2021-07-12T23:01:09,476 Created temporary directory: /tmp/pip-ephem-wheel-cache-znelesiq 2021-07-12T23:01:09,478 Created temporary directory: /tmp/pip-req-tracker-xqplvx2z 2021-07-12T23:01:09,479 Initialized build tracking at /tmp/pip-req-tracker-xqplvx2z 2021-07-12T23:01:09,479 Created build tracker: /tmp/pip-req-tracker-xqplvx2z 2021-07-12T23:01:09,479 Entered build tracker: /tmp/pip-req-tracker-xqplvx2z 2021-07-12T23:01:09,480 Created temporary directory: /tmp/pip-wheel-4t7txk62 2021-07-12T23:01:09,508 1 location(s) to search for versions of libnano: 2021-07-12T23:01:09,508 * https://pypi.org/simple/libnano/ 2021-07-12T23:01:09,509 Fetching project page and analyzing links: https://pypi.org/simple/libnano/ 2021-07-12T23:01:09,509 Getting page https://pypi.org/simple/libnano/ 2021-07-12T23:01:09,511 Found index url https://pypi.org/simple 2021-07-12T23:01:09,621 Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_10_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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/) 2021-07-12T23:01:09,622 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 2021-07-12T23:01:09,622 Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_10_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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/) 2021-07-12T23:01:09,623 Skipping link: none of the wheel's tags (cp36-cp36m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): 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/) 2021-07-12T23:01:09,623 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 2021-07-12T23:01:09,624 Skipping link: none of the wheel's tags (cp36-cp36m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): 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/) 2021-07-12T23:01:09,624 Skipping link: none of the wheel's tags (cp36-cp36m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): 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/) 2021-07-12T23:01:09,624 Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_10_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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/) 2021-07-12T23:01:09,625 Skipping link: none of the wheel's tags (cp36-cp36m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): 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/) 2021-07-12T23:01:09,625 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 2021-07-12T23:01:09,626 Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_10_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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/) 2021-07-12T23:01:09,626 Skipping link: none of the wheel's tags (cp36-cp36m-win_amd64) are compatible (run pip debug --verbose to show compatible tags): 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/) 2021-07-12T23:01:09,626 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 2021-07-12T23:01:09,627 Skipping link: not a file: https://pypi.org/simple/libnano/ 2021-07-12T23:01:09,628 Given no hashes to check 1 links for project 'libnano': discarding no candidates 2021-07-12T23:01:09,647 Collecting libnano==0.1.1.3 2021-07-12T23:01:09,648 Created temporary directory: /tmp/pip-unpack-8jg23cnr 2021-07-12T23:01:10,326 Downloading libnano-0.1.1.3.tar.gz (1.0 MB) 2021-07-12T23:01:11,000 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-xqplvx2z' 2021-07-12T23:01:11,001 Running setup.py (path:/tmp/pip-wheel-4t7txk62/libnano_ff4d2faacbf84477a0659d787f985b4f/setup.py) egg_info for package libnano 2021-07-12T23:01:11,002 Created temporary directory: /tmp/pip-pip-egg-info-96ys8ott 2021-07-12T23:01:11,002 Running command python setup.py egg_info 2021-07-12T23:01:13,242 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-4t7txk62/libnano_ff4d2faacbf84477a0659d787f985b4f/libnano/core/seqint.pxd 2021-07-12T23:01:13,243 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T23:01:13,263 warning: libnano/core/seqint.pxd:13:22: Declarations should not be declared inline. 2021-07-12T23:01:14,307 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-4t7txk62/libnano_ff4d2faacbf84477a0659d787f985b4f/libnano/core/seqmetric/seqrepeat.pyx 2021-07-12T23:01:14,307 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T23:01:16,136 Error compiling Cython file: 2021-07-12T23:01:16,136 ------------------------------------------------------------ 2021-07-12T23:01:16,137 ... 2021-07-12T23:01:16,137 cdef extern from "sr_seqrepeat.h": 2021-07-12T23:01:16,137 int sr_buildRepeatData(char* seq, 2021-07-12T23:01:16,137 int seq_length, 2021-07-12T23:01:16,137 int word_size, 2021-07-12T23:01:16,137 repeatcheck_t** rcheck) 2021-07-12T23:01:16,138 ^ 2021-07-12T23:01:16,138 ------------------------------------------------------------ 2021-07-12T23:01:16,138 libnano/core/seqmetric/seqrepeat.pyx:20:27: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,138 Error compiling Cython file: 2021-07-12T23:01:16,138 ------------------------------------------------------------ 2021-07-12T23:01:16,138 ... 2021-07-12T23:01:16,139 cdef extern from "sr_seqrepeat.h": 2021-07-12T23:01:16,139 int sr_buildRepeatData(char* seq, 2021-07-12T23:01:16,139 int seq_length, 2021-07-12T23:01:16,139 int word_size, 2021-07-12T23:01:16,139 repeatcheck_t** rcheck) 2021-07-12T23:01:16,139 int sr_freeRepeatCheck(repeatcheck_t* rcheck) 2021-07-12T23:01:16,139 ^ 2021-07-12T23:01:16,139 ------------------------------------------------------------ 2021-07-12T23:01:16,140 libnano/core/seqmetric/seqrepeat.pyx:21:27: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,140 Error compiling Cython file: 2021-07-12T23:01:16,140 ------------------------------------------------------------ 2021-07-12T23:01:16,140 ... 2021-07-12T23:01:16,140 int sr_buildRepeatData(char* seq, 2021-07-12T23:01:16,140 int seq_length, 2021-07-12T23:01:16,140 int word_size, 2021-07-12T23:01:16,141 repeatcheck_t** rcheck) 2021-07-12T23:01:16,141 int sr_freeRepeatCheck(repeatcheck_t* rcheck) 2021-07-12T23:01:16,141 int sr_queryRepeatIdx(repeatcheck_t* rcheck, 2021-07-12T23:01:16,141 ^ 2021-07-12T23:01:16,141 ------------------------------------------------------------ 2021-07-12T23:01:16,141 libnano/core/seqmetric/seqrepeat.pyx:22:26: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,142 Error compiling Cython file: 2021-07-12T23:01:16,142 ------------------------------------------------------------ 2021-07-12T23:01:16,142 ... 2021-07-12T23:01:16,142 int sr_freeRepeatCheck(repeatcheck_t* rcheck) 2021-07-12T23:01:16,142 int sr_queryRepeatIdx(repeatcheck_t* rcheck, 2021-07-12T23:01:16,142 char* seq, 2021-07-12T23:01:16,142 char* query, 2021-07-12T23:01:16,142 int query_length) 2021-07-12T23:01:16,142 int sr_repeatWindow(repeatcheck_t* rcheck, 2021-07-12T23:01:16,143 ^ 2021-07-12T23:01:16,143 ------------------------------------------------------------ 2021-07-12T23:01:16,143 libnano/core/seqmetric/seqrepeat.pyx:26:24: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,143 Error compiling Cython file: 2021-07-12T23:01:16,143 ------------------------------------------------------------ 2021-07-12T23:01:16,143 ... 2021-07-12T23:01:16,143 int PyTuple_SET_ITEM(PyObject *p, Py_ssize_t pos, PyObject *o) 2021-07-12T23:01:16,144 cdef class RepeatCheck: 2021-07-12T23:01:16,144 """ 2021-07-12T23:01:16,144 """ 2021-07-12T23:01:16,144 cdef repeatcheck_t *rcheck 2021-07-12T23:01:16,144 ^ 2021-07-12T23:01:16,144 ------------------------------------------------------------ 2021-07-12T23:01:16,144 libnano/core/seqmetric/seqrepeat.pyx:43:9: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,145 Error compiling Cython file: 2021-07-12T23:01:16,145 ------------------------------------------------------------ 2021-07-12T23:01:16,145 ... 2021-07-12T23:01:16,145 sr_freeRepeatCheck(self.rcheck) 2021-07-12T23:01:16,145 PyMem_Free(self.rcheck) 2021-07-12T23:01:16,145 self.rcheck = NULL 2021-07-12T23:01:16,145 # end def 2021-07-12T23:01:16,146 cdef inline repeatcheck_t* data(RepeatCheck self): 2021-07-12T23:01:16,146 ^ 2021-07-12T23:01:16,146 ------------------------------------------------------------ 2021-07-12T23:01:16,146 libnano/core/seqmetric/seqrepeat.pyx:86:16: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,146 Error compiling Cython file: 2021-07-12T23:01:16,146 ------------------------------------------------------------ 2021-07-12T23:01:16,147 ... 2021-07-12T23:01:16,147 seq_obj (str): string sequence 2021-07-12T23:01:16,147 word_size (int): the smallest considered repeat length 2021-07-12T23:01:16,147 """ 2021-07-12T23:01:16,147 cdef Py_ssize_t seq_length 2021-07-12T23:01:16,147 cdef char* seq = c_util.obj_to_cstr_len(seq_obj, &seq_length) 2021-07-12T23:01:16,147 cdef repeatcheck_t *rck = NULL 2021-07-12T23:01:16,147 ^ 2021-07-12T23:01:16,147 ------------------------------------------------------------ 2021-07-12T23:01:16,148 libnano/core/seqmetric/seqrepeat.pyx:57:13: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,148 Error compiling Cython file: 2021-07-12T23:01:16,148 ------------------------------------------------------------ 2021-07-12T23:01:16,148 ... 2021-07-12T23:01:16,148 returns: object (list) of indices 2021-07-12T23:01:16,149 """ 2021-07-12T23:01:16,149 cdef Py_ssize_t query_length 2021-07-12T23:01:16,149 cdef char* query = c_util.obj_to_cstr_len(query_obj, &query_length) 2021-07-12T23:01:16,149 cdef repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,149 ^ 2021-07-12T23:01:16,149 ------------------------------------------------------------ 2021-07-12T23:01:16,149 libnano/core/seqmetric/seqrepeat.pyx:103:13: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,150 Error compiling Cython file: 2021-07-12T23:01:16,150 ------------------------------------------------------------ 2021-07-12T23:01:16,150 ... 2021-07-12T23:01:16,150 Returns: 2021-07-12T23:01:16,150 Tuple[bool, bool]: (True/False, True/False) whether the 5' or 3' end have 2021-07-12T23:01:16,150 repeats 2021-07-12T23:01:16,150 """ 2021-07-12T23:01:16,151 cdef repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,151 ^ 2021-07-12T23:01:16,151 ------------------------------------------------------------ 2021-07-12T23:01:16,151 libnano/core/seqmetric/seqrepeat.pyx:130:13: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,151 Error compiling Cython file: 2021-07-12T23:01:16,151 ------------------------------------------------------------ 2021-07-12T23:01:16,151 ... 2021-07-12T23:01:16,152 length of the repeat at those indices of the form::: 2021-07-12T23:01:16,152 [(i, j, repeat length), ...] 2021-07-12T23:01:16,152 """ 2021-07-12T23:01:16,152 cdef int i, j, k, next_idx 2021-07-12T23:01:16,152 cdef repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,152 ^ 2021-07-12T23:01:16,152 ------------------------------------------------------------ 2021-07-12T23:01:16,153 libnano/core/seqmetric/seqrepeat.pyx:161:13: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,153 Error compiling Cython file: 2021-07-12T23:01:16,153 ------------------------------------------------------------ 2021-07-12T23:01:16,153 ... 2021-07-12T23:01:16,153 {key: [i, j, ...], 2021-07-12T23:01:16,153 ... 2021-07-12T23:01:16,153 } 2021-07-12T23:01:16,153 """ 2021-07-12T23:01:16,154 cdef int z, i, j, k, next_idx 2021-07-12T23:01:16,154 cdef repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,154 ^ 2021-07-12T23:01:16,154 ------------------------------------------------------------ 2021-07-12T23:01:16,154 libnano/core/seqmetric/seqrepeat.pyx:198:13: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,159 Error compiling Cython file: 2021-07-12T23:01:16,159 ------------------------------------------------------------ 2021-07-12T23:01:16,159 ... 2021-07-12T23:01:16,159 """ 2021-07-12T23:01:16,159 cdef: 2021-07-12T23:01:16,159 int violation_count = 0 2021-07-12T23:01:16,159 int* repeat_violation_idxs = NULL 2021-07-12T23:01:16,160 int* repeat_counts = NULL 2021-07-12T23:01:16,160 repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,160 ^ 2021-07-12T23:01:16,160 ------------------------------------------------------------ 2021-07-12T23:01:16,160 libnano/core/seqmetric/seqrepeat.pyx:291:12: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,163 Error compiling Cython file: 2021-07-12T23:01:16,163 ------------------------------------------------------------ 2021-07-12T23:01:16,163 ... 2021-07-12T23:01:16,163 Raises: 2021-07-12T23:01:16,163 IndexError 2021-07-12T23:01:16,163 """ 2021-07-12T23:01:16,163 cdef: 2021-07-12T23:01:16,163 repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,164 ^ 2021-07-12T23:01:16,164 ------------------------------------------------------------ 2021-07-12T23:01:16,164 libnano/core/seqmetric/seqrepeat.pyx:338:12: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,165 Error compiling Cython file: 2021-07-12T23:01:16,165 ------------------------------------------------------------ 2021-07-12T23:01:16,165 ... 2021-07-12T23:01:16,165 Returns: 2021-07-12T23:01:16,166 float: fraction in range [0, 1] 2021-07-12T23:01:16,166 """ 2021-07-12T23:01:16,166 cdef: 2021-07-12T23:01:16,166 repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,166 ^ 2021-07-12T23:01:16,166 ------------------------------------------------------------ 2021-07-12T23:01:16,166 libnano/core/seqmetric/seqrepeat.pyx:371:12: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,168 Error compiling Cython file: 2021-07-12T23:01:16,168 ------------------------------------------------------------ 2021-07-12T23:01:16,168 ... 2021-07-12T23:01:16,168 (index of max violation, max_fraction) ) 2021-07-12T23:01:16,168 Raises: 2021-07-12T23:01:16,168 ValueError 2021-07-12T23:01:16,168 """ 2021-07-12T23:01:16,168 cdef: 2021-07-12T23:01:16,168 repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,169 ^ 2021-07-12T23:01:16,169 ------------------------------------------------------------ 2021-07-12T23:01:16,169 libnano/core/seqmetric/seqrepeat.pyx:412:12: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,313 Error compiling Cython file: 2021-07-12T23:01:16,313 ------------------------------------------------------------ 2021-07-12T23:01:16,313 ... 2021-07-12T23:01:16,313 err = "word_size {} must be less than or equal to 32" 2021-07-12T23:01:16,314 raise ValueError(err.format(word_size)) 2021-07-12T23:01:16,314 if word_size > seq_length: 2021-07-12T23:01:16,314 err = "word_size {} must be less than or equal to seq_length {}" 2021-07-12T23:01:16,314 raise ValueError(err.format(word_size, seq_length)) 2021-07-12T23:01:16,314 rck = PyMem_Malloc(sizeof(repeatcheck_t)) 2021-07-12T23:01:16,314 ^ 2021-07-12T23:01:16,314 ------------------------------------------------------------ 2021-07-12T23:01:16,314 libnano/core/seqmetric/seqrepeat.pyx:66:15: 'repeatcheck_t' is not a type identifier 2021-07-12T23:01:16,315 Error compiling Cython file: 2021-07-12T23:01:16,315 ------------------------------------------------------------ 2021-07-12T23:01:16,315 ... 2021-07-12T23:01:16,315 err = "word_size {} must be less than or equal to 32" 2021-07-12T23:01:16,315 raise ValueError(err.format(word_size)) 2021-07-12T23:01:16,315 if word_size > seq_length: 2021-07-12T23:01:16,315 err = "word_size {} must be less than or equal to seq_length {}" 2021-07-12T23:01:16,316 raise ValueError(err.format(word_size, seq_length)) 2021-07-12T23:01:16,316 rck = PyMem_Malloc(sizeof(repeatcheck_t)) 2021-07-12T23:01:16,316 ^ 2021-07-12T23:01:16,316 ------------------------------------------------------------ 2021-07-12T23:01:16,316 libnano/core/seqmetric/seqrepeat.pyx:66:64: undeclared name not builtin: repeatcheck_t 2021-07-12T23:01:16,316 Error compiling Cython file: 2021-07-12T23:01:16,316 ------------------------------------------------------------ 2021-07-12T23:01:16,317 ... 2021-07-12T23:01:16,317 rck = PyMem_Malloc(sizeof(repeatcheck_t)) 2021-07-12T23:01:16,317 if rck == NULL: 2021-07-12T23:01:16,317 raise OSError("RepeatCheck_init: problem allocating repeatcheck_t") 2021-07-12T23:01:16,317 else: 2021-07-12T23:01:16,317 self.rcheck = rck 2021-07-12T23:01:16,317 rck.repeatroot_arr = NULL 2021-07-12T23:01:16,317 ^ 2021-07-12T23:01:16,317 ------------------------------------------------------------ 2021-07-12T23:01:16,318 libnano/core/seqmetric/seqrepeat.pyx:71:33: Cannot convert 'void *' to Python object 2021-07-12T23:01:16,318 Error compiling Cython file: 2021-07-12T23:01:16,318 ------------------------------------------------------------ 2021-07-12T23:01:16,318 ... 2021-07-12T23:01:16,318 if rck == NULL: 2021-07-12T23:01:16,318 raise OSError("RepeatCheck_init: problem allocating repeatcheck_t") 2021-07-12T23:01:16,318 else: 2021-07-12T23:01:16,319 self.rcheck = rck 2021-07-12T23:01:16,319 rck.repeatroot_arr = NULL 2021-07-12T23:01:16,319 rck.repeat_idx_arr = NULL 2021-07-12T23:01:16,319 ^ 2021-07-12T23:01:16,319 ------------------------------------------------------------ 2021-07-12T23:01:16,319 libnano/core/seqmetric/seqrepeat.pyx:72:33: Cannot convert 'void *' to Python object 2021-07-12T23:01:16,320 Error compiling Cython file: 2021-07-12T23:01:16,320 ------------------------------------------------------------ 2021-07-12T23:01:16,320 ... 2021-07-12T23:01:16,320 """ 2021-07-12T23:01:16,320 cdef Py_ssize_t query_length 2021-07-12T23:01:16,320 cdef char* query = c_util.obj_to_cstr_len(query_obj, &query_length) 2021-07-12T23:01:16,320 cdef repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,320 cdef int idx = sr_queryRepeatIdx(rcheck, self.seq, query, query_length) 2021-07-12T23:01:16,320 cdef int* arr_query = rcheck.repeat_idx_arr 2021-07-12T23:01:16,321 ^ 2021-07-12T23:01:16,321 ------------------------------------------------------------ 2021-07-12T23:01:16,321 libnano/core/seqmetric/seqrepeat.pyx:105:36: Cannot convert Python object to 'int *' 2021-07-12T23:01:16,322 Error compiling Cython file: 2021-07-12T23:01:16,323 ------------------------------------------------------------ 2021-07-12T23:01:16,323 ... 2021-07-12T23:01:16,323 Returns: 2021-07-12T23:01:16,323 Tuple[bool, bool]: (True/False, True/False) whether the 5' or 3' end have 2021-07-12T23:01:16,323 repeats 2021-07-12T23:01:16,323 """ 2021-07-12T23:01:16,323 cdef repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,323 cdef int* arr_query = rcheck.repeat_idx_arr 2021-07-12T23:01:16,323 ^ 2021-07-12T23:01:16,324 ------------------------------------------------------------ 2021-07-12T23:01:16,324 libnano/core/seqmetric/seqrepeat.pyx:131:36: Cannot convert Python object to 'int *' 2021-07-12T23:01:16,327 Error compiling Cython file: 2021-07-12T23:01:16,328 ------------------------------------------------------------ 2021-07-12T23:01:16,328 ... 2021-07-12T23:01:16,328 [(i, j, repeat length), ...] 2021-07-12T23:01:16,328 """ 2021-07-12T23:01:16,328 cdef int i, j, k, next_idx 2021-07-12T23:01:16,328 cdef repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,328 cdef int word_size = rcheck.word_size 2021-07-12T23:01:16,328 cdef int* query_arr = rcheck.repeat_idx_arr 2021-07-12T23:01:16,328 ^ 2021-07-12T23:01:16,329 ------------------------------------------------------------ 2021-07-12T23:01:16,329 libnano/core/seqmetric/seqrepeat.pyx:163:36: Cannot convert Python object to 'int *' 2021-07-12T23:01:16,333 Error compiling Cython file: 2021-07-12T23:01:16,334 ------------------------------------------------------------ 2021-07-12T23:01:16,334 ... 2021-07-12T23:01:16,334 } 2021-07-12T23:01:16,334 """ 2021-07-12T23:01:16,334 cdef int z, i, j, k, next_idx 2021-07-12T23:01:16,334 cdef repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,334 cdef int word_size = rcheck.word_size 2021-07-12T23:01:16,334 cdef int* query_arr = rcheck.repeat_idx_arr 2021-07-12T23:01:16,334 ^ 2021-07-12T23:01:16,335 ------------------------------------------------------------ 2021-07-12T23:01:16,335 libnano/core/seqmetric/seqrepeat.pyx:200:36: Cannot convert Python object to 'int *' 2021-07-12T23:01:16,365 Error compiling Cython file: 2021-07-12T23:01:16,366 ------------------------------------------------------------ 2021-07-12T23:01:16,366 ... 2021-07-12T23:01:16,366 Raises: 2021-07-12T23:01:16,366 IndexError 2021-07-12T23:01:16,366 """ 2021-07-12T23:01:16,366 cdef: 2021-07-12T23:01:16,366 repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,366 int *repeat_idx_array = rcheck.repeat_idx_arr 2021-07-12T23:01:16,366 ^ 2021-07-12T23:01:16,367 ------------------------------------------------------------ 2021-07-12T23:01:16,367 libnano/core/seqmetric/seqrepeat.pyx:339:42: Cannot convert Python object to 'int *' 2021-07-12T23:01:16,373 Error compiling Cython file: 2021-07-12T23:01:16,373 ------------------------------------------------------------ 2021-07-12T23:01:16,373 ... 2021-07-12T23:01:16,373 Returns: 2021-07-12T23:01:16,373 float: fraction in range [0, 1] 2021-07-12T23:01:16,373 """ 2021-07-12T23:01:16,373 cdef: 2021-07-12T23:01:16,374 repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,374 int* repeat_idx_array = rcheck.repeat_idx_arr 2021-07-12T23:01:16,374 ^ 2021-07-12T23:01:16,374 ------------------------------------------------------------ 2021-07-12T23:01:16,374 libnano/core/seqmetric/seqrepeat.pyx:372:42: Cannot convert Python object to 'int *' 2021-07-12T23:01:16,378 Error compiling Cython file: 2021-07-12T23:01:16,379 ------------------------------------------------------------ 2021-07-12T23:01:16,379 ... 2021-07-12T23:01:16,379 Raises: 2021-07-12T23:01:16,379 ValueError 2021-07-12T23:01:16,379 """ 2021-07-12T23:01:16,379 cdef: 2021-07-12T23:01:16,379 repeatcheck_t* rcheck = self.rcheck 2021-07-12T23:01:16,379 int* repeat_idx_array = rcheck.repeat_idx_arr 2021-07-12T23:01:16,380 ^ 2021-07-12T23:01:16,380 ------------------------------------------------------------ 2021-07-12T23:01:16,380 libnano/core/seqmetric/seqrepeat.pyx:413:42: Cannot convert Python object to 'int *' 2021-07-12T23:01:16,576 Traceback (most recent call last): 2021-07-12T23:01:16,577 File "", line 1, in 2021-07-12T23:01:16,577 File "/tmp/pip-wheel-4t7txk62/libnano_ff4d2faacbf84477a0659d787f985b4f/setup.py", line 290, in 2021-07-12T23:01:16,577 cython_ext_list = cythonize(cython_extensions) 2021-07-12T23:01:16,578 File "/usr/local/lib/python3.9/dist-packages/Cython/Build/Dependencies.py", line 1102, in cythonize 2021-07-12T23:01:16,579 cythonize_one(*args) 2021-07-12T23:01:16,579 File "/usr/local/lib/python3.9/dist-packages/Cython/Build/Dependencies.py", line 1225, in cythonize_one 2021-07-12T23:01:16,580 raise CompileError(None, pyx_file) 2021-07-12T23:01:16,580 Cython.Compiler.Errors.CompileError: libnano/core/seqmetric/seqrepeat.pyx 2021-07-12T23:01:16,580 Compiling libnano/core/seqmetric/seqrepeat.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T23:01:16,580 Compiling libnano/cymem/cymem.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T23:01:16,581 Compiling libnano/core/seqsearch/seedmatch.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T23:01:16,581 Compiling libnano/core/seqint.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/cpython/mem.pxd. 2021-07-12T23:01:16,581 Compiling libnano/core/seqstr.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T23:01:16,581 Compiling libnano/core/seqgraph.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T23:01:16,581 Compiling libnano/core/seqmetric/seqmetric.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T23:01:16,582 Compiling libnano/datastructures/seqrecord/feature.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T23:01:16,582 Compiling libnano/datastructures/seqrecord/seqrecordbase.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-12T23:01:16,582 [1/9] Cythonizing libnano/core/seqint.pyx 2021-07-12T23:01:16,582 [2/9] Cythonizing libnano/core/seqmetric/seqrepeat.pyx 2021-07-12T23:01:16,802 WARNING: Discarding https://files.pythonhosted.org/packages/f2/96/614dee55cbd312744bd02b60a877abda9ed52223070509cc9bd7a8a6f200/libnano-0.1.1.3.tar.gz#sha256=0884c16cc572086e56efc69f94a6402cbd3cc952c0beee19a435236223e5ac3f (from https://pypi.org/simple/libnano/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. 2021-07-12T23:01:16,803 ERROR: Could not find a version that satisfies the requirement libnano==0.1.1.3 (from versions: 0.1.1.1, 0.1.1.3, 0.2.2.0, 0.2.3.0) 2021-07-12T23:01:16,804 ERROR: No matching distribution found for libnano==0.1.1.3 2021-07-12T23:01:16,804 Exception information: 2021-07-12T23:01:16,804 Traceback (most recent call last): 2021-07-12T23:01:16,804 File "/usr/local/lib/python3.9/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 341, in resolve 2021-07-12T23:01:16,804 name, crit = self._merge_into_criterion(r, parent=None) 2021-07-12T23:01:16,804 File "/usr/local/lib/python3.9/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _merge_into_criterion 2021-07-12T23:01:16,804 raise RequirementsConflicted(criterion) 2021-07-12T23:01:16,804 pip._vendor.resolvelib.resolvers.RequirementsConflicted: Requirements conflict: SpecifierRequirement('libnano==0.1.1.3') 2021-07-12T23:01:16,804 2021-07-12T23:01:16,804 During handling of the above exception, another exception occurred: 2021-07-12T23:01:16,804 2021-07-12T23:01:16,804 Traceback (most recent call last): 2021-07-12T23:01:16,804 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 127, in resolve 2021-07-12T23:01:16,804 result = self._result = resolver.resolve( 2021-07-12T23:01:16,804 File "/usr/local/lib/python3.9/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 473, in resolve 2021-07-12T23:01:16,804 state = resolution.resolve(requirements, max_rounds=max_rounds) 2021-07-12T23:01:16,804 File "/usr/local/lib/python3.9/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 343, in resolve 2021-07-12T23:01:16,804 raise ResolutionImpossible(e.criterion.information) 2021-07-12T23:01:16,804 pip._vendor.resolvelib.resolvers.ResolutionImpossible: [RequirementInformation(requirement=SpecifierRequirement('libnano==0.1.1.3'), parent=None)] 2021-07-12T23:01:16,804 2021-07-12T23:01:16,804 The above exception was the direct cause of the following exception: 2021-07-12T23:01:16,804 2021-07-12T23:01:16,804 Traceback (most recent call last): 2021-07-12T23:01:16,804 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-12T23:01:16,804 status = self.run(options, args) 2021-07-12T23:01:16,804 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-12T23:01:16,804 return func(self, options, args) 2021-07-12T23:01:16,804 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 142, in run 2021-07-12T23:01:16,804 requirement_set = resolver.resolve( 2021-07-12T23:01:16,804 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 136, in resolve 2021-07-12T23:01:16,804 raise error from e 2021-07-12T23:01:16,804 pip._internal.exceptions.DistributionNotFound: No matching distribution found for libnano==0.1.1.3 2021-07-12T23:01:16,809 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-xqplvx2z' 2021-07-12T23:01:16,809 Removed build tracker: '/tmp/pip-req-tracker-xqplvx2z'