2019-07-07T09:00:59 Created temporary directory: /tmp/pip-ephem-wheel-cache-ayrlijfv 2019-07-07T09:00:59 Created temporary directory: /tmp/pip-req-tracker-gpunfw21 2019-07-07T09:00:59 Created requirements tracker '/tmp/pip-req-tracker-gpunfw21' 2019-07-07T09:00:59 Created temporary directory: /tmp/pip-wheel-raufnweo 2019-07-07T09:00:59 Collecting uta-align==0.1.11 2019-07-07T09:00:59 1 location(s) to search for versions of uta-align: 2019-07-07T09:00:59 * https://pypi.org/simple/uta-align/ 2019-07-07T09:00:59 Getting page https://pypi.org/simple/uta-align/ 2019-07-07T09:00:59 Analyzing links from page https://pypi.org/simple/uta-align/ 2019-07-07T09:00:59 Found link https://files.pythonhosted.org/packages/60/a2/47df4fbbbf9800199f0b9363ba2b02c7f234d074ad2693d09cb499a18b2f/uta-align-0.0.1dev-c749ca8b22a0.tar.gz#sha256=be2bea43e93b36fb91ed4d3cf0dafc9e9d26c754c1c7e7d091e4faec223395c1 (from https://pypi.org/simple/uta-align/), version: 0.0.1dev-c749ca8b22a0 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/08/ed/16116fd416d69101c3cda7290be8a3a4f82f9d3c9e7902c783633ed78f21/uta_align-0.0.1dev_c749ca8b22a0-py2.7-linux-x86_64.egg#sha256=11e7bf9911132edebbcfefbd7628396c2ede205ca2e3d002c5b6b5e9d05be423 (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Found link https://files.pythonhosted.org/packages/c5/c4/e4c65f29cdbcec6ec0269ae305bba6b2a228ff67699de315154dcda99f68/uta-align-0.1.0.tar.gz#sha256=e132e120722a1684309dc3baa6f272a84cd856b2bad8b8efed7c9d790990f7ec (from https://pypi.org/simple/uta-align/), version: 0.1.0 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/66/50/0cf3cc125b6ba7ad99012bedf436c15e56cdf19c677edd4d25f24c51cfe2/uta_align-0.1.0-py2.7-linux-x86_64.egg#sha256=4f38852f9e1646b23a19c00ea43f42ced3b75fb7a100a0634b3babb644f43c8d (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Found link https://files.pythonhosted.org/packages/f5/7f/c7c7d3043fa52fe7d6c8d3a870409f9cc9126ca11c113ca05bcd889a123d/uta-align-0.1.2.tar.gz#sha256=e70615dceeb48cd34bfa5632896db2e588ff74502e7d0f499fd6206d5b867076 (from https://pypi.org/simple/uta-align/), version: 0.1.2 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/fe/38/a811e7ea2cfa3d1447302b1e0bf650a6b7394c85a308416ae9acbde5c0b9/uta_align-0.1.2-py2.7-linux-x86_64.egg#sha256=2c8d200c1d7ec3ea7fccf3882c81b0d0d95e8f15593c6d88f37e548a19545f4c (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/c8/ef/d709856489d8883fa96dfa2732a7cdf33a2b6eb7319e2d8f245e1fbe299a/uta_align-0.1.4-py2.7-linux-x86_64.egg#sha256=54061fe3de1ba3e807a995daf933073c6ee5e62cf10dba247dfc9b4365b85269 (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Found link https://files.pythonhosted.org/packages/4f/98/6c282d715088d99d0e4ad4574bd7ae06ae0157f9b4c94843bf215a2b13fd/uta-align-0.1.5.tar.gz#sha256=8504275cbcfa88a73935633b9b8dcff86216480597ab0e887b38514dbe574473 (from https://pypi.org/simple/uta-align/), version: 0.1.5 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/d3/86/7a17a92e6730db93d570dde8d4f6ed2ebde235a4a2b1067fe41aa73e6d56/uta_align-0.1.5-py2.7-linux-x86_64.egg#sha256=7448c12fcbf369f8439cbca59b19148c79a082014a7d6f8153a5fad51ac875aa (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Found link https://files.pythonhosted.org/packages/20/a0/944d267127f1cc2b188f8afbc3684232ebd576ccad97cec399179f29ada3/uta-align-0.1.6.tar.gz#sha256=6c2368b2375690fa5fcc649841fa1b07d26c327f6c6108c1f6ee6cb1993fe475 (from https://pypi.org/simple/uta-align/), version: 0.1.6 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/8a/79/ab5ccbbf4854c8dc038871306dccb76e18680581267e876528f829089b6a/uta_align-0.1.6-py2.7-linux-x86_64.egg#sha256=547eb1595f2201faa0723bed37480fe739e872fcabf5dc95ebfada86d8a03237 (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Found link https://files.pythonhosted.org/packages/42/c0/9999b551deffc63c27066cffdac0c2bdd6413d3741b775a6f0441ce82c94/uta-align-0.1.7.tar.gz#sha256=9d34fa4c128faa303ed059271e564678a482303fe4f64273e6f977f542916250 (from https://pypi.org/simple/uta-align/), version: 0.1.7 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/8a/fc/a620e23d04f03f60881831b48f4e05e3fbd8b8cd9c797b06245f7783d8b4/uta_align-0.1.7-py2.7-linux-x86_64.egg#sha256=d8e9e7a35c561ec6aa633ce0069f31f6304a1622de94d3441c6f319cecebd66a (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Found link https://files.pythonhosted.org/packages/f1/f2/ae2c44e1009a4c94be0a228a17ba41327cbb14ca4d205b9d30a6d03907e0/uta-align-0.1.8.tar.gz#sha256=9fb48ba209517ddf1bbc7678280ab52f14a5e47131c0b647249cc2f295e398b1 (from https://pypi.org/simple/uta-align/), version: 0.1.8 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/0a/e1/dfb0593828e024c1a8c1b40539a892d613a52221deec59e1916e6271c49d/uta_align-0.1.8-py2.7-linux-x86_64.egg#sha256=6221a1b03c2ac8730965ee66f3693ff51705f81670cb1a0fc0845899a6476d2e (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Found link https://files.pythonhosted.org/packages/53/9a/f8e1cab0dc5e7f59277cad128fcead3897c03c74c743b6ef05927a49914e/uta-align-0.1.9.tar.gz#sha256=47751429b2a3860a0ecb62f4b21a80e13d6c81a6a72a679c61468ab9dc668b17 (from https://pypi.org/simple/uta-align/), version: 0.1.9 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/12/b6/bedbe1aa646f76d72de5a2e269b0771d04704ab97be399ebe34a7b4a31ac/uta_align-0.1.9-py2.7-linux-x86_64.egg#sha256=09b267559e4c203bb88043430ec86612d463355c4b858d57e38aa9d4d12c2894 (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Found link https://files.pythonhosted.org/packages/94/6b/0b73dc6d3391468e9d5229a262129763672296d41f1a26d4f128c66a99dd/uta-align-0.1.10.tar.gz#sha256=98bbd07287834f681670a4f0d93a8ccd79ed2482dcdce715c8d0531e804ac098 (from https://pypi.org/simple/uta-align/), version: 0.1.10 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/af/ec/2ec104fea2c5ad78e85b77df92d92a77c75fca18b9fd5efe75e970c4d6ed/uta_align-0.1.10-py2.7-linux-x86_64.egg#sha256=0ee4e6d1bbb96a6202276e3669c8571995ab6b61b1583b3869081ebb7608600d (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Found link https://files.pythonhosted.org/packages/46/1c/47de77a2b89f0339022a5ae5a03f4a919f1afa18d47b5640c3e87c0f5e68/uta-align-0.1.11.tar.gz#sha256=c57b7a4b0d7440469d9fe166e279055e64c362f48b7c08d1ff9e4355c77e46e9 (from https://pypi.org/simple/uta-align/), version: 0.1.11 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/dd/a7/46496d2d48416e55e45b4f7a77103d53a80f9165552d81ffba27e51ff99b/uta_align-0.1.11-py2.7-linux-x86_64.egg#sha256=05b12a98224dfb96c4430a78741a9b7828963ee4234d5915cae24f43ee9ab1b4 (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Skipping link https://files.pythonhosted.org/packages/0f/7c/ffe50738dd367f7378193f892584392015f4b62aa3ebce7ff721b0cddbc4/uta_align-0.1.11-py3.6-linux-x86_64.egg#sha256=6af6b46d95ebe2e3bd06b51ed976e2a954555bc226f1f7a609acf5d0221ad783 (from https://pypi.org/simple/uta-align/); unsupported archive format: .egg 2019-07-07T09:00:59 Using version 0.1.11 (newest of versions: 0.1.11) 2019-07-07T09:00:59 Created temporary directory: /tmp/pip-unpack-v6mlqpw1 2019-07-07T09:00:59 Downloading https://files.pythonhosted.org/packages/46/1c/47de77a2b89f0339022a5ae5a03f4a919f1afa18d47b5640c3e87c0f5e68/uta-align-0.1.11.tar.gz (73kB) 2019-07-07T09:00:59 Downloading from URL https://files.pythonhosted.org/packages/46/1c/47de77a2b89f0339022a5ae5a03f4a919f1afa18d47b5640c3e87c0f5e68/uta-align-0.1.11.tar.gz#sha256=c57b7a4b0d7440469d9fe166e279055e64c362f48b7c08d1ff9e4355c77e46e9 (from https://pypi.org/simple/uta-align/) 2019-07-07T09:00:59 Added uta-align==0.1.11 from https://files.pythonhosted.org/packages/46/1c/47de77a2b89f0339022a5ae5a03f4a919f1afa18d47b5640c3e87c0f5e68/uta-align-0.1.11.tar.gz#sha256=c57b7a4b0d7440469d9fe166e279055e64c362f48b7c08d1ff9e4355c77e46e9 to build tracker '/tmp/pip-req-tracker-gpunfw21' 2019-07-07T09:00:59 Running setup.py (path:/tmp/pip-wheel-raufnweo/uta-align/setup.py) egg_info for package uta-align 2019-07-07T09:00:59 Running command python setup.py egg_info 2019-07-07T09:01:04 Collecting pysam 2019-07-07T09:01:05 Downloading https://files.pythonhosted.org/packages/15/f6/ce0611aaa1865a616f7dc164fbf046eaf38f2b17c6d404403c56250beb93/pysam-0.15.2.tar.gz (3.2MB) 2019-07-07T09:01:32 Building wheels for collected packages: pysam 2019-07-07T09:01:33 Building wheel for pysam (setup.py): started 2019-07-07T09:02:37 Building wheel for pysam (setup.py): still running... 2019-07-07T09:03:49 Building wheel for pysam (setup.py): still running... 2019-07-07T09:04:59 Building wheel for pysam (setup.py): still running... 2019-07-07T09:06:08 Building wheel for pysam (setup.py): still running... 2019-07-07T09:07:08 Building wheel for pysam (setup.py): still running... 2019-07-07T09:08:14 Building wheel for pysam (setup.py): still running... 2019-07-07T09:10:25 Building wheel for pysam (setup.py): still running... 2019-07-07T09:12:10 Building wheel for pysam (setup.py): still running... 2019-07-07T09:13:17 Building wheel for pysam (setup.py): still running... 2019-07-07T09:15:39 Building wheel for pysam (setup.py): still running... 2019-07-07T09:17:34 Building wheel for pysam (setup.py): still running... 2019-07-07T09:18:54 Building wheel for pysam (setup.py): still running... 2019-07-07T09:19:06 Building wheel for pysam (setup.py): finished with status 'done' 2019-07-07T09:19:06 Stored in directory: /home/piwheels/.cache/pip/wheels/34/3b/bc/f3faaba907f333632357aae7bf09a453209a8c9c3cec4cddae 2019-07-07T09:19:09 Successfully built pysam 2019-07-07T09:19:11 Installing collected packages: pysam 2019-07-07T09:19:11 ERROR: Could not install packages due to an EnvironmentError: [Errno 13] Permission denied: '/usr/local/lib/python3.7/dist-packages/pysam-0.15.2.dist-info' 2019-07-07T09:19:11 Consider using the `--user` option or check the permissions. 2019-07-07T09:19:15 [WARNING] pysam not found, attempting to install using a raw "pip install" call! 2019-07-07T09:19:15 running egg_info 2019-07-07T09:19:15 creating pip-egg-info/uta_align.egg-info 2019-07-07T09:19:15 writing pip-egg-info/uta_align.egg-info/PKG-INFO 2019-07-07T09:19:15 writing dependency_links to pip-egg-info/uta_align.egg-info/dependency_links.txt 2019-07-07T09:19:15 writing requirements to pip-egg-info/uta_align.egg-info/requires.txt 2019-07-07T09:19:15 writing top-level names to pip-egg-info/uta_align.egg-info/top_level.txt 2019-07-07T09:19:15 writing manifest file 'pip-egg-info/uta_align.egg-info/SOURCES.txt' 2019-07-07T09:19:15 reading manifest file 'pip-egg-info/uta_align.egg-info/SOURCES.txt' 2019-07-07T09:19:15 writing manifest file 'pip-egg-info/uta_align.egg-info/SOURCES.txt' 2019-07-07T09:19:16 Source in /tmp/pip-wheel-raufnweo/uta-align has version 0.1.11, which satisfies requirement uta-align==0.1.11 from https://files.pythonhosted.org/packages/46/1c/47de77a2b89f0339022a5ae5a03f4a919f1afa18d47b5640c3e87c0f5e68/uta-align-0.1.11.tar.gz#sha256=c57b7a4b0d7440469d9fe166e279055e64c362f48b7c08d1ff9e4355c77e46e9 2019-07-07T09:19:16 Removed uta-align==0.1.11 from https://files.pythonhosted.org/packages/46/1c/47de77a2b89f0339022a5ae5a03f4a919f1afa18d47b5640c3e87c0f5e68/uta-align-0.1.11.tar.gz#sha256=c57b7a4b0d7440469d9fe166e279055e64c362f48b7c08d1ff9e4355c77e46e9 from build tracker '/tmp/pip-req-tracker-gpunfw21' 2019-07-07T09:19:16 Building wheels for collected packages: uta-align 2019-07-07T09:19:16 Created temporary directory: /tmp/pip-wheel-tfqjl4wk 2019-07-07T09:19:16 Building wheel for uta-align (setup.py): started 2019-07-07T09:19:16 Destination directory: /tmp/pip-wheel-tfqjl4wk 2019-07-07T09:19:16 Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-raufnweo/uta-align/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-tfqjl4wk 2019-07-07T09:19:17 [WARNING] pysam not found, attempting to install using a raw "pip install" call! 2019-07-07T09:19:20 Collecting pysam 2019-07-07T09:19:24 Installing collected packages: pysam 2019-07-07T09:19:24 ERROR: Could not install packages due to an EnvironmentError: [Errno 13] Permission denied: '/usr/local/lib/python3.7/dist-packages/pysam-0.15.2.dist-info' 2019-07-07T09:19:24 Consider using the `--user` option or check the permissions. 2019-07-07T09:19:26 running bdist_wheel 2019-07-07T09:19:26 running build 2019-07-07T09:19:26 running build_py 2019-07-07T09:19:27 creating build 2019-07-07T09:19:27 creating build/lib.linux-armv7l-3.7 2019-07-07T09:19:27 creating build/lib.linux-armv7l-3.7/uta_align 2019-07-07T09:19:27 copying uta_align/__init__.py -> build/lib.linux-armv7l-3.7/uta_align 2019-07-07T09:19:27 creating build/lib.linux-armv7l-3.7/uta_align/align 2019-07-07T09:19:27 copying uta_align/align/__init__.py -> build/lib.linux-armv7l-3.7/uta_align/align 2019-07-07T09:19:27 running build_ext 2019-07-07T09:19:27 cythoning uta_align/align/cigar_utils.pyx to uta_align/align/cigar_utils.c 2019-07-07T09:19:28 /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-raufnweo/uta-align/uta_align/align/cigar_utils.pxd 2019-07-07T09:19:28 tree = Parsing.p_module(s, pxd, full_module_name) 2019-07-07T09:19:28 Error compiling Cython file: 2019-07-07T09:19:28 ------------------------------------------------------------ 2019-07-07T09:19:28 ... 2019-07-07T09:19:28 # -*- coding: utf-8 -*- 2019-07-07T09:19:28 from libc.stdint cimport uint32_t 2019-07-07T09:19:28 from pysam.libcsamfile cimport AlignedRead 2019-07-07T09:19:28 ^ 2019-07-07T09:19:28 ------------------------------------------------------------ 2019-07-07T09:19:28 uta_align/align/cigar_utils.pxd:4:0: 'pysam/libcsamfile.pxd' not found 2019-07-07T09:19:28 Error compiling Cython file: 2019-07-07T09:19:28 ------------------------------------------------------------ 2019-07-07T09:19:28 ... 2019-07-07T09:19:28 # -*- coding: utf-8 -*- 2019-07-07T09:19:28 from libc.stdint cimport uint32_t 2019-07-07T09:19:28 from pysam.libcsamfile cimport AlignedRead 2019-07-07T09:19:28 ^ 2019-07-07T09:19:28 ------------------------------------------------------------ 2019-07-07T09:19:28 uta_align/align/cigar_utils.pxd:4:0: 'pysam/libcsamfile/AlignedRead.pxd' not found 2019-07-07T09:19:28 Error compiling Cython file: 2019-07-07T09:19:28 ------------------------------------------------------------ 2019-07-07T09:19:28 ... 2019-07-07T09:19:28 cdef class CigarSequence(object): 2019-07-07T09:19:28 cdef Py_ssize_t cigar_buf_len, cigar_len 2019-07-07T09:19:28 cdef uint32_t* cigar_buf 2019-07-07T09:19:28 cdef _extend_from_binary(self, uint32_t other_cigar_len, uint32_t* other_cigar_buf) 2019-07-07T09:19:28 cdef _extend_from_align(self, AlignedRead align) 2019-07-07T09:19:28 ^ 2019-07-07T09:19:28 ------------------------------------------------------------ 2019-07-07T09:19:28 uta_align/align/cigar_utils.pxd:29:34: 'AlignedRead' is not a type identifier 2019-07-07T09:19:29 Error compiling Cython file: 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 ... 2019-07-07T09:19:29 from libc.stdio cimport sprintf 2019-07-07T09:19:29 from libc.stdlib cimport malloc, realloc, free 2019-07-07T09:19:29 from libc.string cimport memcpy 2019-07-07T09:19:29 from cpython.ref cimport PyObject 2019-07-07T09:19:29 from cpython.string cimport PyString_FromStringAndSize 2019-07-07T09:19:29 from pysam.libchtslib cimport bam_get_cigar, bam1_t 2019-07-07T09:19:29 ^ 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 uta_align/align/cigar_utils.pyx:14:0: 'pysam/libchtslib.pxd' not found 2019-07-07T09:19:29 Error compiling Cython file: 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 ... 2019-07-07T09:19:29 from libc.stdio cimport sprintf 2019-07-07T09:19:29 from libc.stdlib cimport malloc, realloc, free 2019-07-07T09:19:29 from libc.string cimport memcpy 2019-07-07T09:19:29 from cpython.ref cimport PyObject 2019-07-07T09:19:29 from cpython.string cimport PyString_FromStringAndSize 2019-07-07T09:19:29 from pysam.libchtslib cimport bam_get_cigar, bam1_t 2019-07-07T09:19:29 ^ 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 uta_align/align/cigar_utils.pyx:14:0: 'pysam/libchtslib/bam_get_cigar.pxd' not found 2019-07-07T09:19:29 Error compiling Cython file: 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 ... 2019-07-07T09:19:29 from libc.stdio cimport sprintf 2019-07-07T09:19:29 from libc.stdlib cimport malloc, realloc, free 2019-07-07T09:19:29 from libc.string cimport memcpy 2019-07-07T09:19:29 from cpython.ref cimport PyObject 2019-07-07T09:19:29 from cpython.string cimport PyString_FromStringAndSize 2019-07-07T09:19:29 from pysam.libchtslib cimport bam_get_cigar, bam1_t 2019-07-07T09:19:29 ^ 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 uta_align/align/cigar_utils.pyx:14:0: 'pysam/libchtslib/bam1_t.pxd' not found 2019-07-07T09:19:29 Error compiling Cython file: 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 ... 2019-07-07T09:19:29 self._alloc_buf(self.cigar_len + other_cigar_len) 2019-07-07T09:19:29 memcpy(self.cigar_buf + self.cigar_len, other_cigar_buf, other_cigar_len * sizeof(uint32_t)) 2019-07-07T09:19:29 self.cigar_len += other_cigar_len 2019-07-07T09:19:29 cdef _extend_from_align(self, AlignedRead align): 2019-07-07T09:19:29 ^ 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 uta_align/align/cigar_utils.pyx:211:34: 'AlignedRead' is not a type identifier 2019-07-07T09:19:29 Error compiling Cython file: 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 ... 2019-07-07T09:19:29 self._alloc_buf(self.cigar_len + other_cigar_len) 2019-07-07T09:19:29 memcpy(self.cigar_buf + self.cigar_len, other_cigar_buf, other_cigar_len * sizeof(uint32_t)) 2019-07-07T09:19:29 self.cigar_len += other_cigar_len 2019-07-07T09:19:29 cdef _extend_from_align(self, AlignedRead align): 2019-07-07T09:19:29 cdef bam1_t* src = align._delegate 2019-07-07T09:19:29 ^ 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 uta_align/align/cigar_utils.pyx:212:13: 'bam1_t' is not a type identifier 2019-07-07T09:19:29 Error compiling Cython file: 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 ... 2019-07-07T09:19:29 memcpy(self.cigar_buf + self.cigar_len, other_cigar_buf, other_cigar_len * sizeof(uint32_t)) 2019-07-07T09:19:29 self.cigar_len += other_cigar_len 2019-07-07T09:19:29 cdef _extend_from_align(self, AlignedRead align): 2019-07-07T09:19:29 cdef bam1_t* src = align._delegate 2019-07-07T09:19:29 self._extend_from_binary(src.core.n_cigar, bam_get_cigar(src)) 2019-07-07T09:19:29 ^ 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 uta_align/align/cigar_utils.pyx:213:51: 'bam_get_cigar' is not a constant, variable or function identifier 2019-07-07T09:19:29 Error compiling Cython file: 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 ... 2019-07-07T09:19:29 memcpy(self.cigar_buf + self.cigar_len, other_cigar_buf, other_cigar_len * sizeof(uint32_t)) 2019-07-07T09:19:29 self.cigar_len += other_cigar_len 2019-07-07T09:19:29 cdef _extend_from_align(self, AlignedRead align): 2019-07-07T09:19:29 cdef bam1_t* src = align._delegate 2019-07-07T09:19:29 self._extend_from_binary(src.core.n_cigar, bam_get_cigar(src)) 2019-07-07T09:19:29 ^ 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 uta_align/align/cigar_utils.pyx:213:64: Cannot convert Python object to 'uint32_t *' 2019-07-07T09:19:29 Error compiling Cython file: 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 ... 2019-07-07T09:19:29 '1I520M10I10M' 2019-07-07T09:19:29 >>> c.extend( [(SOFT_CLIP, 5)] ) 2019-07-07T09:19:29 >>> c.to_string() 2019-07-07T09:19:29 '1I520M10I10M5S' 2019-07-07T09:19:29 ''' 2019-07-07T09:19:29 if isinstance(items, AlignedRead): 2019-07-07T09:19:29 ^ 2019-07-07T09:19:29 ------------------------------------------------------------ 2019-07-07T09:19:29 uta_align/align/cigar_utils.pyx:533:29: 'AlignedRead' is not a constant, variable or function identifier 2019-07-07T09:19:29 Traceback (most recent call last): 2019-07-07T09:19:29 File "", line 1, in 2019-07-07T09:19:29 File "/tmp/pip-wheel-raufnweo/uta-align/setup.py", line 102, in 2019-07-07T09:19:29 zip_safe=False, 2019-07-07T09:19:29 File "/usr/local/lib/python3.7/dist-packages/setuptools/__init__.py", line 145, in setup 2019-07-07T09:19:29 return distutils.core.setup(**attrs) 2019-07-07T09:19:29 File "/usr/lib/python3.7/distutils/core.py", line 148, in setup 2019-07-07T09:19:29 dist.run_commands() 2019-07-07T09:19:29 File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands 2019-07-07T09:19:29 self.run_command(cmd) 2019-07-07T09:19:29 File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command 2019-07-07T09:19:29 cmd_obj.run() 2019-07-07T09:19:29 File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 188, in run 2019-07-07T09:19:29 self.run_command('build') 2019-07-07T09:19:29 File "/usr/lib/python3.7/distutils/cmd.py", line 313, in run_command 2019-07-07T09:19:29 self.distribution.run_command(command) 2019-07-07T09:19:29 File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command 2019-07-07T09:19:29 cmd_obj.run() 2019-07-07T09:19:29 File "/usr/lib/python3.7/distutils/command/build.py", line 135, in run 2019-07-07T09:19:29 self.run_command(cmd_name) 2019-07-07T09:19:29 File "/usr/lib/python3.7/distutils/cmd.py", line 313, in run_command 2019-07-07T09:19:29 self.distribution.run_command(command) 2019-07-07T09:19:29 File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command 2019-07-07T09:19:29 cmd_obj.run() 2019-07-07T09:19:29 File "/usr/lib/python3/dist-packages/Cython/Distutils/old_build_ext.py", line 186, in run 2019-07-07T09:19:29 _build_ext.build_ext.run(self) 2019-07-07T09:19:29 File "/usr/lib/python3.7/distutils/command/build_ext.py", line 340, in run 2019-07-07T09:19:29 self.build_extensions() 2019-07-07T09:19:29 File "/usr/lib/python3/dist-packages/Cython/Distutils/old_build_ext.py", line 194, in build_extensions 2019-07-07T09:19:29 self.build_extension(ext) 2019-07-07T09:19:29 File "/tmp/pip-wheel-raufnweo/uta-align/cy_distribute.py", line 39, in build_extension 2019-07-07T09:19:29 ext._init_func(ext) 2019-07-07T09:19:29 File "/tmp/pip-wheel-raufnweo/uta-align/setup.py", line 72, in pysam_incl 2019-07-07T09:19:29 import pysam 2019-07-07T09:19:29 ModuleNotFoundError: No module named 'pysam' 2019-07-07T09:19:30 Building wheel for uta-align (setup.py): finished with status 'error' 2019-07-07T09:19:30 ERROR: Failed building wheel for uta-align 2019-07-07T09:19:30 Running setup.py clean for uta-align 2019-07-07T09:19:30 Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-raufnweo/uta-align/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2019-07-07T09:19:31 [WARNING] pysam not found, attempting to install using a raw "pip install" call! 2019-07-07T09:19:34 Collecting pysam 2019-07-07T09:19:38 Installing collected packages: pysam 2019-07-07T09:19:38 ERROR: Could not install packages due to an EnvironmentError: [Errno 13] Permission denied: '/usr/local/lib/python3.7/dist-packages/pysam-0.15.2.dist-info' 2019-07-07T09:19:38 Consider using the `--user` option or check the permissions. 2019-07-07T09:19:40 running clean 2019-07-07T09:19:40 removing 'build/lib.linux-armv7l-3.7' (and everything under it) 2019-07-07T09:19:40 'build/bdist.linux-armv7l' does not exist -- can't clean it 2019-07-07T09:19:40 'build/scripts-3.7' does not exist -- can't clean it 2019-07-07T09:19:40 removing 'build' 2019-07-07T09:19:40 Failed to build uta-align 2019-07-07T09:19:40 Cleaning up... 2019-07-07T09:19:40 Removing source in /tmp/pip-wheel-raufnweo/uta-align 2019-07-07T09:19:40 Removed build tracker '/tmp/pip-req-tracker-gpunfw21' 2019-07-07T09:19:40 ERROR: Failed to build one or more wheels 2019-07-07T09:19:40 Exception information: 2019-07-07T09:19:40 Traceback (most recent call last): 2019-07-07T09:19:40 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 178, in main 2019-07-07T09:19:40 status = self.run(options, args) 2019-07-07T09:19:40 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/commands/wheel.py", line 178, in run 2019-07-07T09:19:40 "Failed to build one or more wheels" 2019-07-07T09:19:40 pip._internal.exceptions.CommandError: Failed to build one or more wheels