2019-07-04T09:26:19 Created temporary directory: /tmp/pip-ephem-wheel-cache-jmok3na4 2019-07-04T09:26:19 Created temporary directory: /tmp/pip-req-tracker-m7lnvdas 2019-07-04T09:26:19 Created requirements tracker '/tmp/pip-req-tracker-m7lnvdas' 2019-07-04T09:26:19 Created temporary directory: /tmp/pip-wheel-p2yamkmb 2019-07-04T09:26:19 Collecting gat==1.3.1 2019-07-04T09:26:19 1 location(s) to search for versions of gat: 2019-07-04T09:26:19 * https://pypi.org/simple/gat/ 2019-07-04T09:26:19 Getting page https://pypi.org/simple/gat/ 2019-07-04T09:26:19 Analyzing links from page https://pypi.org/simple/gat/ 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/be/34/ecadd24a9bddad07a74b99483aceaec524ad1bed92933ec264f44051627b/gat-0.1.tar.gz#sha256=3c7add7953a3cc64570ed1bc1ce87054db85d28a61382d93a0f5f79ae9e86e9f (from https://pypi.org/simple/gat/), version: 0.1 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/f3/ef/2af035c07eb1809d227f768e6bc765ba93d79e12575e3bd968463d3ce118/gat-0.2.tar.gz#sha256=c0a1823ff9993b02988817e0f5201e5bb1da47a5f0adddeee43a8a5d54dff494 (from https://pypi.org/simple/gat/), version: 0.2 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/2e/d8/0173f218fc3ae63114c3ac7b58846aca1b223d7addc861265c004ff2f7ce/gat-1.1.tar.gz#sha256=d7c31d7b1a4f97182b52f895a64bede4c38da315e1bdcae2b3ec7e9548ada046 (from https://pypi.org/simple/gat/), version: 1.1 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/3d/8e/6156471a92f77b99ac5d5e476da2562db2a960fd965545c155d8cd321e00/gat-1.2.tar.gz#sha256=55d84003d2d34d8aba5499351e407a0def9a50c24ead4a567245fc560b3840d4 (from https://pypi.org/simple/gat/), version: 1.2 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/7b/aa/3417ecbf21b216bff79e02a23f7bdef070a6251eafe98793b0691bf2f425/gat-1.2.1.tar.gz#sha256=64f8bf40e4db6047e8241b941e442b1a37b305c74ac4e4525d209e0d13ab71cc (from https://pypi.org/simple/gat/), version: 1.2.1 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/52/99/7fa1bd580335036e28ca2a2af491323889c445f4a2e0e6495f92159172e4/gat-1.2.2.tar.gz#sha256=e34d80169289e938aefbbebc4c50a3d5cdc8b38bab2cf63ae9716089bfda5968 (from https://pypi.org/simple/gat/), version: 1.2.2 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/01/ed/d8d67087f877efebf80fefafb8b871d3f081d497e2ce9198f6b733d0a76c/gat-1.3.0.tar.gz#sha256=e60e6fd8c9116dc8e76fa71f174dddb7d37f962e4320294cfc6c4aebec8aede4 (from https://pypi.org/simple/gat/), version: 1.3.0 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/32/3b/379a4aab16fd4c225b39cb62c67b24e09d35cec68b50d7a7372f8d5a4b92/gat-1.3.1.tar.gz#sha256=36ca788dea02eab62beba8fab7d7abaf9f41bd8b6af2df8371f1009f9fb3500f (from https://pypi.org/simple/gat/), version: 1.3.1 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/72/9d/6fdbeac74825fee621d61d2d305744591aa5fbf67a9f4c7b9233fd7f7322/gat-1.3.2.tar.gz#sha256=839fa3bff62c7a21194d0d9bcda6e4eac8bfc3ce956ac3e7aa0795d72784ce3e (from https://pypi.org/simple/gat/), version: 1.3.2 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/50/f7/bfb0ff1373c78ff58d0c51b2a9851582c6f2ef681b99a1280325031c6a90/gat-1.3.3.tar.gz#sha256=0964e454a8cfd388172a40be4bf3d9129ea88c39ab83a31655d81db70e452967 (from https://pypi.org/simple/gat/), version: 1.3.3 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/10/d1/e39e8f205cc15f047c8b6af6970dbbf53678b2c1e5623bec693578769899/gat-1.3.4.tar.gz#sha256=b35826959a055d090170c24eb3ac3cd0fc53f0e443c0c9792bc4faa73df50297 (from https://pypi.org/simple/gat/), version: 1.3.4 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/ef/87/3a03ea89abd49690f0c5115bcfb232212475d8e642d65bc886e2498f7b96/gat-1.3.5.tar.gz#sha256=95a268f64e555d14d2af7621cd488486ce4a791236e6a43af46dbbf4051b4d1a (from https://pypi.org/simple/gat/), version: 1.3.5 2019-07-04T09:26:19 Found link https://files.pythonhosted.org/packages/50/73/ec45938cab4c86e4fd9ad967276ceab2c11aed9fcb5325cf8cec1a4d1e4c/gat-1.3.6.tar.gz#sha256=1f4a3357f326fab5cbcda3b6de049cb00bb49a7e570243fc7db6c76c2bb2df2a (from https://pypi.org/simple/gat/), version: 1.3.6 2019-07-04T09:26:19 Using version 1.3.1 (newest of versions: 1.3.1) 2019-07-04T09:26:19 Created temporary directory: /tmp/pip-unpack-oo7fyypz 2019-07-04T09:26:19 Downloading https://files.pythonhosted.org/packages/32/3b/379a4aab16fd4c225b39cb62c67b24e09d35cec68b50d7a7372f8d5a4b92/gat-1.3.1.tar.gz (89kB) 2019-07-04T09:26:19 Downloading from URL https://files.pythonhosted.org/packages/32/3b/379a4aab16fd4c225b39cb62c67b24e09d35cec68b50d7a7372f8d5a4b92/gat-1.3.1.tar.gz#sha256=36ca788dea02eab62beba8fab7d7abaf9f41bd8b6af2df8371f1009f9fb3500f (from https://pypi.org/simple/gat/) 2019-07-04T09:26:20 Added gat==1.3.1 from https://files.pythonhosted.org/packages/32/3b/379a4aab16fd4c225b39cb62c67b24e09d35cec68b50d7a7372f8d5a4b92/gat-1.3.1.tar.gz#sha256=36ca788dea02eab62beba8fab7d7abaf9f41bd8b6af2df8371f1009f9fb3500f to build tracker '/tmp/pip-req-tracker-m7lnvdas' 2019-07-04T09:26:20 Running setup.py (path:/tmp/pip-wheel-p2yamkmb/gat/setup.py) egg_info for package gat 2019-07-04T09:26:20 Running command python setup.py egg_info 2019-07-04T09:26:22 running egg_info 2019-07-04T09:26:22 creating pip-egg-info/gat.egg-info 2019-07-04T09:26:22 writing pip-egg-info/gat.egg-info/PKG-INFO 2019-07-04T09:26:22 writing dependency_links to pip-egg-info/gat.egg-info/dependency_links.txt 2019-07-04T09:26:22 writing requirements to pip-egg-info/gat.egg-info/requires.txt 2019-07-04T09:26:22 writing top-level names to pip-egg-info/gat.egg-info/top_level.txt 2019-07-04T09:26:22 writing manifest file 'pip-egg-info/gat.egg-info/SOURCES.txt' 2019-07-04T09:26:22 reading manifest file 'pip-egg-info/gat.egg-info/SOURCES.txt' 2019-07-04T09:26:22 reading manifest template 'MANIFEST.in' 2019-07-04T09:26:22 warning: no files found matching 'COPYING' 2019-07-04T09:26:22 warning: no files found matching 'INSTALL' 2019-07-04T09:26:22 warning: no files found matching 'KNOWN_BUGS' 2019-07-04T09:26:22 warning: no files found matching 'THANKS' 2019-07-04T09:26:22 warning: no files found matching 'GatEngine/GatEngine.*' 2019-07-04T09:26:22 warning: no files found matching 'GatSegmentList/GatSegmentList.*' 2019-07-04T09:26:22 writing manifest file 'pip-egg-info/gat.egg-info/SOURCES.txt' 2019-07-04T09:26:23 Source in /tmp/pip-wheel-p2yamkmb/gat has version 1.3.1, which satisfies requirement gat==1.3.1 from https://files.pythonhosted.org/packages/32/3b/379a4aab16fd4c225b39cb62c67b24e09d35cec68b50d7a7372f8d5a4b92/gat-1.3.1.tar.gz#sha256=36ca788dea02eab62beba8fab7d7abaf9f41bd8b6af2df8371f1009f9fb3500f 2019-07-04T09:26:23 Removed gat==1.3.1 from https://files.pythonhosted.org/packages/32/3b/379a4aab16fd4c225b39cb62c67b24e09d35cec68b50d7a7372f8d5a4b92/gat-1.3.1.tar.gz#sha256=36ca788dea02eab62beba8fab7d7abaf9f41bd8b6af2df8371f1009f9fb3500f from build tracker '/tmp/pip-req-tracker-m7lnvdas' 2019-07-04T09:26:23 Building wheels for collected packages: gat 2019-07-04T09:26:23 Created temporary directory: /tmp/pip-wheel-f0yeszmu 2019-07-04T09:26:23 Building wheel for gat (setup.py): started 2019-07-04T09:26:23 Destination directory: /tmp/pip-wheel-f0yeszmu 2019-07-04T09:26:23 Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-p2yamkmb/gat/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-f0yeszmu 2019-07-04T09:26:25 running bdist_wheel 2019-07-04T09:26:25 running build 2019-07-04T09:26:25 running build_py 2019-07-04T09:26:25 creating build 2019-07-04T09:26:25 creating build/lib.linux-armv7l-3.7 2019-07-04T09:26:25 creating build/lib.linux-armv7l-3.7/gat 2019-07-04T09:26:25 copying gat/__init__.py -> build/lib.linux-armv7l-3.7/gat 2019-07-04T09:26:25 copying gat/Stats.py -> build/lib.linux-armv7l-3.7/gat 2019-07-04T09:26:25 copying gat/IO.py -> build/lib.linux-armv7l-3.7/gat 2019-07-04T09:26:25 copying gat/Experiment.py -> build/lib.linux-armv7l-3.7/gat 2019-07-04T09:26:25 copying gat/IOTools.py -> build/lib.linux-armv7l-3.7/gat 2019-07-04T09:26:25 copying gat/Bed.py -> build/lib.linux-armv7l-3.7/gat 2019-07-04T09:26:25 running build_ext 2019-07-04T09:26:25 cythoning gat/CoordinateList.pyx to gat/CoordinateList.c 2019-07-04T09:26:26 /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-p2yamkmb/gat/gat/CoordinateList.pyx 2019-07-04T09:26:26 tree = Parsing.p_module(s, pxd, full_module_name) 2019-07-04T09:26:27 building 'gat.CoordinateList' extension 2019-07-04T09:26:27 creating build/temp.linux-armv7l-3.7 2019-07-04T09:26:27 creating build/temp.linux-armv7l-3.7/gat 2019-07-04T09:26:27 creating build/temp.linux-armv7l-3.7/utils 2019-07-04T09:26:27 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I./utils -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c gat/CoordinateList.c -o build/temp.linux-armv7l-3.7/gat/CoordinateList.o 2019-07-04T09:26:33 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I./utils -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c utils/gat_utils.c -o build/temp.linux-armv7l-3.7/utils/gat_utils.o 2019-07-04T09:26:33 utils/gat_utils.c: In function ‘fromCompressedFile’: 2019-07-04T09:26:33 utils/gat_utils.c:110:33: warning: passing argument 2 of ‘uncompress’ from incompatible pointer type [-Wincompatible-pointer-types] 2019-07-04T09:26:33 int zok = uncompress (buffer, &uncompressed_size, compressed, compressed_size); 2019-07-04T09:26:33 ^~~~~~~~~~~~~~~~~~ 2019-07-04T09:26:33 In file included from /usr/include/zlib.h:34, 2019-07-04T09:26:33 from utils/gat_utils.c:2: 2019-07-04T09:26:33 /usr/include/zlib.h:1265:32: note: expected ‘uLongf *’ {aka ‘long unsigned int *’} but argument is of type ‘size_t *’ {aka ‘unsigned int *’} 2019-07-04T09:26:33 ZEXTERN int ZEXPORT uncompress OF((Bytef *dest, uLongf *destLen, 2019-07-04T09:26:33 ^~ 2019-07-04T09:26:33 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.7/gat/CoordinateList.o build/temp.linux-armv7l-3.7/utils/gat_utils.o -lz -lrt -o build/lib.linux-armv7l-3.7/gat/CoordinateList.cpython-37m-arm-linux-gnueabihf.so 2019-07-04T09:26:33 cythoning gat/SegmentList.pyx to gat/SegmentList.c 2019-07-04T09:26:33 /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-p2yamkmb/gat/gat/SegmentList.pyx 2019-07-04T09:26:33 tree = Parsing.p_module(s, pxd, full_module_name) 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 return sizeof(Segment) // 2, sizeof(Segment) 2019-07-04T09:26:39 # min/max are not optimized, so declare them as C functions 2019-07-04T09:26:39 # declare as signed comparisons as a Position might be negative 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference lmin(PositionDifference a, PositionDifference b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:68:12: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 return sizeof(Segment) // 2, sizeof(Segment) 2019-07-04T09:26:39 # min/max are not optimized, so declare them as C functions 2019-07-04T09:26:39 # declare as signed comparisons as a Position might be negative 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference lmin(PositionDifference a, PositionDifference b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:68:36: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 return sizeof(Segment) // 2, sizeof(Segment) 2019-07-04T09:26:39 # min/max are not optimized, so declare them as C functions 2019-07-04T09:26:39 # declare as signed comparisons as a Position might be negative 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference lmin(PositionDifference a, PositionDifference b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:68:58: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 if a < b: 2019-07-04T09:26:39 return a 2019-07-04T09:26:39 return b 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference lmax(PositionDifference a, PositionDifference b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:74:12: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 if a < b: 2019-07-04T09:26:39 return a 2019-07-04T09:26:39 return b 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference lmax(PositionDifference a, PositionDifference b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:74:36: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 if a < b: 2019-07-04T09:26:39 return a 2019-07-04T09:26:39 return b 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference lmax(PositionDifference a, PositionDifference b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:74:58: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 if a > b: 2019-07-04T09:26:39 return a 2019-07-04T09:26:39 return b 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:92:12: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 if a > b: 2019-07-04T09:26:39 return a 2019-07-04T09:26:39 return b 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:92:47: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 if a > b: 2019-07-04T09:26:39 return a 2019-07-04T09:26:39 return b 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:92:58: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 return lmax(0, 2019-07-04T09:26:39 lmin( a.end, b.end) - 2019-07-04T09:26:39 lmax(a.start, b.start)) 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference range_overlap( 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:99:12: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 lmin( a.end, b.end) - 2019-07-04T09:26:39 lmax(a.start, b.start)) 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference range_overlap( 2019-07-04T09:26:39 Position astart, Position aend, Position bstart, Position bend) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:100:4: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 lmin( a.end, b.end) - 2019-07-04T09:26:39 lmax(a.start, b.start)) 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference range_overlap( 2019-07-04T09:26:39 Position astart, Position aend, Position bstart, Position bend) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:100:21: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 lmin( a.end, b.end) - 2019-07-04T09:26:39 lmax(a.start, b.start)) 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference range_overlap( 2019-07-04T09:26:39 Position astart, Position aend, Position bstart, Position bend) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:100:36: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 lmin( a.end, b.end) - 2019-07-04T09:26:39 lmax(a.start, b.start)) 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference range_overlap( 2019-07-04T09:26:39 Position astart, Position aend, Position bstart, Position bend) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:100:53: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 return lmax(0, 2019-07-04T09:26:39 lmin( aend, bend) - 2019-07-04T09:26:39 lmax(astart, bstart)) 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:106:12: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 return lmax(0, 2019-07-04T09:26:39 lmin( aend, bend) - 2019-07-04T09:26:39 lmax(astart, bstart)) 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:106:51: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 return lmax(0, 2019-07-04T09:26:39 lmin( aend, bend) - 2019-07-04T09:26:39 lmax(astart, bstart)) 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:106:62: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:39 return lmin(a.end, b.end) - \ 2019-07-04T09:26:39 lmax(a.start, b.start) 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference segment_length(Segment a) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:111:12: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:39 return lmin(a.end, b.end) - \ 2019-07-04T09:26:39 lmax(a.start, b.start) 2019-07-04T09:26:39 @cython.profile(False) 2019-07-04T09:26:39 cdef inline PositionDifference segment_length(Segment a) nogil: 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:111:46: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 other.nsegments * sizeof(Segment ) ) 2019-07-04T09:26:39 self.nsegments = new_size 2019-07-04T09:26:39 self.flag = 0 2019-07-04T09:26:39 return self 2019-07-04T09:26:39 cdef _add(self, Segment segment): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:513:20: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 self.segments[self.nsegments] = segment 2019-07-04T09:26:39 self.nsegments += 1 2019-07-04T09:26:39 self.flag = 0 2019-07-04T09:26:39 cpdef add(self, Position start, Position end): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:539:20: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 self.segments[self.nsegments] = segment 2019-07-04T09:26:39 self.nsegments += 1 2019-07-04T09:26:39 self.flag = 0 2019-07-04T09:26:39 cpdef add(self, Position start, Position end): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:539:36: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 cdef Segment segment 2019-07-04T09:26:39 assert start <= end, "attempting to add invalid segment %i-%i" % (start, end) 2019-07-04T09:26:39 segment = Segment(start, end) 2019-07-04T09:26:39 self._add(segment) 2019-07-04T09:26:39 cpdef trim_ends( self, Position pos, Position size, int forward ): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:545:27: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 cdef Segment segment 2019-07-04T09:26:39 assert start <= end, "attempting to add invalid segment %i-%i" % (start, end) 2019-07-04T09:26:39 segment = Segment(start, end) 2019-07-04T09:26:39 self._add(segment) 2019-07-04T09:26:39 cpdef trim_ends( self, Position pos, Position size, int forward ): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:545:41: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 raise MemoryError("out of memory when allocation %i bytes" % 2019-07-04T09:26:39 sizeof(self.nsegments * sizeof(Segment))) 2019-07-04T09:26:39 self.allocated = nsegments 2019-07-04T09:26:39 cdef insert(self, int idx, Segment seg): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:621:31: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 sizeof(Segment) * (self.nsegments - idx)) 2019-07-04T09:26:39 self.nsegments += 1 2019-07-04T09:26:39 self.segments[idx] = seg 2019-07-04T09:26:39 cpdef trim(self, Position pos, Position size): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:637:21: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 sizeof(Segment) * (self.nsegments - idx)) 2019-07-04T09:26:39 self.nsegments += 1 2019-07-04T09:26:39 self.segments[idx] = seg 2019-07-04T09:26:39 cpdef trim(self, Position pos, Position size): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:637:35: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 insertion_idx += 1 2019-07-04T09:26:39 self.nsegments = insertion_idx 2019-07-04T09:26:39 self._resize(self.nsegments) 2019-07-04T09:26:39 self.flag = 1 2019-07-04T09:26:39 cpdef merge(self, PositionDifference distance): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:756:22: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 self.flag = 1 2019-07-04T09:26:39 return self.flag 2019-07-04T09:26:39 cdef int _getInsertionPoint( self, Segment other ): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:853:39: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 def __get__(self): return self.flag 2019-07-04T09:26:39 property isEmpty: 2019-07-04T09:26:39 def __get__(self): return self.nsegments == 0 2019-07-04T09:26:39 cpdef Position getRandomPosition(self): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:902:10: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 pos -= l 2019-07-04T09:26:39 else: 2019-07-04T09:26:39 return self.segments[idx].start + pos 2019-07-04T09:26:39 assert False 2019-07-04T09:26:39 cdef Position overlap(self, Segment other): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:919:9: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 pos -= l 2019-07-04T09:26:39 else: 2019-07-04T09:26:39 return self.segments[idx].start + pos 2019-07-04T09:26:39 assert False 2019-07-04T09:26:39 cdef Position overlap(self, Segment other): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:919:32: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 while idx < self.nsegments and self.segments[idx].start <= other.end: 2019-07-04T09:26:39 count += segment_overlap(self.segments[idx], other) 2019-07-04T09:26:39 idx += 1 2019-07-04T09:26:39 return count 2019-07-04T09:26:39 cdef SegmentList getOverlappingSegments(self, Segment other): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:952:50: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 while idx < self.nsegments and self.segments[idx].start <= other.end: 2019-07-04T09:26:39 result._add(self.segments[idx]) 2019-07-04T09:26:39 idx += 1 2019-07-04T09:26:39 return result 2019-07-04T09:26:39 cpdef Position overlapWithRange(self, Position start, Position end): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:985:10: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 while idx < self.nsegments and self.segments[idx].start <= other.end: 2019-07-04T09:26:39 result._add(self.segments[idx]) 2019-07-04T09:26:39 idx += 1 2019-07-04T09:26:39 return result 2019-07-04T09:26:39 cpdef Position overlapWithRange(self, Position start, Position end): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:985:42: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 while idx < self.nsegments and self.segments[idx].start <= other.end: 2019-07-04T09:26:39 result._add(self.segments[idx]) 2019-07-04T09:26:39 idx += 1 2019-07-04T09:26:39 return result 2019-07-04T09:26:39 cpdef Position overlapWithRange(self, Position start, Position end): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:985:58: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 cdef Segment s 2019-07-04T09:26:39 s = Segment(start, end) 2019-07-04T09:26:39 return self.overlap(s) 2019-07-04T09:26:39 cpdef SegmentList getOverlappingSegmentsWithRange( 2019-07-04T09:26:39 self, Position start, Position end): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1006:14: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 cdef Segment s 2019-07-04T09:26:39 s = Segment(start, end) 2019-07-04T09:26:39 return self.overlap(s) 2019-07-04T09:26:39 cpdef SegmentList getOverlappingSegmentsWithRange( 2019-07-04T09:26:39 self, Position start, Position end): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1006:30: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 cdef Segment s 2019-07-04T09:26:39 s = Segment(start, end) 2019-07-04T09:26:39 return self.getOverlappingSegments(s) 2019-07-04T09:26:39 cpdef Position overlapWithSegments(self, SegmentList other): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1026:10: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 this_idx += 1 2019-07-04T09:26:39 other_idx += 1 2019-07-04T09:26:39 return overlap 2019-07-04T09:26:39 cpdef Position intersectionWithSegments( 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1078:10: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 l 2019-07-04T09:26:39 )) 2019-07-04T09:26:39 histogram[i] += 1 2019-07-04T09:26:39 return histogram, bucket_size 2019-07-04T09:26:39 cdef void truncate(self, Segment other): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1186:29: 'Segment' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 cdef double mean_length = total_length / self.nsegments 2019-07-04T09:26:39 return mean_length, min_length, max_length, total_length 2019-07-04T09:26:39 cpdef SegmentList getFilledSegmentsFromStart( self, Position start, PositionDifference remainder ): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1314:56: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 cdef double mean_length = total_length / self.nsegments 2019-07-04T09:26:39 return mean_length, min_length, max_length, total_length 2019-07-04T09:26:39 cpdef SegmentList getFilledSegmentsFromStart( self, Position start, PositionDifference remainder ): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1314:72: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 result.normalize() 2019-07-04T09:26:39 return result 2019-07-04T09:26:39 cpdef SegmentList getFilledSegmentsFromEnd( 2019-07-04T09:26:39 self, Position end, PositionDifference remainder): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1358:14: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 result.normalize() 2019-07-04T09:26:39 return result 2019-07-04T09:26:39 cpdef SegmentList getFilledSegmentsFromEnd( 2019-07-04T09:26:39 self, Position end, PositionDifference remainder): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1358:28: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 extension = floor(l * e_1 ) 2019-07-04T09:26:39 s.start -= lmin( extension, s.start) 2019-07-04T09:26:39 s.end += extension 2019-07-04T09:26:39 self.flag = False 2019-07-04T09:26:39 def shift(self, PositionDifference offset): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1593:20: 'PositionDifference' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 s.end += offset 2019-07-04T09:26:39 s.start += offset 2019-07-04T09:26:39 if s.start < 0: 2019-07-04T09:26:39 raise ValueError("shift creates negative coordinates") 2019-07-04T09:26:39 cpdef Position sum(self): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1607:10: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 if l > max_value: 2019-07-04T09:26:39 max_idx = idx 2019-07-04T09:26:39 max_value = l 2019-07-04T09:26:39 return self.segments[max_idx] 2019-07-04T09:26:39 cpdef Position max(self): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1638:10: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 '''return maximum coordinate.''' 2019-07-04T09:26:39 assert self.flag & SEG_NORMALIZED, "maximum from non-normalized list" 2019-07-04T09:26:39 if self.nsegments == 0: return 0 2019-07-04T09:26:39 return self.segments[self.nsegments - 1].end 2019-07-04T09:26:39 cpdef Position min(self): 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1644:10: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 # SegmentTuple = collections.namedtuple( "SegmentTuple", "start, end" ) 2019-07-04T09:26:39 cdef class SegmentListIterator: 2019-07-04T09:26:39 cdef SegmentList segment_list 2019-07-04T09:26:39 cdef Position idx 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 gat/SegmentList.pyx:1753:9: 'Position' is not a type identifier 2019-07-04T09:26:39 Error compiling Cython file: 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:39 ... 2019-07-04T09:26:39 fd = shm_unlink(self.key) 2019-07-04T09:26:39 if fd == -1: 2019-07-04T09:26:39 raise OSError( "could not unlink shared memory" ) 2019-07-04T09:26:39 # copy data back to unshared memory 2019-07-04T09:26:39 cdef Segment * s 2019-07-04T09:26:39 ^ 2019-07-04T09:26:39 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:410:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef void fromMMAP(self): 2019-07-04T09:26:40 '''retrieve data from mmapped location to private copy. 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 # copy data back to unshared memory 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:431:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if self.nsegments == 0: 2019-07-04T09:26:40 # do not move empty segment lists 2019-07-04T09:26:40 return offset 2019-07-04T09:26:40 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2019-07-04T09:26:40 cdef Segment * p = mmap + offset 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:463:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.segments[self.nsegments] = segment 2019-07-04T09:26:40 self.nsegments += 1 2019-07-04T09:26:40 self.flag = 0 2019-07-04T09:26:40 cpdef add(self, Position start, Position end): 2019-07-04T09:26:40 cdef Segment segment 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:540:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if self.nsegments == 0: return 2019-07-04T09:26:40 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Position l 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:556:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Position l 2019-07-04T09:26:40 cdef PositionDifference s = size 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:557:13: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Position l 2019-07-04T09:26:40 cdef PositionDifference s = size 2019-07-04T09:26:40 cdef Segment other, seg 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:558:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if self.nsegments == 0: return 2019-07-04T09:26:40 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef PositionDifference l 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:650:13: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef PositionDifference l 2019-07-04T09:26:40 cdef PositionDifference s = size 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:651:13: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef PositionDifference l 2019-07-04T09:26:40 cdef PositionDifference s = size 2019-07-04T09:26:40 cdef PositionDifference p = pos 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:652:13: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef PositionDifference l 2019-07-04T09:26:40 cdef PositionDifference s = size 2019-07-04T09:26:40 cdef PositionDifference p = pos 2019-07-04T09:26:40 cdef Segment other, seg 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:653:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 This function works in-place. 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 cdef int idx, insertion_idx 2019-07-04T09:26:40 cdef Position max_end 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:706:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 *n* bases will be merged. 2019-07-04T09:26:40 This function works in-place. 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 cdef PositionDifference max_end 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:770:13: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return self.flag 2019-07-04T09:26:40 self.flag = 0 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Segment segment 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:832:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 '''return a random position within the workspace. 2019-07-04T09:26:40 Not efficient, see the specialized samplers instead if 2019-07-04T09:26:40 you want to sample repeatedly from the same workspace. 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 cdef Position pos = numpy.random.randint( 0, self.sum() ) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:908:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 Not efficient, see the specialized samplers instead if 2019-07-04T09:26:40 you want to sample repeatedly from the same workspace. 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 cdef Position pos = numpy.random.randint( 0, self.sum() ) 2019-07-04T09:26:40 cdef idx 2019-07-04T09:26:40 cdef Position l 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:910:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if idx == self.nsegments: 2019-07-04T09:26:40 idx -=1 2019-07-04T09:26:40 elif idx == -1: 2019-07-04T09:26:40 idx=0 2019-07-04T09:26:40 cdef Position count 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:944:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 ------ 2019-07-04T09:26:40 overlap : int 2019-07-04T09:26:40 Number of residues overlapping 2019-07-04T09:26:40 """ 2019-07-04T09:26:40 cdef Segment s 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1001:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 ------- 2019-07-04T09:26:40 segmentlist : SegmentList 2019-07-04T09:26:40 A new segment list 2019-07-04T09:26:40 """ 2019-07-04T09:26:40 cdef Segment s 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1022:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return self.sum() 2019-07-04T09:26:40 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2019-07-04T09:26:40 this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1042:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2019-07-04T09:26:40 this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Segment other_segment = Segment(0,0) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1043:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Segment other_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Position overlap 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1045:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if other.segments == self.segments: return self.sum() 2019-07-04T09:26:40 cdef int this_idx, other_idx, last_this_idx, last_other_idx 2019-07-04T09:26:40 this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1111:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef int this_idx, other_idx, last_this_idx, last_other_idx 2019-07-04T09:26:40 this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Segment other_segment = Segment(0,0) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1112:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Segment other_segment = Segment(0,0) 2019-07-04T09:26:40 cdef int midpoint_overlap = mode == "midpoint" 2019-07-04T09:26:40 cdef Position noverlap 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1116:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 assert bucket_size >= 0, 'bucket_size is 0' 2019-07-04T09:26:40 assert nbuckets > 0, 'nbuckets is 0' 2019-07-04T09:26:40 cdef int idx, i 2019-07-04T09:26:40 cdef Position l 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1160:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 assert bucket_size >= 0, 'bucket_size is 0' 2019-07-04T09:26:40 assert nbuckets > 0, 'nbuckets is 0' 2019-07-04T09:26:40 cdef int idx, i 2019-07-04T09:26:40 cdef Position l 2019-07-04T09:26:40 cdef Segment s 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1161:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef void truncate(self, Segment other): 2019-07-04T09:26:40 '''truncate Segment list to range given by segment *other*.''' 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1190:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef void truncate(self, Segment other): 2019-07-04T09:26:40 '''truncate Segment list to range given by segment *other*.''' 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 cdef Position start = other.start 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1191:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 '''truncate Segment list to range given by segment *other*.''' 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 cdef Position start = other.start 2019-07-04T09:26:40 cdef Position end = other.end 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1192:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return 2019-07-04T09:26:40 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2019-07-04T09:26:40 working_idx = this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1227:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2019-07-04T09:26:40 working_idx = this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Segment other_segment = Segment(0,0) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1228:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 working_idx = this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Segment other_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Segment * new_segments 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1230:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cpdef summarize(self): 2019-07-04T09:26:40 '''returns summary statistics for segments.''' 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Position min_length, max_length, length 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1291:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cpdef summarize(self): 2019-07-04T09:26:40 '''returns summary statistics for segments.''' 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Position min_length, max_length, length 2019-07-04T09:26:40 cdef Position total_length 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1292:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 '''returns summary statistics for segments.''' 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Position min_length, max_length, length 2019-07-04T09:26:40 cdef Position total_length 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1293:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef SegmentList result = SegmentList() 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 idx = self.getInsertionPoint( start, start + 1 ) 2019-07-04T09:26:40 cdef Position end 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1332:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef SegmentList result = SegmentList() 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 idx = self.getInsertionPoint( end, end + 1 ) 2019-07-04T09:26:40 cdef Position start 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1376:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.clear() 2019-07-04T09:26:40 return 2019-07-04T09:26:40 if self.nsegments == 0: 2019-07-04T09:26:40 return 2019-07-04T09:26:40 cdef Segment * new_segments 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1414:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 sizeof(self.nsegments * sizeof(Segment))) 2019-07-04T09:26:40 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2019-07-04T09:26:40 working_idx = this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1426:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2019-07-04T09:26:40 working_idx = this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Segment other_segment = Segment(0,0) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1427:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 working_idx = this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Segment other_segment = Segment(0,0) 2019-07-04T09:26:40 # for negative segments, do not use -1 2019-07-04T09:26:40 cdef Position last_start = self.segments[0].start - 1 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1429:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return 2019-07-04T09:26:40 if self.nsegments == 0: 2019-07-04T09:26:40 return 2019-07-04T09:26:40 cdef Segment * new_segments 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1492:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 sizeof(allocated * sizeof(Segment))) 2019-07-04T09:26:40 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2019-07-04T09:26:40 working_idx = this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1505:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2019-07-04T09:26:40 working_idx = this_idx = other_idx = 0 2019-07-04T09:26:40 last_this_idx = last_other_idx = -1 2019-07-04T09:26:40 cdef Segment this_segment = Segment(0,0) 2019-07-04T09:26:40 cdef Segment other_segment = Segment(0,0) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1506:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 start, the interval is truncated. 2019-07-04T09:26:40 The segment list will not be normalized afterwards.''' 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1560:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 start, the interval is truncated. 2019-07-04T09:26:40 The segment list will not be normalized afterwards.''' 2019-07-04T09:26:40 cdef int idx, 2019-07-04T09:26:40 cdef PositionDifference l, extension 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1579:13: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 The segment list will not be normalized afterwards.''' 2019-07-04T09:26:40 cdef int idx, 2019-07-04T09:26:40 cdef PositionDifference l, extension 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1580:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 '''shift segments by a certain offset. 2019-07-04T09:26:40 raises ValueError if segment coordinates become negative. 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1599:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if s.start < 0: 2019-07-04T09:26:40 raise ValueError("shift creates negative coordinates") 2019-07-04T09:26:40 cpdef Position sum(self): 2019-07-04T09:26:40 '''return total length of all segments.''' 2019-07-04T09:26:40 cdef Position total 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1609:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cpdef Position sum(self): 2019-07-04T09:26:40 '''return total length of all segments.''' 2019-07-04T09:26:40 cdef Position total 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Segment s 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1611:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 if self.nsegments == 0: 2019-07-04T09:26:40 raise ValueError("largest segment from empty list") 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef int max_idx = 0 2019-07-04T09:26:40 cdef Position max_value = 0 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1628:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if self.nsegments == 0: 2019-07-04T09:26:40 raise ValueError("largest segment from empty list") 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef int max_idx = 0 2019-07-04T09:26:40 cdef Position max_value = 0 2019-07-04T09:26:40 cdef Position l 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1629:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 def __iter__(self): 2019-07-04T09:26:40 return self 2019-07-04T09:26:40 def __next__(self): 2019-07-04T09:26:40 cdef Position t 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1763:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 def __iter__(self): 2019-07-04T09:26:40 return self 2019-07-04T09:26:40 def __next__(self): 2019-07-04T09:26:40 cdef Position t 2019-07-04T09:26:40 cdef Segment v 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1764:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 DTYPE_FLOAT = numpy.float 2019-07-04T09:26:40 ctypedef numpy.float_t DTYPE_FLOAT_t 2019-07-04T09:26:40 def getSegmentSize(): 2019-07-04T09:26:40 '''return size of coordinate and size of a segment.''' 2019-07-04T09:26:40 return sizeof(Segment) // 2, sizeof(Segment) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:63:25: undeclared name not builtin: Segment 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:40 """return number of positions overlapping between to Segments.""" 2019-07-04T09:26:40 return lmax(0, 2019-07-04T09:26:40 lmin( a.end, b.end) - 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:95:17: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:40 """return number of positions overlapping between to Segments.""" 2019-07-04T09:26:40 return lmax(0, 2019-07-04T09:26:40 lmin( a.end, b.end) - 2019-07-04T09:26:40 lmax(a.start, b.start)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:96:17: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef inline PositionDifference range_overlap( 2019-07-04T09:26:40 Position astart, Position aend, Position bstart, Position bend) nogil: 2019-07-04T09:26:40 return lmax(0, 2019-07-04T09:26:40 lmin( aend, bend) - 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:102:17: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef inline PositionDifference range_overlap( 2019-07-04T09:26:40 Position astart, Position aend, Position bstart, Position bend) nogil: 2019-07-04T09:26:40 return lmax(0, 2019-07-04T09:26:40 lmin( aend, bend) - 2019-07-04T09:26:40 lmax(astart, bstart)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:103:17: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 lmin( aend, bend) - 2019-07-04T09:26:40 lmax(astart, bstart)) 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:40 return lmin(a.end, b.end) - \ 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:107:12: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 lmax(astart, bstart)) 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:40 return lmin(a.end, b.end) - \ 2019-07-04T09:26:40 lmax(a.start, b.start) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:108:9: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return lmin(a.end, b.end) - \ 2019-07-04T09:26:40 lmax(a.start, b.start) 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef inline PositionDifference segment_length(Segment a) nogil: 2019-07-04T09:26:40 return a.end - a.start 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:112:12: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return lmin(a.end, b.end) - \ 2019-07-04T09:26:40 lmax(a.start, b.start) 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef inline PositionDifference segment_length(Segment a) nogil: 2019-07-04T09:26:40 return a.end - a.start 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:112:40: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef extern from *: 2019-07-04T09:26:40 ctypedef void * const_void_ptr "const void*" 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:40 return (s1).start - \ 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:120:12: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef extern from *: 2019-07-04T09:26:40 ctypedef void * const_void_ptr "const void*" 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:40 return (s1).start - \ 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:120:33: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 ctypedef void * const_void_ptr "const void*" 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:40 return (s1).start - \ 2019-07-04T09:26:40 (s2).start 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:121:9: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 ctypedef void * const_void_ptr "const void*" 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:40 return (s1).start - \ 2019-07-04T09:26:40 (s2).start 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:121:30: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 (s2).start 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:40 cdef int x 2019-07-04T09:26:40 x = (s1).start - \ 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:126:9: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 (s2).start 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:40 cdef int x 2019-07-04T09:26:40 x = (s1).start - \ 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:126:30: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:40 cdef int x 2019-07-04T09:26:40 x = (s1).start - \ 2019-07-04T09:26:40 (s2).start 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:127:9: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:40 cdef int x 2019-07-04T09:26:40 x = (s1).start - \ 2019-07-04T09:26:40 (s2).start 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:127:30: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef int x 2019-07-04T09:26:40 x = (s1).start - \ 2019-07-04T09:26:40 (s2).start 2019-07-04T09:26:40 if x != 0: 2019-07-04T09:26:40 return x 2019-07-04T09:26:40 return (s1).end - \ 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:130:12: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef int x 2019-07-04T09:26:40 x = (s1).start - \ 2019-07-04T09:26:40 (s2).start 2019-07-04T09:26:40 if x != 0: 2019-07-04T09:26:40 return x 2019-07-04T09:26:40 return (s1).end - \ 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:130:33: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 x = (s1).start - \ 2019-07-04T09:26:40 (s2).start 2019-07-04T09:26:40 if x != 0: 2019-07-04T09:26:40 return x 2019-07-04T09:26:40 return (s1).end - \ 2019-07-04T09:26:40 (s2).end 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:131:9: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 x = (s1).start - \ 2019-07-04T09:26:40 (s2).start 2019-07-04T09:26:40 if x != 0: 2019-07-04T09:26:40 return x 2019-07-04T09:26:40 return (s1).end - \ 2019-07-04T09:26:40 (s2).end 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:131:30: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return (s1).end - \ 2019-07-04T09:26:40 (s2).end 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef int cmpPosition(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:40 return (s1)[0] - (s2)[0] 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:135:13: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return (s1).end - \ 2019-07-04T09:26:40 (s2).end 2019-07-04T09:26:40 @cython.profile(False) 2019-07-04T09:26:40 cdef int cmpPosition(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:40 return (s1)[0] - (s2)[0] 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:135:34: 'Position' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef void * retval 2019-07-04T09:26:40 cdef int error_number 2019-07-04T09:26:40 cdef char * buffer 2019-07-04T09:26:40 # initialize empty list 2019-07-04T09:26:40 self.segments = NULL 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:193:24: Cannot convert 'void *' to Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.allocated = 0 2019-07-04T09:26:40 self.flag = share.flag 2019-07-04T09:26:40 self.is_shared = True 2019-07-04T09:26:40 self.is_slave = True 2019-07-04T09:26:40 self.chunk_size = share.chunk_size 2019-07-04T09:26:40 retval = mmap(NULL, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:235:26: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if retval == -1: 2019-07-04T09:26:40 raise ValueError( 2019-07-04T09:26:40 "could not read list from shared segment - error=%i" % 2019-07-04T09:26:40 error_number) 2019-07-04T09:26:40 self.segments = retval 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:248:33: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if retval == -1: 2019-07-04T09:26:40 raise ValueError( 2019-07-04T09:26:40 "could not unpickle as slave - error=%i" % error_number) 2019-07-04T09:26:40 self.segments = retval 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:273:33: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.shared_fd = -1 2019-07-04T09:26:40 self.is_shared = True 2019-07-04T09:26:40 self.is_slave = True 2019-07-04T09:26:40 else: 2019-07-04T09:26:40 p = PyBytes_AsString(unreduce[5]) 2019-07-04T09:26:40 self.segments = malloc(self.nsegments * sizeof(Segment)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:282:33: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.is_shared = True 2019-07-04T09:26:40 self.is_slave = True 2019-07-04T09:26:40 else: 2019-07-04T09:26:40 p = PyBytes_AsString(unreduce[5]) 2019-07-04T09:26:40 self.segments = malloc(self.nsegments * sizeof(Segment)) 2019-07-04T09:26:40 memcpy(self.segments, p, cython.sizeof(Position) * 2 * self.nsegments) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:283:55: undeclared name not builtin: Position 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.is_shared = True 2019-07-04T09:26:40 self.is_slave = True 2019-07-04T09:26:40 else: 2019-07-04T09:26:40 p = PyBytes_AsString(unreduce[5]) 2019-07-04T09:26:40 self.segments = malloc(self.nsegments * sizeof(Segment)) 2019-07-04T09:26:40 memcpy(self.segments, p, cython.sizeof(Position) * 2 * self.nsegments) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:283:27: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 memcpy(self.segments, p, cython.sizeof(Position) * 2 * self.nsegments) 2019-07-04T09:26:40 # clone from another list 2019-07-04T09:26:40 elif clone != None: 2019-07-04T09:26:40 self.nsegments = self.allocated = clone.nsegments 2019-07-04T09:26:40 self.segments = calloc(clone.nsegments, sizeof( Segment)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:288:29: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 # clone from another list 2019-07-04T09:26:40 elif clone != None: 2019-07-04T09:26:40 self.nsegments = self.allocated = clone.nsegments 2019-07-04T09:26:40 self.segments = calloc(clone.nsegments, sizeof( Segment)) 2019-07-04T09:26:40 memcpy(self.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:289:23: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 # clone from another list 2019-07-04T09:26:40 elif clone != None: 2019-07-04T09:26:40 self.nsegments = self.allocated = clone.nsegments 2019-07-04T09:26:40 self.segments = calloc(clone.nsegments, sizeof( Segment)) 2019-07-04T09:26:40 memcpy(self.segments, 2019-07-04T09:26:40 clone.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:290:24: Cannot convert Python object to 'const void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 # create from an iterable 2019-07-04T09:26:40 elif iter: 2019-07-04T09:26:40 a = tuple(iter) 2019-07-04T09:26:40 nsegments = len(a) 2019-07-04T09:26:40 self.nsegments = self.allocated = nsegments 2019-07-04T09:26:40 self.segments = calloc(self.nsegments, sizeof(Segment)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:299:29: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.flag = 0 2019-07-04T09:26:40 # allocated memory, list remains empty 2019-07-04T09:26:40 elif allocate: 2019-07-04T09:26:40 self.allocated = allocate 2019-07-04T09:26:40 self.segments = calloc(allocate, sizeof(Segment)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:309:29: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if p == -1: 2019-07-04T09:26:40 raise ValueError("could not create memory mapped file" ) 2019-07-04T09:26:40 # copy data to shared memory location 2019-07-04T09:26:40 memcpy( p, self.segments, nbytes) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:381:23: Cannot convert Python object to 'const void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 memcpy( p, self.segments, nbytes) 2019-07-04T09:26:40 self.key = key 2019-07-04T09:26:40 # free allocated private memory 2019-07-04T09:26:40 self.allocated = 0 2019-07-04T09:26:40 free(self.segments) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:386:17: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 # free allocated private memory 2019-07-04T09:26:40 self.allocated = 0 2019-07-04T09:26:40 free(self.segments) 2019-07-04T09:26:40 self.segments = p 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:388:25: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 raise OSError( "could not unlink shared memory" ) 2019-07-04T09:26:40 # copy data back to unshared memory 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2019-07-04T09:26:40 s = malloc(nbytes) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:412:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2019-07-04T09:26:40 s = malloc(nbytes) 2019-07-04T09:26:40 if s == NULL: 2019-07-04T09:26:40 raise ValueError( "could not allocate memory when unsharing" ) 2019-07-04T09:26:40 memcpy(s, self.segments, nbytes) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:416:22: Cannot convert Python object to 'const void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 raise ValueError( "could not allocate memory when unsharing" ) 2019-07-04T09:26:40 memcpy(s, self.segments, nbytes) 2019-07-04T09:26:40 # unmap 2019-07-04T09:26:40 if munmap(self.segments, nbytes) == -1: 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:419:22: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2019-07-04T09:26:40 if self.nsegments == 0: 2019-07-04T09:26:40 return 2019-07-04T09:26:40 s = malloc(nbytes) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:437:13: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 s = malloc(nbytes) 2019-07-04T09:26:40 if s == NULL: 2019-07-04T09:26:40 raise ValueError( "could not allocate memory when unsharing" ) 2019-07-04T09:26:40 memcpy(s, self.segments, nbytes) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:441:22: Cannot convert Python object to 'const void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if self.nsegments == 0: 2019-07-04T09:26:40 # do not move empty segment lists 2019-07-04T09:26:40 return offset 2019-07-04T09:26:40 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2019-07-04T09:26:40 cdef Segment * p = mmap + offset 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:463:28: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2019-07-04T09:26:40 cdef Segment * p = mmap + offset 2019-07-04T09:26:40 # copy data 2019-07-04T09:26:40 memcpy(p, self.segments, nbytes) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:466:22: Cannot convert Python object to 'const void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 # copy data 2019-07-04T09:26:40 memcpy(p, self.segments, nbytes) 2019-07-04T09:26:40 # free allocated private memory 2019-07-04T09:26:40 self.allocated = 0 2019-07-04T09:26:40 free(self.segments) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:470:17: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 :meth:`SegmentList.normalize`. 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 cdef size_t new_size 2019-07-04T09:26:40 new_size = other.nsegments + self.nsegments 2019-07-04T09:26:40 if self.allocated == 0: 2019-07-04T09:26:40 self.segments = malloc( new_size * sizeof( Segment ) ) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:497:29: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.segments = malloc( new_size * sizeof( Segment ) ) 2019-07-04T09:26:40 if not self.segments: 2019-07-04T09:26:40 raise MemoryError( "out of memory when allocation %i bytes" % sizeof( new_size * sizeof( Segment ) )) 2019-07-04T09:26:40 self.allocated = new_size 2019-07-04T09:26:40 elif new_size >= self.allocated: 2019-07-04T09:26:40 self.segments = realloc( self.segments, new_size * sizeof( Segment ) ) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:502:29: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 elif new_size >= self.allocated: 2019-07-04T09:26:40 self.segments = realloc( self.segments, new_size * sizeof( Segment ) ) 2019-07-04T09:26:40 if not self.segments: 2019-07-04T09:26:40 raise MemoryError( "out of memory when allocation %i bytes" % sizeof( new_size * sizeof( Segment ) )) 2019-07-04T09:26:40 self.allocated = new_size 2019-07-04T09:26:40 memcpy( &self.segments[self.nsegments], 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:506:16: Cannot take address of Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.segments = realloc( self.segments, new_size * sizeof( Segment ) ) 2019-07-04T09:26:40 if not self.segments: 2019-07-04T09:26:40 raise MemoryError( "out of memory when allocation %i bytes" % sizeof( new_size * sizeof( Segment ) )) 2019-07-04T09:26:40 self.allocated = new_size 2019-07-04T09:26:40 memcpy( &self.segments[self.nsegments], 2019-07-04T09:26:40 other.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:507:22: Cannot convert Python object to 'const void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 The list will not be normalized automatically - call 2019-07-04T09:26:40 :meth:`SegmentList.normalize`. 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 if self.allocated == 0: 2019-07-04T09:26:40 self.segments = malloc(self.chunk_size * sizeof(Segment)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:521:29: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 raise MemoryError("out of memory when allocation %i bytes" % 2019-07-04T09:26:40 sizeof( self.chunk_size * sizeof(Segment))) 2019-07-04T09:26:40 self.allocated = self.chunk_size 2019-07-04T09:26:40 elif self.nsegments == self.allocated: 2019-07-04T09:26:40 self.allocated *= 2 2019-07-04T09:26:40 self.segments = realloc(self.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:528:29: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 raise MemoryError("out of memory when allocation %i bytes" % 2019-07-04T09:26:40 sizeof( self.chunk_size * sizeof(Segment))) 2019-07-04T09:26:40 self.allocated = self.chunk_size 2019-07-04T09:26:40 elif self.nsegments == self.allocated: 2019-07-04T09:26:40 self.allocated *= 2 2019-07-04T09:26:40 self.segments = realloc(self.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:528:50: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 l = segment_length( seg ) 2019-07-04T09:26:40 if segment_length( seg ) < s: 2019-07-04T09:26:40 self.segments[idx] = Segment(0,0) 2019-07-04T09:26:40 s -= l 2019-07-04T09:26:40 else: 2019-07-04T09:26:40 self.segments[idx] = Segment( seg.start, seg.end - s ) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:591:62: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 nsegments = 1 2019-07-04T09:26:40 assert nsegments >= self.nsegments, "resizing will loose segments" 2019-07-04T09:26:40 if self.allocated == 0: 2019-07-04T09:26:40 self.segments = malloc(nsegments * sizeof(Segment)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:608:29: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.segments = malloc(nsegments * sizeof(Segment)) 2019-07-04T09:26:40 if not self.segments: 2019-07-04T09:26:40 raise MemoryError("out of memory when allocation %i bytes" % 2019-07-04T09:26:40 sizeof(nsegments * sizeof(Segment))) 2019-07-04T09:26:40 else: 2019-07-04T09:26:40 self.segments = realloc(self.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:613:29: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.segments = malloc(nsegments * sizeof(Segment)) 2019-07-04T09:26:40 if not self.segments: 2019-07-04T09:26:40 raise MemoryError("out of memory when allocation %i bytes" % 2019-07-04T09:26:40 sizeof(nsegments * sizeof(Segment))) 2019-07-04T09:26:40 else: 2019-07-04T09:26:40 self.segments = realloc(self.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:613:50: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 idx = max(idx, self.nsegments) 2019-07-04T09:26:40 if self.allocated == self.nsegments: 2019-07-04T09:26:40 self._resize(self.allocated * 2) 2019-07-04T09:26:40 memmove(&self.segments[idx+1], 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:630:16: Cannot take address of Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 idx = max(idx, self.nsegments) 2019-07-04T09:26:40 if self.allocated == self.nsegments: 2019-07-04T09:26:40 self._resize(self.allocated * 2) 2019-07-04T09:26:40 memmove(&self.segments[idx+1], 2019-07-04T09:26:40 &self.segments[idx], 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:631:16: Cannot take address of Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 #assert p < self.segments[idx].end, "pos=%i, %i, %s, %s" % (p, idx, str(self.segments[idx]), str(self.asList())) 2019-07-04T09:26:40 while s > 0: 2019-07-04T09:26:40 seg = self.segments[idx] 2019-07-04T09:26:40 l = self.segments[idx].end - p 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:673:17: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if self.segments[idx].start == self.segments[idx].end: 2019-07-04T09:26:40 idx += 1 2019-07-04T09:26:40 continue 2019-07-04T09:26:40 # no overlap - save segment 2019-07-04T09:26:40 # note the cange from > to >= 2019-07-04T09:26:40 if self.segments[idx].start - distance > max_end: 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:801:16: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if other.start >= self.segments[self.nsegments-1].end: 2019-07-04T09:26:40 return self.nsegments 2019-07-04T09:26:40 if other.end <= self.segments[0].start: 2019-07-04T09:26:40 return -1 2019-07-04T09:26:40 idx = searchsorted(self.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:876:14: undeclared name not builtin: searchsorted 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 idx = searchsorted(self.segments, 2019-07-04T09:26:40 self.nsegments, 2019-07-04T09:26:40 sizeof(Segment), 2019-07-04T09:26:40 &other, 2019-07-04T09:26:40 &cmpSegments) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:880:27: Cannot convert 'int (*)(const_void_ptr, const_void_ptr) nogil' to Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 cdef Position start = other.start 2019-07-04T09:26:40 cdef Position end = other.end 2019-07-04T09:26:40 for idx from 0 <= idx < self.nsegments: 2019-07-04T09:26:40 s = & self.segments[idx] 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1195:16: Cannot take address of Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef Segment * new_segments 2019-07-04T09:26:40 cdef size_t allocated 2019-07-04T09:26:40 # create new list with 10% overhead 2019-07-04T09:26:40 allocated = int(lmax( self.nsegments, other.nsegments) * 1.1) 2019-07-04T09:26:40 new_segments =malloc( allocated * sizeof( Segment ) ) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1235:23: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 while this_idx < self.nsegments and other_idx < other.nsegments: 2019-07-04T09:26:40 # re-allocated before adding 2019-07-04T09:26:40 if working_idx >= allocated: 2019-07-04T09:26:40 allocated *= 2 2019-07-04T09:26:40 new_segments = realloc(new_segments, allocated * sizeof(Segment)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1245:32: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if this_segment.start < this_segment.end: 2019-07-04T09:26:40 new_segments[working_idx].start = this_segment.start 2019-07-04T09:26:40 new_segments[working_idx].end = this_segment.end 2019-07-04T09:26:40 working_idx += 1 2019-07-04T09:26:40 free(self.segments) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1282:17: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 min_length = UINT32_MAX 2019-07-04T09:26:40 max_length = 0 2019-07-04T09:26:40 total_length = 0 2019-07-04T09:26:40 for idx from 0 <= idx < self.nsegments: 2019-07-04T09:26:40 s = & self.segments[idx] 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1304:16: Cannot take address of Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return 2019-07-04T09:26:40 cdef Segment * new_segments 2019-07-04T09:26:40 cdef size_t allocated 2019-07-04T09:26:40 # create new list 2019-07-04T09:26:40 new_segments =malloc( self.nsegments * sizeof(Segment)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1417:23: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 other_idx += 1 2019-07-04T09:26:40 else: 2019-07-04T09:26:40 this_idx += 1 2019-07-04T09:26:40 other_idx += 1 2019-07-04T09:26:40 free(self.segments) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1464:17: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef Segment * new_segments 2019-07-04T09:26:40 cdef size_t allocated 2019-07-04T09:26:40 # create new list with 10% overhead 2019-07-04T09:26:40 allocated = int(lmax(self.nsegments, other.nsegments) * 1.1) 2019-07-04T09:26:40 new_segments =malloc(allocated * sizeof(Segment)) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1497:23: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 new_segments[working_idx].end = lmin(this_segment.end, 2019-07-04T09:26:40 other_segment.end) 2019-07-04T09:26:40 working_idx += 1 2019-07-04T09:26:40 if working_idx >= allocated: 2019-07-04T09:26:40 allocated *= 2 2019-07-04T09:26:40 new_segments = realloc(new_segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1534:36: 'Segment' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 other_idx += 1 2019-07-04T09:26:40 else: 2019-07-04T09:26:40 this_idx += 1 2019-07-04T09:26:40 other_idx += 1 2019-07-04T09:26:40 free(self.segments) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1546:17: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 The segment list will not be normalized afterwards.''' 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 for idx from 0 <= idx < self.nsegments: 2019-07-04T09:26:40 s = &self.segments[idx] 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1562:16: Cannot take address of Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cdef double e_1 = (expansion - 1.0) / 2.0 2019-07-04T09:26:40 if expansion <= 0: raise ValueError( "invalid expansion: %f <= 0" % expansion) 2019-07-04T09:26:40 for idx from 0 <= idx < self.nsegments: 2019-07-04T09:26:40 s = &self.segments[idx] 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1586:16: Cannot take address of Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if expansion <= 0: raise ValueError( "invalid expansion: %f <= 0" % expansion) 2019-07-04T09:26:40 for idx from 0 <= idx < self.nsegments: 2019-07-04T09:26:40 s = &self.segments[idx] 2019-07-04T09:26:40 l = s.end - s.start 2019-07-04T09:26:40 extension = floor(l * e_1 ) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1588:25: 'PositionDifference' is not a type identifier 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 raises ValueError if segment coordinates become negative. 2019-07-04T09:26:40 ''' 2019-07-04T09:26:40 cdef int idx 2019-07-04T09:26:40 cdef Segment * s 2019-07-04T09:26:40 for idx from 0 <= idx < self.nsegments: 2019-07-04T09:26:40 s = &self.segments[idx] 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1601:16: Cannot take address of Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 self.flag = 1 2019-07-04T09:26:40 cpdef SegmentList clone(self): 2019-07-04T09:26:40 """return a copy of self.""" 2019-07-04T09:26:40 clone = SegmentList(allocate=self.nsegments) 2019-07-04T09:26:40 memcpy(clone.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1661:20: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 cpdef SegmentList clone(self): 2019-07-04T09:26:40 """return a copy of self.""" 2019-07-04T09:26:40 clone = SegmentList(allocate=self.nsegments) 2019-07-04T09:26:40 memcpy(clone.segments, 2019-07-04T09:26:40 self.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1662:19: Cannot convert Python object to 'const void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return self.nsegments 2019-07-04T09:26:40 def __dealloc__(self): 2019-07-04T09:26:40 cdef int fd 2019-07-04T09:26:40 if self.segments != NULL: 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1674:25: Invalid types for '!=' (Python object, void *) 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 if self.is_shared: 2019-07-04T09:26:40 if self.is_slave: 2019-07-04T09:26:40 pass 2019-07-04T09:26:40 else: 2019-07-04T09:26:40 # free shared memory as master 2019-07-04T09:26:40 munmap(self.segments, 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1681:31: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 # free shared memory as master 2019-07-04T09:26:40 munmap(self.segments, 2019-07-04T09:26:40 self.nsegments * sizeof(Segment)) 2019-07-04T09:26:40 else: 2019-07-04T09:26:40 # free private copy 2019-07-04T09:26:40 free(self.segments) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1685:25: Cannot convert Python object to 'void *' 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return -1 2019-07-04T09:26:40 cdef int l2 = len(other) 2019-07-04T09:26:40 if l2 - l1 != 0: 2019-07-04T09:26:40 return l2 - l1 2019-07-04T09:26:40 for idx from 0 <= idx < self.nsegments: 2019-07-04T09:26:40 x = cmpSegmentsStartAndEnd(&self.segments[idx], &other.segments[idx]) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1727:39: Cannot take address of Python object 2019-07-04T09:26:40 Error compiling Cython file: 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 ... 2019-07-04T09:26:40 return -1 2019-07-04T09:26:40 cdef int l2 = len(other) 2019-07-04T09:26:40 if l2 - l1 != 0: 2019-07-04T09:26:40 return l2 - l1 2019-07-04T09:26:40 for idx from 0 <= idx < self.nsegments: 2019-07-04T09:26:40 x = cmpSegmentsStartAndEnd(&self.segments[idx], &other.segments[idx]) 2019-07-04T09:26:40 ^ 2019-07-04T09:26:40 ------------------------------------------------------------ 2019-07-04T09:26:40 gat/SegmentList.pyx:1727:60: Cannot take address of Python object 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:41 """return number of positions overlapping between to Segments.""" 2019-07-04T09:26:41 return lmax(0, 2019-07-04T09:26:41 lmin( a.end, b.end) - 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:95:43: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:41 """return number of positions overlapping between to Segments.""" 2019-07-04T09:26:41 return lmax(0, 2019-07-04T09:26:41 lmin( a.end, b.end) - 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:95:43: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:41 """return number of positions overlapping between to Segments.""" 2019-07-04T09:26:41 return lmax(0, 2019-07-04T09:26:41 lmin( a.end, b.end) - 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:95:50: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:41 """return number of positions overlapping between to Segments.""" 2019-07-04T09:26:41 return lmax(0, 2019-07-04T09:26:41 lmin( a.end, b.end) - 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:95:50: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:41 """return number of positions overlapping between to Segments.""" 2019-07-04T09:26:41 return lmax(0, 2019-07-04T09:26:41 lmin( a.end, b.end) - 2019-07-04T09:26:41 lmax(a.start, b.start)) 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:96:42: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:41 """return number of positions overlapping between to Segments.""" 2019-07-04T09:26:41 return lmax(0, 2019-07-04T09:26:41 lmin( a.end, b.end) - 2019-07-04T09:26:41 lmax(a.start, b.start)) 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:96:42: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:41 """return number of positions overlapping between to Segments.""" 2019-07-04T09:26:41 return lmax(0, 2019-07-04T09:26:41 lmin( a.end, b.end) - 2019-07-04T09:26:41 lmax(a.start, b.start)) 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:96:51: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2019-07-04T09:26:41 """return number of positions overlapping between to Segments.""" 2019-07-04T09:26:41 return lmax(0, 2019-07-04T09:26:41 lmin( a.end, b.end) - 2019-07-04T09:26:41 lmax(a.start, b.start)) 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:96:51: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 lmin( aend, bend) - 2019-07-04T09:26:41 lmax(astart, bstart)) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:107:37: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 lmin( aend, bend) - 2019-07-04T09:26:41 lmax(astart, bstart)) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:107:37: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 lmin( aend, bend) - 2019-07-04T09:26:41 lmax(astart, bstart)) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:107:44: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 lmin( aend, bend) - 2019-07-04T09:26:41 lmax(astart, bstart)) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:107:44: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 lmax(astart, bstart)) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 lmax(a.start, b.start) 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:108:34: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 lmax(astart, bstart)) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 lmax(a.start, b.start) 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:108:34: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 lmax(astart, bstart)) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 lmax(a.start, b.start) 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:108:43: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 lmax(astart, bstart)) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 lmax(a.start, b.start) 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:108:43: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 lmax(a.start, b.start) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_length(Segment a) nogil: 2019-07-04T09:26:41 return a.end - a.start 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:112:32: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 lmax(a.start, b.start) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_length(Segment a) nogil: 2019-07-04T09:26:41 return a.end - a.start 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:112:32: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 lmax(a.start, b.start) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_length(Segment a) nogil: 2019-07-04T09:26:41 return a.end - a.start 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:112:60: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 return lmin(a.end, b.end) - \ 2019-07-04T09:26:41 lmax(a.start, b.start) 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef inline PositionDifference segment_length(Segment a) nogil: 2019-07-04T09:26:41 return a.end - a.start 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:112:60: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 cdef extern from *: 2019-07-04T09:26:41 ctypedef void * const_void_ptr "const void*" 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:41 return (s1).start - \ 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:120:46: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 cdef extern from *: 2019-07-04T09:26:41 ctypedef void * const_void_ptr "const void*" 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:41 return (s1).start - \ 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:120:46: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 ctypedef void * const_void_ptr "const void*" 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:41 return (s1).start - \ 2019-07-04T09:26:41 (s2).start 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:121:43: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 ctypedef void * const_void_ptr "const void*" 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:41 return (s1).start - \ 2019-07-04T09:26:41 (s2).start 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:121:43: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 (s2).start 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:41 cdef int x 2019-07-04T09:26:41 x = (s1).start - \ 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:126:43: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 (s2).start 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:41 cdef int x 2019-07-04T09:26:41 x = (s1).start - \ 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:126:43: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:41 cdef int x 2019-07-04T09:26:41 x = (s1).start - \ 2019-07-04T09:26:41 (s2).start 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:127:43: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 @cython.profile(False) 2019-07-04T09:26:41 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2019-07-04T09:26:41 cdef int x 2019-07-04T09:26:41 x = (s1).start - \ 2019-07-04T09:26:41 (s2).start 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:127:43: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 cdef int x 2019-07-04T09:26:41 x = (s1).start - \ 2019-07-04T09:26:41 (s2).start 2019-07-04T09:26:41 if x != 0: 2019-07-04T09:26:41 return x 2019-07-04T09:26:41 return (s1).end - \ 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:130:46: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 cdef int x 2019-07-04T09:26:41 x = (s1).start - \ 2019-07-04T09:26:41 (s2).start 2019-07-04T09:26:41 if x != 0: 2019-07-04T09:26:41 return x 2019-07-04T09:26:41 return (s1).end - \ 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:130:46: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 x = (s1).start - \ 2019-07-04T09:26:41 (s2).start 2019-07-04T09:26:41 if x != 0: 2019-07-04T09:26:41 return x 2019-07-04T09:26:41 return (s1).end - \ 2019-07-04T09:26:41 (s2).end 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:131:43: Coercion from Python not allowed without the GIL 2019-07-04T09:26:41 Error compiling Cython file: 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 ... 2019-07-04T09:26:41 x = (s1).start - \ 2019-07-04T09:26:41 (s2).start 2019-07-04T09:26:41 if x != 0: 2019-07-04T09:26:41 return x 2019-07-04T09:26:41 return (s1).end - \ 2019-07-04T09:26:41 (s2).end 2019-07-04T09:26:41 ^ 2019-07-04T09:26:41 ------------------------------------------------------------ 2019-07-04T09:26:41 gat/SegmentList.pyx:131:43: Accessing Python attribute not allowed without gil 2019-07-04T09:26:41 building 'gat.SegmentList' extension 2019-07-04T09:26:41 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I./utils -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c gat/SegmentList.c -o build/temp.linux-armv7l-3.7/gat/SegmentList.o 2019-07-04T09:26:41 gat/SegmentList.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation. 2019-07-04T09:26:41 #error Do not use this file, it is the result of a failed Cython compilation. 2019-07-04T09:26:41 ^~~~~ 2019-07-04T09:26:41 error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1 2019-07-04T09:26:42 Building wheel for gat (setup.py): finished with status 'error' 2019-07-04T09:26:42 ERROR: Failed building wheel for gat 2019-07-04T09:26:42 Running setup.py clean for gat 2019-07-04T09:26:42 Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-p2yamkmb/gat/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2019-07-04T09:26:44 running clean 2019-07-04T09:26:44 removing 'build/temp.linux-armv7l-3.7' (and everything under it) 2019-07-04T09:26:44 removing 'build/lib.linux-armv7l-3.7' (and everything under it) 2019-07-04T09:26:44 'build/bdist.linux-armv7l' does not exist -- can't clean it 2019-07-04T09:26:44 'build/scripts-3.7' does not exist -- can't clean it 2019-07-04T09:26:44 removing 'build' 2019-07-04T09:26:44 Failed to build gat 2019-07-04T09:26:44 Cleaning up... 2019-07-04T09:26:44 Removing source in /tmp/pip-wheel-p2yamkmb/gat 2019-07-04T09:26:44 Removed build tracker '/tmp/pip-req-tracker-m7lnvdas' 2019-07-04T09:26:44 ERROR: Failed to build one or more wheels 2019-07-04T09:26:44 Exception information: 2019-07-04T09:26:44 Traceback (most recent call last): 2019-07-04T09:26:44 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 178, in main 2019-07-04T09:26:44 status = self.run(options, args) 2019-07-04T09:26:44 File "/home/piwheels/.local/lib/python3.7/site-packages/pip/_internal/commands/wheel.py", line 178, in run 2019-07-04T09:26:44 "Failed to build one or more wheels" 2019-07-04T09:26:44 pip._internal.exceptions.CommandError: Failed to build one or more wheels