2021-07-08T19:42:10,733 Created temporary directory: /tmp/pip-ephem-wheel-cache-tjh9meuh 2021-07-08T19:42:10,736 Created temporary directory: /tmp/pip-req-tracker-jre3yzl8 2021-07-08T19:42:10,737 Initialized build tracking at /tmp/pip-req-tracker-jre3yzl8 2021-07-08T19:42:10,737 Created build tracker: /tmp/pip-req-tracker-jre3yzl8 2021-07-08T19:42:10,737 Entered build tracker: /tmp/pip-req-tracker-jre3yzl8 2021-07-08T19:42:10,738 Created temporary directory: /tmp/pip-wheel-0p2akz1q 2021-07-08T19:42:10,772 1 location(s) to search for versions of nwalign: 2021-07-08T19:42:10,772 * https://pypi.org/simple/nwalign/ 2021-07-08T19:42:10,772 Fetching project page and analyzing links: https://pypi.org/simple/nwalign/ 2021-07-08T19:42:10,773 Getting page https://pypi.org/simple/nwalign/ 2021-07-08T19:42:10,774 Found index url https://pypi.org/simple 2021-07-08T19:42:10,961 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 2021-07-08T19:42:10,961 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 2021-07-08T19:42:10,961 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 2021-07-08T19:42:10,962 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 2021-07-08T19:42:10,962 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 2021-07-08T19:42:10,962 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 2021-07-08T19:42:10,962 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 2021-07-08T19:42:10,963 Skipping link: not a file: https://pypi.org/simple/nwalign/ 2021-07-08T19:42:10,980 Given no hashes to check 1 links for project 'nwalign': discarding no candidates 2021-07-08T19:42:10,997 Collecting nwalign==0.1 2021-07-08T19:42:10,999 Created temporary directory: /tmp/pip-unpack-t98ynqrq 2021-07-08T19:42:11,174 Downloading nwalign-0.1.tar.gz (42 kB) 2021-07-08T19:42:11,239 Added nwalign==0.1 from https://files.pythonhosted.org/packages/c8/26/9ca7ef2ddd1680a8a56c8b9c04f0b97f6c5a4b1fdd32f4795022317823a8/nwalign-0.1.tar.gz#sha256=4faa5fa9e60b19bee52adbf0a511b970bd29ad01d91112088c468c0bd58085cd to build tracker '/tmp/pip-req-tracker-jre3yzl8' 2021-07-08T19:42:11,240 Running setup.py (path:/tmp/pip-wheel-0p2akz1q/nwalign_caac988e081d4d689c6f7775e660a9b2/setup.py) egg_info for package nwalign 2021-07-08T19:42:11,241 Created temporary directory: /tmp/pip-pip-egg-info-pgexy2nt 2021-07-08T19:42:11,241 Running command python setup.py egg_info 2021-07-08T19:42:12,298 running egg_info 2021-07-08T19:42:12,300 creating /tmp/pip-pip-egg-info-pgexy2nt/nwalign.egg-info 2021-07-08T19:42:12,301 writing /tmp/pip-pip-egg-info-pgexy2nt/nwalign.egg-info/PKG-INFO 2021-07-08T19:42:12,304 writing dependency_links to /tmp/pip-pip-egg-info-pgexy2nt/nwalign.egg-info/dependency_links.txt 2021-07-08T19:42:12,306 writing entry points to /tmp/pip-pip-egg-info-pgexy2nt/nwalign.egg-info/entry_points.txt 2021-07-08T19:42:12,307 writing requirements to /tmp/pip-pip-egg-info-pgexy2nt/nwalign.egg-info/requires.txt 2021-07-08T19:42:12,308 writing top-level names to /tmp/pip-pip-egg-info-pgexy2nt/nwalign.egg-info/top_level.txt 2021-07-08T19:42:12,309 writing manifest file '/tmp/pip-pip-egg-info-pgexy2nt/nwalign.egg-info/SOURCES.txt' 2021-07-08T19:42:12,526 reading manifest file '/tmp/pip-pip-egg-info-pgexy2nt/nwalign.egg-info/SOURCES.txt' 2021-07-08T19:42:12,530 writing manifest file '/tmp/pip-pip-egg-info-pgexy2nt/nwalign.egg-info/SOURCES.txt' 2021-07-08T19:42:12,630 Source in /tmp/pip-wheel-0p2akz1q/nwalign_caac988e081d4d689c6f7775e660a9b2 has version 0.1, which satisfies requirement nwalign==0.1 from https://files.pythonhosted.org/packages/c8/26/9ca7ef2ddd1680a8a56c8b9c04f0b97f6c5a4b1fdd32f4795022317823a8/nwalign-0.1.tar.gz#sha256=4faa5fa9e60b19bee52adbf0a511b970bd29ad01d91112088c468c0bd58085cd 2021-07-08T19:42:12,631 Removed nwalign==0.1 from https://files.pythonhosted.org/packages/c8/26/9ca7ef2ddd1680a8a56c8b9c04f0b97f6c5a4b1fdd32f4795022317823a8/nwalign-0.1.tar.gz#sha256=4faa5fa9e60b19bee52adbf0a511b970bd29ad01d91112088c468c0bd58085cd from build tracker '/tmp/pip-req-tracker-jre3yzl8' 2021-07-08T19:42:12,635 Created temporary directory: /tmp/pip-unpack-6_cb4xw3 2021-07-08T19:42:12,636 Building wheels for collected packages: nwalign 2021-07-08T19:42:12,640 Created temporary directory: /tmp/pip-wheel-kf1952su 2021-07-08T19:42:12,641 Building wheel for nwalign (setup.py): started 2021-07-08T19:42:12,641 Destination directory: /tmp/pip-wheel-kf1952su 2021-07-08T19:42:12,641 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-0p2akz1q/nwalign_caac988e081d4d689c6f7775e660a9b2/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-0p2akz1q/nwalign_caac988e081d4d689c6f7775e660a9b2/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-kf1952su 2021-07-08T19:42:13,676 running bdist_wheel 2021-07-08T19:42:13,869 running build 2021-07-08T19:42:13,870 running build_ext 2021-07-08T19:42:13,875 building 'nwalign' extension 2021-07-08T19:42:13,875 creating build 2021-07-08T19:42:13,875 creating build/temp.linux-armv7l-3.9 2021-07-08T19:42:13,876 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 2021-07-08T19:42:14,289 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-08T19:42:14,290 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-08T19:42:14,290 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-08T19:42:14,290 from nwalign.c:133: 2021-07-08T19:42:14,290 /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] 2021-07-08T19:42:14,290 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-08T19:42:14,291 | ^~~~~~~ 2021-07-08T19:42:14,336 nwalign.c: In function ‘__pyx_pf_7nwalign_read_matrix’: 2021-07-08T19:42:14,337 nwalign.c:1025:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,337 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;} 2021-07-08T19:42:14,337 | ^~~~~~~~~ 2021-07-08T19:42:14,337 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,337 from nwalign.c:4: 2021-07-08T19:42:14,338 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,338 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,338 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,342 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] 2021-07-08T19:42:14,343 1142 | for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_4; __pyx_t_12+=1) { 2021-07-08T19:42:14,343 | ^ 2021-07-08T19:42:14,344 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] 2021-07-08T19:42:14,344 1205 | if (unlikely(!(__pyx_v_ai == __pyx_t_4))) { 2021-07-08T19:42:14,344 | ^~ 2021-07-08T19:42:14,345 nwalign.c:206:41: note: in definition of macro ‘unlikely’ 2021-07-08T19:42:14,345 206 | #define unlikely(x) __builtin_expect(!!(x), 0) 2021-07-08T19:42:14,345 | ^ 2021-07-08T19:42:14,347 nwalign.c:793:14: warning: variable ‘__pyx_bshape_1_a’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:42:14,347 793 | Py_ssize_t __pyx_bshape_1_a = 0; 2021-07-08T19:42:14,347 | ^~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,347 nwalign.c:792:14: warning: variable ‘__pyx_bshape_0_a’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:42:14,347 792 | Py_ssize_t __pyx_bshape_0_a = 0; 2021-07-08T19:42:14,347 | ^~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,351 nwalign.c: In function ‘__pyx_f_7nwalign_global_align’: 2021-07-08T19:42:14,352 nwalign.c:1623:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,352 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;} 2021-07-08T19:42:14,352 | ^~~~~~~~~ 2021-07-08T19:42:14,352 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,352 from nwalign.c:4: 2021-07-08T19:42:14,353 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,353 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,353 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,355 nwalign.c:1678:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,355 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;} 2021-07-08T19:42:14,355 | ^~~~~~~~~ 2021-07-08T19:42:14,355 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,356 from nwalign.c:4: 2021-07-08T19:42:14,356 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,356 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,356 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,358 nwalign.c:1733:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,358 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;} 2021-07-08T19:42:14,358 | ^~~~~~~~~ 2021-07-08T19:42:14,359 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,359 from nwalign.c:4: 2021-07-08T19:42:14,359 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,359 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,359 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,366 nwalign.c:1962:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,366 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;} 2021-07-08T19:42:14,366 | ^~~~~~~~~ 2021-07-08T19:42:14,366 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,366 from nwalign.c:4: 2021-07-08T19:42:14,366 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,367 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,367 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,369 nwalign.c:2020:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,370 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;} 2021-07-08T19:42:14,370 | ^~~~~~~~~ 2021-07-08T19:42:14,370 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,370 from nwalign.c:4: 2021-07-08T19:42:14,370 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,370 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,370 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,374 nwalign.c:2212:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-08T19:42:14,375 2212 | if (!(__pyx_v_ii == -1)) { 2021-07-08T19:42:14,375 | ^~ 2021-07-08T19:42:14,376 nwalign.c:2213:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-08T19:42:14,376 2213 | __pyx_t_25 = (__pyx_v_jj == -1); 2021-07-08T19:42:14,376 | ^~ 2021-07-08T19:42:14,377 nwalign.c:2215:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-08T19:42:14,378 2215 | __pyx_t_25 = (__pyx_v_ii == -1); 2021-07-08T19:42:14,378 | ^~ 2021-07-08T19:42:14,379 nwalign.c:2226:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-08T19:42:14,379 2226 | __pyx_t_25 = (__pyx_v_ii == -1); 2021-07-08T19:42:14,380 | ^~ 2021-07-08T19:42:14,391 nwalign.c:2236:26: warning: implicit declaration of function ‘PyString_FromStringAndSize’; did you mean ‘PyBytes_FromStringAndSize’? [-Wimplicit-function-declaration] 2021-07-08T19:42:14,391 2236 | __pyx_t_26 = PyString_FromStringAndSize((&__pyx_v_ci), ((size_t)1)); 2021-07-08T19:42:14,391 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,391 | PyBytes_FromStringAndSize 2021-07-08T19:42:14,393 nwalign.c:2236:24: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:42:14,393 2236 | __pyx_t_26 = PyString_FromStringAndSize((&__pyx_v_ci), ((size_t)1)); 2021-07-08T19:42:14,393 | ^ 2021-07-08T19:42:14,396 nwalign.c:2291:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-08T19:42:14,396 2291 | __pyx_t_25 = (__pyx_v_jj == -1); 2021-07-08T19:42:14,396 | ^~ 2021-07-08T19:42:14,397 nwalign.c:2301:24: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:42:14,398 2301 | __pyx_t_26 = PyString_FromStringAndSize((&__pyx_v_cj), ((size_t)1)); 2021-07-08T19:42:14,398 | ^ 2021-07-08T19:42:14,404 nwalign.c:2633:14: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:42:14,404 2633 | __pyx_v_ai = PyString_FromStringAndSize(NULL, __pyx_v_seqlen); 2021-07-08T19:42:14,404 | ^ 2021-07-08T19:42:14,406 nwalign.c:2642:14: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:42:14,406 2642 | __pyx_v_aj = PyString_FromStringAndSize(NULL, __pyx_v_seqlen); 2021-07-08T19:42:14,406 | ^ 2021-07-08T19:42:14,421 nwalign.c:2651:21: warning: implicit declaration of function ‘PyString_AS_STRING’; did you mean ‘PyBytes_AS_STRING’? [-Wimplicit-function-declaration] 2021-07-08T19:42:14,422 2651 | __pyx_v_align_j = PyString_AS_STRING(__pyx_v_aj); 2021-07-08T19:42:14,422 | ^~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,422 | PyBytes_AS_STRING 2021-07-08T19:42:14,423 nwalign.c:2651:19: warning: assignment to ‘char *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:42:14,424 2651 | __pyx_v_align_j = PyString_AS_STRING(__pyx_v_aj); 2021-07-08T19:42:14,424 | ^ 2021-07-08T19:42:14,425 nwalign.c:2660:19: warning: assignment to ‘char *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-08T19:42:14,425 2660 | __pyx_v_align_i = PyString_AS_STRING(__pyx_v_ai); 2021-07-08T19:42:14,425 | ^ 2021-07-08T19:42:14,443 nwalign.c:2864:3: warning: implicit declaration of function ‘_PyString_Resize’ [-Wimplicit-function-declaration] 2021-07-08T19:42:14,444 2864 | _PyString_Resize((&__pyx_v_aj), __pyx_v_align_counter); 2021-07-08T19:42:14,444 | ^~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,447 nwalign.c:1435:14: warning: variable ‘__pyx_bshape_1_agap’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:42:14,447 1435 | Py_ssize_t __pyx_bshape_1_agap = 0; 2021-07-08T19:42:14,447 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,448 nwalign.c:1434:14: warning: variable ‘__pyx_bshape_0_agap’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:42:14,448 1434 | Py_ssize_t __pyx_bshape_0_agap = 0; 2021-07-08T19:42:14,448 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,449 nwalign.c:1430:14: warning: variable ‘__pyx_bshape_1_score’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:42:14,449 1430 | Py_ssize_t __pyx_bshape_1_score = 0; 2021-07-08T19:42:14,449 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,450 nwalign.c:1429:14: warning: variable ‘__pyx_bshape_0_score’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:42:14,450 1429 | Py_ssize_t __pyx_bshape_0_score = 0; 2021-07-08T19:42:14,450 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,451 nwalign.c:1425:14: warning: variable ‘__pyx_bshape_1_pointer’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:42:14,451 1425 | Py_ssize_t __pyx_bshape_1_pointer = 0; 2021-07-08T19:42:14,451 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,452 nwalign.c:1424:14: warning: variable ‘__pyx_bshape_0_pointer’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:42:14,452 1424 | Py_ssize_t __pyx_bshape_0_pointer = 0; 2021-07-08T19:42:14,452 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,453 nwalign.c:1420:14: warning: variable ‘__pyx_bshape_1_amatrix’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:42:14,453 1420 | Py_ssize_t __pyx_bshape_1_amatrix = 0; 2021-07-08T19:42:14,453 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,454 nwalign.c:1419:14: warning: variable ‘__pyx_bshape_0_amatrix’ set but not used [-Wunused-but-set-variable] 2021-07-08T19:42:14,454 1419 | Py_ssize_t __pyx_bshape_0_amatrix = 0; 2021-07-08T19:42:14,454 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,460 nwalign.c: In function ‘__pyx_pf_7nwalign_main’: 2021-07-08T19:42:14,462 nwalign.c:3164:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,462 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;} 2021-07-08T19:42:14,462 | ^~~~~~~~~ 2021-07-08T19:42:14,462 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,463 from nwalign.c:4: 2021-07-08T19:42:14,463 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,463 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,463 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,465 nwalign.c:3192:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,465 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;} 2021-07-08T19:42:14,466 | ^~~~~~~~~ 2021-07-08T19:42:14,466 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,466 from nwalign.c:4: 2021-07-08T19:42:14,466 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,466 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,466 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,469 nwalign.c:3219:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,469 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;} 2021-07-08T19:42:14,469 | ^~~~~~~~~ 2021-07-08T19:42:14,469 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,469 from nwalign.c:4: 2021-07-08T19:42:14,469 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,469 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,470 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,472 nwalign.c:3246:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,472 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;} 2021-07-08T19:42:14,472 | ^~~~~~~~~ 2021-07-08T19:42:14,472 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,472 from nwalign.c:4: 2021-07-08T19:42:14,473 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,473 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,473 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,475 nwalign.c:3273:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,475 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;} 2021-07-08T19:42:14,475 | ^~~~~~~~~ 2021-07-08T19:42:14,476 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,476 from nwalign.c:4: 2021-07-08T19:42:14,476 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,476 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,476 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,478 nwalign.c:3307:3: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,478 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;} 2021-07-08T19:42:14,479 | ^~~~~~~~~ 2021-07-08T19:42:14,479 In file included from /usr/include/python3.9/Python.h:145, 2021-07-08T19:42:14,479 from nwalign.c:4: 2021-07-08T19:42:14,479 /usr/include/python3.9/ceval.h:17:43: note: declared here 2021-07-08T19:42:14,479 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( 2021-07-08T19:42:14,479 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,527 nwalign.c: In function ‘__Pyx_ErrRestore’: 2021-07-08T19:42:14,534 nwalign.c:5306:18: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:42:14,534 5306 | if ((tstate->exc_type != NULL) & (tstate->exc_type != Py_None)) { 2021-07-08T19:42:14,534 | ^~~~~~~~ 2021-07-08T19:42:14,534 | curexc_type 2021-07-08T19:42:14,541 nwalign.c:5306:47: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:42:14,541 5306 | if ((tstate->exc_type != NULL) & (tstate->exc_type != Py_None)) { 2021-07-08T19:42:14,541 | ^~~~~~~~ 2021-07-08T19:42:14,541 | curexc_type 2021-07-08T19:42:14,548 nwalign.c:5307:28: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:42:14,548 5307 | tmp_type = tstate->exc_type; 2021-07-08T19:42:14,548 | ^~~~~~~~ 2021-07-08T19:42:14,548 | curexc_type 2021-07-08T19:42:14,554 nwalign.c:5308:29: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:42:14,555 5308 | tmp_value = tstate->exc_value; 2021-07-08T19:42:14,555 | ^~~~~~~~~ 2021-07-08T19:42:14,555 | curexc_value 2021-07-08T19:42:14,561 nwalign.c:5309:26: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:42:14,561 5309 | tmp_tb = tstate->exc_traceback; 2021-07-08T19:42:14,561 | ^~~~~~~~~~~~~ 2021-07-08T19:42:14,561 | curexc_traceback 2021-07-08T19:42:14,568 nwalign.c:5312:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:42:14,568 5312 | tstate->exc_type = 0; 2021-07-08T19:42:14,568 | ^~~~~~~~ 2021-07-08T19:42:14,568 | curexc_type 2021-07-08T19:42:14,575 nwalign.c:5313:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:42:14,575 5313 | tstate->exc_value = 0; 2021-07-08T19:42:14,575 | ^~~~~~~~~ 2021-07-08T19:42:14,575 | curexc_value 2021-07-08T19:42:14,581 nwalign.c:5314:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:42:14,581 5314 | tstate->exc_traceback = 0; 2021-07-08T19:42:14,582 | ^~~~~~~~~~~~~ 2021-07-08T19:42:14,582 | curexc_traceback 2021-07-08T19:42:14,607 nwalign.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-08T19:42:14,611 nwalign.c:5531:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,612 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,612 | ^~ 2021-07-08T19:42:14,612 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,612 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,612 from nwalign.c:4: 2021-07-08T19:42:14,612 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:42:14,613 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:42:14,613 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,617 nwalign.c:5531:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,617 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,617 | ^~ 2021-07-08T19:42:14,617 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,618 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,618 from nwalign.c:4: 2021-07-08T19:42:14,618 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-08T19:42:14,618 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-08T19:42:14,618 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,623 nwalign.c:5531:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,623 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,623 | ^~ 2021-07-08T19:42:14,624 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,624 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,624 from nwalign.c:4: 2021-07-08T19:42:14,624 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:42:14,624 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:42:14,624 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,628 nwalign.c:5531:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,628 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,628 | ^~ 2021-07-08T19:42:14,628 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,628 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,629 from nwalign.c:4: 2021-07-08T19:42:14,629 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:42:14,629 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:42:14,629 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,633 nwalign.c:5531:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,633 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,633 | ^~ 2021-07-08T19:42:14,633 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,633 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,633 from nwalign.c:4: 2021-07-08T19:42:14,633 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-08T19:42:14,634 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-08T19:42:14,634 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,638 nwalign.c:5531:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,638 5531 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,638 | ^~ 2021-07-08T19:42:14,638 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,638 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,638 from nwalign.c:4: 2021-07-08T19:42:14,638 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:42:14,639 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:42:14,639 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,644 nwalign.c:5545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,644 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,644 | ^~ 2021-07-08T19:42:14,644 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,644 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,644 from nwalign.c:4: 2021-07-08T19:42:14,644 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:42:14,644 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:42:14,645 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,648 nwalign.c:5545:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,649 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,649 | ^~ 2021-07-08T19:42:14,649 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,649 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,649 from nwalign.c:4: 2021-07-08T19:42:14,649 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-08T19:42:14,649 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-08T19:42:14,649 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,653 nwalign.c:5545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,653 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,653 | ^~ 2021-07-08T19:42:14,654 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,654 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,654 from nwalign.c:4: 2021-07-08T19:42:14,654 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:42:14,654 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:42:14,654 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,658 nwalign.c:5545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,658 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,658 | ^~ 2021-07-08T19:42:14,658 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,659 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,659 from nwalign.c:4: 2021-07-08T19:42:14,659 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:42:14,659 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:42:14,659 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,663 nwalign.c:5545:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,663 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,663 | ^~ 2021-07-08T19:42:14,663 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,663 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,663 from nwalign.c:4: 2021-07-08T19:42:14,663 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-08T19:42:14,664 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-08T19:42:14,664 | ^~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,668 nwalign.c:5545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-08T19:42:14,668 5545 | if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && 2021-07-08T19:42:14,668 | ^~ 2021-07-08T19:42:14,668 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-08T19:42:14,668 from /usr/include/python3.9/Python.h:97, 2021-07-08T19:42:14,668 from nwalign.c:4: 2021-07-08T19:42:14,668 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-08T19:42:14,669 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-08T19:42:14,669 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,669 nwalign.c: In function ‘__Pyx_GetException’: 2021-07-08T19:42:14,676 nwalign.c:5597:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:42:14,676 5597 | tmp_type = tstate->exc_type; 2021-07-08T19:42:14,676 | ^~~~~~~~ 2021-07-08T19:42:14,676 | curexc_type 2021-07-08T19:42:14,683 nwalign.c:5598:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:42:14,683 5598 | tmp_value = tstate->exc_value; 2021-07-08T19:42:14,683 | ^~~~~~~~~ 2021-07-08T19:42:14,683 | curexc_value 2021-07-08T19:42:14,690 nwalign.c:5599:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:42:14,690 5599 | tmp_tb = tstate->exc_traceback; 2021-07-08T19:42:14,690 | ^~~~~~~~~~~~~ 2021-07-08T19:42:14,690 | curexc_traceback 2021-07-08T19:42:14,697 nwalign.c:5600:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:42:14,697 5600 | tstate->exc_type = *type; 2021-07-08T19:42:14,697 | ^~~~~~~~ 2021-07-08T19:42:14,697 | curexc_type 2021-07-08T19:42:14,704 nwalign.c:5601:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:42:14,704 5601 | tstate->exc_value = *value; 2021-07-08T19:42:14,704 | ^~~~~~~~~ 2021-07-08T19:42:14,704 | curexc_value 2021-07-08T19:42:14,711 nwalign.c:5602:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:42:14,711 5602 | tstate->exc_traceback = *tb; 2021-07-08T19:42:14,711 | ^~~~~~~~~~~~~ 2021-07-08T19:42:14,711 | curexc_traceback 2021-07-08T19:42:14,712 nwalign.c: In function ‘__Pyx_ExceptionSave’: 2021-07-08T19:42:14,719 nwalign.c:5619:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:42:14,719 5619 | *type = tstate->exc_type; 2021-07-08T19:42:14,719 | ^~~~~~~~ 2021-07-08T19:42:14,719 | curexc_type 2021-07-08T19:42:14,726 nwalign.c:5620:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:42:14,726 5620 | *value = tstate->exc_value; 2021-07-08T19:42:14,726 | ^~~~~~~~~ 2021-07-08T19:42:14,726 | curexc_value 2021-07-08T19:42:14,733 nwalign.c:5621:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:42:14,733 5621 | *tb = tstate->exc_traceback; 2021-07-08T19:42:14,733 | ^~~~~~~~~~~~~ 2021-07-08T19:42:14,733 | curexc_traceback 2021-07-08T19:42:14,734 nwalign.c: In function ‘__Pyx_ExceptionReset’: 2021-07-08T19:42:14,740 nwalign.c:5630:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:42:14,740 5630 | tmp_type = tstate->exc_type; 2021-07-08T19:42:14,741 | ^~~~~~~~ 2021-07-08T19:42:14,741 | curexc_type 2021-07-08T19:42:14,747 nwalign.c:5631:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:42:14,748 5631 | tmp_value = tstate->exc_value; 2021-07-08T19:42:14,748 | ^~~~~~~~~ 2021-07-08T19:42:14,748 | curexc_value 2021-07-08T19:42:14,755 nwalign.c:5632:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:42:14,755 5632 | tmp_tb = tstate->exc_traceback; 2021-07-08T19:42:14,755 | ^~~~~~~~~~~~~ 2021-07-08T19:42:14,755 | curexc_traceback 2021-07-08T19:42:14,762 nwalign.c:5633:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-08T19:42:14,762 5633 | tstate->exc_type = type; 2021-07-08T19:42:14,762 | ^~~~~~~~ 2021-07-08T19:42:14,762 | curexc_type 2021-07-08T19:42:14,769 nwalign.c:5634:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-08T19:42:14,769 5634 | tstate->exc_value = value; 2021-07-08T19:42:14,769 | ^~~~~~~~~ 2021-07-08T19:42:14,769 | curexc_value 2021-07-08T19:42:14,776 nwalign.c:5635:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-08T19:42:14,776 5635 | tstate->exc_traceback = tb; 2021-07-08T19:42:14,776 | ^~~~~~~~~~~~~ 2021-07-08T19:42:14,777 | curexc_traceback 2021-07-08T19:42:14,905 At top level: 2021-07-08T19:42:14,908 nwalign.c:4232:13: warning: ‘__pyx_pf_5numpy_7ndarray___releasebuffer__’ defined but not used [-Wunused-function] 2021-07-08T19:42:14,908 4232 | static void __pyx_pf_5numpy_7ndarray___releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { 2021-07-08T19:42:14,909 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,911 nwalign.c:3569:12: warning: ‘__pyx_pf_5numpy_7ndarray___getbuffer__’ defined but not used [-Wunused-function] 2021-07-08T19:42:14,911 3569 | static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { 2021-07-08T19:42:14,912 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-08T19:42:14,912 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:21, 2021-07-08T19:42:14,912 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-08T19:42:14,912 from nwalign.c:133: 2021-07-08T19:42:14,913 /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] 2021-07-08T19:42:14,913 1464 | _import_array(void) 2021-07-08T19:42:14,913 | ^~~~~~~~~~~~~ 2021-07-08T19:42:14,918 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-08T19:42:15,031 Building wheel for nwalign (setup.py): finished with status 'error' 2021-07-08T19:42:15,031 ERROR: Failed building wheel for nwalign 2021-07-08T19:42:15,032 Running setup.py clean for nwalign 2021-07-08T19:42:15,032 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-0p2akz1q/nwalign_caac988e081d4d689c6f7775e660a9b2/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-0p2akz1q/nwalign_caac988e081d4d689c6f7775e660a9b2/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 2021-07-08T19:42:16,040 running clean 2021-07-08T19:42:16,042 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-08T19:42:16,043 'build/lib.linux-armv7l-3.9' does not exist -- can't clean it 2021-07-08T19:42:16,044 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-08T19:42:16,044 'build/scripts-3.9' does not exist -- can't clean it 2021-07-08T19:42:16,044 removing 'build' 2021-07-08T19:42:16,130 Failed to build nwalign 2021-07-08T19:42:16,130 ERROR: Failed to build one or more wheels 2021-07-08T19:42:16,131 Exception information: 2021-07-08T19:42:16,131 Traceback (most recent call last): 2021-07-08T19:42:16,131 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-08T19:42:16,131 status = self.run(options, args) 2021-07-08T19:42:16,131 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-08T19:42:16,131 return func(self, options, args) 2021-07-08T19:42:16,131 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-08T19:42:16,131 raise CommandError( 2021-07-08T19:42:16,131 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-08T19:42:16,134 Removed build tracker: '/tmp/pip-req-tracker-jre3yzl8'