/simple/nwalign/), version: 0.1 2021-07-08T19:44:44,909 Found link https://files.pythonhosted.org/packages/a1/c8/1e9a68782c95d700d695c8b1f3a8934e1072e8ed60491e430896b834f961/nwalign-0.1.1.tar.gz#sha256=6fad7673d67932c0c670f564f8d9c8c7af264c7300c8038a245014a9d62b50dd (from https://pypi.org/simple/nwalign/), version: 0.1.1 2021-07-08T19:44:44,910 Found link https://files.pythonhosted.org/packages/b0/88/af6b4592f61add748195ef777dce0892bde1e2520d81b92e80e76b86deb4/nwalign-0.1.2.tar.gz#sha256=46db767c135bd698649657f17fdd091c6eb12acc0061fb0559df94e15ab7b149 (from https://pypi.org/simple/nwalign/), version: 0.1.2 2021-07-08T19:44:44,910 Found link https://files.pythonhosted.org/packages/e4/56/1e74d542efb45570042356a81bbad81cc6adc23bb4d5fcf6fd642ec2658b/nwalign-0.1.3.tar.gz#sha256=4fa6ca37c80650269e58437c4ac7969fa69ef7929ecfff279f6529e9f3a86fd9 (from https://pypi.org/simple/nwalign/), version: 0.1.3 2021-07-08T19:44:44,910 Found link https://files.pythonhosted.org/packages/5d/35/f962c0a6d870ea7ff96ba2465b276054192d36597cee2832972a0736bbb1/nwalign-0.2.tar.gz#sha256=c0984d30a9e7b95ceffda4265c8c2f4faf3ebf41ade008744df870bfa83c0b18 (from https://pypi.org/simple/nwalign/), version: 0.2 2021-07-08T19:44:44,911 Found link https://files.pythonhosted.org/packages/d1/2e/44355ba45f5a7ae0f0e1dcce833952470a95353669307a9a90affcbb757e/nwalign-0.3.0.tar.gz#sha256=8bd5786ad2d43282e5f5163f298cb232a7a154769398189a130eb34e61adc952 (from https://pypi.org/simple/nwalign/), version: 0.3.0 2021-07-08T19:44:44,911 Found link https://files.pythonhosted.org/packages/33/f9/96fdb624719c4122d559af37275c9af258ca9b1b93411e16ef0ec4899c3f/nwalign-0.3.1.tar.gz#sha256=bdbf1948df8421ef744ebf2993341df1f8431bbe41f4ce31241fff88d4d8e781 (from https://pypi.org/simple/nwalign/), version: 0.3.1 2021-07-08T19:44:44,911 Skipping link: not a file: https://pypi.org/simple/nwalign/ 2021-07-08T19:44:44,928 Given no hashes to check 1 links for project 'nwalign': discarding no candidates 2021-07-08T19:44:44,945 Collecting nwalign==0.1.1 2021-07-08T19:44:44,947 Created temporary directory: /tmp/pip-unpack-g6jju65e 2021-07-08T19:44:45,143 Downloading nwalign-0.1.1.tar.gz (37 kB) 2021-07-08T19:44:45,196 Added nwalign==0.1.1 from https://files.pythonhosted.org/packages/a1/c8/1e9a68782c95d700d695c8b1f3a8934e1072e8ed60491e430896b834f961/nwalign-0.1.1.tar.gz#sha256=6fad7673d67932c0c670f564f8d9c8c7af264c7300c8038a245014a9d62b50dd to build tracker '/tmp/pip-req-tracker-i_p9s3se' 2021-07-08T19:44:45,197 Running setup.py (path:/tmp/pip-wheel-dtxaxguy/nwalign_b497598aa74f4bd98778d5a625d4e494/setup.py) egg_info for package nwalign 2021-07-08T19:44:45,198 Created temporary directory: /tmp/pip-pip-egg-info-y169grki 2021-07-08T19:44:45,198 Running command python setup.py egg_info 2021-07-08T19:44:46,266 running egg_info 2021-07-08T19:44:46,268 creating /tmp/pip-pip-egg-info-y169grki/nwalign.egg-info 2021-07-08T19:44:46,269 writing /tmp/pip-pip-egg-info-y169grki/nwalign.egg-info/PKG-INFO 2021-07-08T19:44:46,272 writing dependency_links to /tmp/pip-pip-egg-info-y169grki/nwalign.egg-info/dependency_links.txt 2021-07-08T19:44:46,274 writing entry points to /tmp/pip-pip-egg-info-y169grki/nwalign.egg-info/entry_points.txt 2021-07-08T19:44:46,275 writing requirements to /tmp/pip-pip-egg-info-y169grki/nwalign.egg-info/requires.txt 2021-07-08T19:44:46,276 writing top-level names to /tmp/pip-pip-egg-info-y169grki/nwalign.egg-info/top_level.txt 2021-07-08T19:44:46,278 writing manifest file '/tmp/pip-pip-egg-info-y169grki/nwalign.egg-info/SOURCES.txt' 2021-07-08T19:44:46,495 reading manifest file '/tmp/pip-pip-egg-info-y169grki/nwalign.egg-info/SOURCES.txt' 2021-07-08T19:44:46,499 writing manifest file '/tmp/pip-pip-egg-info-y169grki/nwalign.egg-info/SOURCES.txt' 2021-07-08T19:44:46,599 Source in /tmp/pip-wheel-dtxaxguy/nwalign_b497598aa74f4bd98778d5a625d4e494 has version 0.1.1, which satisfies requirement nwalign==0.1.1 from https://files.pythonhosted.org/packages/a1/c8/1e9a68782c95d700d695c8b1f3a8934e1072e8ed60491e430896b834f961/nwalign-0.1.1.tar.gz#sha256=6fad7673d67932c0c670f564f8d9c8c7af264c7300c8038a245014a9d62b50dd 2021-07-08T19:44:46,600 Removed nwalign==0.1.1 from https://files.pythonhosted.org/packages/a1/c8/1e9a68782c95d700d695c8b1f3a8934e1072e8ed60491e430896b834f961/nwalign-0.1.1.tar.gz#sha256=6fad7673d67932c0c670f564f8d9c8c7af264c7300c8038a245014a9d62b50dd from build tracker '/tmp/pip-req-tracker-i_p9s3se' 2021-07-08T19:44:46,604 Created temporary directory: /tmp/pip-unpack-150vp2wu 2021-07-08T19:44:46,605 Building wheels for collected packages: nwalign 2021-07-08T19:44:46,610 Created temporary directory: /tmp/pip-wheel-vzpa_ht3 2021-07-08T19:44:46,610 Building wheel for nwalign (setup.py): started 2021-07-08T19:44:46,610 Destination directory: /tmp/pip-wheel-vzpa_ht3 2021-07-08T19:44:46,611 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-dtxaxguy/nwalign_b497598aa74f4bd98778d5a625d4e494/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-dtxaxguy/nwalign_b497598aa74f4bd98778d5a625d4e494/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-vzpa_ht3 2021-07-08T19:44:47,668 running bdist_wheel 2021-07-08T19:44:47,864 running build 2021-07-08T19:44:47,865 running build_ext 2021-07-08T19:44:47,870 building 'nwalign' extension 2021-07-08T19:44:47,871 creating build 2021-07-08T19:44:47,871 creating build/temp.linux-armv7l-3.9 2021-07-08T19:44:47,872 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I. -I/usr/include/python3.9 -c nwalign.c -o build/temp.linux-armv7l-3.9/nwalign.o 2021-07-08T19:44:48,297 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-08T19:44:48,297 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-08T19:44:48,297 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-08T19:44:48,297 from nwalign.c:133: 2021-07-08T19:44:48,297 /usr/local/lib/python3.9/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] 2021-07-08T19:44:48,298 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-08T19:44:48,298 | ^~~~~~~ 2021-07-08T19:44:48,347 nwalign.c: In function ‘__pyx_pf_7nwalign_read_matrix’: 2021-07-08T19:44:48,348 nwalign.c:1025:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,348 1025 | __pyx_t_6 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_5numpy_ndarray)), ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,348 | ^~~~~~~~~ 2021-07-08T19:44:48,349 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,349 from nwalign.c:4: 2021-07-08T19:44:48,349 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,349 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,349 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,355 nwalign.c:1142:37: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-07-08T19:44:48,355 1142 | for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_4; __pyx_t_12+=1) { 2021-07-08T19:44:48,355 | ^ 2021-07-08T19:44:48,357 nwalign.c:1205:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-07-08T19:44:48,357 1205 | if (unlikely(!(__pyx_v_ai == __pyx_t_4))) { 2021-07-08T19:44:48,357 | ^~ 2021-07-08T19:44:48,357 nwalign.c:206:41: note: in definition of macro ‘unlikely’ 2021-07-08T19:44:48,357 206 | #define unlikely(x) __builtin_expect(!!(x), 0) 2021-07-08T19:44:48,358 | ^ 2021-07-08T19:44:48,360 nwalign.c:793:14: warning: variable ‘__pyx_bshape_1_a’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:44:48,360 793 | Py_ssize_t __pyx_bshape_1_a = 0; 2021-07-08T19:44:48,361 | ^~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,361 nwalign.c:792:14: warning: variable ‘__pyx_bshape_0_a’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:44:48,361 792 | Py_ssize_t __pyx_bshape_0_a = 0; 2021-07-08T19:44:48,361 | ^~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,365 nwalign.c: In function ‘__pyx_f_7nwalign_global_align’: 2021-07-08T19:44:48,366 nwalign.c:1623:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,366 1623 | __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_t_4), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,366 | ^~~~~~~~~ 2021-07-08T19:44:48,367 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,367 from nwalign.c:4: 2021-07-08T19:44:48,367 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,367 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,367 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,370 nwalign.c:1678:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,371 1678 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_5, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,371 | ^~~~~~~~~ 2021-07-08T19:44:48,371 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,371 from nwalign.c:4: 2021-07-08T19:44:48,371 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,371 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,372 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,374 nwalign.c:1733:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,375 1733 | __pyx_t_4 = PyEval_CallObjectWithKeywords(__pyx_t_3, ((PyObject *)__pyx_t_5), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,375 | ^~~~~~~~~ 2021-07-08T19:44:48,375 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,375 from nwalign.c:4: 2021-07-08T19:44:48,375 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,375 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,376 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,383 nwalign.c:1962:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,383 1962 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_4, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 164; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,383 | ^~~~~~~~~ 2021-07-08T19:44:48,384 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,384 from nwalign.c:4: 2021-07-08T19:44:48,384 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,384 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,384 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,387 nwalign.c:2020:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,388 2020 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_5, ((PyObject *)__pyx_t_4), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,388 | ^~~~~~~~~ 2021-07-08T19:44:48,388 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,388 from nwalign.c:4: 2021-07-08T19:44:48,388 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,389 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,389 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,393 nwalign.c:2212:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-08T19:44:48,394 2212 | if (!(__pyx_v_ii == -1)) { 2021-07-08T19:44:48,394 | ^~ 2021-07-08T19:44:48,395 nwalign.c:2213:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-08T19:44:48,395 2213 | __pyx_t_25 = (__pyx_v_jj == -1); 2021-07-08T19:44:48,395 | ^~ 2021-07-08T19:44:48,397 nwalign.c:2215:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-08T19:44:48,397 2215 | __pyx_t_25 = (__pyx_v_ii == -1); 2021-07-08T19:44:48,397 | ^~ 2021-07-08T19:44:48,398 nwalign.c:2226:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-08T19:44:48,399 2226 | __pyx_t_25 = (__pyx_v_ii == -1); 2021-07-08T19:44:48,399 | ^~ 2021-07-08T19:44:48,410 nwalign.c:2236:26: warning: implicit declaration of function ‘PyString_FromStringAndSize’; did you mean ‘PyBytes_FromStringAndSize’? [-Wimplicit-function-declaration] 2021-07-08T19:44:48,410 2236 | __pyx_t_26 = PyString_FromStringAndSize((&__pyx_v_ci), ((size_t)1)); 2021-07-08T19:44:48,411 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,411 | PyBytes_FromStringAndSize 2021-07-08T19:44:48,412 nwalign.c:2236:24: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:44:48,413 2236 | __pyx_t_26 = PyString_FromStringAndSize((&__pyx_v_ci), ((size_t)1)); 2021-07-08T19:44:48,413 | ^ 2021-07-08T19:44:48,416 nwalign.c:2291:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-08T19:44:48,416 2291 | __pyx_t_25 = (__pyx_v_jj == -1); 2021-07-08T19:44:48,416 | ^~ 2021-07-08T19:44:48,418 nwalign.c:2301:24: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:44:48,418 2301 | __pyx_t_26 = PyString_FromStringAndSize((&__pyx_v_cj), ((size_t)1)); 2021-07-08T19:44:48,418 | ^ 2021-07-08T19:44:48,424 nwalign.c:2633:14: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:44:48,424 2633 | __pyx_v_ai = PyString_FromStringAndSize(NULL, __pyx_v_seqlen); 2021-07-08T19:44:48,424 | ^ 2021-07-08T19:44:48,426 nwalign.c:2642:14: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:44:48,426 2642 | __pyx_v_aj = PyString_FromStringAndSize(NULL, __pyx_v_seqlen); 2021-07-08T19:44:48,426 | ^ 2021-07-08T19:44:48,441 nwalign.c:2651:21: warning: implicit declaration of function ‘PyString_AS_STRING’; did you mean ‘PyBytes_AS_STRING’? [-Wimplicit-function-declaration] 2021-07-08T19:44:48,441 2651 | __pyx_v_align_j = PyString_AS_STRING(__pyx_v_aj); 2021-07-08T19:44:48,441 | ^~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,441 | PyBytes_AS_STRING 2021-07-08T19:44:48,443 nwalign.c:2651:19: warning: assignment to ‘char *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:44:48,443 2651 | __pyx_v_align_j = PyString_AS_STRING(__pyx_v_aj); 2021-07-08T19:44:48,443 | ^ 2021-07-08T19:44:48,445 nwalign.c:2660:19: warning: assignment to ‘char *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:44:48,445 2660 | __pyx_v_align_i = PyString_AS_STRING(__pyx_v_ai); 2021-07-08T19:44:48,445 | ^ 2021-07-08T19:44:48,463 nwalign.c:2864:3: warning: implicit declaration of function ‘_PyString_Resize’ [-Wimplicit-function-declaration] 2021-07-08T19:44:48,463 2864 | _PyString_Resize((&__pyx_v_aj), __pyx_v_align_counter); 2021-07-08T19:44:48,463 | ^~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,467 nwalign.c:1435:14: warning: variable ‘__pyx_bshape_1_agap’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:44:48,467 1435 | Py_ssize_t __pyx_bshape_1_agap = 0; 2021-07-08T19:44:48,467 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,468 nwalign.c:1434:14: warning: variable ‘__pyx_bshape_0_agap’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:44:48,469 1434 | Py_ssize_t __pyx_bshape_0_agap = 0; 2021-07-08T19:44:48,469 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,470 nwalign.c:1430:14: warning: variable ‘__pyx_bshape_1_score’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:44:48,470 1430 | Py_ssize_t __pyx_bshape_1_score = 0; 2021-07-08T19:44:48,470 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,471 nwalign.c:1429:14: warning: variable ‘__pyx_bshape_0_score’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:44:48,471 1429 | Py_ssize_t __pyx_bshape_0_score = 0; 2021-07-08T19:44:48,471 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,472 nwalign.c:1425:14: warning: variable ‘__pyx_bshape_1_pointer’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:44:48,472 1425 | Py_ssize_t __pyx_bshape_1_pointer = 0; 2021-07-08T19:44:48,472 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,473 nwalign.c:1424:14: warning: variable ‘__pyx_bshape_0_pointer’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:44:48,473 1424 | Py_ssize_t __pyx_bshape_0_pointer = 0; 2021-07-08T19:44:48,473 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,474 nwalign.c:1420:14: warning: variable ‘__pyx_bshape_1_amatrix’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:44:48,474 1420 | Py_ssize_t __pyx_bshape_1_amatrix = 0; 2021-07-08T19:44:48,474 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,475 nwalign.c:1419:14: warning: variable ‘__pyx_bshape_0_amatrix’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:44:48,475 1419 | Py_ssize_t __pyx_bshape_0_amatrix = 0; 2021-07-08T19:44:48,476 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,482 nwalign.c: In function ‘__pyx_pf_7nwalign_main’: 2021-07-08T19:44:48,484 nwalign.c:3164:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,484 3164 | __pyx_t_2 = PyEval_CallObjectWithKeywords(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 252; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,484 | ^~~~~~~~~ 2021-07-08T19:44:48,484 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,484 from nwalign.c:4: 2021-07-08T19:44:48,484 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,484 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,485 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,487 nwalign.c:3192:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,488 3192 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 255; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,488 | ^~~~~~~~~ 2021-07-08T19:44:48,488 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,488 from nwalign.c:4: 2021-07-08T19:44:48,488 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,488 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,488 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,491 nwalign.c:3219:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,491 3219 | __pyx_t_2 = PyEval_CallObjectWithKeywords(__pyx_t_3, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,491 | ^~~~~~~~~ 2021-07-08T19:44:48,492 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,492 from nwalign.c:4: 2021-07-08T19:44:48,492 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,492 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,492 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,494 nwalign.c:3246:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,494 3246 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,494 | ^~~~~~~~~ 2021-07-08T19:44:48,494 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,494 from nwalign.c:4: 2021-07-08T19:44:48,495 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,495 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,495 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,497 nwalign.c:3273:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,497 3273 | __pyx_t_2 = PyEval_CallObjectWithKeywords(__pyx_t_3, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,497 | ^~~~~~~~~ 2021-07-08T19:44:48,497 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,497 from nwalign.c:4: 2021-07-08T19:44:48,497 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,497 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,498 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,499 nwalign.c:3307:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,499 3307 | __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2021-07-08T19:44:48,500 | ^~~~~~~~~ 2021-07-08T19:44:48,500 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:44:48,500 from nwalign.c:4: 2021-07-08T19:44:48,500 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:44:48,500 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:44:48,500 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,546 nwalign.c: In function ‘__Pyx_ErrRestore’: 2021-07-08T19:44:48,551 nwalign.c:5306:18: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:44:48,551 5306 | if ((tstate->exc_type != NULL) & (tstate->exc_type != Py_None)) { 2021-07-08T19:44:48,551 | ^~~~~~~~ 2021-07-08T19:44:48,551 | curexc_type 2021-07-08T19:44:48,557 nwalign.c:5306:47: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:44:48,557 5306 | if ((tstate->exc_type != NULL) & (tstate->exc_type != Py_None)) { 2021-07-08T19:44:48,557 | ^~~~~~~~ 2021-07-08T19:44:48,557 | curexc_type 2021-07-08T19:44:48,562 nwalign.c:5307:28: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:44:48,562 5307 | tmp_type = tstate->exc_type; 2021-07-08T19:44:48,562 | ^~~~~~~~ 2021-07-08T19:44:48,562 | curexc_type 2021-07-08T19:44:48,567 nwalign.c:5308:29: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:44:48,567 5308 | tmp_value = tstate->exc_value; 2021-07-08T19:44:48,567 | ^~~~~~~~~ 2021-07-08T19:44:48,567 | curexc_value 2021-07-08T19:44:48,572 nwalign.c:5309:26: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:44:48,572 5309 | tmp_tb = tstate->exc_traceback; 2021-07-08T19:44:48,572 | ^~~~~~~~~~~~~ 2021-07-08T19:44:48,572 | curexc_traceback 2021-07-08T19:44:48,577 nwalign.c:5312:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:44:48,577 5312 | tstate->exc_type = 0; 2021-07-08T19:44:48,577 | ^~~~~~~~ 2021-07-08T19:44:48,577 | curexc_type 2021-07-08T19:44:48,582 nwalign.c:5313:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:44:48,582 5313 | tstate->exc_value = 0; 2021-07-08T19:44:48,582 | ^~~~~~~~~ 2021-07-08T19:44:48,582 | curexc_value 2021-07-08T19:44:48,587 nwalign.c:5314:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:44:48,587 5314 | tstate->exc_traceback = 0; 2021-07-08T19:44:48,587 | ^~~~~~~~~~~~~ 2021-07-08T19:44:48,587 | curexc_traceback 2021-07-08T19:44:48,607 nwalign.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-08T19:44:48,610 nwalign.c:5531:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,610 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,610 | ^~ 2021-07-08T19:44:48,610 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,610 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,611 from nwalign.c:4: 2021-07-08T19:44:48,611 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:44:48,611 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:44:48,611 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,614 nwalign.c:5531:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,614 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,614 | ^~ 2021-07-08T19:44:48,614 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,614 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,615 from nwalign.c:4: 2021-07-08T19:44:48,615 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-08T19:44:48,615 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-08T19:44:48,615 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,619 nwalign.c:5531:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,619 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,619 | ^~ 2021-07-08T19:44:48,619 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,619 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,619 from nwalign.c:4: 2021-07-08T19:44:48,619 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:44:48,620 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:44:48,620 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,622 nwalign.c:5531:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,622 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,623 | ^~ 2021-07-08T19:44:48,623 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,623 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,623 from nwalign.c:4: 2021-07-08T19:44:48,623 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:44:48,623 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:44:48,623 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,626 nwalign.c:5531:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,626 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,626 | ^~ 2021-07-08T19:44:48,626 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,626 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,626 from nwalign.c:4: 2021-07-08T19:44:48,627 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-08T19:44:48,627 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-08T19:44:48,627 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,629 nwalign.c:5531:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,630 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,630 | ^~ 2021-07-08T19:44:48,630 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,630 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,630 from nwalign.c:4: 2021-07-08T19:44:48,630 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:44:48,630 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:44:48,630 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,634 nwalign.c:5545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,634 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,634 | ^~ 2021-07-08T19:44:48,634 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,634 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,635 from nwalign.c:4: 2021-07-08T19:44:48,635 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:44:48,635 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:44:48,635 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,637 nwalign.c:5545:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,638 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,638 | ^~ 2021-07-08T19:44:48,638 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,638 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,638 from nwalign.c:4: 2021-07-08T19:44:48,638 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-08T19:44:48,638 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-08T19:44:48,638 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,641 nwalign.c:5545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,641 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,641 | ^~ 2021-07-08T19:44:48,641 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,642 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,642 from nwalign.c:4: 2021-07-08T19:44:48,642 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:44:48,642 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:44:48,642 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,645 nwalign.c:5545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,645 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,645 | ^~ 2021-07-08T19:44:48,645 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,645 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,645 from nwalign.c:4: 2021-07-08T19:44:48,645 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:44:48,645 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:44:48,646 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,648 nwalign.c:5545:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,648 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,648 | ^~ 2021-07-08T19:44:48,649 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,649 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,649 from nwalign.c:4: 2021-07-08T19:44:48,649 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-08T19:44:48,649 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-08T19:44:48,649 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,652 nwalign.c:5545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:44:48,652 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:44:48,652 | ^~ 2021-07-08T19:44:48,652 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:44:48,652 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:44:48,652 from nwalign.c:4: 2021-07-08T19:44:48,653 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:44:48,653 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:44:48,653 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,653 nwalign.c: In function ‘__Pyx_GetException’: 2021-07-08T19:44:48,658 nwalign.c:5597:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:44:48,658 5597 | tmp_type = tstate->exc_type; 2021-07-08T19:44:48,658 | ^~~~~~~~ 2021-07-08T19:44:48,658 | curexc_type 2021-07-08T19:44:48,663 nwalign.c:5598:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:44:48,663 5598 | tmp_value = tstate->exc_value; 2021-07-08T19:44:48,663 | ^~~~~~~~~ 2021-07-08T19:44:48,664 | curexc_value 2021-07-08T19:44:48,668 nwalign.c:5599:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:44:48,669 5599 | tmp_tb = tstate->exc_traceback; 2021-07-08T19:44:48,669 | ^~~~~~~~~~~~~ 2021-07-08T19:44:48,669 | curexc_traceback 2021-07-08T19:44:48,674 nwalign.c:5600:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:44:48,674 5600 | tstate->exc_type = *type; 2021-07-08T19:44:48,674 | ^~~~~~~~ 2021-07-08T19:44:48,674 | curexc_type 2021-07-08T19:44:48,679 nwalign.c:5601:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:44:48,679 5601 | tstate->exc_value = *value; 2021-07-08T19:44:48,679 | ^~~~~~~~~ 2021-07-08T19:44:48,679 | curexc_value 2021-07-08T19:44:48,684 nwalign.c:5602:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:44:48,684 5602 | tstate->exc_traceback = *tb; 2021-07-08T19:44:48,685 | ^~~~~~~~~~~~~ 2021-07-08T19:44:48,685 | curexc_traceback 2021-07-08T19:44:48,685 nwalign.c: In function ‘__Pyx_ExceptionSave’: 2021-07-08T19:44:48,690 nwalign.c:5619:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:44:48,690 5619 | *type = tstate->exc_type; 2021-07-08T19:44:48,690 | ^~~~~~~~ 2021-07-08T19:44:48,690 | curexc_type 2021-07-08T19:44:48,695 nwalign.c:5620:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:44:48,695 5620 | *value = tstate->exc_value; 2021-07-08T19:44:48,695 | ^~~~~~~~~ 2021-07-08T19:44:48,696 | curexc_value 2021-07-08T19:44:48,700 nwalign.c:5621:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:44:48,701 5621 | *tb = tstate->exc_traceback; 2021-07-08T19:44:48,701 | ^~~~~~~~~~~~~ 2021-07-08T19:44:48,701 | curexc_traceback 2021-07-08T19:44:48,701 nwalign.c: In function ‘__Pyx_ExceptionReset’: 2021-07-08T19:44:48,706 nwalign.c:5630:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:44:48,706 5630 | tmp_type = tstate->exc_type; 2021-07-08T19:44:48,706 | ^~~~~~~~ 2021-07-08T19:44:48,706 | curexc_type 2021-07-08T19:44:48,711 nwalign.c:5631:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:44:48,711 5631 | tmp_value = tstate->exc_value; 2021-07-08T19:44:48,712 | ^~~~~~~~~ 2021-07-08T19:44:48,712 | curexc_value 2021-07-08T19:44:48,717 nwalign.c:5632:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:44:48,717 5632 | tmp_tb = tstate->exc_traceback; 2021-07-08T19:44:48,717 | ^~~~~~~~~~~~~ 2021-07-08T19:44:48,717 | curexc_traceback 2021-07-08T19:44:48,722 nwalign.c:5633:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:44:48,722 5633 | tstate->exc_type = type; 2021-07-08T19:44:48,722 | ^~~~~~~~ 2021-07-08T19:44:48,722 | curexc_type 2021-07-08T19:44:48,727 nwalign.c:5634:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:44:48,727 5634 | tstate->exc_value = value; 2021-07-08T19:44:48,727 | ^~~~~~~~~ 2021-07-08T19:44:48,728 | curexc_value 2021-07-08T19:44:48,732 nwalign.c:5635:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:44:48,733 5635 | tstate->exc_traceback = tb; 2021-07-08T19:44:48,733 | ^~~~~~~~~~~~~ 2021-07-08T19:44:48,733 | curexc_traceback 2021-07-08T19:44:48,843 At top level: 2021-07-08T19:44:48,846 nwalign.c:4232:13: warning: ‘__pyx_pf_5numpy_7ndarray___releasebuffer__’ defined but not used [-Wunused-function] 2021-07-08T19:44:48,846 4232 | static void __pyx_pf_5numpy_7ndarray___releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2021-07-08T19:44:48,846 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,848 nwalign.c:3569:12: warning: ‘__pyx_pf_5numpy_7ndarray___getbuffer__’ defined but not used [-Wunused-function] 2021-07-08T19:44:48,848 3569 | static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2021-07-08T19:44:48,849 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:44:48,849 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:21, 2021-07-08T19:44:48,849 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-08T19:44:48,849 from nwalign.c:133: 2021-07-08T19:44:48,850 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1464:1: warning: ‘_import_array’ defined but not used [-Wunused-function] 2021-07-08T19:44:48,850 1464 | _import_array(void) 2021-07-08T19:44:48,850 | ^~~~~~~~~~~~~ 2021-07-08T19:44:48,855 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-08T19:44:48,965 Building wheel for nwalign (setup.py): finished with status 'error' 2021-07-08T19:44:48,966 ERROR: Failed building wheel for nwalign 2021-07-08T19:44:48,967 Running setup.py clean for nwalign 2021-07-08T19:44:48,967 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-dtxaxguy/nwalign_b497598aa74f4bd98778d5a625d4e494/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-dtxaxguy/nwalign_b497598aa74f4bd98778d5a625d4e494/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2021-07-08T19:44:49,982 running clean 2021-07-08T19:44:49,984 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-08T19:44:49,985 'build/lib.linux-armv7l-3.9' does not exist -- can't clean it 2021-07-08T19:44:49,986 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-08T19:44:49,986 'build/scripts-3.9' does not exist -- can't clean it 2021-07-08T19:44:49,986 removing 'build' 2021-07-08T19:44:50,072 Failed to build nwalign 2021-07-08T19:44:50,072 ERROR: Failed to build one or more wheels 2021-07-08T19:44:50,073 Exception information: 2021-07-08T19:44:50,073 Traceback (most recent call last): 2021-07-08T19:44:50,073 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-08T19:44:50,073 status = self.run(options, args) 2021-07-08T19:44:50,073 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-08T19:44:50,073 return func(self, options, args) 2021-07-08T19:44:50,073 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-08T19:44:50,073 raise CommandError( 2021-07-08T19:44:50,073 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-08T19:44:50,076 Removed build tracker: '/tmp/pip-req-tracker-i_p9s3se'