2019-07-06T11:06:02 Created temporary directory: /tmp/pip-ephem-wheel-cache-67_zzamq 2019-07-06T11:06:02 Created temporary directory: /tmp/pip-req-tracker-bwqm2bog 2019-07-06T11:06:02 Created requirements tracker '/tmp/pip-req-tracker-bwqm2bog' 2019-07-06T11:06:02 Created temporary directory: /tmp/pip-wheel-tq_9685b 2019-07-06T11:06:02 Collecting libnano==0.1.1.3 2019-07-06T11:06:02 1 location(s) to search for versions of libnano: 2019-07-06T11:06:02 * https://pypi.org/simple/libnano/ 2019-07-06T11:06:02 Getting page https://pypi.org/simple/libnano/ 2019-07-06T11:06:02 Analyzing links from page https://pypi.org/simple/libnano/ 2019-07-06T11:06:02 Skipping link https://files.pythonhosted.org/packages/1c/56/4b638e208d676e55ed11418337d7732bf5930de7d3ca197ae4174e0e945d/libnano-0.1.1.1-cp36-cp36m-macosx_10_10_x86_64.whl#sha256=a1cb088527dfa29b558ac87f0fe738a8d261b6737a6d7a7e7afb17173998f205 (from https://pypi.org/simple/libnano/); it is not compatible with this Python 2019-07-06T11:06:02 Found link https://files.pythonhosted.org/packages/06/9a/7c0fec038abaa2fc52a0a0635b00e73bc689c0528670aa5b96ed9c0d2bab/libnano-0.1.1.1.tar.gz#sha256=352c4f908b61892b31cccf7b2b6c1e959708ac56b77c383376254ab402d749a1 (from https://pypi.org/simple/libnano/), version: 0.1.1.1 2019-07-06T11:06:02 Skipping link https://files.pythonhosted.org/packages/88/76/ad4de2d7f145b9fa66758481106b58d250a669559b917bc9b696b79c3a02/libnano-0.1.1.3-cp36-cp36m-macosx_10_10_x86_64.whl#sha256=8ebb6b0b1352048aa2f95b0035eac4ef14595fb153ab4712a899edaf0d197fe4 (from https://pypi.org/simple/libnano/); it is not compatible with this Python 2019-07-06T11:06:02 Skipping link https://files.pythonhosted.org/packages/84/ef/ec4e045c9cda34c249d509637fcb0c33b5b161ba37dd62e3e9d956ffc341/libnano-0.1.1.3-cp36-cp36m-win_amd64.whl#sha256=f273a5569a2f08214740b7663e22106e72b2ca3640b6a1e3ee9c20cef7733cc4 (from https://pypi.org/simple/libnano/); it is not compatible with this Python 2019-07-06T11:06:02 Found link https://files.pythonhosted.org/packages/f2/96/614dee55cbd312744bd02b60a877abda9ed52223070509cc9bd7a8a6f200/libnano-0.1.1.3.tar.gz#sha256=0884c16cc572086e56efc69f94a6402cbd3cc952c0beee19a435236223e5ac3f (from https://pypi.org/simple/libnano/), version: 0.1.1.3 2019-07-06T11:06:02 Skipping link https://files.pythonhosted.org/packages/bb/62/5647c7e6990de3c5ef2724c4021aa64e37318b058c44f86c0a22fc203255/libnano-0.2.0.0-cp36-cp36m-win_amd64.whl#sha256=ade8654471cfe4a394a54d898393b95b8d35285f3438467567c388fec2a1a772 (from https://pypi.org/simple/libnano/); it is not compatible with this Python 2019-07-06T11:06:02 Skipping link https://files.pythonhosted.org/packages/df/5e/3cb8809c58f2ab23b551364403b6129b32394ae051ac4469f8c3b93f5a01/libnano-0.2.1.0-cp36-cp36m-win_amd64.whl#sha256=82ac0541ff92863d606de28bd4fad0ec7684a95e953c52f2ece02f1ace7f2027 (from https://pypi.org/simple/libnano/); it is not compatible with this Python 2019-07-06T11:06:02 Skipping link https://files.pythonhosted.org/packages/17/c6/3b1ee948a1029affb74d1e82fc913d862495d000f23e1a7c560f6b779241/libnano-0.2.2.0-cp36-cp36m-macosx_10_10_x86_64.whl#sha256=298d937476ee93b625a77473b026d135ed364555997edc4f6675e9a344beb984 (from https://pypi.org/simple/libnano/); it is not compatible with this Python 2019-07-06T11:06:02 Skipping link https://files.pythonhosted.org/packages/a9/c3/88ee4c76805371457f731ccf572c37cea0d790cb9c093a4f154c52c4a3ac/libnano-0.2.2.0-cp36-cp36m-win_amd64.whl#sha256=4fc5e863d5fd0f97fb317274623c09746e3ee0f302e6f929de8b32ba5f45052b (from https://pypi.org/simple/libnano/); it is not compatible with this Python 2019-07-06T11:06:02 Found link https://files.pythonhosted.org/packages/01/52/3aaab3109334438c77d98bb9599e000fd690213a2a3149bfad6e8a868fb8/libnano-0.2.2.0.tar.gz#sha256=79b3260dc52380548d4ca0dda47af997d211e1ddaebd4df43cae38e0d885fd54 (from https://pypi.org/simple/libnano/), version: 0.2.2.0 2019-07-06T11:06:02 Skipping link https://files.pythonhosted.org/packages/cf/1b/c67c9cc92c58796895599d528bf04b76a0459f1c8b69f171feca2600ae14/libnano-0.2.3.0-cp36-cp36m-macosx_10_10_x86_64.whl#sha256=3b8f7a76b6e2870aeb14ef6fb2d2cd60cadf68dd7151ccaccadcf6e3cd7dfd10 (from https://pypi.org/simple/libnano/); it is not compatible with this Python 2019-07-06T11:06:02 Skipping link https://files.pythonhosted.org/packages/4a/fa/2ceace20e498c9d5f01e898a052f9da465cc138d9f6edcbecabadb207952/libnano-0.2.3.0-cp36-cp36m-win_amd64.whl#sha256=33d3f0628b19f5a79aa3fdee468c70a6385475431b14548a0b4f139ee0d5f412 (from https://pypi.org/simple/libnano/); it is not compatible with this Python 2019-07-06T11:06:02 Found link https://files.pythonhosted.org/packages/77/e6/49f98e4537b0a2531fa36ed9e45e272f3ea4ac99a154e10628011d68e647/libnano-0.2.3.0.tar.gz#sha256=0c36b41f3d362d781a9bd98a6382b95fadca0a7393889839d75fad01d2679bf6 (from https://pypi.org/simple/libnano/), version: 0.2.3.0 2019-07-06T11:06:02 Using version 0.1.1.3 (newest of versions: 0.1.1.3) 2019-07-06T11:06:02 Created temporary directory: /tmp/pip-unpack-bcm3wvb1 2019-07-06T11:06:02 Downloading https://files.pythonhosted.org/packages/f2/96/614dee55cbd312744bd02b60a877abda9ed52223070509cc9bd7a8a6f200/libnano-0.1.1.3.tar.gz (1.0MB) 2019-07-06T11:06:02 Downloading from URL https://files.pythonhosted.org/packages/f2/96/614dee55cbd312744bd02b60a877abda9ed52223070509cc9bd7a8a6f200/libnano-0.1.1.3.tar.gz#sha256=0884c16cc572086e56efc69f94a6402cbd3cc952c0beee19a435236223e5ac3f (from https://pypi.org/simple/libnano/) 2019-07-06T11:06:04 Added libnano==0.1.1.3 from https://files.pythonhosted.org/packages/f2/96/614dee55cbd312744bd02b60a877abda9ed52223070509cc9bd7a8a6f200/libnano-0.1.1.3.tar.gz#sha256=0884c16cc572086e56efc69f94a6402cbd3cc952c0beee19a435236223e5ac3f to build tracker '/tmp/pip-req-tracker-bwqm2bog' 2019-07-06T11:06:04 Running setup.py (path:/tmp/pip-wheel-tq_9685b/libnano/setup.py) egg_info for package libnano 2019-07-06T11:06:04 Running command python setup.py egg_info 2019-07-06T11:06:21 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-tq_9685b/libnano/libnano/core/seqgraph.pyx 2019-07-06T11:06:21 tree = Parsing.p_module(s, pxd, full_module_name) 2019-07-06T11:06:21 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-tq_9685b/libnano/libnano/core/seqint.pxd 2019-07-06T11:06:21 tree = Parsing.p_module(s, pxd, full_module_name) 2019-07-06T11:06:21 warning: libnano/core/seqint.pxd:13:22: Declarations should not be declared inline. 2019-07-06T11:06:21 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-tq_9685b/libnano/libnano/core/seqmetric/seqrepeat.pyx 2019-07-06T11:06:21 tree = Parsing.p_module(s, pxd, full_module_name) 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 cdef extern from "sr_seqrepeat.h": 2019-07-06T11:06:21 int sr_buildRepeatData(char* seq, 2019-07-06T11:06:21 int seq_length, 2019-07-06T11:06:21 int word_size, 2019-07-06T11:06:21 repeatcheck_t** rcheck) 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:20:27: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 cdef extern from "sr_seqrepeat.h": 2019-07-06T11:06:21 int sr_buildRepeatData(char* seq, 2019-07-06T11:06:21 int seq_length, 2019-07-06T11:06:21 int word_size, 2019-07-06T11:06:21 repeatcheck_t** rcheck) 2019-07-06T11:06:21 int sr_freeRepeatCheck(repeatcheck_t* rcheck) 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:21:27: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 int sr_buildRepeatData(char* seq, 2019-07-06T11:06:21 int seq_length, 2019-07-06T11:06:21 int word_size, 2019-07-06T11:06:21 repeatcheck_t** rcheck) 2019-07-06T11:06:21 int sr_freeRepeatCheck(repeatcheck_t* rcheck) 2019-07-06T11:06:21 int sr_queryRepeatIdx(repeatcheck_t* rcheck, 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:22:26: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 int sr_freeRepeatCheck(repeatcheck_t* rcheck) 2019-07-06T11:06:21 int sr_queryRepeatIdx(repeatcheck_t* rcheck, 2019-07-06T11:06:21 char* seq, 2019-07-06T11:06:21 char* query, 2019-07-06T11:06:21 int query_length) 2019-07-06T11:06:21 int sr_repeatWindow(repeatcheck_t* rcheck, 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:26:24: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 int PyTuple_SET_ITEM(PyObject *p, Py_ssize_t pos, PyObject *o) 2019-07-06T11:06:21 cdef class RepeatCheck: 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef repeatcheck_t *rcheck 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:43:9: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 sr_freeRepeatCheck(self.rcheck) 2019-07-06T11:06:21 PyMem_Free(self.rcheck) 2019-07-06T11:06:21 self.rcheck = NULL 2019-07-06T11:06:21 # end def 2019-07-06T11:06:21 cdef inline repeatcheck_t* data(RepeatCheck self): 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:86:16: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 seq_obj (str): string sequence 2019-07-06T11:06:21 word_size (int): the smallest considered repeat length 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef Py_ssize_t seq_length 2019-07-06T11:06:21 cdef char* seq = c_util.obj_to_cstr_len(seq_obj, &seq_length) 2019-07-06T11:06:21 cdef repeatcheck_t *rck = NULL 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:57:13: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 returns: object (list) of indices 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef Py_ssize_t query_length 2019-07-06T11:06:21 cdef char* query = c_util.obj_to_cstr_len(query_obj, &query_length) 2019-07-06T11:06:21 cdef repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:103:13: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 Returns: 2019-07-06T11:06:21 Tuple[bool, bool]: (True/False, True/False) whether the 5' or 3' end have 2019-07-06T11:06:21 repeats 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:130:13: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 length of the repeat at those indices of the form::: 2019-07-06T11:06:21 [(i, j, repeat length), ...] 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef int i, j, k, next_idx 2019-07-06T11:06:21 cdef repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:161:13: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 {key: [i, j, ...], 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 } 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef int z, i, j, k, next_idx 2019-07-06T11:06:21 cdef repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:198:13: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef: 2019-07-06T11:06:21 int violation_count = 0 2019-07-06T11:06:21 int* repeat_violation_idxs = NULL 2019-07-06T11:06:21 int* repeat_counts = NULL 2019-07-06T11:06:21 repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:291:12: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 Raises: 2019-07-06T11:06:21 IndexError 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef: 2019-07-06T11:06:21 repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:338:12: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 Returns: 2019-07-06T11:06:21 float: fraction in range [0, 1] 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef: 2019-07-06T11:06:21 repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:371:12: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 (index of max violation, max_fraction) ) 2019-07-06T11:06:21 Raises: 2019-07-06T11:06:21 ValueError 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef: 2019-07-06T11:06:21 repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:412:12: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 err = "word_size {} must be less than or equal to 32" 2019-07-06T11:06:21 raise ValueError(err.format(word_size)) 2019-07-06T11:06:21 if word_size > seq_length: 2019-07-06T11:06:21 err = "word_size {} must be less than or equal to seq_length {}" 2019-07-06T11:06:21 raise ValueError(err.format(word_size, seq_length)) 2019-07-06T11:06:21 rck = PyMem_Malloc(sizeof(repeatcheck_t)) 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:66:15: 'repeatcheck_t' is not a type identifier 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 err = "word_size {} must be less than or equal to 32" 2019-07-06T11:06:21 raise ValueError(err.format(word_size)) 2019-07-06T11:06:21 if word_size > seq_length: 2019-07-06T11:06:21 err = "word_size {} must be less than or equal to seq_length {}" 2019-07-06T11:06:21 raise ValueError(err.format(word_size, seq_length)) 2019-07-06T11:06:21 rck = PyMem_Malloc(sizeof(repeatcheck_t)) 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:66:64: undeclared name not builtin: repeatcheck_t 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 rck = PyMem_Malloc(sizeof(repeatcheck_t)) 2019-07-06T11:06:21 if rck == NULL: 2019-07-06T11:06:21 raise OSError("RepeatCheck_init: problem allocating repeatcheck_t") 2019-07-06T11:06:21 else: 2019-07-06T11:06:21 self.rcheck = rck 2019-07-06T11:06:21 rck.repeatroot_arr = NULL 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:71:33: Cannot convert 'void *' to Python object 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 if rck == NULL: 2019-07-06T11:06:21 raise OSError("RepeatCheck_init: problem allocating repeatcheck_t") 2019-07-06T11:06:21 else: 2019-07-06T11:06:21 self.rcheck = rck 2019-07-06T11:06:21 rck.repeatroot_arr = NULL 2019-07-06T11:06:21 rck.repeat_idx_arr = NULL 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:72:33: Cannot convert 'void *' to Python object 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef Py_ssize_t query_length 2019-07-06T11:06:21 cdef char* query = c_util.obj_to_cstr_len(query_obj, &query_length) 2019-07-06T11:06:21 cdef repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 cdef int idx = sr_queryRepeatIdx(rcheck, self.seq, query, query_length) 2019-07-06T11:06:21 cdef int* arr_query = rcheck.repeat_idx_arr 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:105:36: Cannot convert Python object to 'int *' 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 Returns: 2019-07-06T11:06:21 Tuple[bool, bool]: (True/False, True/False) whether the 5' or 3' end have 2019-07-06T11:06:21 repeats 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 cdef int* arr_query = rcheck.repeat_idx_arr 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:131:36: Cannot convert Python object to 'int *' 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 [(i, j, repeat length), ...] 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef int i, j, k, next_idx 2019-07-06T11:06:21 cdef repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 cdef int word_size = rcheck.word_size 2019-07-06T11:06:21 cdef int* query_arr = rcheck.repeat_idx_arr 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:163:36: Cannot convert Python object to 'int *' 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 } 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef int z, i, j, k, next_idx 2019-07-06T11:06:21 cdef repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 cdef int word_size = rcheck.word_size 2019-07-06T11:06:21 cdef int* query_arr = rcheck.repeat_idx_arr 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:200:36: Cannot convert Python object to 'int *' 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 Raises: 2019-07-06T11:06:21 IndexError 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef: 2019-07-06T11:06:21 repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 int *repeat_idx_array = rcheck.repeat_idx_arr 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:339:42: Cannot convert Python object to 'int *' 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 Returns: 2019-07-06T11:06:21 float: fraction in range [0, 1] 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef: 2019-07-06T11:06:21 repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 int* repeat_idx_array = rcheck.repeat_idx_arr 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:372:42: Cannot convert Python object to 'int *' 2019-07-06T11:06:21 Error compiling Cython file: 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 ... 2019-07-06T11:06:21 Raises: 2019-07-06T11:06:21 ValueError 2019-07-06T11:06:21 """ 2019-07-06T11:06:21 cdef: 2019-07-06T11:06:21 repeatcheck_t* rcheck = self.rcheck 2019-07-06T11:06:21 int* repeat_idx_array = rcheck.repeat_idx_arr 2019-07-06T11:06:21 ^ 2019-07-06T11:06:21 ------------------------------------------------------------ 2019-07-06T11:06:21 libnano/core/seqmetric/seqrepeat.pyx:413:42: Cannot convert Python object to 'int *' 2019-07-06T11:06:21 Traceback (most recent call last): 2019-07-06T11:06:21 File "", line 1, in 2019-07-06T11:06:21 File "/tmp/pip-wheel-tq_9685b/libnano/setup.py", line 290, in 2019-07-06T11:06:21 cython_ext_list = cythonize(cython_extensions) 2019-07-06T11:06:21 File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", line 1097, in cythonize 2019-07-06T11:06:21 cythonize_one(*args) 2019-07-06T11:06:21 File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", line 1220, in cythonize_one 2019-07-06T11:06:21 raise CompileError(None, pyx_file) 2019-07-06T11:06:21 Cython.Compiler.Errors.CompileError: libnano/core/seqmetric/seqrepeat.pyx 2019-07-06T11:06:21 Compiling libnano/core/seqmetric/seqrepeat.pyx because it depends on /usr/lib/python3/dist-packages/Cython/Includes/numpy/__init__.pxd. 2019-07-06T11:06:21 Compiling libnano/cymem/cymem.pyx because it depends on /usr/lib/python3/dist-packages/Cython/Includes/cpython/mem.pxd. 2019-07-06T11:06:21 Compiling libnano/core/seqsearch/seedmatch.pyx because it depends on /usr/lib/python3/dist-packages/Cython/Includes/cpython/object.pxd. 2019-07-06T11:06:21 Compiling libnano/core/seqint.pyx because it depends on /usr/lib/python3/dist-packages/Cython/Includes/cpython/mem.pxd. 2019-07-06T11:06:21 Compiling libnano/core/seqstr.pyx because it depends on /usr/lib/python3/dist-packages/Cython/Includes/numpy/__init__.pxd. 2019-07-06T11:06:21 Compiling libnano/core/seqgraph.pyx because it depends on /usr/lib/python3/dist-packages/Cython/Includes/numpy/__init__.pxd. 2019-07-06T11:06:21 Compiling libnano/core/seqmetric/seqmetric.pyx because it depends on /usr/lib/python3/dist-packages/Cython/Includes/cpython/pystate.pxd. 2019-07-06T11:06:21 Compiling libnano/datastructures/seqrecord/feature.pyx because it depends on /usr/lib/python3/dist-packages/Cython/Includes/cpython/object.pxd. 2019-07-06T11:06:21 Compiling libnano/datastructures/seqrecord/seqrecordbase.pyx because it depends on /usr/lib/python3/dist-packages/Cython/Includes/cpython/object.pxd. 2019-07-06T11:06:21 [1/9] Cythonizing libnano/core/seqgraph.pyx 2019-07-06T11:06:21 [2/9] Cythonizing libnano/core/seqint.pyx 2019-07-06T11:06:21 [3/9] Cythonizing libnano/core/seqmetric/seqrepeat.pyx 2019-07-06T11:06:22 Cleaning up... 2019-07-06T11:06:22 Removing source in /tmp/pip-wheel-tq_9685b/libnano 2019-07-06T11:06:22 Removed libnano==0.1.1.3 from https://files.pythonhosted.org/packages/f2/96/614dee55cbd312744bd02b60a877abda9ed52223070509cc9bd7a8a6f200/libnano-0.1.1.3.tar.gz#sha256=0884c16cc572086e56efc69f94a6402cbd3cc952c0beee19a435236223e5ac3f from build tracker '/tmp/pip-req-tracker-bwqm2bog' 2019-07-06T11:06:22 Removed build tracker '/tmp/pip-req-tracker-bwqm2bog' 2019-07-06T11:06:22 ERROR: Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-wheel-tq_9685b/libnano/ 2019-07-06T11:06:22 Exception information: 2019-07-06T11:06:22 Traceback (most recent call last): 2019-07-06T11:06:22 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 178, in main 2019-07-06T11:06:22 status = self.run(options, args) 2019-07-06T11:06:22 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/commands/wheel.py", line 164, in run 2019-07-06T11:06:22 resolver.resolve(requirement_set) 2019-07-06T11:06:22 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/resolve.py", line 131, in resolve 2019-07-06T11:06:22 self._resolve_one(requirement_set, req) 2019-07-06T11:06:22 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/resolve.py", line 294, in _resolve_one 2019-07-06T11:06:22 abstract_dist = self._get_abstract_dist_for(req_to_install) 2019-07-06T11:06:22 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/resolve.py", line 242, in _get_abstract_dist_for 2019-07-06T11:06:22 self.require_hashes 2019-07-06T11:06:22 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 362, in prepare_linked_requirement 2019-07-06T11:06:22 abstract_dist.prep_for_dist(finder, self.build_isolation) 2019-07-06T11:06:22 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/operations/prepare.py", line 171, in prep_for_dist 2019-07-06T11:06:22 self.req.prepare_metadata() 2019-07-06T11:06:22 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 537, in prepare_metadata 2019-07-06T11:06:22 self.run_egg_info() 2019-07-06T11:06:22 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 615, in run_egg_info 2019-07-06T11:06:22 command_desc='python setup.py egg_info') 2019-07-06T11:06:22 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/utils/misc.py", line 776, in call_subprocess 2019-07-06T11:06:22 % (command_desc, proc.returncode, cwd)) 2019-07-06T11:06:22 pip._internal.exceptions.InstallationError: Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-wheel-tq_9685b/libnano/