2021-07-12T08:16:07,970 Created temporary directory: /tmp/pip-ephem-wheel-cache-1ncxnf88 2021-07-12T08:16:07,973 Created temporary directory: /tmp/pip-req-tracker-nj0p_fwh 2021-07-12T08:16:07,973 Initialized build tracking at /tmp/pip-req-tracker-nj0p_fwh 2021-07-12T08:16:07,974 Created build tracker: /tmp/pip-req-tracker-nj0p_fwh 2021-07-12T08:16:07,974 Entered build tracker: /tmp/pip-req-tracker-nj0p_fwh 2021-07-12T08:16:07,974 Created temporary directory: /tmp/pip-wheel-sammuaxk 2021-07-12T08:16:08,004 1 location(s) to search for versions of gat: 2021-07-12T08:16:08,004 * https://pypi.org/simple/gat/ 2021-07-12T08:16:08,005 Fetching project page and analyzing links: https://pypi.org/simple/gat/ 2021-07-12T08:16:08,005 Getting page https://pypi.org/simple/gat/ 2021-07-12T08:16:08,007 Found index url https://pypi.org/simple 2021-07-12T08:16:08,192 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 2021-07-12T08:16:08,192 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 2021-07-12T08:16:08,193 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 2021-07-12T08:16:08,193 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 2021-07-12T08:16:08,193 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 2021-07-12T08:16:08,193 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 2021-07-12T08:16:08,194 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 2021-07-12T08:16:08,194 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 2021-07-12T08:16:08,194 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 2021-07-12T08:16:08,195 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 2021-07-12T08:16:08,195 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 2021-07-12T08:16:08,195 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 2021-07-12T08:16:08,195 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 2021-07-12T08:16:08,196 Skipping link: not a file: https://pypi.org/simple/gat/ 2021-07-12T08:16:08,215 Given no hashes to check 1 links for project 'gat': discarding no candidates 2021-07-12T08:16:08,233 Collecting gat==1.3.1 2021-07-12T08:16:08,235 Created temporary directory: /tmp/pip-unpack-4zfzhphd 2021-07-12T08:16:08,534 Downloading gat-1.3.1.tar.gz (89 kB) 2021-07-12T08:16:08,663 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-nj0p_fwh' 2021-07-12T08:16:08,664 Running setup.py (path:/tmp/pip-wheel-sammuaxk/gat_98fddb3111d94ae9bf647f384bede459/setup.py) egg_info for package gat 2021-07-12T08:16:08,665 Created temporary directory: /tmp/pip-pip-egg-info-xoh0k8o5 2021-07-12T08:16:08,665 Running command python setup.py egg_info 2021-07-12T08:16:09,963 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'distribution-name' will not be supported in future versions. Please use the underscore name 'distribution_name' instead 2021-07-12T08:16:09,964 warnings.warn( 2021-07-12T08:16:10,090 running egg_info 2021-07-12T08:16:10,092 creating /tmp/pip-pip-egg-info-xoh0k8o5/gat.egg-info 2021-07-12T08:16:10,093 writing /tmp/pip-pip-egg-info-xoh0k8o5/gat.egg-info/PKG-INFO 2021-07-12T08:16:10,095 writing dependency_links to /tmp/pip-pip-egg-info-xoh0k8o5/gat.egg-info/dependency_links.txt 2021-07-12T08:16:10,097 writing requirements to /tmp/pip-pip-egg-info-xoh0k8o5/gat.egg-info/requires.txt 2021-07-12T08:16:10,098 writing top-level names to /tmp/pip-pip-egg-info-xoh0k8o5/gat.egg-info/top_level.txt 2021-07-12T08:16:10,099 writing manifest file '/tmp/pip-pip-egg-info-xoh0k8o5/gat.egg-info/SOURCES.txt' 2021-07-12T08:16:10,249 reading manifest file '/tmp/pip-pip-egg-info-xoh0k8o5/gat.egg-info/SOURCES.txt' 2021-07-12T08:16:10,250 reading manifest template 'MANIFEST.in' 2021-07-12T08:16:10,251 warning: no files found matching 'COPYING' 2021-07-12T08:16:10,251 warning: no files found matching 'INSTALL' 2021-07-12T08:16:10,252 warning: no files found matching 'KNOWN_BUGS' 2021-07-12T08:16:10,252 warning: no files found matching 'THANKS' 2021-07-12T08:16:10,253 warning: no files found matching 'GatEngine/GatEngine.*' 2021-07-12T08:16:10,253 warning: no files found matching 'GatSegmentList/GatSegmentList.*' 2021-07-12T08:16:10,257 writing manifest file '/tmp/pip-pip-egg-info-xoh0k8o5/gat.egg-info/SOURCES.txt' 2021-07-12T08:16:10,354 Source in /tmp/pip-wheel-sammuaxk/gat_98fddb3111d94ae9bf647f384bede459 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 2021-07-12T08:16:10,355 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-nj0p_fwh' 2021-07-12T08:16:10,360 Created temporary directory: /tmp/pip-unpack-q2113n23 2021-07-12T08:16:10,360 Building wheels for collected packages: gat 2021-07-12T08:16:10,364 Created temporary directory: /tmp/pip-wheel-2vzeu_w_ 2021-07-12T08:16:10,365 Building wheel for gat (setup.py): started 2021-07-12T08:16:10,365 Destination directory: /tmp/pip-wheel-2vzeu_w_ 2021-07-12T08:16:10,365 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-sammuaxk/gat_98fddb3111d94ae9bf647f384bede459/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-sammuaxk/gat_98fddb3111d94ae9bf647f384bede459/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-2vzeu_w_ 2021-07-12T08:16:11,588 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'distribution-name' will not be supported in future versions. Please use the underscore name 'distribution_name' instead 2021-07-12T08:16:11,588 warnings.warn( 2021-07-12T08:16:11,726 running bdist_wheel 2021-07-12T08:16:11,730 running build 2021-07-12T08:16:11,730 running build_py 2021-07-12T08:16:11,862 creating build 2021-07-12T08:16:11,862 creating build/lib.linux-armv7l-3.9 2021-07-12T08:16:11,863 creating build/lib.linux-armv7l-3.9/gat 2021-07-12T08:16:11,864 copying gat/Stats.py -> build/lib.linux-armv7l-3.9/gat 2021-07-12T08:16:11,867 copying gat/__init__.py -> build/lib.linux-armv7l-3.9/gat 2021-07-12T08:16:11,870 copying gat/Bed.py -> build/lib.linux-armv7l-3.9/gat 2021-07-12T08:16:11,872 copying gat/IO.py -> build/lib.linux-armv7l-3.9/gat 2021-07-12T08:16:11,875 copying gat/IOTools.py -> build/lib.linux-armv7l-3.9/gat 2021-07-12T08:16:11,878 copying gat/Experiment.py -> build/lib.linux-armv7l-3.9/gat 2021-07-12T08:16:11,881 running build_ext 2021-07-12T08:16:11,948 cythoning gat/CoordinateList.pyx to gat/CoordinateList.c 2021-07-12T08:16:12,566 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-sammuaxk/gat_98fddb3111d94ae9bf647f384bede459/gat/CoordinateList.pyx 2021-07-12T08:16:12,566 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T08:16:12,846 cythoning gat/SegmentList.pyx to gat/SegmentList.c 2021-07-12T08:16:12,857 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-sammuaxk/gat_98fddb3111d94ae9bf647f384bede459/gat/SegmentList.pyx 2021-07-12T08:16:12,857 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T08:16:16,688 Error compiling Cython file: 2021-07-12T08:16:16,688 ------------------------------------------------------------ 2021-07-12T08:16:16,688 ... 2021-07-12T08:16:16,688 return sizeof(Segment) // 2, sizeof(Segment) 2021-07-12T08:16:16,688 # min/max are not optimized, so declare them as C functions 2021-07-12T08:16:16,688 # declare as signed comparisons as a Position might be negative 2021-07-12T08:16:16,689 @cython.profile(False) 2021-07-12T08:16:16,689 cdef inline PositionDifference lmin(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:16,689 ^ 2021-07-12T08:16:16,689 ------------------------------------------------------------ 2021-07-12T08:16:16,689 gat/SegmentList.pyx:68:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,690 Error compiling Cython file: 2021-07-12T08:16:16,690 ------------------------------------------------------------ 2021-07-12T08:16:16,690 ... 2021-07-12T08:16:16,690 return sizeof(Segment) // 2, sizeof(Segment) 2021-07-12T08:16:16,690 # min/max are not optimized, so declare them as C functions 2021-07-12T08:16:16,690 # declare as signed comparisons as a Position might be negative 2021-07-12T08:16:16,690 @cython.profile(False) 2021-07-12T08:16:16,690 cdef inline PositionDifference lmin(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:16,691 ^ 2021-07-12T08:16:16,691 ------------------------------------------------------------ 2021-07-12T08:16:16,691 gat/SegmentList.pyx:68:36: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,691 Error compiling Cython file: 2021-07-12T08:16:16,691 ------------------------------------------------------------ 2021-07-12T08:16:16,691 ... 2021-07-12T08:16:16,692 return sizeof(Segment) // 2, sizeof(Segment) 2021-07-12T08:16:16,692 # min/max are not optimized, so declare them as C functions 2021-07-12T08:16:16,692 # declare as signed comparisons as a Position might be negative 2021-07-12T08:16:16,692 @cython.profile(False) 2021-07-12T08:16:16,692 cdef inline PositionDifference lmin(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:16,692 ^ 2021-07-12T08:16:16,693 ------------------------------------------------------------ 2021-07-12T08:16:16,693 gat/SegmentList.pyx:68:58: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,693 Error compiling Cython file: 2021-07-12T08:16:16,693 ------------------------------------------------------------ 2021-07-12T08:16:16,693 ... 2021-07-12T08:16:16,693 if a < b: 2021-07-12T08:16:16,693 return a 2021-07-12T08:16:16,694 return b 2021-07-12T08:16:16,694 @cython.profile(False) 2021-07-12T08:16:16,694 cdef inline PositionDifference lmax(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:16,694 ^ 2021-07-12T08:16:16,694 ------------------------------------------------------------ 2021-07-12T08:16:16,694 gat/SegmentList.pyx:74:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,695 Error compiling Cython file: 2021-07-12T08:16:16,695 ------------------------------------------------------------ 2021-07-12T08:16:16,695 ... 2021-07-12T08:16:16,695 if a < b: 2021-07-12T08:16:16,695 return a 2021-07-12T08:16:16,695 return b 2021-07-12T08:16:16,695 @cython.profile(False) 2021-07-12T08:16:16,696 cdef inline PositionDifference lmax(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:16,696 ^ 2021-07-12T08:16:16,696 ------------------------------------------------------------ 2021-07-12T08:16:16,696 gat/SegmentList.pyx:74:36: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,696 Error compiling Cython file: 2021-07-12T08:16:16,696 ------------------------------------------------------------ 2021-07-12T08:16:16,696 ... 2021-07-12T08:16:16,697 if a < b: 2021-07-12T08:16:16,697 return a 2021-07-12T08:16:16,697 return b 2021-07-12T08:16:16,697 @cython.profile(False) 2021-07-12T08:16:16,697 cdef inline PositionDifference lmax(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:16,697 ^ 2021-07-12T08:16:16,697 ------------------------------------------------------------ 2021-07-12T08:16:16,698 gat/SegmentList.pyx:74:58: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,698 Error compiling Cython file: 2021-07-12T08:16:16,698 ------------------------------------------------------------ 2021-07-12T08:16:16,698 ... 2021-07-12T08:16:16,698 if a > b: 2021-07-12T08:16:16,698 return a 2021-07-12T08:16:16,699 return b 2021-07-12T08:16:16,699 @cython.profile(False) 2021-07-12T08:16:16,699 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:16,699 ^ 2021-07-12T08:16:16,699 ------------------------------------------------------------ 2021-07-12T08:16:16,699 gat/SegmentList.pyx:92:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,700 Error compiling Cython file: 2021-07-12T08:16:16,700 ------------------------------------------------------------ 2021-07-12T08:16:16,700 ... 2021-07-12T08:16:16,700 if a > b: 2021-07-12T08:16:16,700 return a 2021-07-12T08:16:16,700 return b 2021-07-12T08:16:16,700 @cython.profile(False) 2021-07-12T08:16:16,701 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:16,701 ^ 2021-07-12T08:16:16,701 ------------------------------------------------------------ 2021-07-12T08:16:16,701 gat/SegmentList.pyx:92:47: 'Segment' is not a type identifier 2021-07-12T08:16:16,701 Error compiling Cython file: 2021-07-12T08:16:16,701 ------------------------------------------------------------ 2021-07-12T08:16:16,701 ... 2021-07-12T08:16:16,702 if a > b: 2021-07-12T08:16:16,702 return a 2021-07-12T08:16:16,702 return b 2021-07-12T08:16:16,702 @cython.profile(False) 2021-07-12T08:16:16,702 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:16,702 ^ 2021-07-12T08:16:16,703 ------------------------------------------------------------ 2021-07-12T08:16:16,703 gat/SegmentList.pyx:92:58: 'Segment' is not a type identifier 2021-07-12T08:16:16,703 Error compiling Cython file: 2021-07-12T08:16:16,703 ------------------------------------------------------------ 2021-07-12T08:16:16,703 ... 2021-07-12T08:16:16,703 return lmax(0, 2021-07-12T08:16:16,703 lmin( a.end, b.end) - 2021-07-12T08:16:16,704 lmax(a.start, b.start)) 2021-07-12T08:16:16,704 @cython.profile(False) 2021-07-12T08:16:16,704 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:16,704 ^ 2021-07-12T08:16:16,704 ------------------------------------------------------------ 2021-07-12T08:16:16,704 gat/SegmentList.pyx:99:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,705 Error compiling Cython file: 2021-07-12T08:16:16,705 ------------------------------------------------------------ 2021-07-12T08:16:16,705 ... 2021-07-12T08:16:16,705 lmin( a.end, b.end) - 2021-07-12T08:16:16,705 lmax(a.start, b.start)) 2021-07-12T08:16:16,705 @cython.profile(False) 2021-07-12T08:16:16,705 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:16,706 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:16,706 ^ 2021-07-12T08:16:16,706 ------------------------------------------------------------ 2021-07-12T08:16:16,706 gat/SegmentList.pyx:100:4: 'Position' is not a type identifier 2021-07-12T08:16:16,706 Error compiling Cython file: 2021-07-12T08:16:16,706 ------------------------------------------------------------ 2021-07-12T08:16:16,706 ... 2021-07-12T08:16:16,707 lmin( a.end, b.end) - 2021-07-12T08:16:16,707 lmax(a.start, b.start)) 2021-07-12T08:16:16,707 @cython.profile(False) 2021-07-12T08:16:16,707 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:16,707 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:16,707 ^ 2021-07-12T08:16:16,707 ------------------------------------------------------------ 2021-07-12T08:16:16,708 gat/SegmentList.pyx:100:21: 'Position' is not a type identifier 2021-07-12T08:16:16,708 Error compiling Cython file: 2021-07-12T08:16:16,708 ------------------------------------------------------------ 2021-07-12T08:16:16,708 ... 2021-07-12T08:16:16,708 lmin( a.end, b.end) - 2021-07-12T08:16:16,708 lmax(a.start, b.start)) 2021-07-12T08:16:16,709 @cython.profile(False) 2021-07-12T08:16:16,709 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:16,709 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:16,709 ^ 2021-07-12T08:16:16,709 ------------------------------------------------------------ 2021-07-12T08:16:16,709 gat/SegmentList.pyx:100:36: 'Position' is not a type identifier 2021-07-12T08:16:16,709 Error compiling Cython file: 2021-07-12T08:16:16,710 ------------------------------------------------------------ 2021-07-12T08:16:16,710 ... 2021-07-12T08:16:16,710 lmin( a.end, b.end) - 2021-07-12T08:16:16,710 lmax(a.start, b.start)) 2021-07-12T08:16:16,710 @cython.profile(False) 2021-07-12T08:16:16,710 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:16,710 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:16,710 ^ 2021-07-12T08:16:16,711 ------------------------------------------------------------ 2021-07-12T08:16:16,711 gat/SegmentList.pyx:100:53: 'Position' is not a type identifier 2021-07-12T08:16:16,711 Error compiling Cython file: 2021-07-12T08:16:16,711 ------------------------------------------------------------ 2021-07-12T08:16:16,711 ... 2021-07-12T08:16:16,711 return lmax(0, 2021-07-12T08:16:16,712 lmin( aend, bend) - 2021-07-12T08:16:16,712 lmax(astart, bstart)) 2021-07-12T08:16:16,712 @cython.profile(False) 2021-07-12T08:16:16,712 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:16,712 ^ 2021-07-12T08:16:16,712 ------------------------------------------------------------ 2021-07-12T08:16:16,713 gat/SegmentList.pyx:106:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,713 Error compiling Cython file: 2021-07-12T08:16:16,713 ------------------------------------------------------------ 2021-07-12T08:16:16,713 ... 2021-07-12T08:16:16,713 return lmax(0, 2021-07-12T08:16:16,713 lmin( aend, bend) - 2021-07-12T08:16:16,713 lmax(astart, bstart)) 2021-07-12T08:16:16,714 @cython.profile(False) 2021-07-12T08:16:16,714 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:16,714 ^ 2021-07-12T08:16:16,714 ------------------------------------------------------------ 2021-07-12T08:16:16,714 gat/SegmentList.pyx:106:51: 'Segment' is not a type identifier 2021-07-12T08:16:16,714 Error compiling Cython file: 2021-07-12T08:16:16,714 ------------------------------------------------------------ 2021-07-12T08:16:16,715 ... 2021-07-12T08:16:16,715 return lmax(0, 2021-07-12T08:16:16,715 lmin( aend, bend) - 2021-07-12T08:16:16,715 lmax(astart, bstart)) 2021-07-12T08:16:16,715 @cython.profile(False) 2021-07-12T08:16:16,715 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:16,715 ^ 2021-07-12T08:16:16,716 ------------------------------------------------------------ 2021-07-12T08:16:16,716 gat/SegmentList.pyx:106:62: 'Segment' is not a type identifier 2021-07-12T08:16:16,716 Error compiling Cython file: 2021-07-12T08:16:16,716 ------------------------------------------------------------ 2021-07-12T08:16:16,716 ... 2021-07-12T08:16:16,716 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:16,716 return lmin(a.end, b.end) - \ 2021-07-12T08:16:16,717 lmax(a.start, b.start) 2021-07-12T08:16:16,717 @cython.profile(False) 2021-07-12T08:16:16,717 cdef inline PositionDifference segment_length(Segment a) nogil: 2021-07-12T08:16:16,717 ^ 2021-07-12T08:16:16,717 ------------------------------------------------------------ 2021-07-12T08:16:16,717 gat/SegmentList.pyx:111:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,718 Error compiling Cython file: 2021-07-12T08:16:16,718 ------------------------------------------------------------ 2021-07-12T08:16:16,718 ... 2021-07-12T08:16:16,718 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:16,718 return lmin(a.end, b.end) - \ 2021-07-12T08:16:16,718 lmax(a.start, b.start) 2021-07-12T08:16:16,718 @cython.profile(False) 2021-07-12T08:16:16,719 cdef inline PositionDifference segment_length(Segment a) nogil: 2021-07-12T08:16:16,719 ^ 2021-07-12T08:16:16,719 ------------------------------------------------------------ 2021-07-12T08:16:16,719 gat/SegmentList.pyx:111:46: 'Segment' is not a type identifier 2021-07-12T08:16:16,719 Error compiling Cython file: 2021-07-12T08:16:16,719 ------------------------------------------------------------ 2021-07-12T08:16:16,719 ... 2021-07-12T08:16:16,720 other.nsegments * sizeof(Segment ) ) 2021-07-12T08:16:16,720 self.nsegments = new_size 2021-07-12T08:16:16,720 self.flag = 0 2021-07-12T08:16:16,720 return self 2021-07-12T08:16:16,720 cdef _add(self, Segment segment): 2021-07-12T08:16:16,720 ^ 2021-07-12T08:16:16,720 ------------------------------------------------------------ 2021-07-12T08:16:16,720 gat/SegmentList.pyx:513:20: 'Segment' is not a type identifier 2021-07-12T08:16:16,721 Error compiling Cython file: 2021-07-12T08:16:16,721 ------------------------------------------------------------ 2021-07-12T08:16:16,721 ... 2021-07-12T08:16:16,721 self.segments[self.nsegments] = segment 2021-07-12T08:16:16,721 self.nsegments += 1 2021-07-12T08:16:16,721 self.flag = 0 2021-07-12T08:16:16,722 cpdef add(self, Position start, Position end): 2021-07-12T08:16:16,722 ^ 2021-07-12T08:16:16,722 ------------------------------------------------------------ 2021-07-12T08:16:16,722 gat/SegmentList.pyx:539:20: 'Position' is not a type identifier 2021-07-12T08:16:16,722 Error compiling Cython file: 2021-07-12T08:16:16,722 ------------------------------------------------------------ 2021-07-12T08:16:16,723 ... 2021-07-12T08:16:16,723 self.segments[self.nsegments] = segment 2021-07-12T08:16:16,723 self.nsegments += 1 2021-07-12T08:16:16,723 self.flag = 0 2021-07-12T08:16:16,723 cpdef add(self, Position start, Position end): 2021-07-12T08:16:16,723 ^ 2021-07-12T08:16:16,723 ------------------------------------------------------------ 2021-07-12T08:16:16,724 gat/SegmentList.pyx:539:36: 'Position' is not a type identifier 2021-07-12T08:16:16,724 Error compiling Cython file: 2021-07-12T08:16:16,724 ------------------------------------------------------------ 2021-07-12T08:16:16,724 ... 2021-07-12T08:16:16,724 cdef Segment segment 2021-07-12T08:16:16,724 assert start <= end, "attempting to add invalid segment %i-%i" % (start, end) 2021-07-12T08:16:16,724 segment = Segment(start, end) 2021-07-12T08:16:16,725 self._add(segment) 2021-07-12T08:16:16,725 cpdef trim_ends( self, Position pos, Position size, int forward ): 2021-07-12T08:16:16,725 ^ 2021-07-12T08:16:16,725 ------------------------------------------------------------ 2021-07-12T08:16:16,725 gat/SegmentList.pyx:545:27: 'Position' is not a type identifier 2021-07-12T08:16:16,726 Error compiling Cython file: 2021-07-12T08:16:16,726 ------------------------------------------------------------ 2021-07-12T08:16:16,726 ... 2021-07-12T08:16:16,726 cdef Segment segment 2021-07-12T08:16:16,726 assert start <= end, "attempting to add invalid segment %i-%i" % (start, end) 2021-07-12T08:16:16,726 segment = Segment(start, end) 2021-07-12T08:16:16,726 self._add(segment) 2021-07-12T08:16:16,727 cpdef trim_ends( self, Position pos, Position size, int forward ): 2021-07-12T08:16:16,727 ^ 2021-07-12T08:16:16,727 ------------------------------------------------------------ 2021-07-12T08:16:16,727 gat/SegmentList.pyx:545:41: 'Position' is not a type identifier 2021-07-12T08:16:16,727 Error compiling Cython file: 2021-07-12T08:16:16,727 ------------------------------------------------------------ 2021-07-12T08:16:16,727 ... 2021-07-12T08:16:16,727 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:16,728 sizeof(self.nsegments * sizeof(Segment))) 2021-07-12T08:16:16,728 self.allocated = nsegments 2021-07-12T08:16:16,728 cdef insert(self, int idx, Segment seg): 2021-07-12T08:16:16,728 ^ 2021-07-12T08:16:16,728 ------------------------------------------------------------ 2021-07-12T08:16:16,728 gat/SegmentList.pyx:621:31: 'Segment' is not a type identifier 2021-07-12T08:16:16,729 Error compiling Cython file: 2021-07-12T08:16:16,729 ------------------------------------------------------------ 2021-07-12T08:16:16,729 ... 2021-07-12T08:16:16,729 sizeof(Segment) * (self.nsegments - idx)) 2021-07-12T08:16:16,729 self.nsegments += 1 2021-07-12T08:16:16,729 self.segments[idx] = seg 2021-07-12T08:16:16,730 cpdef trim(self, Position pos, Position size): 2021-07-12T08:16:16,730 ^ 2021-07-12T08:16:16,730 ------------------------------------------------------------ 2021-07-12T08:16:16,730 gat/SegmentList.pyx:637:21: 'Position' is not a type identifier 2021-07-12T08:16:16,730 Error compiling Cython file: 2021-07-12T08:16:16,730 ------------------------------------------------------------ 2021-07-12T08:16:16,730 ... 2021-07-12T08:16:16,731 sizeof(Segment) * (self.nsegments - idx)) 2021-07-12T08:16:16,731 self.nsegments += 1 2021-07-12T08:16:16,731 self.segments[idx] = seg 2021-07-12T08:16:16,731 cpdef trim(self, Position pos, Position size): 2021-07-12T08:16:16,731 ^ 2021-07-12T08:16:16,731 ------------------------------------------------------------ 2021-07-12T08:16:16,732 gat/SegmentList.pyx:637:35: 'Position' is not a type identifier 2021-07-12T08:16:16,732 Error compiling Cython file: 2021-07-12T08:16:16,732 ------------------------------------------------------------ 2021-07-12T08:16:16,732 ... 2021-07-12T08:16:16,732 insertion_idx += 1 2021-07-12T08:16:16,732 self.nsegments = insertion_idx 2021-07-12T08:16:16,732 self._resize(self.nsegments) 2021-07-12T08:16:16,732 self.flag = 1 2021-07-12T08:16:16,733 cpdef merge(self, PositionDifference distance): 2021-07-12T08:16:16,733 ^ 2021-07-12T08:16:16,733 ------------------------------------------------------------ 2021-07-12T08:16:16,733 gat/SegmentList.pyx:756:22: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,733 Error compiling Cython file: 2021-07-12T08:16:16,733 ------------------------------------------------------------ 2021-07-12T08:16:16,734 ... 2021-07-12T08:16:16,734 self.flag = 1 2021-07-12T08:16:16,734 return self.flag 2021-07-12T08:16:16,734 cdef int _getInsertionPoint( self, Segment other ): 2021-07-12T08:16:16,734 ^ 2021-07-12T08:16:16,734 ------------------------------------------------------------ 2021-07-12T08:16:16,735 gat/SegmentList.pyx:853:39: 'Segment' is not a type identifier 2021-07-12T08:16:16,735 Error compiling Cython file: 2021-07-12T08:16:16,735 ------------------------------------------------------------ 2021-07-12T08:16:16,735 ... 2021-07-12T08:16:16,735 def __get__(self): return self.flag 2021-07-12T08:16:16,735 property isEmpty: 2021-07-12T08:16:16,736 def __get__(self): return self.nsegments == 0 2021-07-12T08:16:16,736 cpdef Position getRandomPosition(self): 2021-07-12T08:16:16,736 ^ 2021-07-12T08:16:16,736 ------------------------------------------------------------ 2021-07-12T08:16:16,736 gat/SegmentList.pyx:902:10: 'Position' is not a type identifier 2021-07-12T08:16:16,736 Error compiling Cython file: 2021-07-12T08:16:16,737 ------------------------------------------------------------ 2021-07-12T08:16:16,737 ... 2021-07-12T08:16:16,737 pos -= l 2021-07-12T08:16:16,737 else: 2021-07-12T08:16:16,737 return self.segments[idx].start + pos 2021-07-12T08:16:16,737 assert False 2021-07-12T08:16:16,737 cdef Position overlap(self, Segment other): 2021-07-12T08:16:16,737 ^ 2021-07-12T08:16:16,738 ------------------------------------------------------------ 2021-07-12T08:16:16,738 gat/SegmentList.pyx:919:9: 'Position' is not a type identifier 2021-07-12T08:16:16,738 Error compiling Cython file: 2021-07-12T08:16:16,738 ------------------------------------------------------------ 2021-07-12T08:16:16,738 ... 2021-07-12T08:16:16,738 pos -= l 2021-07-12T08:16:16,738 else: 2021-07-12T08:16:16,739 return self.segments[idx].start + pos 2021-07-12T08:16:16,739 assert False 2021-07-12T08:16:16,739 cdef Position overlap(self, Segment other): 2021-07-12T08:16:16,739 ^ 2021-07-12T08:16:16,739 ------------------------------------------------------------ 2021-07-12T08:16:16,739 gat/SegmentList.pyx:919:32: 'Segment' is not a type identifier 2021-07-12T08:16:16,740 Error compiling Cython file: 2021-07-12T08:16:16,740 ------------------------------------------------------------ 2021-07-12T08:16:16,740 ... 2021-07-12T08:16:16,740 while idx < self.nsegments and self.segments[idx].start <= other.end: 2021-07-12T08:16:16,740 count += segment_overlap(self.segments[idx], other) 2021-07-12T08:16:16,740 idx += 1 2021-07-12T08:16:16,740 return count 2021-07-12T08:16:16,740 cdef SegmentList getOverlappingSegments(self, Segment other): 2021-07-12T08:16:16,741 ^ 2021-07-12T08:16:16,741 ------------------------------------------------------------ 2021-07-12T08:16:16,741 gat/SegmentList.pyx:952:50: 'Segment' is not a type identifier 2021-07-12T08:16:16,741 Error compiling Cython file: 2021-07-12T08:16:16,741 ------------------------------------------------------------ 2021-07-12T08:16:16,741 ... 2021-07-12T08:16:16,741 while idx < self.nsegments and self.segments[idx].start <= other.end: 2021-07-12T08:16:16,742 result._add(self.segments[idx]) 2021-07-12T08:16:16,742 idx += 1 2021-07-12T08:16:16,742 return result 2021-07-12T08:16:16,742 cpdef Position overlapWithRange(self, Position start, Position end): 2021-07-12T08:16:16,742 ^ 2021-07-12T08:16:16,742 ------------------------------------------------------------ 2021-07-12T08:16:16,742 gat/SegmentList.pyx:985:10: 'Position' is not a type identifier 2021-07-12T08:16:16,743 Error compiling Cython file: 2021-07-12T08:16:16,743 ------------------------------------------------------------ 2021-07-12T08:16:16,743 ... 2021-07-12T08:16:16,743 while idx < self.nsegments and self.segments[idx].start <= other.end: 2021-07-12T08:16:16,743 result._add(self.segments[idx]) 2021-07-12T08:16:16,743 idx += 1 2021-07-12T08:16:16,743 return result 2021-07-12T08:16:16,744 cpdef Position overlapWithRange(self, Position start, Position end): 2021-07-12T08:16:16,744 ^ 2021-07-12T08:16:16,744 ------------------------------------------------------------ 2021-07-12T08:16:16,744 gat/SegmentList.pyx:985:42: 'Position' is not a type identifier 2021-07-12T08:16:16,744 Error compiling Cython file: 2021-07-12T08:16:16,744 ------------------------------------------------------------ 2021-07-12T08:16:16,744 ... 2021-07-12T08:16:16,745 while idx < self.nsegments and self.segments[idx].start <= other.end: 2021-07-12T08:16:16,745 result._add(self.segments[idx]) 2021-07-12T08:16:16,745 idx += 1 2021-07-12T08:16:16,745 return result 2021-07-12T08:16:16,745 cpdef Position overlapWithRange(self, Position start, Position end): 2021-07-12T08:16:16,745 ^ 2021-07-12T08:16:16,745 ------------------------------------------------------------ 2021-07-12T08:16:16,746 gat/SegmentList.pyx:985:58: 'Position' is not a type identifier 2021-07-12T08:16:16,746 Error compiling Cython file: 2021-07-12T08:16:16,746 ------------------------------------------------------------ 2021-07-12T08:16:16,746 ... 2021-07-12T08:16:16,746 cdef Segment s 2021-07-12T08:16:16,746 s = Segment(start, end) 2021-07-12T08:16:16,746 return self.overlap(s) 2021-07-12T08:16:16,747 cpdef SegmentList getOverlappingSegmentsWithRange( 2021-07-12T08:16:16,747 self, Position start, Position end): 2021-07-12T08:16:16,747 ^ 2021-07-12T08:16:16,747 ------------------------------------------------------------ 2021-07-12T08:16:16,747 gat/SegmentList.pyx:1006:14: 'Position' is not a type identifier 2021-07-12T08:16:16,747 Error compiling Cython file: 2021-07-12T08:16:16,747 ------------------------------------------------------------ 2021-07-12T08:16:16,748 ... 2021-07-12T08:16:16,748 cdef Segment s 2021-07-12T08:16:16,748 s = Segment(start, end) 2021-07-12T08:16:16,748 return self.overlap(s) 2021-07-12T08:16:16,748 cpdef SegmentList getOverlappingSegmentsWithRange( 2021-07-12T08:16:16,748 self, Position start, Position end): 2021-07-12T08:16:16,748 ^ 2021-07-12T08:16:16,748 ------------------------------------------------------------ 2021-07-12T08:16:16,749 gat/SegmentList.pyx:1006:30: 'Position' is not a type identifier 2021-07-12T08:16:16,749 Error compiling Cython file: 2021-07-12T08:16:16,749 ------------------------------------------------------------ 2021-07-12T08:16:16,749 ... 2021-07-12T08:16:16,749 cdef Segment s 2021-07-12T08:16:16,749 s = Segment(start, end) 2021-07-12T08:16:16,749 return self.getOverlappingSegments(s) 2021-07-12T08:16:16,750 cpdef Position overlapWithSegments(self, SegmentList other): 2021-07-12T08:16:16,750 ^ 2021-07-12T08:16:16,750 ------------------------------------------------------------ 2021-07-12T08:16:16,750 gat/SegmentList.pyx:1026:10: 'Position' is not a type identifier 2021-07-12T08:16:16,750 Error compiling Cython file: 2021-07-12T08:16:16,750 ------------------------------------------------------------ 2021-07-12T08:16:16,751 ... 2021-07-12T08:16:16,751 this_idx += 1 2021-07-12T08:16:16,751 other_idx += 1 2021-07-12T08:16:16,751 return overlap 2021-07-12T08:16:16,751 cpdef Position intersectionWithSegments( 2021-07-12T08:16:16,751 ^ 2021-07-12T08:16:16,751 ------------------------------------------------------------ 2021-07-12T08:16:16,752 gat/SegmentList.pyx:1078:10: 'Position' is not a type identifier 2021-07-12T08:16:16,752 Error compiling Cython file: 2021-07-12T08:16:16,752 ------------------------------------------------------------ 2021-07-12T08:16:16,752 ... 2021-07-12T08:16:16,752 l 2021-07-12T08:16:16,752 )) 2021-07-12T08:16:16,752 histogram[i] += 1 2021-07-12T08:16:16,753 return histogram, bucket_size 2021-07-12T08:16:16,753 cdef void truncate(self, Segment other): 2021-07-12T08:16:16,753 ^ 2021-07-12T08:16:16,753 ------------------------------------------------------------ 2021-07-12T08:16:16,753 gat/SegmentList.pyx:1186:29: 'Segment' is not a type identifier 2021-07-12T08:16:16,754 Error compiling Cython file: 2021-07-12T08:16:16,754 ------------------------------------------------------------ 2021-07-12T08:16:16,754 ... 2021-07-12T08:16:16,754 cdef double mean_length = total_length / self.nsegments 2021-07-12T08:16:16,754 return mean_length, min_length, max_length, total_length 2021-07-12T08:16:16,754 cpdef SegmentList getFilledSegmentsFromStart( self, Position start, PositionDifference remainder ): 2021-07-12T08:16:16,755 ^ 2021-07-12T08:16:16,755 ------------------------------------------------------------ 2021-07-12T08:16:16,755 gat/SegmentList.pyx:1314:56: 'Position' is not a type identifier 2021-07-12T08:16:16,755 Error compiling Cython file: 2021-07-12T08:16:16,755 ------------------------------------------------------------ 2021-07-12T08:16:16,755 ... 2021-07-12T08:16:16,756 cdef double mean_length = total_length / self.nsegments 2021-07-12T08:16:16,756 return mean_length, min_length, max_length, total_length 2021-07-12T08:16:16,756 cpdef SegmentList getFilledSegmentsFromStart( self, Position start, PositionDifference remainder ): 2021-07-12T08:16:16,756 ^ 2021-07-12T08:16:16,756 ------------------------------------------------------------ 2021-07-12T08:16:16,757 gat/SegmentList.pyx:1314:72: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,757 Error compiling Cython file: 2021-07-12T08:16:16,757 ------------------------------------------------------------ 2021-07-12T08:16:16,757 ... 2021-07-12T08:16:16,757 result.normalize() 2021-07-12T08:16:16,757 return result 2021-07-12T08:16:16,758 cpdef SegmentList getFilledSegmentsFromEnd( 2021-07-12T08:16:16,758 self, Position end, PositionDifference remainder): 2021-07-12T08:16:16,758 ^ 2021-07-12T08:16:16,758 ------------------------------------------------------------ 2021-07-12T08:16:16,758 gat/SegmentList.pyx:1358:14: 'Position' is not a type identifier 2021-07-12T08:16:16,758 Error compiling Cython file: 2021-07-12T08:16:16,758 ------------------------------------------------------------ 2021-07-12T08:16:16,759 ... 2021-07-12T08:16:16,759 result.normalize() 2021-07-12T08:16:16,759 return result 2021-07-12T08:16:16,759 cpdef SegmentList getFilledSegmentsFromEnd( 2021-07-12T08:16:16,759 self, Position end, PositionDifference remainder): 2021-07-12T08:16:16,759 ^ 2021-07-12T08:16:16,759 ------------------------------------------------------------ 2021-07-12T08:16:16,760 gat/SegmentList.pyx:1358:28: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,760 Error compiling Cython file: 2021-07-12T08:16:16,760 ------------------------------------------------------------ 2021-07-12T08:16:16,760 ... 2021-07-12T08:16:16,760 extension = floor(l * e_1 ) 2021-07-12T08:16:16,760 s.start -= lmin( extension, s.start) 2021-07-12T08:16:16,760 s.end += extension 2021-07-12T08:16:16,761 self.flag = False 2021-07-12T08:16:16,761 def shift(self, PositionDifference offset): 2021-07-12T08:16:16,761 ^ 2021-07-12T08:16:16,761 ------------------------------------------------------------ 2021-07-12T08:16:16,761 gat/SegmentList.pyx:1593:20: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,761 Error compiling Cython file: 2021-07-12T08:16:16,762 ------------------------------------------------------------ 2021-07-12T08:16:16,762 ... 2021-07-12T08:16:16,762 s.end += offset 2021-07-12T08:16:16,762 s.start += offset 2021-07-12T08:16:16,762 if s.start < 0: 2021-07-12T08:16:16,762 raise ValueError("shift creates negative coordinates") 2021-07-12T08:16:16,762 cpdef Position sum(self): 2021-07-12T08:16:16,762 ^ 2021-07-12T08:16:16,763 ------------------------------------------------------------ 2021-07-12T08:16:16,763 gat/SegmentList.pyx:1607:10: 'Position' is not a type identifier 2021-07-12T08:16:16,763 Error compiling Cython file: 2021-07-12T08:16:16,763 ------------------------------------------------------------ 2021-07-12T08:16:16,763 ... 2021-07-12T08:16:16,763 if l > max_value: 2021-07-12T08:16:16,763 max_idx = idx 2021-07-12T08:16:16,764 max_value = l 2021-07-12T08:16:16,764 return self.segments[max_idx] 2021-07-12T08:16:16,764 cpdef Position max(self): 2021-07-12T08:16:16,764 ^ 2021-07-12T08:16:16,764 ------------------------------------------------------------ 2021-07-12T08:16:16,764 gat/SegmentList.pyx:1638:10: 'Position' is not a type identifier 2021-07-12T08:16:16,765 Error compiling Cython file: 2021-07-12T08:16:16,765 ------------------------------------------------------------ 2021-07-12T08:16:16,765 ... 2021-07-12T08:16:16,765 '''return maximum coordinate.''' 2021-07-12T08:16:16,765 assert self.flag & SEG_NORMALIZED, "maximum from non-normalized list" 2021-07-12T08:16:16,765 if self.nsegments == 0: return 0 2021-07-12T08:16:16,765 return self.segments[self.nsegments - 1].end 2021-07-12T08:16:16,765 cpdef Position min(self): 2021-07-12T08:16:16,766 ^ 2021-07-12T08:16:16,766 ------------------------------------------------------------ 2021-07-12T08:16:16,766 gat/SegmentList.pyx:1644:10: 'Position' is not a type identifier 2021-07-12T08:16:16,766 Error compiling Cython file: 2021-07-12T08:16:16,766 ------------------------------------------------------------ 2021-07-12T08:16:16,766 ... 2021-07-12T08:16:16,766 # SegmentTuple = collections.namedtuple( "SegmentTuple", "start, end" ) 2021-07-12T08:16:16,767 cdef class SegmentListIterator: 2021-07-12T08:16:16,767 cdef SegmentList segment_list 2021-07-12T08:16:16,767 cdef Position idx 2021-07-12T08:16:16,767 ^ 2021-07-12T08:16:16,767 ------------------------------------------------------------ 2021-07-12T08:16:16,767 gat/SegmentList.pyx:1753:9: 'Position' is not a type identifier 2021-07-12T08:16:16,768 Error compiling Cython file: 2021-07-12T08:16:16,768 ------------------------------------------------------------ 2021-07-12T08:16:16,768 ... 2021-07-12T08:16:16,768 fd = shm_unlink(self.key) 2021-07-12T08:16:16,768 if fd == -1: 2021-07-12T08:16:16,768 raise OSError( "could not unlink shared memory" ) 2021-07-12T08:16:16,768 # copy data back to unshared memory 2021-07-12T08:16:16,769 cdef Segment * s 2021-07-12T08:16:16,769 ^ 2021-07-12T08:16:16,769 ------------------------------------------------------------ 2021-07-12T08:16:16,769 gat/SegmentList.pyx:410:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,769 Error compiling Cython file: 2021-07-12T08:16:16,769 ------------------------------------------------------------ 2021-07-12T08:16:16,769 ... 2021-07-12T08:16:16,770 cdef void fromMMAP(self): 2021-07-12T08:16:16,770 '''retrieve data from mmapped location to private copy. 2021-07-12T08:16:16,770 ''' 2021-07-12T08:16:16,770 # copy data back to unshared memory 2021-07-12T08:16:16,770 cdef Segment * s 2021-07-12T08:16:16,770 ^ 2021-07-12T08:16:16,770 ------------------------------------------------------------ 2021-07-12T08:16:16,771 gat/SegmentList.pyx:431:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,771 Error compiling Cython file: 2021-07-12T08:16:16,771 ------------------------------------------------------------ 2021-07-12T08:16:16,771 ... 2021-07-12T08:16:16,771 if self.nsegments == 0: 2021-07-12T08:16:16,771 # do not move empty segment lists 2021-07-12T08:16:16,771 return offset 2021-07-12T08:16:16,771 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2021-07-12T08:16:16,772 cdef Segment * p = mmap + offset 2021-07-12T08:16:16,772 ^ 2021-07-12T08:16:16,772 ------------------------------------------------------------ 2021-07-12T08:16:16,772 gat/SegmentList.pyx:463:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,772 Error compiling Cython file: 2021-07-12T08:16:16,772 ------------------------------------------------------------ 2021-07-12T08:16:16,773 ... 2021-07-12T08:16:16,773 self.segments[self.nsegments] = segment 2021-07-12T08:16:16,773 self.nsegments += 1 2021-07-12T08:16:16,773 self.flag = 0 2021-07-12T08:16:16,773 cpdef add(self, Position start, Position end): 2021-07-12T08:16:16,773 cdef Segment segment 2021-07-12T08:16:16,773 ^ 2021-07-12T08:16:16,773 ------------------------------------------------------------ 2021-07-12T08:16:16,774 gat/SegmentList.pyx:540:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,774 Error compiling Cython file: 2021-07-12T08:16:16,774 ------------------------------------------------------------ 2021-07-12T08:16:16,774 ... 2021-07-12T08:16:16,774 if self.nsegments == 0: return 2021-07-12T08:16:16,774 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2021-07-12T08:16:16,775 cdef int idx 2021-07-12T08:16:16,775 cdef Position l 2021-07-12T08:16:16,775 ^ 2021-07-12T08:16:16,775 ------------------------------------------------------------ 2021-07-12T08:16:16,775 gat/SegmentList.pyx:556:13: 'Position' is not a type identifier 2021-07-12T08:16:16,775 Error compiling Cython file: 2021-07-12T08:16:16,776 ------------------------------------------------------------ 2021-07-12T08:16:16,776 ... 2021-07-12T08:16:16,776 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2021-07-12T08:16:16,776 cdef int idx 2021-07-12T08:16:16,776 cdef Position l 2021-07-12T08:16:16,776 cdef PositionDifference s = size 2021-07-12T08:16:16,776 ^ 2021-07-12T08:16:16,777 ------------------------------------------------------------ 2021-07-12T08:16:16,777 gat/SegmentList.pyx:557:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,777 Error compiling Cython file: 2021-07-12T08:16:16,777 ------------------------------------------------------------ 2021-07-12T08:16:16,777 ... 2021-07-12T08:16:16,777 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2021-07-12T08:16:16,778 cdef int idx 2021-07-12T08:16:16,778 cdef Position l 2021-07-12T08:16:16,778 cdef PositionDifference s = size 2021-07-12T08:16:16,778 cdef Segment other, seg 2021-07-12T08:16:16,778 ^ 2021-07-12T08:16:16,778 ------------------------------------------------------------ 2021-07-12T08:16:16,778 gat/SegmentList.pyx:558:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,779 Error compiling Cython file: 2021-07-12T08:16:16,779 ------------------------------------------------------------ 2021-07-12T08:16:16,779 ... 2021-07-12T08:16:16,779 if self.nsegments == 0: return 2021-07-12T08:16:16,779 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2021-07-12T08:16:16,779 cdef int idx 2021-07-12T08:16:16,779 cdef PositionDifference l 2021-07-12T08:16:16,780 ^ 2021-07-12T08:16:16,780 ------------------------------------------------------------ 2021-07-12T08:16:16,780 gat/SegmentList.pyx:650:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,780 Error compiling Cython file: 2021-07-12T08:16:16,780 ------------------------------------------------------------ 2021-07-12T08:16:16,780 ... 2021-07-12T08:16:16,780 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2021-07-12T08:16:16,781 cdef int idx 2021-07-12T08:16:16,781 cdef PositionDifference l 2021-07-12T08:16:16,781 cdef PositionDifference s = size 2021-07-12T08:16:16,781 ^ 2021-07-12T08:16:16,781 ------------------------------------------------------------ 2021-07-12T08:16:16,781 gat/SegmentList.pyx:651:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,782 Error compiling Cython file: 2021-07-12T08:16:16,782 ------------------------------------------------------------ 2021-07-12T08:16:16,782 ... 2021-07-12T08:16:16,782 assert self.flag & SEG_NORMALIZED, "trimming in non-normalized list" 2021-07-12T08:16:16,782 cdef int idx 2021-07-12T08:16:16,782 cdef PositionDifference l 2021-07-12T08:16:16,782 cdef PositionDifference s = size 2021-07-12T08:16:16,783 cdef PositionDifference p = pos 2021-07-12T08:16:16,783 ^ 2021-07-12T08:16:16,783 ------------------------------------------------------------ 2021-07-12T08:16:16,783 gat/SegmentList.pyx:652:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,783 Error compiling Cython file: 2021-07-12T08:16:16,783 ------------------------------------------------------------ 2021-07-12T08:16:16,783 ... 2021-07-12T08:16:16,784 cdef int idx 2021-07-12T08:16:16,784 cdef PositionDifference l 2021-07-12T08:16:16,784 cdef PositionDifference s = size 2021-07-12T08:16:16,784 cdef PositionDifference p = pos 2021-07-12T08:16:16,784 cdef Segment other, seg 2021-07-12T08:16:16,784 ^ 2021-07-12T08:16:16,784 ------------------------------------------------------------ 2021-07-12T08:16:16,785 gat/SegmentList.pyx:653:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,785 Error compiling Cython file: 2021-07-12T08:16:16,785 ------------------------------------------------------------ 2021-07-12T08:16:16,785 ... 2021-07-12T08:16:16,785 This function works in-place. 2021-07-12T08:16:16,785 ''' 2021-07-12T08:16:16,786 cdef int idx, insertion_idx 2021-07-12T08:16:16,786 cdef Position max_end 2021-07-12T08:16:16,786 ^ 2021-07-12T08:16:16,786 ------------------------------------------------------------ 2021-07-12T08:16:16,786 gat/SegmentList.pyx:706:13: 'Position' is not a type identifier 2021-07-12T08:16:16,786 Error compiling Cython file: 2021-07-12T08:16:16,786 ------------------------------------------------------------ 2021-07-12T08:16:16,787 ... 2021-07-12T08:16:16,787 *n* bases will be merged. 2021-07-12T08:16:16,787 This function works in-place. 2021-07-12T08:16:16,787 ''' 2021-07-12T08:16:16,787 cdef PositionDifference max_end 2021-07-12T08:16:16,787 ^ 2021-07-12T08:16:16,787 ------------------------------------------------------------ 2021-07-12T08:16:16,788 gat/SegmentList.pyx:770:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,788 Error compiling Cython file: 2021-07-12T08:16:16,788 ------------------------------------------------------------ 2021-07-12T08:16:16,788 ... 2021-07-12T08:16:16,788 return self.flag 2021-07-12T08:16:16,788 self.flag = 0 2021-07-12T08:16:16,789 cdef int idx 2021-07-12T08:16:16,789 cdef Segment segment 2021-07-12T08:16:16,789 ^ 2021-07-12T08:16:16,789 ------------------------------------------------------------ 2021-07-12T08:16:16,789 gat/SegmentList.pyx:832:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,789 Error compiling Cython file: 2021-07-12T08:16:16,790 ------------------------------------------------------------ 2021-07-12T08:16:16,790 ... 2021-07-12T08:16:16,790 '''return a random position within the workspace. 2021-07-12T08:16:16,790 Not efficient, see the specialized samplers instead if 2021-07-12T08:16:16,790 you want to sample repeatedly from the same workspace. 2021-07-12T08:16:16,790 ''' 2021-07-12T08:16:16,790 cdef Position pos = numpy.random.randint( 0, self.sum() ) 2021-07-12T08:16:16,791 ^ 2021-07-12T08:16:16,791 ------------------------------------------------------------ 2021-07-12T08:16:16,791 gat/SegmentList.pyx:908:13: 'Position' is not a type identifier 2021-07-12T08:16:16,791 Error compiling Cython file: 2021-07-12T08:16:16,791 ------------------------------------------------------------ 2021-07-12T08:16:16,791 ... 2021-07-12T08:16:16,791 Not efficient, see the specialized samplers instead if 2021-07-12T08:16:16,791 you want to sample repeatedly from the same workspace. 2021-07-12T08:16:16,792 ''' 2021-07-12T08:16:16,792 cdef Position pos = numpy.random.randint( 0, self.sum() ) 2021-07-12T08:16:16,792 cdef idx 2021-07-12T08:16:16,792 cdef Position l 2021-07-12T08:16:16,792 ^ 2021-07-12T08:16:16,792 ------------------------------------------------------------ 2021-07-12T08:16:16,792 gat/SegmentList.pyx:910:13: 'Position' is not a type identifier 2021-07-12T08:16:16,793 Error compiling Cython file: 2021-07-12T08:16:16,793 ------------------------------------------------------------ 2021-07-12T08:16:16,793 ... 2021-07-12T08:16:16,793 if idx == self.nsegments: 2021-07-12T08:16:16,793 idx -=1 2021-07-12T08:16:16,793 elif idx == -1: 2021-07-12T08:16:16,793 idx=0 2021-07-12T08:16:16,794 cdef Position count 2021-07-12T08:16:16,794 ^ 2021-07-12T08:16:16,794 ------------------------------------------------------------ 2021-07-12T08:16:16,794 gat/SegmentList.pyx:944:13: 'Position' is not a type identifier 2021-07-12T08:16:16,794 Error compiling Cython file: 2021-07-12T08:16:16,794 ------------------------------------------------------------ 2021-07-12T08:16:16,794 ... 2021-07-12T08:16:16,795 ------ 2021-07-12T08:16:16,795 overlap : int 2021-07-12T08:16:16,795 Number of residues overlapping 2021-07-12T08:16:16,795 """ 2021-07-12T08:16:16,795 cdef Segment s 2021-07-12T08:16:16,795 ^ 2021-07-12T08:16:16,795 ------------------------------------------------------------ 2021-07-12T08:16:16,796 gat/SegmentList.pyx:1001:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,796 Error compiling Cython file: 2021-07-12T08:16:16,796 ------------------------------------------------------------ 2021-07-12T08:16:16,796 ... 2021-07-12T08:16:16,796 ------- 2021-07-12T08:16:16,796 segmentlist : SegmentList 2021-07-12T08:16:16,796 A new segment list 2021-07-12T08:16:16,796 """ 2021-07-12T08:16:16,797 cdef Segment s 2021-07-12T08:16:16,797 ^ 2021-07-12T08:16:16,797 ------------------------------------------------------------ 2021-07-12T08:16:16,797 gat/SegmentList.pyx:1022:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,797 Error compiling Cython file: 2021-07-12T08:16:16,797 ------------------------------------------------------------ 2021-07-12T08:16:16,798 ... 2021-07-12T08:16:16,798 return self.sum() 2021-07-12T08:16:16,798 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2021-07-12T08:16:16,798 this_idx = other_idx = 0 2021-07-12T08:16:16,798 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,798 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,798 ^ 2021-07-12T08:16:16,799 ------------------------------------------------------------ 2021-07-12T08:16:16,799 gat/SegmentList.pyx:1042:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,799 Error compiling Cython file: 2021-07-12T08:16:16,799 ------------------------------------------------------------ 2021-07-12T08:16:16,800 ... 2021-07-12T08:16:16,800 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2021-07-12T08:16:16,800 this_idx = other_idx = 0 2021-07-12T08:16:16,800 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,800 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,800 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:16,800 ^ 2021-07-12T08:16:16,800 ------------------------------------------------------------ 2021-07-12T08:16:16,801 gat/SegmentList.pyx:1043:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,801 Error compiling Cython file: 2021-07-12T08:16:16,801 ------------------------------------------------------------ 2021-07-12T08:16:16,801 ... 2021-07-12T08:16:16,801 this_idx = other_idx = 0 2021-07-12T08:16:16,801 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,801 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,802 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:16,802 cdef Position overlap 2021-07-12T08:16:16,802 ^ 2021-07-12T08:16:16,802 ------------------------------------------------------------ 2021-07-12T08:16:16,802 gat/SegmentList.pyx:1045:13: 'Position' is not a type identifier 2021-07-12T08:16:16,802 Error compiling Cython file: 2021-07-12T08:16:16,803 ------------------------------------------------------------ 2021-07-12T08:16:16,803 ... 2021-07-12T08:16:16,803 if other.segments == self.segments: return self.sum() 2021-07-12T08:16:16,803 cdef int this_idx, other_idx, last_this_idx, last_other_idx 2021-07-12T08:16:16,803 this_idx = other_idx = 0 2021-07-12T08:16:16,803 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,803 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,803 ^ 2021-07-12T08:16:16,803 ------------------------------------------------------------ 2021-07-12T08:16:16,804 gat/SegmentList.pyx:1111:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,804 Error compiling Cython file: 2021-07-12T08:16:16,804 ------------------------------------------------------------ 2021-07-12T08:16:16,804 ... 2021-07-12T08:16:16,804 cdef int this_idx, other_idx, last_this_idx, last_other_idx 2021-07-12T08:16:16,804 this_idx = other_idx = 0 2021-07-12T08:16:16,805 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,805 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,805 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:16,805 ^ 2021-07-12T08:16:16,805 ------------------------------------------------------------ 2021-07-12T08:16:16,805 gat/SegmentList.pyx:1112:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,805 Error compiling Cython file: 2021-07-12T08:16:16,806 ------------------------------------------------------------ 2021-07-12T08:16:16,806 ... 2021-07-12T08:16:16,806 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,806 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:16,806 cdef int midpoint_overlap = mode == "midpoint" 2021-07-12T08:16:16,806 cdef Position noverlap 2021-07-12T08:16:16,806 ^ 2021-07-12T08:16:16,807 ------------------------------------------------------------ 2021-07-12T08:16:16,807 gat/SegmentList.pyx:1116:13: 'Position' is not a type identifier 2021-07-12T08:16:16,807 Error compiling Cython file: 2021-07-12T08:16:16,807 ------------------------------------------------------------ 2021-07-12T08:16:16,807 ... 2021-07-12T08:16:16,807 ''' 2021-07-12T08:16:16,807 assert bucket_size >= 0, 'bucket_size is 0' 2021-07-12T08:16:16,807 assert nbuckets > 0, 'nbuckets is 0' 2021-07-12T08:16:16,808 cdef int idx, i 2021-07-12T08:16:16,808 cdef Position l 2021-07-12T08:16:16,808 ^ 2021-07-12T08:16:16,808 ------------------------------------------------------------ 2021-07-12T08:16:16,808 gat/SegmentList.pyx:1160:13: 'Position' is not a type identifier 2021-07-12T08:16:16,808 Error compiling Cython file: 2021-07-12T08:16:16,809 ------------------------------------------------------------ 2021-07-12T08:16:16,809 ... 2021-07-12T08:16:16,809 assert bucket_size >= 0, 'bucket_size is 0' 2021-07-12T08:16:16,809 assert nbuckets > 0, 'nbuckets is 0' 2021-07-12T08:16:16,809 cdef int idx, i 2021-07-12T08:16:16,809 cdef Position l 2021-07-12T08:16:16,809 cdef Segment s 2021-07-12T08:16:16,809 ^ 2021-07-12T08:16:16,810 ------------------------------------------------------------ 2021-07-12T08:16:16,810 gat/SegmentList.pyx:1161:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,810 Error compiling Cython file: 2021-07-12T08:16:16,810 ------------------------------------------------------------ 2021-07-12T08:16:16,810 ... 2021-07-12T08:16:16,810 cdef void truncate(self, Segment other): 2021-07-12T08:16:16,810 '''truncate Segment list to range given by segment *other*.''' 2021-07-12T08:16:16,811 cdef int idx 2021-07-12T08:16:16,811 cdef Segment * s 2021-07-12T08:16:16,811 ^ 2021-07-12T08:16:16,811 ------------------------------------------------------------ 2021-07-12T08:16:16,811 gat/SegmentList.pyx:1190:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,811 Error compiling Cython file: 2021-07-12T08:16:16,812 ------------------------------------------------------------ 2021-07-12T08:16:16,812 ... 2021-07-12T08:16:16,812 cdef void truncate(self, Segment other): 2021-07-12T08:16:16,812 '''truncate Segment list to range given by segment *other*.''' 2021-07-12T08:16:16,812 cdef int idx 2021-07-12T08:16:16,812 cdef Segment * s 2021-07-12T08:16:16,812 cdef Position start = other.start 2021-07-12T08:16:16,812 ^ 2021-07-12T08:16:16,813 ------------------------------------------------------------ 2021-07-12T08:16:16,813 gat/SegmentList.pyx:1191:13: 'Position' is not a type identifier 2021-07-12T08:16:16,813 Error compiling Cython file: 2021-07-12T08:16:16,813 ------------------------------------------------------------ 2021-07-12T08:16:16,813 ... 2021-07-12T08:16:16,813 '''truncate Segment list to range given by segment *other*.''' 2021-07-12T08:16:16,813 cdef int idx 2021-07-12T08:16:16,814 cdef Segment * s 2021-07-12T08:16:16,814 cdef Position start = other.start 2021-07-12T08:16:16,814 cdef Position end = other.end 2021-07-12T08:16:16,814 ^ 2021-07-12T08:16:16,814 ------------------------------------------------------------ 2021-07-12T08:16:16,814 gat/SegmentList.pyx:1192:13: 'Position' is not a type identifier 2021-07-12T08:16:16,814 Error compiling Cython file: 2021-07-12T08:16:16,815 ------------------------------------------------------------ 2021-07-12T08:16:16,815 ... 2021-07-12T08:16:16,815 return 2021-07-12T08:16:16,815 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2021-07-12T08:16:16,815 working_idx = this_idx = other_idx = 0 2021-07-12T08:16:16,815 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,815 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,815 ^ 2021-07-12T08:16:16,816 ------------------------------------------------------------ 2021-07-12T08:16:16,816 gat/SegmentList.pyx:1227:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,816 Error compiling Cython file: 2021-07-12T08:16:16,816 ------------------------------------------------------------ 2021-07-12T08:16:16,816 ... 2021-07-12T08:16:16,816 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2021-07-12T08:16:16,816 working_idx = this_idx = other_idx = 0 2021-07-12T08:16:16,817 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,817 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,817 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:16,817 ^ 2021-07-12T08:16:16,817 ------------------------------------------------------------ 2021-07-12T08:16:16,817 gat/SegmentList.pyx:1228:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,817 Error compiling Cython file: 2021-07-12T08:16:16,818 ------------------------------------------------------------ 2021-07-12T08:16:16,818 ... 2021-07-12T08:16:16,818 working_idx = this_idx = other_idx = 0 2021-07-12T08:16:16,818 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,818 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,818 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:16,818 cdef Segment * new_segments 2021-07-12T08:16:16,818 ^ 2021-07-12T08:16:16,818 ------------------------------------------------------------ 2021-07-12T08:16:16,819 gat/SegmentList.pyx:1230:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,819 Error compiling Cython file: 2021-07-12T08:16:16,819 ------------------------------------------------------------ 2021-07-12T08:16:16,819 ... 2021-07-12T08:16:16,819 cpdef summarize(self): 2021-07-12T08:16:16,819 '''returns summary statistics for segments.''' 2021-07-12T08:16:16,820 cdef int idx 2021-07-12T08:16:16,820 cdef Position min_length, max_length, length 2021-07-12T08:16:16,820 ^ 2021-07-12T08:16:16,820 ------------------------------------------------------------ 2021-07-12T08:16:16,820 gat/SegmentList.pyx:1291:13: 'Position' is not a type identifier 2021-07-12T08:16:16,820 Error compiling Cython file: 2021-07-12T08:16:16,820 ------------------------------------------------------------ 2021-07-12T08:16:16,821 ... 2021-07-12T08:16:16,821 cpdef summarize(self): 2021-07-12T08:16:16,821 '''returns summary statistics for segments.''' 2021-07-12T08:16:16,821 cdef int idx 2021-07-12T08:16:16,821 cdef Position min_length, max_length, length 2021-07-12T08:16:16,821 cdef Position total_length 2021-07-12T08:16:16,821 ^ 2021-07-12T08:16:16,821 ------------------------------------------------------------ 2021-07-12T08:16:16,822 gat/SegmentList.pyx:1292:13: 'Position' is not a type identifier 2021-07-12T08:16:16,822 Error compiling Cython file: 2021-07-12T08:16:16,822 ------------------------------------------------------------ 2021-07-12T08:16:16,822 ... 2021-07-12T08:16:16,822 '''returns summary statistics for segments.''' 2021-07-12T08:16:16,822 cdef int idx 2021-07-12T08:16:16,823 cdef Position min_length, max_length, length 2021-07-12T08:16:16,823 cdef Position total_length 2021-07-12T08:16:16,823 cdef Segment * s 2021-07-12T08:16:16,823 ^ 2021-07-12T08:16:16,823 ------------------------------------------------------------ 2021-07-12T08:16:16,823 gat/SegmentList.pyx:1293:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,823 Error compiling Cython file: 2021-07-12T08:16:16,823 ------------------------------------------------------------ 2021-07-12T08:16:16,824 ... 2021-07-12T08:16:16,824 cdef SegmentList result = SegmentList() 2021-07-12T08:16:16,824 cdef int idx 2021-07-12T08:16:16,824 idx = self.getInsertionPoint( start, start + 1 ) 2021-07-12T08:16:16,824 cdef Position end 2021-07-12T08:16:16,824 ^ 2021-07-12T08:16:16,824 ------------------------------------------------------------ 2021-07-12T08:16:16,825 gat/SegmentList.pyx:1332:13: 'Position' is not a type identifier 2021-07-12T08:16:16,825 Error compiling Cython file: 2021-07-12T08:16:16,825 ------------------------------------------------------------ 2021-07-12T08:16:16,825 ... 2021-07-12T08:16:16,825 cdef SegmentList result = SegmentList() 2021-07-12T08:16:16,825 cdef int idx 2021-07-12T08:16:16,826 idx = self.getInsertionPoint( end, end + 1 ) 2021-07-12T08:16:16,826 cdef Position start 2021-07-12T08:16:16,826 ^ 2021-07-12T08:16:16,826 ------------------------------------------------------------ 2021-07-12T08:16:16,826 gat/SegmentList.pyx:1376:13: 'Position' is not a type identifier 2021-07-12T08:16:16,826 Error compiling Cython file: 2021-07-12T08:16:16,826 ------------------------------------------------------------ 2021-07-12T08:16:16,827 ... 2021-07-12T08:16:16,827 self.clear() 2021-07-12T08:16:16,827 return 2021-07-12T08:16:16,827 if self.nsegments == 0: 2021-07-12T08:16:16,827 return 2021-07-12T08:16:16,827 cdef Segment * new_segments 2021-07-12T08:16:16,827 ^ 2021-07-12T08:16:16,827 ------------------------------------------------------------ 2021-07-12T08:16:16,828 gat/SegmentList.pyx:1414:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,828 Error compiling Cython file: 2021-07-12T08:16:16,828 ------------------------------------------------------------ 2021-07-12T08:16:16,828 ... 2021-07-12T08:16:16,828 sizeof(self.nsegments * sizeof(Segment))) 2021-07-12T08:16:16,828 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2021-07-12T08:16:16,828 working_idx = this_idx = other_idx = 0 2021-07-12T08:16:16,829 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,829 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,829 ^ 2021-07-12T08:16:16,829 ------------------------------------------------------------ 2021-07-12T08:16:16,829 gat/SegmentList.pyx:1426:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,829 Error compiling Cython file: 2021-07-12T08:16:16,829 ------------------------------------------------------------ 2021-07-12T08:16:16,830 ... 2021-07-12T08:16:16,830 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2021-07-12T08:16:16,830 working_idx = this_idx = other_idx = 0 2021-07-12T08:16:16,830 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,830 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,830 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:16,830 ^ 2021-07-12T08:16:16,830 ------------------------------------------------------------ 2021-07-12T08:16:16,831 gat/SegmentList.pyx:1427:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,831 Error compiling Cython file: 2021-07-12T08:16:16,831 ------------------------------------------------------------ 2021-07-12T08:16:16,831 ... 2021-07-12T08:16:16,831 working_idx = this_idx = other_idx = 0 2021-07-12T08:16:16,831 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,831 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,831 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:16,832 # for negative segments, do not use -1 2021-07-12T08:16:16,832 cdef Position last_start = self.segments[0].start - 1 2021-07-12T08:16:16,832 ^ 2021-07-12T08:16:16,832 ------------------------------------------------------------ 2021-07-12T08:16:16,832 gat/SegmentList.pyx:1429:13: 'Position' is not a type identifier 2021-07-12T08:16:16,832 Error compiling Cython file: 2021-07-12T08:16:16,832 ------------------------------------------------------------ 2021-07-12T08:16:16,832 ... 2021-07-12T08:16:16,833 return 2021-07-12T08:16:16,833 if self.nsegments == 0: 2021-07-12T08:16:16,833 return 2021-07-12T08:16:16,833 cdef Segment * new_segments 2021-07-12T08:16:16,833 ^ 2021-07-12T08:16:16,833 ------------------------------------------------------------ 2021-07-12T08:16:16,834 gat/SegmentList.pyx:1492:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,834 Error compiling Cython file: 2021-07-12T08:16:16,834 ------------------------------------------------------------ 2021-07-12T08:16:16,834 ... 2021-07-12T08:16:16,834 sizeof(allocated * sizeof(Segment))) 2021-07-12T08:16:16,834 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2021-07-12T08:16:16,834 working_idx = this_idx = other_idx = 0 2021-07-12T08:16:16,834 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,835 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,835 ^ 2021-07-12T08:16:16,835 ------------------------------------------------------------ 2021-07-12T08:16:16,835 gat/SegmentList.pyx:1505:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,835 Error compiling Cython file: 2021-07-12T08:16:16,835 ------------------------------------------------------------ 2021-07-12T08:16:16,835 ... 2021-07-12T08:16:16,836 cdef int this_idx, other_idx, working_idx, last_this_idx, last_other_idx 2021-07-12T08:16:16,836 working_idx = this_idx = other_idx = 0 2021-07-12T08:16:16,836 last_this_idx = last_other_idx = -1 2021-07-12T08:16:16,836 cdef Segment this_segment = Segment(0,0) 2021-07-12T08:16:16,836 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:16,836 ^ 2021-07-12T08:16:16,836 ------------------------------------------------------------ 2021-07-12T08:16:16,836 gat/SegmentList.pyx:1506:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,837 Error compiling Cython file: 2021-07-12T08:16:16,837 ------------------------------------------------------------ 2021-07-12T08:16:16,837 ... 2021-07-12T08:16:16,837 start, the interval is truncated. 2021-07-12T08:16:16,837 The segment list will not be normalized afterwards.''' 2021-07-12T08:16:16,837 cdef int idx 2021-07-12T08:16:16,838 cdef Segment * s 2021-07-12T08:16:16,838 ^ 2021-07-12T08:16:16,838 ------------------------------------------------------------ 2021-07-12T08:16:16,838 gat/SegmentList.pyx:1560:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,838 Error compiling Cython file: 2021-07-12T08:16:16,838 ------------------------------------------------------------ 2021-07-12T08:16:16,838 ... 2021-07-12T08:16:16,838 start, the interval is truncated. 2021-07-12T08:16:16,839 The segment list will not be normalized afterwards.''' 2021-07-12T08:16:16,839 cdef int idx, 2021-07-12T08:16:16,839 cdef PositionDifference l, extension 2021-07-12T08:16:16,839 ^ 2021-07-12T08:16:16,839 ------------------------------------------------------------ 2021-07-12T08:16:16,839 gat/SegmentList.pyx:1579:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:16,840 Error compiling Cython file: 2021-07-12T08:16:16,840 ------------------------------------------------------------ 2021-07-12T08:16:16,840 ... 2021-07-12T08:16:16,840 The segment list will not be normalized afterwards.''' 2021-07-12T08:16:16,840 cdef int idx, 2021-07-12T08:16:16,840 cdef PositionDifference l, extension 2021-07-12T08:16:16,840 cdef Segment * s 2021-07-12T08:16:16,841 ^ 2021-07-12T08:16:16,841 ------------------------------------------------------------ 2021-07-12T08:16:16,841 gat/SegmentList.pyx:1580:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,841 Error compiling Cython file: 2021-07-12T08:16:16,841 ------------------------------------------------------------ 2021-07-12T08:16:16,841 ... 2021-07-12T08:16:16,841 '''shift segments by a certain offset. 2021-07-12T08:16:16,842 raises ValueError if segment coordinates become negative. 2021-07-12T08:16:16,842 ''' 2021-07-12T08:16:16,842 cdef int idx 2021-07-12T08:16:16,842 cdef Segment * s 2021-07-12T08:16:16,842 ^ 2021-07-12T08:16:16,842 ------------------------------------------------------------ 2021-07-12T08:16:16,842 gat/SegmentList.pyx:1599:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,843 Error compiling Cython file: 2021-07-12T08:16:16,843 ------------------------------------------------------------ 2021-07-12T08:16:16,843 ... 2021-07-12T08:16:16,843 if s.start < 0: 2021-07-12T08:16:16,843 raise ValueError("shift creates negative coordinates") 2021-07-12T08:16:16,843 cpdef Position sum(self): 2021-07-12T08:16:16,843 '''return total length of all segments.''' 2021-07-12T08:16:16,843 cdef Position total 2021-07-12T08:16:16,844 ^ 2021-07-12T08:16:16,844 ------------------------------------------------------------ 2021-07-12T08:16:16,844 gat/SegmentList.pyx:1609:13: 'Position' is not a type identifier 2021-07-12T08:16:16,844 Error compiling Cython file: 2021-07-12T08:16:16,844 ------------------------------------------------------------ 2021-07-12T08:16:16,844 ... 2021-07-12T08:16:16,845 cpdef Position sum(self): 2021-07-12T08:16:16,845 '''return total length of all segments.''' 2021-07-12T08:16:16,845 cdef Position total 2021-07-12T08:16:16,845 cdef int idx 2021-07-12T08:16:16,845 cdef Segment s 2021-07-12T08:16:16,845 ^ 2021-07-12T08:16:16,845 ------------------------------------------------------------ 2021-07-12T08:16:16,845 gat/SegmentList.pyx:1611:13: 'Segment' is not a type identifier 2021-07-12T08:16:16,846 Error compiling Cython file: 2021-07-12T08:16:16,846 ------------------------------------------------------------ 2021-07-12T08:16:16,846 ... 2021-07-12T08:16:16,846 ''' 2021-07-12T08:16:16,846 if self.nsegments == 0: 2021-07-12T08:16:16,846 raise ValueError("largest segment from empty list") 2021-07-12T08:16:16,846 cdef int idx 2021-07-12T08:16:16,846 cdef int max_idx = 0 2021-07-12T08:16:16,846 cdef Position max_value = 0 2021-07-12T08:16:16,847 ^ 2021-07-12T08:16:16,847 ------------------------------------------------------------ 2021-07-12T08:16:16,847 gat/SegmentList.pyx:1628:13: 'Position' is not a type identifier 2021-07-12T08:16:16,847 Error compiling Cython file: 2021-07-12T08:16:16,847 ------------------------------------------------------------ 2021-07-12T08:16:16,847 ... 2021-07-12T08:16:16,847 if self.nsegments == 0: 2021-07-12T08:16:16,847 raise ValueError("largest segment from empty list") 2021-07-12T08:16:16,848 cdef int idx 2021-07-12T08:16:16,848 cdef int max_idx = 0 2021-07-12T08:16:16,848 cdef Position max_value = 0 2021-07-12T08:16:16,848 cdef Position l 2021-07-12T08:16:16,848 ^ 2021-07-12T08:16:16,848 ------------------------------------------------------------ 2021-07-12T08:16:16,848 gat/SegmentList.pyx:1629:13: 'Position' is not a type identifier 2021-07-12T08:16:16,848 Error compiling Cython file: 2021-07-12T08:16:16,849 ------------------------------------------------------------ 2021-07-12T08:16:16,849 ... 2021-07-12T08:16:16,849 def __iter__(self): 2021-07-12T08:16:16,849 return self 2021-07-12T08:16:16,849 def __next__(self): 2021-07-12T08:16:16,849 cdef Position t 2021-07-12T08:16:16,849 ^ 2021-07-12T08:16:16,850 ------------------------------------------------------------ 2021-07-12T08:16:16,850 gat/SegmentList.pyx:1763:13: 'Position' is not a type identifier 2021-07-12T08:16:16,850 Error compiling Cython file: 2021-07-12T08:16:16,850 ------------------------------------------------------------ 2021-07-12T08:16:16,850 ... 2021-07-12T08:16:16,850 def __iter__(self): 2021-07-12T08:16:16,850 return self 2021-07-12T08:16:16,851 def __next__(self): 2021-07-12T08:16:16,851 cdef Position t 2021-07-12T08:16:16,851 cdef Segment v 2021-07-12T08:16:16,851 ^ 2021-07-12T08:16:16,851 ------------------------------------------------------------ 2021-07-12T08:16:16,851 gat/SegmentList.pyx:1764:13: 'Segment' is not a type identifier 2021-07-12T08:16:17,261 Error compiling Cython file: 2021-07-12T08:16:17,261 ------------------------------------------------------------ 2021-07-12T08:16:17,261 ... 2021-07-12T08:16:17,261 DTYPE_FLOAT = numpy.float 2021-07-12T08:16:17,261 ctypedef numpy.float_t DTYPE_FLOAT_t 2021-07-12T08:16:17,261 def getSegmentSize(): 2021-07-12T08:16:17,261 '''return size of coordinate and size of a segment.''' 2021-07-12T08:16:17,262 return sizeof(Segment) // 2, sizeof(Segment) 2021-07-12T08:16:17,262 ^ 2021-07-12T08:16:17,262 ------------------------------------------------------------ 2021-07-12T08:16:17,262 gat/SegmentList.pyx:63:25: undeclared name not builtin: Segment 2021-07-12T08:16:17,264 Error compiling Cython file: 2021-07-12T08:16:17,264 ------------------------------------------------------------ 2021-07-12T08:16:17,265 ... 2021-07-12T08:16:17,265 @cython.profile(False) 2021-07-12T08:16:17,265 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:17,265 """return number of positions overlapping between to Segments.""" 2021-07-12T08:16:17,265 return lmax(0, 2021-07-12T08:16:17,265 lmin( a.end, b.end) - 2021-07-12T08:16:17,265 ^ 2021-07-12T08:16:17,265 ------------------------------------------------------------ 2021-07-12T08:16:17,266 gat/SegmentList.pyx:95:17: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,266 Error compiling Cython file: 2021-07-12T08:16:17,266 ------------------------------------------------------------ 2021-07-12T08:16:17,266 ... 2021-07-12T08:16:17,266 @cython.profile(False) 2021-07-12T08:16:17,266 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:17,267 """return number of positions overlapping between to Segments.""" 2021-07-12T08:16:17,267 return lmax(0, 2021-07-12T08:16:17,267 lmin( a.end, b.end) - 2021-07-12T08:16:17,267 lmax(a.start, b.start)) 2021-07-12T08:16:17,267 ^ 2021-07-12T08:16:17,267 ------------------------------------------------------------ 2021-07-12T08:16:17,267 gat/SegmentList.pyx:96:17: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,268 Error compiling Cython file: 2021-07-12T08:16:17,268 ------------------------------------------------------------ 2021-07-12T08:16:17,268 ... 2021-07-12T08:16:17,268 @cython.profile(False) 2021-07-12T08:16:17,268 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:17,268 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:17,268 return lmax(0, 2021-07-12T08:16:17,268 lmin( aend, bend) - 2021-07-12T08:16:17,269 ^ 2021-07-12T08:16:17,269 ------------------------------------------------------------ 2021-07-12T08:16:17,269 gat/SegmentList.pyx:102:17: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,269 Error compiling Cython file: 2021-07-12T08:16:17,269 ------------------------------------------------------------ 2021-07-12T08:16:17,269 ... 2021-07-12T08:16:17,269 @cython.profile(False) 2021-07-12T08:16:17,270 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:17,270 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:17,270 return lmax(0, 2021-07-12T08:16:17,270 lmin( aend, bend) - 2021-07-12T08:16:17,270 lmax(astart, bstart)) 2021-07-12T08:16:17,270 ^ 2021-07-12T08:16:17,270 ------------------------------------------------------------ 2021-07-12T08:16:17,270 gat/SegmentList.pyx:103:17: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,271 Error compiling Cython file: 2021-07-12T08:16:17,271 ------------------------------------------------------------ 2021-07-12T08:16:17,271 ... 2021-07-12T08:16:17,271 lmin( aend, bend) - 2021-07-12T08:16:17,271 lmax(astart, bstart)) 2021-07-12T08:16:17,271 @cython.profile(False) 2021-07-12T08:16:17,272 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:17,272 return lmin(a.end, b.end) - \ 2021-07-12T08:16:17,272 ^ 2021-07-12T08:16:17,272 ------------------------------------------------------------ 2021-07-12T08:16:17,272 gat/SegmentList.pyx:107:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,272 Error compiling Cython file: 2021-07-12T08:16:17,272 ------------------------------------------------------------ 2021-07-12T08:16:17,273 ... 2021-07-12T08:16:17,273 lmax(astart, bstart)) 2021-07-12T08:16:17,273 @cython.profile(False) 2021-07-12T08:16:17,273 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:17,273 return lmin(a.end, b.end) - \ 2021-07-12T08:16:17,273 lmax(a.start, b.start) 2021-07-12T08:16:17,273 ^ 2021-07-12T08:16:17,273 ------------------------------------------------------------ 2021-07-12T08:16:17,274 gat/SegmentList.pyx:108:9: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,274 Error compiling Cython file: 2021-07-12T08:16:17,274 ------------------------------------------------------------ 2021-07-12T08:16:17,274 ... 2021-07-12T08:16:17,274 return lmin(a.end, b.end) - \ 2021-07-12T08:16:17,274 lmax(a.start, b.start) 2021-07-12T08:16:17,275 @cython.profile(False) 2021-07-12T08:16:17,275 cdef inline PositionDifference segment_length(Segment a) nogil: 2021-07-12T08:16:17,275 return a.end - a.start 2021-07-12T08:16:17,275 ^ 2021-07-12T08:16:17,275 ------------------------------------------------------------ 2021-07-12T08:16:17,275 gat/SegmentList.pyx:112:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,275 Error compiling Cython file: 2021-07-12T08:16:17,276 ------------------------------------------------------------ 2021-07-12T08:16:17,276 ... 2021-07-12T08:16:17,276 return lmin(a.end, b.end) - \ 2021-07-12T08:16:17,276 lmax(a.start, b.start) 2021-07-12T08:16:17,276 @cython.profile(False) 2021-07-12T08:16:17,276 cdef inline PositionDifference segment_length(Segment a) nogil: 2021-07-12T08:16:17,276 return a.end - a.start 2021-07-12T08:16:17,276 ^ 2021-07-12T08:16:17,277 ------------------------------------------------------------ 2021-07-12T08:16:17,277 gat/SegmentList.pyx:112:40: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,277 Error compiling Cython file: 2021-07-12T08:16:17,277 ------------------------------------------------------------ 2021-07-12T08:16:17,277 ... 2021-07-12T08:16:17,277 cdef extern from *: 2021-07-12T08:16:17,277 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:17,278 @cython.profile(False) 2021-07-12T08:16:17,278 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:17,278 return (s1).start - \ 2021-07-12T08:16:17,278 ^ 2021-07-12T08:16:17,278 ------------------------------------------------------------ 2021-07-12T08:16:17,278 gat/SegmentList.pyx:120:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,279 Error compiling Cython file: 2021-07-12T08:16:17,279 ------------------------------------------------------------ 2021-07-12T08:16:17,279 ... 2021-07-12T08:16:17,279 cdef extern from *: 2021-07-12T08:16:17,279 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:17,279 @cython.profile(False) 2021-07-12T08:16:17,279 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:17,279 return (s1).start - \ 2021-07-12T08:16:17,280 ^ 2021-07-12T08:16:17,280 ------------------------------------------------------------ 2021-07-12T08:16:17,280 gat/SegmentList.pyx:120:33: 'Segment' is not a type identifier 2021-07-12T08:16:17,280 Error compiling Cython file: 2021-07-12T08:16:17,280 ------------------------------------------------------------ 2021-07-12T08:16:17,280 ... 2021-07-12T08:16:17,280 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:17,281 @cython.profile(False) 2021-07-12T08:16:17,281 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:17,281 return (s1).start - \ 2021-07-12T08:16:17,281 (s2).start 2021-07-12T08:16:17,281 ^ 2021-07-12T08:16:17,281 ------------------------------------------------------------ 2021-07-12T08:16:17,281 gat/SegmentList.pyx:121:9: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,282 Error compiling Cython file: 2021-07-12T08:16:17,282 ------------------------------------------------------------ 2021-07-12T08:16:17,282 ... 2021-07-12T08:16:17,282 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:17,282 @cython.profile(False) 2021-07-12T08:16:17,282 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:17,282 return (s1).start - \ 2021-07-12T08:16:17,283 (s2).start 2021-07-12T08:16:17,283 ^ 2021-07-12T08:16:17,283 ------------------------------------------------------------ 2021-07-12T08:16:17,283 gat/SegmentList.pyx:121:30: 'Segment' is not a type identifier 2021-07-12T08:16:17,283 Error compiling Cython file: 2021-07-12T08:16:17,283 ------------------------------------------------------------ 2021-07-12T08:16:17,283 ... 2021-07-12T08:16:17,284 (s2).start 2021-07-12T08:16:17,284 @cython.profile(False) 2021-07-12T08:16:17,284 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:17,284 cdef int x 2021-07-12T08:16:17,284 x = (s1).start - \ 2021-07-12T08:16:17,284 ^ 2021-07-12T08:16:17,284 ------------------------------------------------------------ 2021-07-12T08:16:17,285 gat/SegmentList.pyx:126:9: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,285 Error compiling Cython file: 2021-07-12T08:16:17,285 ------------------------------------------------------------ 2021-07-12T08:16:17,285 ... 2021-07-12T08:16:17,285 (s2).start 2021-07-12T08:16:17,285 @cython.profile(False) 2021-07-12T08:16:17,285 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:17,285 cdef int x 2021-07-12T08:16:17,286 x = (s1).start - \ 2021-07-12T08:16:17,286 ^ 2021-07-12T08:16:17,286 ------------------------------------------------------------ 2021-07-12T08:16:17,286 gat/SegmentList.pyx:126:30: 'Segment' is not a type identifier 2021-07-12T08:16:17,286 Error compiling Cython file: 2021-07-12T08:16:17,286 ------------------------------------------------------------ 2021-07-12T08:16:17,286 ... 2021-07-12T08:16:17,287 @cython.profile(False) 2021-07-12T08:16:17,287 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:17,287 cdef int x 2021-07-12T08:16:17,287 x = (s1).start - \ 2021-07-12T08:16:17,287 (s2).start 2021-07-12T08:16:17,287 ^ 2021-07-12T08:16:17,287 ------------------------------------------------------------ 2021-07-12T08:16:17,288 gat/SegmentList.pyx:127:9: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,288 Error compiling Cython file: 2021-07-12T08:16:17,288 ------------------------------------------------------------ 2021-07-12T08:16:17,288 ... 2021-07-12T08:16:17,288 @cython.profile(False) 2021-07-12T08:16:17,288 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:17,288 cdef int x 2021-07-12T08:16:17,289 x = (s1).start - \ 2021-07-12T08:16:17,289 (s2).start 2021-07-12T08:16:17,289 ^ 2021-07-12T08:16:17,289 ------------------------------------------------------------ 2021-07-12T08:16:17,289 gat/SegmentList.pyx:127:30: 'Segment' is not a type identifier 2021-07-12T08:16:17,289 Error compiling Cython file: 2021-07-12T08:16:17,289 ------------------------------------------------------------ 2021-07-12T08:16:17,290 ... 2021-07-12T08:16:17,290 cdef int x 2021-07-12T08:16:17,290 x = (s1).start - \ 2021-07-12T08:16:17,290 (s2).start 2021-07-12T08:16:17,290 if x != 0: 2021-07-12T08:16:17,290 return x 2021-07-12T08:16:17,290 return (s1).end - \ 2021-07-12T08:16:17,290 ^ 2021-07-12T08:16:17,290 ------------------------------------------------------------ 2021-07-12T08:16:17,291 gat/SegmentList.pyx:130:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,291 Error compiling Cython file: 2021-07-12T08:16:17,291 ------------------------------------------------------------ 2021-07-12T08:16:17,291 ... 2021-07-12T08:16:17,291 cdef int x 2021-07-12T08:16:17,291 x = (s1).start - \ 2021-07-12T08:16:17,291 (s2).start 2021-07-12T08:16:17,292 if x != 0: 2021-07-12T08:16:17,292 return x 2021-07-12T08:16:17,292 return (s1).end - \ 2021-07-12T08:16:17,292 ^ 2021-07-12T08:16:17,292 ------------------------------------------------------------ 2021-07-12T08:16:17,292 gat/SegmentList.pyx:130:33: 'Segment' is not a type identifier 2021-07-12T08:16:17,293 Error compiling Cython file: 2021-07-12T08:16:17,293 ------------------------------------------------------------ 2021-07-12T08:16:17,293 ... 2021-07-12T08:16:17,293 x = (s1).start - \ 2021-07-12T08:16:17,293 (s2).start 2021-07-12T08:16:17,293 if x != 0: 2021-07-12T08:16:17,293 return x 2021-07-12T08:16:17,293 return (s1).end - \ 2021-07-12T08:16:17,293 (s2).end 2021-07-12T08:16:17,294 ^ 2021-07-12T08:16:17,294 ------------------------------------------------------------ 2021-07-12T08:16:17,294 gat/SegmentList.pyx:131:9: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,294 Error compiling Cython file: 2021-07-12T08:16:17,294 ------------------------------------------------------------ 2021-07-12T08:16:17,294 ... 2021-07-12T08:16:17,294 x = (s1).start - \ 2021-07-12T08:16:17,295 (s2).start 2021-07-12T08:16:17,295 if x != 0: 2021-07-12T08:16:17,295 return x 2021-07-12T08:16:17,295 return (s1).end - \ 2021-07-12T08:16:17,295 (s2).end 2021-07-12T08:16:17,295 ^ 2021-07-12T08:16:17,295 ------------------------------------------------------------ 2021-07-12T08:16:17,295 gat/SegmentList.pyx:131:30: 'Segment' is not a type identifier 2021-07-12T08:16:17,296 Error compiling Cython file: 2021-07-12T08:16:17,296 ------------------------------------------------------------ 2021-07-12T08:16:17,296 ... 2021-07-12T08:16:17,296 return (s1).end - \ 2021-07-12T08:16:17,296 (s2).end 2021-07-12T08:16:17,296 @cython.profile(False) 2021-07-12T08:16:17,297 cdef int cmpPosition(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:17,297 return (s1)[0] - (s2)[0] 2021-07-12T08:16:17,297 ^ 2021-07-12T08:16:17,297 ------------------------------------------------------------ 2021-07-12T08:16:17,297 gat/SegmentList.pyx:135:13: 'Position' is not a type identifier 2021-07-12T08:16:17,297 Error compiling Cython file: 2021-07-12T08:16:17,297 ------------------------------------------------------------ 2021-07-12T08:16:17,298 ... 2021-07-12T08:16:17,298 return (s1).end - \ 2021-07-12T08:16:17,298 (s2).end 2021-07-12T08:16:17,298 @cython.profile(False) 2021-07-12T08:16:17,298 cdef int cmpPosition(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:17,298 return (s1)[0] - (s2)[0] 2021-07-12T08:16:17,298 ^ 2021-07-12T08:16:17,298 ------------------------------------------------------------ 2021-07-12T08:16:17,299 gat/SegmentList.pyx:135:34: 'Position' is not a type identifier 2021-07-12T08:16:17,299 Error compiling Cython file: 2021-07-12T08:16:17,299 ------------------------------------------------------------ 2021-07-12T08:16:17,299 ... 2021-07-12T08:16:17,299 cdef void * retval 2021-07-12T08:16:17,300 cdef int error_number 2021-07-12T08:16:17,300 cdef char * buffer 2021-07-12T08:16:17,300 # initialize empty list 2021-07-12T08:16:17,300 self.segments = NULL 2021-07-12T08:16:17,300 ^ 2021-07-12T08:16:17,300 ------------------------------------------------------------ 2021-07-12T08:16:17,300 gat/SegmentList.pyx:193:24: Cannot convert 'void *' to Python object 2021-07-12T08:16:17,301 Error compiling Cython file: 2021-07-12T08:16:17,301 ------------------------------------------------------------ 2021-07-12T08:16:17,301 ... 2021-07-12T08:16:17,301 self.allocated = 0 2021-07-12T08:16:17,301 self.flag = share.flag 2021-07-12T08:16:17,301 self.is_shared = True 2021-07-12T08:16:17,301 self.is_slave = True 2021-07-12T08:16:17,301 self.chunk_size = share.chunk_size 2021-07-12T08:16:17,301 retval = mmap(NULL, 2021-07-12T08:16:17,302 ^ 2021-07-12T08:16:17,302 ------------------------------------------------------------ 2021-07-12T08:16:17,302 gat/SegmentList.pyx:235:26: 'Segment' is not a type identifier 2021-07-12T08:16:17,302 Error compiling Cython file: 2021-07-12T08:16:17,302 ------------------------------------------------------------ 2021-07-12T08:16:17,302 ... 2021-07-12T08:16:17,303 if retval == -1: 2021-07-12T08:16:17,303 raise ValueError( 2021-07-12T08:16:17,303 "could not read list from shared segment - error=%i" % 2021-07-12T08:16:17,303 error_number) 2021-07-12T08:16:17,303 self.segments = retval 2021-07-12T08:16:17,303 ^ 2021-07-12T08:16:17,303 ------------------------------------------------------------ 2021-07-12T08:16:17,303 gat/SegmentList.pyx:248:33: 'Segment' is not a type identifier 2021-07-12T08:16:17,304 Error compiling Cython file: 2021-07-12T08:16:17,304 ------------------------------------------------------------ 2021-07-12T08:16:17,304 ... 2021-07-12T08:16:17,304 if retval == -1: 2021-07-12T08:16:17,304 raise ValueError( 2021-07-12T08:16:17,304 "could not unpickle as slave - error=%i" % error_number) 2021-07-12T08:16:17,305 self.segments = retval 2021-07-12T08:16:17,305 ^ 2021-07-12T08:16:17,305 ------------------------------------------------------------ 2021-07-12T08:16:17,305 gat/SegmentList.pyx:273:33: 'Segment' is not a type identifier 2021-07-12T08:16:17,305 Error compiling Cython file: 2021-07-12T08:16:17,305 ------------------------------------------------------------ 2021-07-12T08:16:17,305 ... 2021-07-12T08:16:17,306 self.shared_fd = -1 2021-07-12T08:16:17,306 self.is_shared = True 2021-07-12T08:16:17,306 self.is_slave = True 2021-07-12T08:16:17,306 else: 2021-07-12T08:16:17,306 p = PyBytes_AsString(unreduce[5]) 2021-07-12T08:16:17,306 self.segments = malloc(self.nsegments * sizeof(Segment)) 2021-07-12T08:16:17,306 ^ 2021-07-12T08:16:17,306 ------------------------------------------------------------ 2021-07-12T08:16:17,307 gat/SegmentList.pyx:282:33: 'Segment' is not a type identifier 2021-07-12T08:16:17,307 Error compiling Cython file: 2021-07-12T08:16:17,307 ------------------------------------------------------------ 2021-07-12T08:16:17,307 ... 2021-07-12T08:16:17,307 self.is_shared = True 2021-07-12T08:16:17,307 self.is_slave = True 2021-07-12T08:16:17,307 else: 2021-07-12T08:16:17,307 p = PyBytes_AsString(unreduce[5]) 2021-07-12T08:16:17,308 self.segments = malloc(self.nsegments * sizeof(Segment)) 2021-07-12T08:16:17,308 memcpy(self.segments, p, cython.sizeof(Position) * 2 * self.nsegments) 2021-07-12T08:16:17,308 ^ 2021-07-12T08:16:17,308 ------------------------------------------------------------ 2021-07-12T08:16:17,308 gat/SegmentList.pyx:283:55: undeclared name not builtin: Position 2021-07-12T08:16:17,308 Error compiling Cython file: 2021-07-12T08:16:17,308 ------------------------------------------------------------ 2021-07-12T08:16:17,309 ... 2021-07-12T08:16:17,309 self.is_shared = True 2021-07-12T08:16:17,309 self.is_slave = True 2021-07-12T08:16:17,309 else: 2021-07-12T08:16:17,309 p = PyBytes_AsString(unreduce[5]) 2021-07-12T08:16:17,309 self.segments = malloc(self.nsegments * sizeof(Segment)) 2021-07-12T08:16:17,309 memcpy(self.segments, p, cython.sizeof(Position) * 2 * self.nsegments) 2021-07-12T08:16:17,309 ^ 2021-07-12T08:16:17,309 ------------------------------------------------------------ 2021-07-12T08:16:17,310 gat/SegmentList.pyx:283:27: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,310 Error compiling Cython file: 2021-07-12T08:16:17,310 ------------------------------------------------------------ 2021-07-12T08:16:17,310 ... 2021-07-12T08:16:17,310 memcpy(self.segments, p, cython.sizeof(Position) * 2 * self.nsegments) 2021-07-12T08:16:17,310 # clone from another list 2021-07-12T08:16:17,310 elif clone != None: 2021-07-12T08:16:17,311 self.nsegments = self.allocated = clone.nsegments 2021-07-12T08:16:17,311 self.segments = calloc(clone.nsegments, sizeof( Segment)) 2021-07-12T08:16:17,311 ^ 2021-07-12T08:16:17,311 ------------------------------------------------------------ 2021-07-12T08:16:17,311 gat/SegmentList.pyx:288:29: 'Segment' is not a type identifier 2021-07-12T08:16:17,311 Error compiling Cython file: 2021-07-12T08:16:17,311 ------------------------------------------------------------ 2021-07-12T08:16:17,312 ... 2021-07-12T08:16:17,312 # clone from another list 2021-07-12T08:16:17,312 elif clone != None: 2021-07-12T08:16:17,312 self.nsegments = self.allocated = clone.nsegments 2021-07-12T08:16:17,312 self.segments = calloc(clone.nsegments, sizeof( Segment)) 2021-07-12T08:16:17,312 memcpy(self.segments, 2021-07-12T08:16:17,312 ^ 2021-07-12T08:16:17,312 ------------------------------------------------------------ 2021-07-12T08:16:17,313 gat/SegmentList.pyx:289:23: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,313 Error compiling Cython file: 2021-07-12T08:16:17,313 ------------------------------------------------------------ 2021-07-12T08:16:17,313 ... 2021-07-12T08:16:17,313 # clone from another list 2021-07-12T08:16:17,313 elif clone != None: 2021-07-12T08:16:17,313 self.nsegments = self.allocated = clone.nsegments 2021-07-12T08:16:17,314 self.segments = calloc(clone.nsegments, sizeof( Segment)) 2021-07-12T08:16:17,314 memcpy(self.segments, 2021-07-12T08:16:17,314 clone.segments, 2021-07-12T08:16:17,314 ^ 2021-07-12T08:16:17,314 ------------------------------------------------------------ 2021-07-12T08:16:17,314 gat/SegmentList.pyx:290:24: Cannot convert Python object to 'const void *' 2021-07-12T08:16:17,315 Error compiling Cython file: 2021-07-12T08:16:17,315 ------------------------------------------------------------ 2021-07-12T08:16:17,315 ... 2021-07-12T08:16:17,315 # create from an iterable 2021-07-12T08:16:17,315 elif iter: 2021-07-12T08:16:17,315 a = tuple(iter) 2021-07-12T08:16:17,315 nsegments = len(a) 2021-07-12T08:16:17,315 self.nsegments = self.allocated = nsegments 2021-07-12T08:16:17,315 self.segments = calloc(self.nsegments, sizeof(Segment)) 2021-07-12T08:16:17,316 ^ 2021-07-12T08:16:17,316 ------------------------------------------------------------ 2021-07-12T08:16:17,316 gat/SegmentList.pyx:299:29: 'Segment' is not a type identifier 2021-07-12T08:16:17,316 Error compiling Cython file: 2021-07-12T08:16:17,316 ------------------------------------------------------------ 2021-07-12T08:16:17,316 ... 2021-07-12T08:16:17,316 self.flag = 0 2021-07-12T08:16:17,317 # allocated memory, list remains empty 2021-07-12T08:16:17,317 elif allocate: 2021-07-12T08:16:17,317 self.allocated = allocate 2021-07-12T08:16:17,317 self.segments = calloc(allocate, sizeof(Segment)) 2021-07-12T08:16:17,317 ^ 2021-07-12T08:16:17,317 ------------------------------------------------------------ 2021-07-12T08:16:17,317 gat/SegmentList.pyx:309:29: 'Segment' is not a type identifier 2021-07-12T08:16:17,320 Error compiling Cython file: 2021-07-12T08:16:17,320 ------------------------------------------------------------ 2021-07-12T08:16:17,320 ... 2021-07-12T08:16:17,320 if p == -1: 2021-07-12T08:16:17,321 raise ValueError("could not create memory mapped file" ) 2021-07-12T08:16:17,321 # copy data to shared memory location 2021-07-12T08:16:17,321 memcpy( p, self.segments, nbytes) 2021-07-12T08:16:17,321 ^ 2021-07-12T08:16:17,321 ------------------------------------------------------------ 2021-07-12T08:16:17,321 gat/SegmentList.pyx:381:23: Cannot convert Python object to 'const void *' 2021-07-12T08:16:17,322 Error compiling Cython file: 2021-07-12T08:16:17,322 ------------------------------------------------------------ 2021-07-12T08:16:17,322 ... 2021-07-12T08:16:17,322 memcpy( p, self.segments, nbytes) 2021-07-12T08:16:17,322 self.key = key 2021-07-12T08:16:17,322 # free allocated private memory 2021-07-12T08:16:17,322 self.allocated = 0 2021-07-12T08:16:17,322 free(self.segments) 2021-07-12T08:16:17,323 ^ 2021-07-12T08:16:17,323 ------------------------------------------------------------ 2021-07-12T08:16:17,323 gat/SegmentList.pyx:386:17: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,323 Error compiling Cython file: 2021-07-12T08:16:17,323 ------------------------------------------------------------ 2021-07-12T08:16:17,323 ... 2021-07-12T08:16:17,324 # free allocated private memory 2021-07-12T08:16:17,324 self.allocated = 0 2021-07-12T08:16:17,324 free(self.segments) 2021-07-12T08:16:17,324 self.segments = p 2021-07-12T08:16:17,324 ^ 2021-07-12T08:16:17,324 ------------------------------------------------------------ 2021-07-12T08:16:17,325 gat/SegmentList.pyx:388:25: 'Segment' is not a type identifier 2021-07-12T08:16:17,325 Error compiling Cython file: 2021-07-12T08:16:17,325 ------------------------------------------------------------ 2021-07-12T08:16:17,325 ... 2021-07-12T08:16:17,325 raise OSError( "could not unlink shared memory" ) 2021-07-12T08:16:17,325 # copy data back to unshared memory 2021-07-12T08:16:17,325 cdef Segment * s 2021-07-12T08:16:17,326 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2021-07-12T08:16:17,326 s = malloc(nbytes) 2021-07-12T08:16:17,326 ^ 2021-07-12T08:16:17,326 ------------------------------------------------------------ 2021-07-12T08:16:17,326 gat/SegmentList.pyx:412:13: 'Segment' is not a type identifier 2021-07-12T08:16:17,326 Error compiling Cython file: 2021-07-12T08:16:17,327 ------------------------------------------------------------ 2021-07-12T08:16:17,327 ... 2021-07-12T08:16:17,327 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2021-07-12T08:16:17,327 s = malloc(nbytes) 2021-07-12T08:16:17,327 if s == NULL: 2021-07-12T08:16:17,327 raise ValueError( "could not allocate memory when unsharing" ) 2021-07-12T08:16:17,327 memcpy(s, self.segments, nbytes) 2021-07-12T08:16:17,327 ^ 2021-07-12T08:16:17,328 ------------------------------------------------------------ 2021-07-12T08:16:17,328 gat/SegmentList.pyx:416:22: Cannot convert Python object to 'const void *' 2021-07-12T08:16:17,328 Error compiling Cython file: 2021-07-12T08:16:17,328 ------------------------------------------------------------ 2021-07-12T08:16:17,328 ... 2021-07-12T08:16:17,328 raise ValueError( "could not allocate memory when unsharing" ) 2021-07-12T08:16:17,329 memcpy(s, self.segments, nbytes) 2021-07-12T08:16:17,329 # unmap 2021-07-12T08:16:17,329 if munmap(self.segments, nbytes) == -1: 2021-07-12T08:16:17,329 ^ 2021-07-12T08:16:17,329 ------------------------------------------------------------ 2021-07-12T08:16:17,329 gat/SegmentList.pyx:419:22: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,330 Error compiling Cython file: 2021-07-12T08:16:17,330 ------------------------------------------------------------ 2021-07-12T08:16:17,330 ... 2021-07-12T08:16:17,330 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2021-07-12T08:16:17,330 if self.nsegments == 0: 2021-07-12T08:16:17,330 return 2021-07-12T08:16:17,331 s = malloc(nbytes) 2021-07-12T08:16:17,331 ^ 2021-07-12T08:16:17,331 ------------------------------------------------------------ 2021-07-12T08:16:17,331 gat/SegmentList.pyx:437:13: 'Segment' is not a type identifier 2021-07-12T08:16:17,331 Error compiling Cython file: 2021-07-12T08:16:17,331 ------------------------------------------------------------ 2021-07-12T08:16:17,332 ... 2021-07-12T08:16:17,332 s = malloc(nbytes) 2021-07-12T08:16:17,332 if s == NULL: 2021-07-12T08:16:17,332 raise ValueError( "could not allocate memory when unsharing" ) 2021-07-12T08:16:17,332 memcpy(s, self.segments, nbytes) 2021-07-12T08:16:17,332 ^ 2021-07-12T08:16:17,332 ------------------------------------------------------------ 2021-07-12T08:16:17,333 gat/SegmentList.pyx:441:22: Cannot convert Python object to 'const void *' 2021-07-12T08:16:17,333 Error compiling Cython file: 2021-07-12T08:16:17,333 ------------------------------------------------------------ 2021-07-12T08:16:17,333 ... 2021-07-12T08:16:17,333 if self.nsegments == 0: 2021-07-12T08:16:17,333 # do not move empty segment lists 2021-07-12T08:16:17,334 return offset 2021-07-12T08:16:17,334 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2021-07-12T08:16:17,334 cdef Segment * p = mmap + offset 2021-07-12T08:16:17,334 ^ 2021-07-12T08:16:17,334 ------------------------------------------------------------ 2021-07-12T08:16:17,334 gat/SegmentList.pyx:463:28: 'Segment' is not a type identifier 2021-07-12T08:16:17,335 Error compiling Cython file: 2021-07-12T08:16:17,335 ------------------------------------------------------------ 2021-07-12T08:16:17,335 ... 2021-07-12T08:16:17,335 cdef off_t nbytes = sizeof(Segment) * self.nsegments 2021-07-12T08:16:17,335 cdef Segment * p = mmap + offset 2021-07-12T08:16:17,335 # copy data 2021-07-12T08:16:17,335 memcpy(p, self.segments, nbytes) 2021-07-12T08:16:17,335 ^ 2021-07-12T08:16:17,336 ------------------------------------------------------------ 2021-07-12T08:16:17,336 gat/SegmentList.pyx:466:22: Cannot convert Python object to 'const void *' 2021-07-12T08:16:17,336 Error compiling Cython file: 2021-07-12T08:16:17,336 ------------------------------------------------------------ 2021-07-12T08:16:17,336 ... 2021-07-12T08:16:17,336 # copy data 2021-07-12T08:16:17,337 memcpy(p, self.segments, nbytes) 2021-07-12T08:16:17,337 # free allocated private memory 2021-07-12T08:16:17,337 self.allocated = 0 2021-07-12T08:16:17,337 free(self.segments) 2021-07-12T08:16:17,337 ^ 2021-07-12T08:16:17,337 ------------------------------------------------------------ 2021-07-12T08:16:17,337 gat/SegmentList.pyx:470:17: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,339 Error compiling Cython file: 2021-07-12T08:16:17,339 ------------------------------------------------------------ 2021-07-12T08:16:17,339 ... 2021-07-12T08:16:17,339 :meth:`SegmentList.normalize`. 2021-07-12T08:16:17,339 ''' 2021-07-12T08:16:17,339 cdef size_t new_size 2021-07-12T08:16:17,339 new_size = other.nsegments + self.nsegments 2021-07-12T08:16:17,340 if self.allocated == 0: 2021-07-12T08:16:17,340 self.segments = malloc( new_size * sizeof( Segment ) ) 2021-07-12T08:16:17,340 ^ 2021-07-12T08:16:17,340 ------------------------------------------------------------ 2021-07-12T08:16:17,340 gat/SegmentList.pyx:497:29: 'Segment' is not a type identifier 2021-07-12T08:16:17,340 Error compiling Cython file: 2021-07-12T08:16:17,340 ------------------------------------------------------------ 2021-07-12T08:16:17,341 ... 2021-07-12T08:16:17,341 self.segments = malloc( new_size * sizeof( Segment ) ) 2021-07-12T08:16:17,341 if not self.segments: 2021-07-12T08:16:17,341 raise MemoryError( "out of memory when allocation %i bytes" % sizeof( new_size * sizeof( Segment ) )) 2021-07-12T08:16:17,341 self.allocated = new_size 2021-07-12T08:16:17,341 elif new_size >= self.allocated: 2021-07-12T08:16:17,341 self.segments = realloc( self.segments, new_size * sizeof( Segment ) ) 2021-07-12T08:16:17,341 ^ 2021-07-12T08:16:17,342 ------------------------------------------------------------ 2021-07-12T08:16:17,342 gat/SegmentList.pyx:502:29: 'Segment' is not a type identifier 2021-07-12T08:16:17,342 Error compiling Cython file: 2021-07-12T08:16:17,342 ------------------------------------------------------------ 2021-07-12T08:16:17,342 ... 2021-07-12T08:16:17,342 elif new_size >= self.allocated: 2021-07-12T08:16:17,343 self.segments = realloc( self.segments, new_size * sizeof( Segment ) ) 2021-07-12T08:16:17,343 if not self.segments: 2021-07-12T08:16:17,343 raise MemoryError( "out of memory when allocation %i bytes" % sizeof( new_size * sizeof( Segment ) )) 2021-07-12T08:16:17,343 self.allocated = new_size 2021-07-12T08:16:17,343 memcpy( &self.segments[self.nsegments], 2021-07-12T08:16:17,343 ^ 2021-07-12T08:16:17,343 ------------------------------------------------------------ 2021-07-12T08:16:17,343 gat/SegmentList.pyx:506:16: Cannot take address of Python object 2021-07-12T08:16:17,344 Error compiling Cython file: 2021-07-12T08:16:17,344 ------------------------------------------------------------ 2021-07-12T08:16:17,344 ... 2021-07-12T08:16:17,344 self.segments = realloc( self.segments, new_size * sizeof( Segment ) ) 2021-07-12T08:16:17,344 if not self.segments: 2021-07-12T08:16:17,344 raise MemoryError( "out of memory when allocation %i bytes" % sizeof( new_size * sizeof( Segment ) )) 2021-07-12T08:16:17,344 self.allocated = new_size 2021-07-12T08:16:17,344 memcpy( &self.segments[self.nsegments], 2021-07-12T08:16:17,345 other.segments, 2021-07-12T08:16:17,345 ^ 2021-07-12T08:16:17,345 ------------------------------------------------------------ 2021-07-12T08:16:17,345 gat/SegmentList.pyx:507:22: Cannot convert Python object to 'const void *' 2021-07-12T08:16:17,345 Error compiling Cython file: 2021-07-12T08:16:17,345 ------------------------------------------------------------ 2021-07-12T08:16:17,346 ... 2021-07-12T08:16:17,346 The list will not be normalized automatically - call 2021-07-12T08:16:17,346 :meth:`SegmentList.normalize`. 2021-07-12T08:16:17,346 ''' 2021-07-12T08:16:17,346 if self.allocated == 0: 2021-07-12T08:16:17,346 self.segments = malloc(self.chunk_size * sizeof(Segment)) 2021-07-12T08:16:17,346 ^ 2021-07-12T08:16:17,346 ------------------------------------------------------------ 2021-07-12T08:16:17,347 gat/SegmentList.pyx:521:29: 'Segment' is not a type identifier 2021-07-12T08:16:17,347 Error compiling Cython file: 2021-07-12T08:16:17,347 ------------------------------------------------------------ 2021-07-12T08:16:17,347 ... 2021-07-12T08:16:17,347 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:17,347 sizeof( self.chunk_size * sizeof(Segment))) 2021-07-12T08:16:17,347 self.allocated = self.chunk_size 2021-07-12T08:16:17,348 elif self.nsegments == self.allocated: 2021-07-12T08:16:17,348 self.allocated *= 2 2021-07-12T08:16:17,348 self.segments = realloc(self.segments, 2021-07-12T08:16:17,348 ^ 2021-07-12T08:16:17,348 ------------------------------------------------------------ 2021-07-12T08:16:17,348 gat/SegmentList.pyx:528:29: 'Segment' is not a type identifier 2021-07-12T08:16:17,348 Error compiling Cython file: 2021-07-12T08:16:17,349 ------------------------------------------------------------ 2021-07-12T08:16:17,349 ... 2021-07-12T08:16:17,349 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:17,349 sizeof( self.chunk_size * sizeof(Segment))) 2021-07-12T08:16:17,349 self.allocated = self.chunk_size 2021-07-12T08:16:17,349 elif self.nsegments == self.allocated: 2021-07-12T08:16:17,349 self.allocated *= 2 2021-07-12T08:16:17,349 self.segments = realloc(self.segments, 2021-07-12T08:16:17,349 ^ 2021-07-12T08:16:17,350 ------------------------------------------------------------ 2021-07-12T08:16:17,350 gat/SegmentList.pyx:528:50: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,358 Error compiling Cython file: 2021-07-12T08:16:17,358 ------------------------------------------------------------ 2021-07-12T08:16:17,358 ... 2021-07-12T08:16:17,359 l = segment_length( seg ) 2021-07-12T08:16:17,359 if segment_length( seg ) < s: 2021-07-12T08:16:17,359 self.segments[idx] = Segment(0,0) 2021-07-12T08:16:17,359 s -= l 2021-07-12T08:16:17,359 else: 2021-07-12T08:16:17,359 self.segments[idx] = Segment( seg.start, seg.end - s ) 2021-07-12T08:16:17,359 ^ 2021-07-12T08:16:17,359 ------------------------------------------------------------ 2021-07-12T08:16:17,360 gat/SegmentList.pyx:591:62: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,363 Error compiling Cython file: 2021-07-12T08:16:17,363 ------------------------------------------------------------ 2021-07-12T08:16:17,363 ... 2021-07-12T08:16:17,363 nsegments = 1 2021-07-12T08:16:17,363 assert nsegments >= self.nsegments, "resizing will loose segments" 2021-07-12T08:16:17,364 if self.allocated == 0: 2021-07-12T08:16:17,364 self.segments = malloc(nsegments * sizeof(Segment)) 2021-07-12T08:16:17,364 ^ 2021-07-12T08:16:17,364 ------------------------------------------------------------ 2021-07-12T08:16:17,364 gat/SegmentList.pyx:608:29: 'Segment' is not a type identifier 2021-07-12T08:16:17,364 Error compiling Cython file: 2021-07-12T08:16:17,365 ------------------------------------------------------------ 2021-07-12T08:16:17,365 ... 2021-07-12T08:16:17,365 self.segments = malloc(nsegments * sizeof(Segment)) 2021-07-12T08:16:17,365 if not self.segments: 2021-07-12T08:16:17,365 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:17,365 sizeof(nsegments * sizeof(Segment))) 2021-07-12T08:16:17,365 else: 2021-07-12T08:16:17,365 self.segments = realloc(self.segments, 2021-07-12T08:16:17,365 ^ 2021-07-12T08:16:17,366 ------------------------------------------------------------ 2021-07-12T08:16:17,366 gat/SegmentList.pyx:613:29: 'Segment' is not a type identifier 2021-07-12T08:16:17,366 Error compiling Cython file: 2021-07-12T08:16:17,366 ------------------------------------------------------------ 2021-07-12T08:16:17,366 ... 2021-07-12T08:16:17,366 self.segments = malloc(nsegments * sizeof(Segment)) 2021-07-12T08:16:17,366 if not self.segments: 2021-07-12T08:16:17,367 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:17,367 sizeof(nsegments * sizeof(Segment))) 2021-07-12T08:16:17,367 else: 2021-07-12T08:16:17,367 self.segments = realloc(self.segments, 2021-07-12T08:16:17,367 ^ 2021-07-12T08:16:17,367 ------------------------------------------------------------ 2021-07-12T08:16:17,367 gat/SegmentList.pyx:613:50: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,368 Error compiling Cython file: 2021-07-12T08:16:17,368 ------------------------------------------------------------ 2021-07-12T08:16:17,368 ... 2021-07-12T08:16:17,369 idx = max(idx, self.nsegments) 2021-07-12T08:16:17,369 if self.allocated == self.nsegments: 2021-07-12T08:16:17,369 self._resize(self.allocated * 2) 2021-07-12T08:16:17,369 memmove(&self.segments[idx+1], 2021-07-12T08:16:17,369 ^ 2021-07-12T08:16:17,369 ------------------------------------------------------------ 2021-07-12T08:16:17,369 gat/SegmentList.pyx:630:16: Cannot take address of Python object 2021-07-12T08:16:17,370 Error compiling Cython file: 2021-07-12T08:16:17,370 ------------------------------------------------------------ 2021-07-12T08:16:17,370 ... 2021-07-12T08:16:17,370 idx = max(idx, self.nsegments) 2021-07-12T08:16:17,370 if self.allocated == self.nsegments: 2021-07-12T08:16:17,370 self._resize(self.allocated * 2) 2021-07-12T08:16:17,370 memmove(&self.segments[idx+1], 2021-07-12T08:16:17,371 &self.segments[idx], 2021-07-12T08:16:17,371 ^ 2021-07-12T08:16:17,371 ------------------------------------------------------------ 2021-07-12T08:16:17,371 gat/SegmentList.pyx:631:16: Cannot take address of Python object 2021-07-12T08:16:17,374 Error compiling Cython file: 2021-07-12T08:16:17,374 ------------------------------------------------------------ 2021-07-12T08:16:17,374 ... 2021-07-12T08:16:17,374 #assert p < self.segments[idx].end, "pos=%i, %i, %s, %s" % (p, idx, str(self.segments[idx]), str(self.asList())) 2021-07-12T08:16:17,375 while s > 0: 2021-07-12T08:16:17,375 seg = self.segments[idx] 2021-07-12T08:16:17,375 l = self.segments[idx].end - p 2021-07-12T08:16:17,375 ^ 2021-07-12T08:16:17,375 ------------------------------------------------------------ 2021-07-12T08:16:17,375 gat/SegmentList.pyx:673:17: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,390 Error compiling Cython file: 2021-07-12T08:16:17,391 ------------------------------------------------------------ 2021-07-12T08:16:17,391 ... 2021-07-12T08:16:17,391 if self.segments[idx].start == self.segments[idx].end: 2021-07-12T08:16:17,391 idx += 1 2021-07-12T08:16:17,391 continue 2021-07-12T08:16:17,391 # no overlap - save segment 2021-07-12T08:16:17,391 # note the cange from > to >= 2021-07-12T08:16:17,391 if self.segments[idx].start - distance > max_end: 2021-07-12T08:16:17,391 ^ 2021-07-12T08:16:17,392 ------------------------------------------------------------ 2021-07-12T08:16:17,392 gat/SegmentList.pyx:801:16: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,402 Error compiling Cython file: 2021-07-12T08:16:17,402 ------------------------------------------------------------ 2021-07-12T08:16:17,402 ... 2021-07-12T08:16:17,402 if other.start >= self.segments[self.nsegments-1].end: 2021-07-12T08:16:17,402 return self.nsegments 2021-07-12T08:16:17,402 if other.end <= self.segments[0].start: 2021-07-12T08:16:17,402 return -1 2021-07-12T08:16:17,403 idx = searchsorted(self.segments, 2021-07-12T08:16:17,403 ^ 2021-07-12T08:16:17,403 ------------------------------------------------------------ 2021-07-12T08:16:17,403 gat/SegmentList.pyx:876:14: undeclared name not builtin: searchsorted 2021-07-12T08:16:17,403 Error compiling Cython file: 2021-07-12T08:16:17,403 ------------------------------------------------------------ 2021-07-12T08:16:17,403 ... 2021-07-12T08:16:17,404 idx = searchsorted(self.segments, 2021-07-12T08:16:17,404 self.nsegments, 2021-07-12T08:16:17,404 sizeof(Segment), 2021-07-12T08:16:17,404 &other, 2021-07-12T08:16:17,404 &cmpSegments) 2021-07-12T08:16:17,404 ^ 2021-07-12T08:16:17,404 ------------------------------------------------------------ 2021-07-12T08:16:17,405 gat/SegmentList.pyx:880:27: Cannot convert 'int (*)(const_void_ptr, const_void_ptr) nogil' to Python object 2021-07-12T08:16:17,435 Error compiling Cython file: 2021-07-12T08:16:17,435 ------------------------------------------------------------ 2021-07-12T08:16:17,435 ... 2021-07-12T08:16:17,435 cdef Segment * s 2021-07-12T08:16:17,436 cdef Position start = other.start 2021-07-12T08:16:17,436 cdef Position end = other.end 2021-07-12T08:16:17,436 for idx from 0 <= idx < self.nsegments: 2021-07-12T08:16:17,436 s = & self.segments[idx] 2021-07-12T08:16:17,436 ^ 2021-07-12T08:16:17,436 ------------------------------------------------------------ 2021-07-12T08:16:17,436 gat/SegmentList.pyx:1195:16: Cannot take address of Python object 2021-07-12T08:16:17,440 Error compiling Cython file: 2021-07-12T08:16:17,440 ------------------------------------------------------------ 2021-07-12T08:16:17,440 ... 2021-07-12T08:16:17,440 cdef Segment * new_segments 2021-07-12T08:16:17,440 cdef size_t allocated 2021-07-12T08:16:17,441 # create new list with 10% overhead 2021-07-12T08:16:17,441 allocated = int(lmax( self.nsegments, other.nsegments) * 1.1) 2021-07-12T08:16:17,441 new_segments =malloc( allocated * sizeof( Segment ) ) 2021-07-12T08:16:17,441 ^ 2021-07-12T08:16:17,441 ------------------------------------------------------------ 2021-07-12T08:16:17,441 gat/SegmentList.pyx:1235:23: 'Segment' is not a type identifier 2021-07-12T08:16:17,442 Error compiling Cython file: 2021-07-12T08:16:17,442 ------------------------------------------------------------ 2021-07-12T08:16:17,442 ... 2021-07-12T08:16:17,442 while this_idx < self.nsegments and other_idx < other.nsegments: 2021-07-12T08:16:17,442 # re-allocated before adding 2021-07-12T08:16:17,442 if working_idx >= allocated: 2021-07-12T08:16:17,442 allocated *= 2 2021-07-12T08:16:17,443 new_segments = realloc(new_segments, allocated * sizeof(Segment)) 2021-07-12T08:16:17,443 ^ 2021-07-12T08:16:17,443 ------------------------------------------------------------ 2021-07-12T08:16:17,443 gat/SegmentList.pyx:1245:32: 'Segment' is not a type identifier 2021-07-12T08:16:17,444 Error compiling Cython file: 2021-07-12T08:16:17,445 ------------------------------------------------------------ 2021-07-12T08:16:17,445 ... 2021-07-12T08:16:17,445 if this_segment.start < this_segment.end: 2021-07-12T08:16:17,445 new_segments[working_idx].start = this_segment.start 2021-07-12T08:16:17,445 new_segments[working_idx].end = this_segment.end 2021-07-12T08:16:17,445 working_idx += 1 2021-07-12T08:16:17,445 free(self.segments) 2021-07-12T08:16:17,445 ^ 2021-07-12T08:16:17,446 ------------------------------------------------------------ 2021-07-12T08:16:17,446 gat/SegmentList.pyx:1282:17: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,450 Error compiling Cython file: 2021-07-12T08:16:17,450 ------------------------------------------------------------ 2021-07-12T08:16:17,450 ... 2021-07-12T08:16:17,451 min_length = UINT32_MAX 2021-07-12T08:16:17,451 max_length = 0 2021-07-12T08:16:17,451 total_length = 0 2021-07-12T08:16:17,451 for idx from 0 <= idx < self.nsegments: 2021-07-12T08:16:17,451 s = & self.segments[idx] 2021-07-12T08:16:17,451 ^ 2021-07-12T08:16:17,451 ------------------------------------------------------------ 2021-07-12T08:16:17,452 gat/SegmentList.pyx:1304:16: Cannot take address of Python object 2021-07-12T08:16:17,466 Error compiling Cython file: 2021-07-12T08:16:17,466 ------------------------------------------------------------ 2021-07-12T08:16:17,466 ... 2021-07-12T08:16:17,466 return 2021-07-12T08:16:17,466 cdef Segment * new_segments 2021-07-12T08:16:17,467 cdef size_t allocated 2021-07-12T08:16:17,467 # create new list 2021-07-12T08:16:17,467 new_segments =malloc( self.nsegments * sizeof(Segment)) 2021-07-12T08:16:17,467 ^ 2021-07-12T08:16:17,467 ------------------------------------------------------------ 2021-07-12T08:16:17,467 gat/SegmentList.pyx:1417:23: 'Segment' is not a type identifier 2021-07-12T08:16:17,470 Error compiling Cython file: 2021-07-12T08:16:17,470 ------------------------------------------------------------ 2021-07-12T08:16:17,471 ... 2021-07-12T08:16:17,471 other_idx += 1 2021-07-12T08:16:17,471 else: 2021-07-12T08:16:17,471 this_idx += 1 2021-07-12T08:16:17,471 other_idx += 1 2021-07-12T08:16:17,471 free(self.segments) 2021-07-12T08:16:17,471 ^ 2021-07-12T08:16:17,471 ------------------------------------------------------------ 2021-07-12T08:16:17,472 gat/SegmentList.pyx:1464:17: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,476 Error compiling Cython file: 2021-07-12T08:16:17,476 ------------------------------------------------------------ 2021-07-12T08:16:17,476 ... 2021-07-12T08:16:17,476 cdef Segment * new_segments 2021-07-12T08:16:17,476 cdef size_t allocated 2021-07-12T08:16:17,476 # create new list with 10% overhead 2021-07-12T08:16:17,476 allocated = int(lmax(self.nsegments, other.nsegments) * 1.1) 2021-07-12T08:16:17,476 new_segments =malloc(allocated * sizeof(Segment)) 2021-07-12T08:16:17,477 ^ 2021-07-12T08:16:17,477 ------------------------------------------------------------ 2021-07-12T08:16:17,477 gat/SegmentList.pyx:1497:23: 'Segment' is not a type identifier 2021-07-12T08:16:17,479 Error compiling Cython file: 2021-07-12T08:16:17,479 ------------------------------------------------------------ 2021-07-12T08:16:17,480 ... 2021-07-12T08:16:17,480 new_segments[working_idx].end = lmin(this_segment.end, 2021-07-12T08:16:17,480 other_segment.end) 2021-07-12T08:16:17,480 working_idx += 1 2021-07-12T08:16:17,480 if working_idx >= allocated: 2021-07-12T08:16:17,480 allocated *= 2 2021-07-12T08:16:17,480 new_segments = realloc(new_segments, 2021-07-12T08:16:17,480 ^ 2021-07-12T08:16:17,480 ------------------------------------------------------------ 2021-07-12T08:16:17,481 gat/SegmentList.pyx:1534:36: 'Segment' is not a type identifier 2021-07-12T08:16:17,481 Error compiling Cython file: 2021-07-12T08:16:17,481 ------------------------------------------------------------ 2021-07-12T08:16:17,481 ... 2021-07-12T08:16:17,481 other_idx += 1 2021-07-12T08:16:17,481 else: 2021-07-12T08:16:17,482 this_idx += 1 2021-07-12T08:16:17,482 other_idx += 1 2021-07-12T08:16:17,482 free(self.segments) 2021-07-12T08:16:17,482 ^ 2021-07-12T08:16:17,482 ------------------------------------------------------------ 2021-07-12T08:16:17,483 gat/SegmentList.pyx:1546:17: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,489 Error compiling Cython file: 2021-07-12T08:16:17,489 ------------------------------------------------------------ 2021-07-12T08:16:17,489 ... 2021-07-12T08:16:17,490 The segment list will not be normalized afterwards.''' 2021-07-12T08:16:17,490 cdef int idx 2021-07-12T08:16:17,490 cdef Segment * s 2021-07-12T08:16:17,490 for idx from 0 <= idx < self.nsegments: 2021-07-12T08:16:17,490 s = &self.segments[idx] 2021-07-12T08:16:17,490 ^ 2021-07-12T08:16:17,490 ------------------------------------------------------------ 2021-07-12T08:16:17,491 gat/SegmentList.pyx:1562:16: Cannot take address of Python object 2021-07-12T08:16:17,492 Error compiling Cython file: 2021-07-12T08:16:17,492 ------------------------------------------------------------ 2021-07-12T08:16:17,493 ... 2021-07-12T08:16:17,493 cdef double e_1 = (expansion - 1.0) / 2.0 2021-07-12T08:16:17,493 if expansion <= 0: raise ValueError( "invalid expansion: %f <= 0" % expansion) 2021-07-12T08:16:17,493 for idx from 0 <= idx < self.nsegments: 2021-07-12T08:16:17,493 s = &self.segments[idx] 2021-07-12T08:16:17,493 ^ 2021-07-12T08:16:17,493 ------------------------------------------------------------ 2021-07-12T08:16:17,494 gat/SegmentList.pyx:1586:16: Cannot take address of Python object 2021-07-12T08:16:17,494 Error compiling Cython file: 2021-07-12T08:16:17,494 ------------------------------------------------------------ 2021-07-12T08:16:17,494 ... 2021-07-12T08:16:17,494 if expansion <= 0: raise ValueError( "invalid expansion: %f <= 0" % expansion) 2021-07-12T08:16:17,494 for idx from 0 <= idx < self.nsegments: 2021-07-12T08:16:17,495 s = &self.segments[idx] 2021-07-12T08:16:17,495 l = s.end - s.start 2021-07-12T08:16:17,495 extension = floor(l * e_1 ) 2021-07-12T08:16:17,495 ^ 2021-07-12T08:16:17,495 ------------------------------------------------------------ 2021-07-12T08:16:17,495 gat/SegmentList.pyx:1588:25: 'PositionDifference' is not a type identifier 2021-07-12T08:16:17,496 Error compiling Cython file: 2021-07-12T08:16:17,496 ------------------------------------------------------------ 2021-07-12T08:16:17,496 ... 2021-07-12T08:16:17,496 raises ValueError if segment coordinates become negative. 2021-07-12T08:16:17,496 ''' 2021-07-12T08:16:17,496 cdef int idx 2021-07-12T08:16:17,496 cdef Segment * s 2021-07-12T08:16:17,496 for idx from 0 <= idx < self.nsegments: 2021-07-12T08:16:17,496 s = &self.segments[idx] 2021-07-12T08:16:17,497 ^ 2021-07-12T08:16:17,497 ------------------------------------------------------------ 2021-07-12T08:16:17,497 gat/SegmentList.pyx:1601:16: Cannot take address of Python object 2021-07-12T08:16:17,505 Error compiling Cython file: 2021-07-12T08:16:17,505 ------------------------------------------------------------ 2021-07-12T08:16:17,505 ... 2021-07-12T08:16:17,505 self.flag = 1 2021-07-12T08:16:17,505 cpdef SegmentList clone(self): 2021-07-12T08:16:17,505 """return a copy of self.""" 2021-07-12T08:16:17,505 clone = SegmentList(allocate=self.nsegments) 2021-07-12T08:16:17,506 memcpy(clone.segments, 2021-07-12T08:16:17,506 ^ 2021-07-12T08:16:17,506 ------------------------------------------------------------ 2021-07-12T08:16:17,506 gat/SegmentList.pyx:1661:20: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,506 Error compiling Cython file: 2021-07-12T08:16:17,506 ------------------------------------------------------------ 2021-07-12T08:16:17,507 ... 2021-07-12T08:16:17,507 cpdef SegmentList clone(self): 2021-07-12T08:16:17,507 """return a copy of self.""" 2021-07-12T08:16:17,507 clone = SegmentList(allocate=self.nsegments) 2021-07-12T08:16:17,507 memcpy(clone.segments, 2021-07-12T08:16:17,507 self.segments, 2021-07-12T08:16:17,507 ^ 2021-07-12T08:16:17,507 ------------------------------------------------------------ 2021-07-12T08:16:17,508 gat/SegmentList.pyx:1662:19: Cannot convert Python object to 'const void *' 2021-07-12T08:16:17,508 Error compiling Cython file: 2021-07-12T08:16:17,508 ------------------------------------------------------------ 2021-07-12T08:16:17,508 ... 2021-07-12T08:16:17,508 return self.nsegments 2021-07-12T08:16:17,509 def __dealloc__(self): 2021-07-12T08:16:17,509 cdef int fd 2021-07-12T08:16:17,509 if self.segments != NULL: 2021-07-12T08:16:17,509 ^ 2021-07-12T08:16:17,509 ------------------------------------------------------------ 2021-07-12T08:16:17,509 gat/SegmentList.pyx:1674:25: Invalid types for '!=' (Python object, void *) 2021-07-12T08:16:17,510 Error compiling Cython file: 2021-07-12T08:16:17,510 ------------------------------------------------------------ 2021-07-12T08:16:17,510 ... 2021-07-12T08:16:17,510 if self.is_shared: 2021-07-12T08:16:17,510 if self.is_slave: 2021-07-12T08:16:17,510 pass 2021-07-12T08:16:17,510 else: 2021-07-12T08:16:17,510 # free shared memory as master 2021-07-12T08:16:17,510 munmap(self.segments, 2021-07-12T08:16:17,511 ^ 2021-07-12T08:16:17,511 ------------------------------------------------------------ 2021-07-12T08:16:17,511 gat/SegmentList.pyx:1681:31: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,511 Error compiling Cython file: 2021-07-12T08:16:17,511 ------------------------------------------------------------ 2021-07-12T08:16:17,511 ... 2021-07-12T08:16:17,511 # free shared memory as master 2021-07-12T08:16:17,512 munmap(self.segments, 2021-07-12T08:16:17,512 self.nsegments * sizeof(Segment)) 2021-07-12T08:16:17,512 else: 2021-07-12T08:16:17,512 # free private copy 2021-07-12T08:16:17,512 free(self.segments) 2021-07-12T08:16:17,512 ^ 2021-07-12T08:16:17,512 ------------------------------------------------------------ 2021-07-12T08:16:17,512 gat/SegmentList.pyx:1685:25: Cannot convert Python object to 'void *' 2021-07-12T08:16:17,516 Error compiling Cython file: 2021-07-12T08:16:17,516 ------------------------------------------------------------ 2021-07-12T08:16:17,516 ... 2021-07-12T08:16:17,516 return -1 2021-07-12T08:16:17,516 cdef int l2 = len(other) 2021-07-12T08:16:17,516 if l2 - l1 != 0: 2021-07-12T08:16:17,517 return l2 - l1 2021-07-12T08:16:17,517 for idx from 0 <= idx < self.nsegments: 2021-07-12T08:16:17,517 x = cmpSegmentsStartAndEnd(&self.segments[idx], &other.segments[idx]) 2021-07-12T08:16:17,517 ^ 2021-07-12T08:16:17,517 ------------------------------------------------------------ 2021-07-12T08:16:17,517 gat/SegmentList.pyx:1727:39: Cannot take address of Python object 2021-07-12T08:16:17,517 Error compiling Cython file: 2021-07-12T08:16:17,518 ------------------------------------------------------------ 2021-07-12T08:16:17,518 ... 2021-07-12T08:16:17,518 return -1 2021-07-12T08:16:17,518 cdef int l2 = len(other) 2021-07-12T08:16:17,518 if l2 - l1 != 0: 2021-07-12T08:16:17,518 return l2 - l1 2021-07-12T08:16:17,518 for idx from 0 <= idx < self.nsegments: 2021-07-12T08:16:17,518 x = cmpSegmentsStartAndEnd(&self.segments[idx], &other.segments[idx]) 2021-07-12T08:16:17,518 ^ 2021-07-12T08:16:17,519 ------------------------------------------------------------ 2021-07-12T08:16:17,519 gat/SegmentList.pyx:1727:60: Cannot take address of Python object 2021-07-12T08:16:18,149 Error compiling Cython file: 2021-07-12T08:16:18,150 ------------------------------------------------------------ 2021-07-12T08:16:18,150 ... 2021-07-12T08:16:18,150 @cython.profile(False) 2021-07-12T08:16:18,150 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:18,150 """return number of positions overlapping between to Segments.""" 2021-07-12T08:16:18,150 return lmax(0, 2021-07-12T08:16:18,150 lmin( a.end, b.end) - 2021-07-12T08:16:18,150 ^ 2021-07-12T08:16:18,151 ------------------------------------------------------------ 2021-07-12T08:16:18,151 gat/SegmentList.pyx:95:43: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,151 Error compiling Cython file: 2021-07-12T08:16:18,151 ------------------------------------------------------------ 2021-07-12T08:16:18,151 ... 2021-07-12T08:16:18,152 @cython.profile(False) 2021-07-12T08:16:18,152 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:18,152 """return number of positions overlapping between to Segments.""" 2021-07-12T08:16:18,152 return lmax(0, 2021-07-12T08:16:18,152 lmin( a.end, b.end) - 2021-07-12T08:16:18,152 ^ 2021-07-12T08:16:18,152 ------------------------------------------------------------ 2021-07-12T08:16:18,153 gat/SegmentList.pyx:95:43: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,153 Error compiling Cython file: 2021-07-12T08:16:18,153 ------------------------------------------------------------ 2021-07-12T08:16:18,153 ... 2021-07-12T08:16:18,153 @cython.profile(False) 2021-07-12T08:16:18,153 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:18,153 """return number of positions overlapping between to Segments.""" 2021-07-12T08:16:18,154 return lmax(0, 2021-07-12T08:16:18,154 lmin( a.end, b.end) - 2021-07-12T08:16:18,154 ^ 2021-07-12T08:16:18,154 ------------------------------------------------------------ 2021-07-12T08:16:18,154 gat/SegmentList.pyx:95:50: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,154 Error compiling Cython file: 2021-07-12T08:16:18,154 ------------------------------------------------------------ 2021-07-12T08:16:18,154 ... 2021-07-12T08:16:18,155 @cython.profile(False) 2021-07-12T08:16:18,155 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:18,155 """return number of positions overlapping between to Segments.""" 2021-07-12T08:16:18,155 return lmax(0, 2021-07-12T08:16:18,155 lmin( a.end, b.end) - 2021-07-12T08:16:18,155 ^ 2021-07-12T08:16:18,155 ------------------------------------------------------------ 2021-07-12T08:16:18,156 gat/SegmentList.pyx:95:50: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,156 Error compiling Cython file: 2021-07-12T08:16:18,156 ------------------------------------------------------------ 2021-07-12T08:16:18,156 ... 2021-07-12T08:16:18,156 @cython.profile(False) 2021-07-12T08:16:18,156 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:18,156 """return number of positions overlapping between to Segments.""" 2021-07-12T08:16:18,156 return lmax(0, 2021-07-12T08:16:18,156 lmin( a.end, b.end) - 2021-07-12T08:16:18,157 lmax(a.start, b.start)) 2021-07-12T08:16:18,157 ^ 2021-07-12T08:16:18,157 ------------------------------------------------------------ 2021-07-12T08:16:18,157 gat/SegmentList.pyx:96:42: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,157 Error compiling Cython file: 2021-07-12T08:16:18,157 ------------------------------------------------------------ 2021-07-12T08:16:18,157 ... 2021-07-12T08:16:18,158 @cython.profile(False) 2021-07-12T08:16:18,158 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:18,158 """return number of positions overlapping between to Segments.""" 2021-07-12T08:16:18,158 return lmax(0, 2021-07-12T08:16:18,158 lmin( a.end, b.end) - 2021-07-12T08:16:18,158 lmax(a.start, b.start)) 2021-07-12T08:16:18,158 ^ 2021-07-12T08:16:18,158 ------------------------------------------------------------ 2021-07-12T08:16:18,159 gat/SegmentList.pyx:96:42: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,159 Error compiling Cython file: 2021-07-12T08:16:18,159 ------------------------------------------------------------ 2021-07-12T08:16:18,159 ... 2021-07-12T08:16:18,159 @cython.profile(False) 2021-07-12T08:16:18,159 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:18,159 """return number of positions overlapping between to Segments.""" 2021-07-12T08:16:18,159 return lmax(0, 2021-07-12T08:16:18,159 lmin( a.end, b.end) - 2021-07-12T08:16:18,160 lmax(a.start, b.start)) 2021-07-12T08:16:18,160 ^ 2021-07-12T08:16:18,160 ------------------------------------------------------------ 2021-07-12T08:16:18,160 gat/SegmentList.pyx:96:51: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,160 Error compiling Cython file: 2021-07-12T08:16:18,160 ------------------------------------------------------------ 2021-07-12T08:16:18,160 ... 2021-07-12T08:16:18,161 @cython.profile(False) 2021-07-12T08:16:18,161 cdef inline PositionDifference segment_overlap(Segment a, Segment b) nogil: 2021-07-12T08:16:18,161 """return number of positions overlapping between to Segments.""" 2021-07-12T08:16:18,161 return lmax(0, 2021-07-12T08:16:18,161 lmin( a.end, b.end) - 2021-07-12T08:16:18,161 lmax(a.start, b.start)) 2021-07-12T08:16:18,161 ^ 2021-07-12T08:16:18,161 ------------------------------------------------------------ 2021-07-12T08:16:18,161 gat/SegmentList.pyx:96:51: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,162 Error compiling Cython file: 2021-07-12T08:16:18,162 ------------------------------------------------------------ 2021-07-12T08:16:18,162 ... 2021-07-12T08:16:18,162 lmin( aend, bend) - 2021-07-12T08:16:18,162 lmax(astart, bstart)) 2021-07-12T08:16:18,162 @cython.profile(False) 2021-07-12T08:16:18,162 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:18,163 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,163 ^ 2021-07-12T08:16:18,163 ------------------------------------------------------------ 2021-07-12T08:16:18,163 gat/SegmentList.pyx:107:37: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,163 Error compiling Cython file: 2021-07-12T08:16:18,163 ------------------------------------------------------------ 2021-07-12T08:16:18,163 ... 2021-07-12T08:16:18,163 lmin( aend, bend) - 2021-07-12T08:16:18,164 lmax(astart, bstart)) 2021-07-12T08:16:18,164 @cython.profile(False) 2021-07-12T08:16:18,164 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:18,164 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,164 ^ 2021-07-12T08:16:18,164 ------------------------------------------------------------ 2021-07-12T08:16:18,164 gat/SegmentList.pyx:107:37: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,165 Error compiling Cython file: 2021-07-12T08:16:18,165 ------------------------------------------------------------ 2021-07-12T08:16:18,165 ... 2021-07-12T08:16:18,165 lmin( aend, bend) - 2021-07-12T08:16:18,165 lmax(astart, bstart)) 2021-07-12T08:16:18,165 @cython.profile(False) 2021-07-12T08:16:18,165 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:18,166 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,166 ^ 2021-07-12T08:16:18,166 ------------------------------------------------------------ 2021-07-12T08:16:18,166 gat/SegmentList.pyx:107:44: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,166 Error compiling Cython file: 2021-07-12T08:16:18,166 ------------------------------------------------------------ 2021-07-12T08:16:18,166 ... 2021-07-12T08:16:18,166 lmin( aend, bend) - 2021-07-12T08:16:18,167 lmax(astart, bstart)) 2021-07-12T08:16:18,167 @cython.profile(False) 2021-07-12T08:16:18,167 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:18,167 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,167 ^ 2021-07-12T08:16:18,167 ------------------------------------------------------------ 2021-07-12T08:16:18,167 gat/SegmentList.pyx:107:44: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,168 Error compiling Cython file: 2021-07-12T08:16:18,168 ------------------------------------------------------------ 2021-07-12T08:16:18,168 ... 2021-07-12T08:16:18,168 lmax(astart, bstart)) 2021-07-12T08:16:18,168 @cython.profile(False) 2021-07-12T08:16:18,168 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:18,168 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,168 lmax(a.start, b.start) 2021-07-12T08:16:18,169 ^ 2021-07-12T08:16:18,169 ------------------------------------------------------------ 2021-07-12T08:16:18,169 gat/SegmentList.pyx:108:34: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,169 Error compiling Cython file: 2021-07-12T08:16:18,169 ------------------------------------------------------------ 2021-07-12T08:16:18,169 ... 2021-07-12T08:16:18,169 lmax(astart, bstart)) 2021-07-12T08:16:18,170 @cython.profile(False) 2021-07-12T08:16:18,170 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:18,170 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,170 lmax(a.start, b.start) 2021-07-12T08:16:18,170 ^ 2021-07-12T08:16:18,170 ------------------------------------------------------------ 2021-07-12T08:16:18,170 gat/SegmentList.pyx:108:34: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,171 Error compiling Cython file: 2021-07-12T08:16:18,171 ------------------------------------------------------------ 2021-07-12T08:16:18,171 ... 2021-07-12T08:16:18,171 lmax(astart, bstart)) 2021-07-12T08:16:18,171 @cython.profile(False) 2021-07-12T08:16:18,171 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:18,171 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,171 lmax(a.start, b.start) 2021-07-12T08:16:18,172 ^ 2021-07-12T08:16:18,172 ------------------------------------------------------------ 2021-07-12T08:16:18,172 gat/SegmentList.pyx:108:43: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,172 Error compiling Cython file: 2021-07-12T08:16:18,172 ------------------------------------------------------------ 2021-07-12T08:16:18,172 ... 2021-07-12T08:16:18,173 lmax(astart, bstart)) 2021-07-12T08:16:18,173 @cython.profile(False) 2021-07-12T08:16:18,173 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:18,173 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,173 lmax(a.start, b.start) 2021-07-12T08:16:18,173 ^ 2021-07-12T08:16:18,173 ------------------------------------------------------------ 2021-07-12T08:16:18,173 gat/SegmentList.pyx:108:43: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,174 Error compiling Cython file: 2021-07-12T08:16:18,174 ------------------------------------------------------------ 2021-07-12T08:16:18,174 ... 2021-07-12T08:16:18,174 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,174 lmax(a.start, b.start) 2021-07-12T08:16:18,174 @cython.profile(False) 2021-07-12T08:16:18,174 cdef inline PositionDifference segment_length(Segment a) nogil: 2021-07-12T08:16:18,174 return a.end - a.start 2021-07-12T08:16:18,175 ^ 2021-07-12T08:16:18,175 ------------------------------------------------------------ 2021-07-12T08:16:18,175 gat/SegmentList.pyx:112:32: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,175 Error compiling Cython file: 2021-07-12T08:16:18,175 ------------------------------------------------------------ 2021-07-12T08:16:18,175 ... 2021-07-12T08:16:18,175 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,176 lmax(a.start, b.start) 2021-07-12T08:16:18,176 @cython.profile(False) 2021-07-12T08:16:18,176 cdef inline PositionDifference segment_length(Segment a) nogil: 2021-07-12T08:16:18,176 return a.end - a.start 2021-07-12T08:16:18,176 ^ 2021-07-12T08:16:18,176 ------------------------------------------------------------ 2021-07-12T08:16:18,176 gat/SegmentList.pyx:112:32: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,177 Error compiling Cython file: 2021-07-12T08:16:18,177 ------------------------------------------------------------ 2021-07-12T08:16:18,177 ... 2021-07-12T08:16:18,177 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,177 lmax(a.start, b.start) 2021-07-12T08:16:18,177 @cython.profile(False) 2021-07-12T08:16:18,177 cdef inline PositionDifference segment_length(Segment a) nogil: 2021-07-12T08:16:18,177 return a.end - a.start 2021-07-12T08:16:18,178 ^ 2021-07-12T08:16:18,178 ------------------------------------------------------------ 2021-07-12T08:16:18,178 gat/SegmentList.pyx:112:60: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,178 Error compiling Cython file: 2021-07-12T08:16:18,178 ------------------------------------------------------------ 2021-07-12T08:16:18,178 ... 2021-07-12T08:16:18,178 return lmin(a.end, b.end) - \ 2021-07-12T08:16:18,178 lmax(a.start, b.start) 2021-07-12T08:16:18,179 @cython.profile(False) 2021-07-12T08:16:18,179 cdef inline PositionDifference segment_length(Segment a) nogil: 2021-07-12T08:16:18,179 return a.end - a.start 2021-07-12T08:16:18,179 ^ 2021-07-12T08:16:18,179 ------------------------------------------------------------ 2021-07-12T08:16:18,179 gat/SegmentList.pyx:112:60: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,180 Error compiling Cython file: 2021-07-12T08:16:18,180 ------------------------------------------------------------ 2021-07-12T08:16:18,180 ... 2021-07-12T08:16:18,180 cdef extern from *: 2021-07-12T08:16:18,180 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:18,180 @cython.profile(False) 2021-07-12T08:16:18,180 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:18,180 return (s1).start - \ 2021-07-12T08:16:18,180 ^ 2021-07-12T08:16:18,181 ------------------------------------------------------------ 2021-07-12T08:16:18,181 gat/SegmentList.pyx:120:46: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,181 Error compiling Cython file: 2021-07-12T08:16:18,181 ------------------------------------------------------------ 2021-07-12T08:16:18,181 ... 2021-07-12T08:16:18,181 cdef extern from *: 2021-07-12T08:16:18,181 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:18,182 @cython.profile(False) 2021-07-12T08:16:18,182 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:18,182 return (s1).start - \ 2021-07-12T08:16:18,182 ^ 2021-07-12T08:16:18,182 ------------------------------------------------------------ 2021-07-12T08:16:18,182 gat/SegmentList.pyx:120:46: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,182 Error compiling Cython file: 2021-07-12T08:16:18,183 ------------------------------------------------------------ 2021-07-12T08:16:18,183 ... 2021-07-12T08:16:18,183 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:18,183 @cython.profile(False) 2021-07-12T08:16:18,183 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:18,183 return (s1).start - \ 2021-07-12T08:16:18,183 (s2).start 2021-07-12T08:16:18,183 ^ 2021-07-12T08:16:18,184 ------------------------------------------------------------ 2021-07-12T08:16:18,184 gat/SegmentList.pyx:121:43: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,184 Error compiling Cython file: 2021-07-12T08:16:18,184 ------------------------------------------------------------ 2021-07-12T08:16:18,184 ... 2021-07-12T08:16:18,184 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:18,184 @cython.profile(False) 2021-07-12T08:16:18,185 cdef int cmpSegments(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:18,185 return (s1).start - \ 2021-07-12T08:16:18,185 (s2).start 2021-07-12T08:16:18,185 ^ 2021-07-12T08:16:18,185 ------------------------------------------------------------ 2021-07-12T08:16:18,185 gat/SegmentList.pyx:121:43: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,185 Error compiling Cython file: 2021-07-12T08:16:18,185 ------------------------------------------------------------ 2021-07-12T08:16:18,186 ... 2021-07-12T08:16:18,186 (s2).start 2021-07-12T08:16:18,186 @cython.profile(False) 2021-07-12T08:16:18,186 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:18,186 cdef int x 2021-07-12T08:16:18,186 x = (s1).start - \ 2021-07-12T08:16:18,186 ^ 2021-07-12T08:16:18,186 ------------------------------------------------------------ 2021-07-12T08:16:18,187 gat/SegmentList.pyx:126:43: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,187 Error compiling Cython file: 2021-07-12T08:16:18,187 ------------------------------------------------------------ 2021-07-12T08:16:18,187 ... 2021-07-12T08:16:18,187 (s2).start 2021-07-12T08:16:18,187 @cython.profile(False) 2021-07-12T08:16:18,188 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:18,188 cdef int x 2021-07-12T08:16:18,188 x = (s1).start - \ 2021-07-12T08:16:18,188 ^ 2021-07-12T08:16:18,188 ------------------------------------------------------------ 2021-07-12T08:16:18,188 gat/SegmentList.pyx:126:43: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,188 Error compiling Cython file: 2021-07-12T08:16:18,188 ------------------------------------------------------------ 2021-07-12T08:16:18,189 ... 2021-07-12T08:16:18,189 @cython.profile(False) 2021-07-12T08:16:18,189 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:18,189 cdef int x 2021-07-12T08:16:18,189 x = (s1).start - \ 2021-07-12T08:16:18,189 (s2).start 2021-07-12T08:16:18,189 ^ 2021-07-12T08:16:18,189 ------------------------------------------------------------ 2021-07-12T08:16:18,190 gat/SegmentList.pyx:127:43: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,190 Error compiling Cython file: 2021-07-12T08:16:18,190 ------------------------------------------------------------ 2021-07-12T08:16:18,190 ... 2021-07-12T08:16:18,190 @cython.profile(False) 2021-07-12T08:16:18,190 cdef int cmpSegmentsStartAndEnd(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:18,190 cdef int x 2021-07-12T08:16:18,191 x = (s1).start - \ 2021-07-12T08:16:18,191 (s2).start 2021-07-12T08:16:18,191 ^ 2021-07-12T08:16:18,191 ------------------------------------------------------------ 2021-07-12T08:16:18,191 gat/SegmentList.pyx:127:43: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,191 Error compiling Cython file: 2021-07-12T08:16:18,191 ------------------------------------------------------------ 2021-07-12T08:16:18,191 ... 2021-07-12T08:16:18,192 cdef int x 2021-07-12T08:16:18,192 x = (s1).start - \ 2021-07-12T08:16:18,192 (s2).start 2021-07-12T08:16:18,192 if x != 0: 2021-07-12T08:16:18,192 return x 2021-07-12T08:16:18,192 return (s1).end - \ 2021-07-12T08:16:18,192 ^ 2021-07-12T08:16:18,192 ------------------------------------------------------------ 2021-07-12T08:16:18,193 gat/SegmentList.pyx:130:46: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,193 Error compiling Cython file: 2021-07-12T08:16:18,193 ------------------------------------------------------------ 2021-07-12T08:16:18,193 ... 2021-07-12T08:16:18,193 cdef int x 2021-07-12T08:16:18,193 x = (s1).start - \ 2021-07-12T08:16:18,193 (s2).start 2021-07-12T08:16:18,193 if x != 0: 2021-07-12T08:16:18,193 return x 2021-07-12T08:16:18,194 return (s1).end - \ 2021-07-12T08:16:18,194 ^ 2021-07-12T08:16:18,194 ------------------------------------------------------------ 2021-07-12T08:16:18,194 gat/SegmentList.pyx:130:46: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,194 Error compiling Cython file: 2021-07-12T08:16:18,194 ------------------------------------------------------------ 2021-07-12T08:16:18,194 ... 2021-07-12T08:16:18,195 x = (s1).start - \ 2021-07-12T08:16:18,195 (s2).start 2021-07-12T08:16:18,195 if x != 0: 2021-07-12T08:16:18,195 return x 2021-07-12T08:16:18,195 return (s1).end - \ 2021-07-12T08:16:18,195 (s2).end 2021-07-12T08:16:18,195 ^ 2021-07-12T08:16:18,195 ------------------------------------------------------------ 2021-07-12T08:16:18,196 gat/SegmentList.pyx:131:43: Coercion from Python not allowed without the GIL 2021-07-12T08:16:18,196 Error compiling Cython file: 2021-07-12T08:16:18,196 ------------------------------------------------------------ 2021-07-12T08:16:18,196 ... 2021-07-12T08:16:18,196 x = (s1).start - \ 2021-07-12T08:16:18,196 (s2).start 2021-07-12T08:16:18,196 if x != 0: 2021-07-12T08:16:18,196 return x 2021-07-12T08:16:18,196 return (s1).end - \ 2021-07-12T08:16:18,197 (s2).end 2021-07-12T08:16:18,197 ^ 2021-07-12T08:16:18,197 ------------------------------------------------------------ 2021-07-12T08:16:18,197 gat/SegmentList.pyx:131:43: Accessing Python attribute not allowed without gil 2021-07-12T08:16:18,223 cythoning gat/PositionList.pyx to gat/PositionList.c 2021-07-12T08:16:18,230 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-sammuaxk/gat_98fddb3111d94ae9bf647f384bede459/gat/PositionList.pyx 2021-07-12T08:16:18,230 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T08:16:20,427 Error compiling Cython file: 2021-07-12T08:16:20,427 ------------------------------------------------------------ 2021-07-12T08:16:20,428 ... 2021-07-12T08:16:20,428 from posix.mman cimport mmap, munmap, shm_open, shm_unlink 2021-07-12T08:16:20,428 from posix.mman cimport MAP_SHARED, PROT_READ, PROT_WRITE 2021-07-12T08:16:20,428 from posix.stat cimport S_IRUSR, S_IWUSR 2021-07-12T08:16:20,428 from posix.fcntl cimport O_CREAT, O_RDWR, O_RDONLY 2021-07-12T08:16:20,428 from SegmentList cimport Position, Segment, SegmentList 2021-07-12T08:16:20,428 ^ 2021-07-12T08:16:20,428 ------------------------------------------------------------ 2021-07-12T08:16:20,429 gat/PositionList.pyx:17:0: 'SegmentList.pxd' not found 2021-07-12T08:16:20,433 Error compiling Cython file: 2021-07-12T08:16:20,433 ------------------------------------------------------------ 2021-07-12T08:16:20,434 ... 2021-07-12T08:16:20,434 from posix.mman cimport mmap, munmap, shm_open, shm_unlink 2021-07-12T08:16:20,434 from posix.mman cimport MAP_SHARED, PROT_READ, PROT_WRITE 2021-07-12T08:16:20,434 from posix.stat cimport S_IRUSR, S_IWUSR 2021-07-12T08:16:20,434 from posix.fcntl cimport O_CREAT, O_RDWR, O_RDONLY 2021-07-12T08:16:20,434 from SegmentList cimport Position, Segment, SegmentList 2021-07-12T08:16:20,435 ^ 2021-07-12T08:16:20,435 ------------------------------------------------------------ 2021-07-12T08:16:20,435 gat/PositionList.pyx:17:0: 'SegmentList/Position.pxd' not found 2021-07-12T08:16:20,438 Error compiling Cython file: 2021-07-12T08:16:20,438 ------------------------------------------------------------ 2021-07-12T08:16:20,438 ... 2021-07-12T08:16:20,438 from posix.mman cimport mmap, munmap, shm_open, shm_unlink 2021-07-12T08:16:20,438 from posix.mman cimport MAP_SHARED, PROT_READ, PROT_WRITE 2021-07-12T08:16:20,439 from posix.stat cimport S_IRUSR, S_IWUSR 2021-07-12T08:16:20,439 from posix.fcntl cimport O_CREAT, O_RDWR, O_RDONLY 2021-07-12T08:16:20,439 from SegmentList cimport Position, Segment, SegmentList 2021-07-12T08:16:20,439 ^ 2021-07-12T08:16:20,439 ------------------------------------------------------------ 2021-07-12T08:16:20,439 gat/PositionList.pyx:17:0: 'SegmentList/Segment.pxd' not found 2021-07-12T08:16:20,442 Error compiling Cython file: 2021-07-12T08:16:20,442 ------------------------------------------------------------ 2021-07-12T08:16:20,442 ... 2021-07-12T08:16:20,443 from posix.mman cimport mmap, munmap, shm_open, shm_unlink 2021-07-12T08:16:20,443 from posix.mman cimport MAP_SHARED, PROT_READ, PROT_WRITE 2021-07-12T08:16:20,443 from posix.stat cimport S_IRUSR, S_IWUSR 2021-07-12T08:16:20,443 from posix.fcntl cimport O_CREAT, O_RDWR, O_RDONLY 2021-07-12T08:16:20,443 from SegmentList cimport Position, Segment, SegmentList 2021-07-12T08:16:20,443 ^ 2021-07-12T08:16:20,444 ------------------------------------------------------------ 2021-07-12T08:16:20,444 gat/PositionList.pyx:17:0: 'SegmentList/SegmentList.pxd' not found 2021-07-12T08:16:20,445 Error compiling Cython file: 2021-07-12T08:16:20,445 ------------------------------------------------------------ 2021-07-12T08:16:20,445 ... 2021-07-12T08:16:20,445 self.is_sorted, 2021-07-12T08:16:20,445 self.is_normalized, 2021-07-12T08:16:20,445 self.chunk_size, 2021-07-12T08:16:20,445 self.key, 2021-07-12T08:16:20,446 data)) 2021-07-12T08:16:20,446 cpdef Position max(self): 2021-07-12T08:16:20,446 ^ 2021-07-12T08:16:20,446 ------------------------------------------------------------ 2021-07-12T08:16:20,446 gat/PositionList.pyx:223:10: 'Position' is not a type identifier 2021-07-12T08:16:20,447 Error compiling Cython file: 2021-07-12T08:16:20,447 ------------------------------------------------------------ 2021-07-12T08:16:20,447 ... 2021-07-12T08:16:20,447 assert self.is_sorted, "PositionList : max from unsorted list" 2021-07-12T08:16:20,447 if self.npositions == 0: 2021-07-12T08:16:20,447 return 0 2021-07-12T08:16:20,447 return self.positions[self.npositions - 1] 2021-07-12T08:16:20,448 cpdef Position min(self): 2021-07-12T08:16:20,448 ^ 2021-07-12T08:16:20,448 ------------------------------------------------------------ 2021-07-12T08:16:20,448 gat/PositionList.pyx:230:10: 'Position' is not a type identifier 2021-07-12T08:16:20,448 Error compiling Cython file: 2021-07-12T08:16:20,448 ------------------------------------------------------------ 2021-07-12T08:16:20,449 ... 2021-07-12T08:16:20,449 assert self.is_sorted, "PositionList : min from unsorted list" 2021-07-12T08:16:20,449 if self.npositions == 0: 2021-07-12T08:16:20,449 return 0 2021-07-12T08:16:20,449 return self.positions[0] 2021-07-12T08:16:20,449 cpdef Position sum(self): 2021-07-12T08:16:20,450 ^ 2021-07-12T08:16:20,450 ------------------------------------------------------------ 2021-07-12T08:16:20,450 gat/PositionList.pyx:237:10: 'Position' is not a type identifier 2021-07-12T08:16:20,450 Error compiling Cython file: 2021-07-12T08:16:20,450 ------------------------------------------------------------ 2021-07-12T08:16:20,450 ... 2021-07-12T08:16:20,451 self.is_normalized = True 2021-07-12T08:16:20,451 def __len__(self): 2021-07-12T08:16:20,451 return self.npositions 2021-07-12T08:16:20,451 cdef _add(self, Position position): 2021-07-12T08:16:20,451 ^ 2021-07-12T08:16:20,452 ------------------------------------------------------------ 2021-07-12T08:16:20,452 gat/PositionList.pyx:253:20: 'Position' is not a type identifier 2021-07-12T08:16:20,452 Error compiling Cython file: 2021-07-12T08:16:20,452 ------------------------------------------------------------ 2021-07-12T08:16:20,453 ... 2021-07-12T08:16:20,453 self.positions[self.npositions] = position 2021-07-12T08:16:20,453 self.npositions += 1 2021-07-12T08:16:20,453 self.is_sorted = False 2021-07-12T08:16:20,453 self.is_normalized = False 2021-07-12T08:16:20,453 cpdef add(self, Position pos): 2021-07-12T08:16:20,453 ^ 2021-07-12T08:16:20,454 ------------------------------------------------------------ 2021-07-12T08:16:20,454 gat/PositionList.pyx:280:20: 'Position' is not a type identifier 2021-07-12T08:16:20,454 Error compiling Cython file: 2021-07-12T08:16:20,454 ------------------------------------------------------------ 2021-07-12T08:16:20,455 ... 2021-07-12T08:16:20,455 The list will not be normalized automatically - call 2021-07-12T08:16:20,455 :meth:`PositionList.normalize`. 2021-07-12T08:16:20,455 ''' 2021-07-12T08:16:20,455 self._add(pos) 2021-07-12T08:16:20,456 def fromSegmentList(self, SegmentList segments, method="midpoint"): 2021-07-12T08:16:20,456 ^ 2021-07-12T08:16:20,456 ------------------------------------------------------------ 2021-07-12T08:16:20,456 gat/PositionList.pyx:288:30: 'SegmentList' is not a type identifier 2021-07-12T08:16:20,457 Error compiling Cython file: 2021-07-12T08:16:20,457 ------------------------------------------------------------ 2021-07-12T08:16:20,457 ... 2021-07-12T08:16:20,457 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:20,457 sizeof(self.npositions * sizeof(Position))) 2021-07-12T08:16:20,458 self.allocated = npositions 2021-07-12T08:16:20,458 cdef int _getInsertionPoint(self, Position other): 2021-07-12T08:16:20,458 ^ 2021-07-12T08:16:20,458 ------------------------------------------------------------ 2021-07-12T08:16:20,458 gat/PositionList.pyx:398:38: 'Position' is not a type identifier 2021-07-12T08:16:20,459 Error compiling Cython file: 2021-07-12T08:16:20,459 ------------------------------------------------------------ 2021-07-12T08:16:20,459 ... 2021-07-12T08:16:20,459 self.npositions, 2021-07-12T08:16:20,459 sizeof(Position), 2021-07-12T08:16:20,459 &other, 2021-07-12T08:16:20,459 &cmpPosition) 2021-07-12T08:16:20,460 cdef Position overlap(self, Segment other): 2021-07-12T08:16:20,460 ^ 2021-07-12T08:16:20,460 ------------------------------------------------------------ 2021-07-12T08:16:20,460 gat/PositionList.pyx:432:9: 'Position' is not a type identifier 2021-07-12T08:16:20,460 Error compiling Cython file: 2021-07-12T08:16:20,460 ------------------------------------------------------------ 2021-07-12T08:16:20,460 ... 2021-07-12T08:16:20,461 self.npositions, 2021-07-12T08:16:20,461 sizeof(Position), 2021-07-12T08:16:20,461 &other, 2021-07-12T08:16:20,461 &cmpPosition) 2021-07-12T08:16:20,461 cdef Position overlap(self, Segment other): 2021-07-12T08:16:20,461 ^ 2021-07-12T08:16:20,461 ------------------------------------------------------------ 2021-07-12T08:16:20,462 gat/PositionList.pyx:432:32: 'Segment' is not a type identifier 2021-07-12T08:16:20,462 Error compiling Cython file: 2021-07-12T08:16:20,462 ------------------------------------------------------------ 2021-07-12T08:16:20,462 ... 2021-07-12T08:16:20,462 self.positions[idx] < other.end: 2021-07-12T08:16:20,462 count += 1 2021-07-12T08:16:20,463 idx += 1 2021-07-12T08:16:20,463 return count 2021-07-12T08:16:20,463 cpdef Position overlapWithRange(self, Position start, Position end): 2021-07-12T08:16:20,463 ^ 2021-07-12T08:16:20,463 ------------------------------------------------------------ 2021-07-12T08:16:20,463 gat/PositionList.pyx:470:10: 'Position' is not a type identifier 2021-07-12T08:16:20,464 Error compiling Cython file: 2021-07-12T08:16:20,464 ------------------------------------------------------------ 2021-07-12T08:16:20,464 ... 2021-07-12T08:16:20,464 self.positions[idx] < other.end: 2021-07-12T08:16:20,464 count += 1 2021-07-12T08:16:20,464 idx += 1 2021-07-12T08:16:20,464 return count 2021-07-12T08:16:20,465 cpdef Position overlapWithRange(self, Position start, Position end): 2021-07-12T08:16:20,465 ^ 2021-07-12T08:16:20,465 ------------------------------------------------------------ 2021-07-12T08:16:20,465 gat/PositionList.pyx:470:42: 'Position' is not a type identifier 2021-07-12T08:16:20,465 Error compiling Cython file: 2021-07-12T08:16:20,465 ------------------------------------------------------------ 2021-07-12T08:16:20,465 ... 2021-07-12T08:16:20,466 self.positions[idx] < other.end: 2021-07-12T08:16:20,466 count += 1 2021-07-12T08:16:20,466 idx += 1 2021-07-12T08:16:20,466 return count 2021-07-12T08:16:20,466 cpdef Position overlapWithRange(self, Position start, Position end): 2021-07-12T08:16:20,466 ^ 2021-07-12T08:16:20,466 ------------------------------------------------------------ 2021-07-12T08:16:20,467 gat/PositionList.pyx:470:58: 'Position' is not a type identifier 2021-07-12T08:16:20,467 Error compiling Cython file: 2021-07-12T08:16:20,467 ------------------------------------------------------------ 2021-07-12T08:16:20,467 ... 2021-07-12T08:16:20,467 cdef Segment s 2021-07-12T08:16:20,467 s = Segment(start, end) 2021-07-12T08:16:20,468 return self.overlap(s) 2021-07-12T08:16:20,468 cpdef Position intersectionWithSegments( 2021-07-12T08:16:20,468 ^ 2021-07-12T08:16:20,468 ------------------------------------------------------------ 2021-07-12T08:16:20,468 gat/PositionList.pyx:490:10: 'Position' is not a type identifier 2021-07-12T08:16:20,468 Error compiling Cython file: 2021-07-12T08:16:20,469 ------------------------------------------------------------ 2021-07-12T08:16:20,469 ... 2021-07-12T08:16:20,469 s = Segment(start, end) 2021-07-12T08:16:20,469 return self.overlap(s) 2021-07-12T08:16:20,469 cpdef Position intersectionWithSegments( 2021-07-12T08:16:20,469 self, 2021-07-12T08:16:20,469 SegmentList other, 2021-07-12T08:16:20,469 ^ 2021-07-12T08:16:20,470 ------------------------------------------------------------ 2021-07-12T08:16:20,470 gat/PositionList.pyx:492:8: 'SegmentList' is not a type identifier 2021-07-12T08:16:20,470 Error compiling Cython file: 2021-07-12T08:16:20,470 ------------------------------------------------------------ 2021-07-12T08:16:20,470 ... 2021-07-12T08:16:20,470 noverlap += 1 2021-07-12T08:16:20,471 this_idx += 1 2021-07-12T08:16:20,471 return noverlap 2021-07-12T08:16:20,471 cpdef void intersect(self, SegmentList other): 2021-07-12T08:16:20,471 ^ 2021-07-12T08:16:20,471 ------------------------------------------------------------ 2021-07-12T08:16:20,471 gat/PositionList.pyx:542:31: 'SegmentList' is not a type identifier 2021-07-12T08:16:20,472 Error compiling Cython file: 2021-07-12T08:16:20,472 ------------------------------------------------------------ 2021-07-12T08:16:20,472 ... 2021-07-12T08:16:20,472 self.is_shared = False 2021-07-12T08:16:20,472 self.is_slave = False 2021-07-12T08:16:20,472 self.shared_fd = -1 2021-07-12T08:16:20,472 self.key = None 2021-07-12T08:16:20,473 cdef int idx 2021-07-12T08:16:20,473 cdef Position pos 2021-07-12T08:16:20,473 ^ 2021-07-12T08:16:20,473 ------------------------------------------------------------ 2021-07-12T08:16:20,473 gat/PositionList.pyx:97:13: 'Position' is not a type identifier 2021-07-12T08:16:20,473 Error compiling Cython file: 2021-07-12T08:16:20,474 ------------------------------------------------------------ 2021-07-12T08:16:20,474 ... 2021-07-12T08:16:20,474 self.sort() 2021-07-12T08:16:20,474 cdef int idx = 0 2021-07-12T08:16:20,474 cdef int insertion_idx = 0 2021-07-12T08:16:20,474 cdef Position last_position = -1 2021-07-12T08:16:20,474 ^ 2021-07-12T08:16:20,475 ------------------------------------------------------------ 2021-07-12T08:16:20,475 gat/PositionList.pyx:363:13: 'Position' is not a type identifier 2021-07-12T08:16:20,475 Error compiling Cython file: 2021-07-12T08:16:20,475 ------------------------------------------------------------ 2021-07-12T08:16:20,475 ... 2021-07-12T08:16:20,475 self.sort() 2021-07-12T08:16:20,476 cdef int idx = 0 2021-07-12T08:16:20,476 cdef int insertion_idx = 0 2021-07-12T08:16:20,476 cdef Position last_position = -1 2021-07-12T08:16:20,476 cdef Position current_position 2021-07-12T08:16:20,476 ^ 2021-07-12T08:16:20,476 ------------------------------------------------------------ 2021-07-12T08:16:20,476 gat/PositionList.pyx:364:13: 'Position' is not a type identifier 2021-07-12T08:16:20,477 Error compiling Cython file: 2021-07-12T08:16:20,477 ------------------------------------------------------------ 2021-07-12T08:16:20,477 ... 2021-07-12T08:16:20,477 overlap : int 2021-07-12T08:16:20,477 Number of residues overlapping 2021-07-12T08:16:20,477 """ 2021-07-12T08:16:20,477 assert self.is_sorted, "PointList is not sorted" 2021-07-12T08:16:20,478 cdef Position count = 0 2021-07-12T08:16:20,478 ^ 2021-07-12T08:16:20,478 ------------------------------------------------------------ 2021-07-12T08:16:20,478 gat/PositionList.pyx:447:13: 'Position' is not a type identifier 2021-07-12T08:16:20,478 Error compiling Cython file: 2021-07-12T08:16:20,479 ------------------------------------------------------------ 2021-07-12T08:16:20,479 ... 2021-07-12T08:16:20,479 ------ 2021-07-12T08:16:20,479 overlap : int 2021-07-12T08:16:20,479 Number of residues overlapping 2021-07-12T08:16:20,479 """ 2021-07-12T08:16:20,479 cdef Segment s 2021-07-12T08:16:20,480 ^ 2021-07-12T08:16:20,480 ------------------------------------------------------------ 2021-07-12T08:16:20,480 gat/PositionList.pyx:486:13: 'Segment' is not a type identifier 2021-07-12T08:16:20,480 Error compiling Cython file: 2021-07-12T08:16:20,480 ------------------------------------------------------------ 2021-07-12T08:16:20,480 ... 2021-07-12T08:16:20,480 assert other.isNormalized, "Intersection with non-normalized segments" 2021-07-12T08:16:20,481 cdef int this_idx, other_idx, last_this_idx, last_other_idx 2021-07-12T08:16:20,481 this_idx = other_idx = 0 2021-07-12T08:16:20,481 last_this_idx = last_other_idx = -1 2021-07-12T08:16:20,481 cdef Position this_position = -1 2021-07-12T08:16:20,481 ^ 2021-07-12T08:16:20,481 ------------------------------------------------------------ 2021-07-12T08:16:20,481 gat/PositionList.pyx:518:13: 'Position' is not a type identifier 2021-07-12T08:16:20,482 Error compiling Cython file: 2021-07-12T08:16:20,482 ------------------------------------------------------------ 2021-07-12T08:16:20,482 ... 2021-07-12T08:16:20,482 cdef int this_idx, other_idx, last_this_idx, last_other_idx 2021-07-12T08:16:20,482 this_idx = other_idx = 0 2021-07-12T08:16:20,482 last_this_idx = last_other_idx = -1 2021-07-12T08:16:20,482 cdef Position this_position = -1 2021-07-12T08:16:20,483 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:20,483 ^ 2021-07-12T08:16:20,483 ------------------------------------------------------------ 2021-07-12T08:16:20,483 gat/PositionList.pyx:519:13: 'Segment' is not a type identifier 2021-07-12T08:16:20,483 Error compiling Cython file: 2021-07-12T08:16:20,483 ------------------------------------------------------------ 2021-07-12T08:16:20,483 ... 2021-07-12T08:16:20,484 cdef int this_idx, other_idx, last_this_idx, last_other_idx 2021-07-12T08:16:20,484 this_idx = other_idx = 0 2021-07-12T08:16:20,484 last_this_idx = last_other_idx = -1 2021-07-12T08:16:20,484 cdef Position this_position = -1 2021-07-12T08:16:20,484 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:20,484 cdef Position noverlap = 0 2021-07-12T08:16:20,484 ^ 2021-07-12T08:16:20,484 ------------------------------------------------------------ 2021-07-12T08:16:20,485 gat/PositionList.pyx:520:13: 'Position' is not a type identifier 2021-07-12T08:16:20,485 Error compiling Cython file: 2021-07-12T08:16:20,485 ------------------------------------------------------------ 2021-07-12T08:16:20,485 ... 2021-07-12T08:16:20,485 return 2021-07-12T08:16:20,485 cdef int this_idx, other_idx, last_this_idx, last_other_idx, working_idx 2021-07-12T08:16:20,485 this_idx = other_idx = working_idx = 0 2021-07-12T08:16:20,486 last_this_idx = last_other_idx = -1 2021-07-12T08:16:20,486 cdef Position this_position = -1 2021-07-12T08:16:20,486 ^ 2021-07-12T08:16:20,486 ------------------------------------------------------------ 2021-07-12T08:16:20,486 gat/PositionList.pyx:562:13: 'Position' is not a type identifier 2021-07-12T08:16:20,486 Error compiling Cython file: 2021-07-12T08:16:20,486 ------------------------------------------------------------ 2021-07-12T08:16:20,487 ... 2021-07-12T08:16:20,487 cdef int this_idx, other_idx, last_this_idx, last_other_idx, working_idx 2021-07-12T08:16:20,487 this_idx = other_idx = working_idx = 0 2021-07-12T08:16:20,487 last_this_idx = last_other_idx = -1 2021-07-12T08:16:20,487 cdef Position this_position = -1 2021-07-12T08:16:20,487 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:20,487 ^ 2021-07-12T08:16:20,487 ------------------------------------------------------------ 2021-07-12T08:16:20,488 gat/PositionList.pyx:563:13: 'Segment' is not a type identifier 2021-07-12T08:16:20,488 Error compiling Cython file: 2021-07-12T08:16:20,488 ------------------------------------------------------------ 2021-07-12T08:16:20,488 ... 2021-07-12T08:16:20,488 cdef int this_idx, other_idx, last_this_idx, last_other_idx, working_idx 2021-07-12T08:16:20,488 this_idx = other_idx = working_idx = 0 2021-07-12T08:16:20,488 last_this_idx = last_other_idx = -1 2021-07-12T08:16:20,489 cdef Position this_position = -1 2021-07-12T08:16:20,489 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:20,489 cdef Position noverlap = 0 2021-07-12T08:16:20,489 ^ 2021-07-12T08:16:20,489 ------------------------------------------------------------ 2021-07-12T08:16:20,489 gat/PositionList.pyx:564:13: 'Position' is not a type identifier 2021-07-12T08:16:20,489 Error compiling Cython file: 2021-07-12T08:16:20,490 ------------------------------------------------------------ 2021-07-12T08:16:20,490 ... 2021-07-12T08:16:20,490 cdef void fromMMAP(self): 2021-07-12T08:16:20,490 '''retrieve data from mmapped location to private copy. 2021-07-12T08:16:20,490 ''' 2021-07-12T08:16:20,490 # copy data back to unshared memory 2021-07-12T08:16:20,490 cdef Position * s 2021-07-12T08:16:20,490 ^ 2021-07-12T08:16:20,491 ------------------------------------------------------------ 2021-07-12T08:16:20,491 gat/PositionList.pyx:634:13: 'Position' is not a type identifier 2021-07-12T08:16:20,491 Error compiling Cython file: 2021-07-12T08:16:20,491 ------------------------------------------------------------ 2021-07-12T08:16:20,491 ... 2021-07-12T08:16:20,491 if self.npositions == 0: 2021-07-12T08:16:20,492 # do not move empty position lists 2021-07-12T08:16:20,492 return offset 2021-07-12T08:16:20,492 cdef off_t nbytes = sizeof(Position) * self.npositions 2021-07-12T08:16:20,492 cdef Position * p = mmap + offset 2021-07-12T08:16:20,492 ^ 2021-07-12T08:16:20,492 ------------------------------------------------------------ 2021-07-12T08:16:20,492 gat/PositionList.pyx:666:13: 'Position' is not a type identifier 2021-07-12T08:16:20,648 Error compiling Cython file: 2021-07-12T08:16:20,648 ------------------------------------------------------------ 2021-07-12T08:16:20,648 ... 2021-07-12T08:16:20,648 cdef extern from *: 2021-07-12T08:16:20,648 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:20,648 @cython.profile(False) 2021-07-12T08:16:20,648 cdef int cmpPosition(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:20,648 return (s1)[0] - (s2)[0] 2021-07-12T08:16:20,649 ^ 2021-07-12T08:16:20,649 ------------------------------------------------------------ 2021-07-12T08:16:20,649 gat/PositionList.pyx:39:13: 'Position' is not a type identifier 2021-07-12T08:16:20,649 Error compiling Cython file: 2021-07-12T08:16:20,649 ------------------------------------------------------------ 2021-07-12T08:16:20,649 ... 2021-07-12T08:16:20,650 cdef extern from *: 2021-07-12T08:16:20,650 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:20,650 @cython.profile(False) 2021-07-12T08:16:20,650 cdef int cmpPosition(const_void_ptr s1, const_void_ptr s2) nogil: 2021-07-12T08:16:20,650 return (s1)[0] - (s2)[0] 2021-07-12T08:16:20,650 ^ 2021-07-12T08:16:20,650 ------------------------------------------------------------ 2021-07-12T08:16:20,651 gat/PositionList.pyx:39:34: 'Position' is not a type identifier 2021-07-12T08:16:20,651 Error compiling Cython file: 2021-07-12T08:16:20,651 ------------------------------------------------------------ 2021-07-12T08:16:20,651 ... 2021-07-12T08:16:20,651 a _slave_. 2021-07-12T08:16:20,651 If *normalize* is set, the list will be normalized. 2021-07-12T08:16:20,651 ''' 2021-07-12T08:16:20,652 # initialize empty list 2021-07-12T08:16:20,652 self.positions = NULL 2021-07-12T08:16:20,652 ^ 2021-07-12T08:16:20,652 ------------------------------------------------------------ 2021-07-12T08:16:20,652 gat/PositionList.pyx:84:25: Cannot convert 'void *' to Python object 2021-07-12T08:16:20,652 Error compiling Cython file: 2021-07-12T08:16:20,653 ------------------------------------------------------------ 2021-07-12T08:16:20,653 ... 2021-07-12T08:16:20,653 self.is_sorted = share.is_sorted 2021-07-12T08:16:20,653 self.is_normalized = share.is_normalized 2021-07-12T08:16:20,653 self.is_shared = True 2021-07-12T08:16:20,653 self.is_slave = True 2021-07-12T08:16:20,653 self.chunk_size = share.chunk_size 2021-07-12T08:16:20,653 retval = mmap(NULL, 2021-07-12T08:16:20,653 ^ 2021-07-12T08:16:20,654 ------------------------------------------------------------ 2021-07-12T08:16:20,654 gat/PositionList.pyx:113:26: 'Position' is not a type identifier 2021-07-12T08:16:20,654 Error compiling Cython file: 2021-07-12T08:16:20,654 ------------------------------------------------------------ 2021-07-12T08:16:20,654 ... 2021-07-12T08:16:20,654 self.is_normalized = share.is_normalized 2021-07-12T08:16:20,654 self.is_shared = True 2021-07-12T08:16:20,655 self.is_slave = True 2021-07-12T08:16:20,655 self.chunk_size = share.chunk_size 2021-07-12T08:16:20,655 retval = mmap(NULL, 2021-07-12T08:16:20,655 self.npositions * sizeof(Segment), 2021-07-12T08:16:20,655 ^ 2021-07-12T08:16:20,655 ------------------------------------------------------------ 2021-07-12T08:16:20,655 gat/PositionList.pyx:114:73: 'Segment' is not a constant, variable or function identifier 2021-07-12T08:16:20,656 Error compiling Cython file: 2021-07-12T08:16:20,656 ------------------------------------------------------------ 2021-07-12T08:16:20,656 ... 2021-07-12T08:16:20,656 if retval == -1: 2021-07-12T08:16:20,656 raise ValueError( 2021-07-12T08:16:20,656 "could not read list from shared segment - error=%i" % 2021-07-12T08:16:20,656 error_number ) 2021-07-12T08:16:20,656 self.positions = retval 2021-07-12T08:16:20,657 ^ 2021-07-12T08:16:20,657 ------------------------------------------------------------ 2021-07-12T08:16:20,657 gat/PositionList.pyx:126:34: 'Position' is not a type identifier 2021-07-12T08:16:20,657 Error compiling Cython file: 2021-07-12T08:16:20,657 ------------------------------------------------------------ 2021-07-12T08:16:20,657 ... 2021-07-12T08:16:20,657 if type(unreduce[6]) == int: 2021-07-12T08:16:20,658 # shared memory 2021-07-12T08:16:20,658 shared_fd = unreduce[6] 2021-07-12T08:16:20,658 retval = mmap(NULL, 2021-07-12T08:16:20,658 self.npositions * sizeof(Position), 2021-07-12T08:16:20,658 ^ 2021-07-12T08:16:20,658 ------------------------------------------------------------ 2021-07-12T08:16:20,659 gat/PositionList.pyx:140:63: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,659 Error compiling Cython file: 2021-07-12T08:16:20,659 ------------------------------------------------------------ 2021-07-12T08:16:20,659 ... 2021-07-12T08:16:20,659 if retval == -1: 2021-07-12T08:16:20,659 raise ValueError( 2021-07-12T08:16:20,659 "could not unpickle as slave - error=%i" % error_number) 2021-07-12T08:16:20,660 self.positions = retval 2021-07-12T08:16:20,660 ^ 2021-07-12T08:16:20,660 ------------------------------------------------------------ 2021-07-12T08:16:20,660 gat/PositionList.pyx:152:34: 'Position' is not a type identifier 2021-07-12T08:16:20,660 Error compiling Cython file: 2021-07-12T08:16:20,660 ------------------------------------------------------------ 2021-07-12T08:16:20,661 ... 2021-07-12T08:16:20,661 self.shared_fd = -1 2021-07-12T08:16:20,661 self.is_shared = True 2021-07-12T08:16:20,661 self.is_slave = True 2021-07-12T08:16:20,661 else: 2021-07-12T08:16:20,661 p = PyBytes_AsString(unreduce[6]) 2021-07-12T08:16:20,661 self.positions = malloc(self.npositions * sizeof(Position)) 2021-07-12T08:16:20,661 ^ 2021-07-12T08:16:20,661 ------------------------------------------------------------ 2021-07-12T08:16:20,662 gat/PositionList.pyx:161:34: 'Position' is not a type identifier 2021-07-12T08:16:20,662 Error compiling Cython file: 2021-07-12T08:16:20,662 ------------------------------------------------------------ 2021-07-12T08:16:20,662 ... 2021-07-12T08:16:20,662 self.shared_fd = -1 2021-07-12T08:16:20,662 self.is_shared = True 2021-07-12T08:16:20,663 self.is_slave = True 2021-07-12T08:16:20,663 else: 2021-07-12T08:16:20,663 p = PyBytes_AsString(unreduce[6]) 2021-07-12T08:16:20,663 self.positions = malloc(self.npositions * sizeof(Position)) 2021-07-12T08:16:20,663 ^ 2021-07-12T08:16:20,663 ------------------------------------------------------------ 2021-07-12T08:16:20,663 gat/PositionList.pyx:161:84: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,664 Error compiling Cython file: 2021-07-12T08:16:20,664 ------------------------------------------------------------ 2021-07-12T08:16:20,664 ... 2021-07-12T08:16:20,664 self.is_shared = True 2021-07-12T08:16:20,664 self.is_slave = True 2021-07-12T08:16:20,664 else: 2021-07-12T08:16:20,664 p = PyBytes_AsString(unreduce[6]) 2021-07-12T08:16:20,664 self.positions = malloc(self.npositions * sizeof(Position)) 2021-07-12T08:16:20,664 memcpy(self.positions, p, cython.sizeof(Position) * self.npositions) 2021-07-12T08:16:20,665 ^ 2021-07-12T08:16:20,665 ------------------------------------------------------------ 2021-07-12T08:16:20,665 gat/PositionList.pyx:162:56: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,665 Error compiling Cython file: 2021-07-12T08:16:20,665 ------------------------------------------------------------ 2021-07-12T08:16:20,665 ... 2021-07-12T08:16:20,665 self.is_shared = True 2021-07-12T08:16:20,665 self.is_slave = True 2021-07-12T08:16:20,666 else: 2021-07-12T08:16:20,666 p = PyBytes_AsString(unreduce[6]) 2021-07-12T08:16:20,666 self.positions = malloc(self.npositions * sizeof(Position)) 2021-07-12T08:16:20,666 memcpy(self.positions, p, cython.sizeof(Position) * self.npositions) 2021-07-12T08:16:20,666 ^ 2021-07-12T08:16:20,666 ------------------------------------------------------------ 2021-07-12T08:16:20,666 gat/PositionList.pyx:162:27: Cannot convert Python object to 'void *' 2021-07-12T08:16:20,667 Error compiling Cython file: 2021-07-12T08:16:20,667 ------------------------------------------------------------ 2021-07-12T08:16:20,667 ... 2021-07-12T08:16:20,667 memcpy(self.positions, p, cython.sizeof(Position) * self.npositions) 2021-07-12T08:16:20,667 # clone from another list 2021-07-12T08:16:20,667 elif clone != None: 2021-07-12T08:16:20,667 self.npositions = self.allocated = clone.npositions 2021-07-12T08:16:20,667 self.positions = calloc(clone.npositions, sizeof(Position)) 2021-07-12T08:16:20,667 ^ 2021-07-12T08:16:20,668 ------------------------------------------------------------ 2021-07-12T08:16:20,668 gat/PositionList.pyx:167:30: 'Position' is not a type identifier 2021-07-12T08:16:20,668 Error compiling Cython file: 2021-07-12T08:16:20,668 ------------------------------------------------------------ 2021-07-12T08:16:20,668 ... 2021-07-12T08:16:20,668 memcpy(self.positions, p, cython.sizeof(Position) * self.npositions) 2021-07-12T08:16:20,669 # clone from another list 2021-07-12T08:16:20,669 elif clone != None: 2021-07-12T08:16:20,669 self.npositions = self.allocated = clone.npositions 2021-07-12T08:16:20,669 self.positions = calloc(clone.npositions, sizeof(Position)) 2021-07-12T08:16:20,669 ^ 2021-07-12T08:16:20,669 ------------------------------------------------------------ 2021-07-12T08:16:20,669 gat/PositionList.pyx:167:80: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,670 Error compiling Cython file: 2021-07-12T08:16:20,670 ------------------------------------------------------------ 2021-07-12T08:16:20,670 ... 2021-07-12T08:16:20,670 elif clone != None: 2021-07-12T08:16:20,670 self.npositions = self.allocated = clone.npositions 2021-07-12T08:16:20,670 self.positions = calloc(clone.npositions, sizeof(Position)) 2021-07-12T08:16:20,670 memcpy(self.positions, 2021-07-12T08:16:20,670 clone.positions, 2021-07-12T08:16:20,671 clone.npositions * sizeof(Position)) 2021-07-12T08:16:20,671 ^ 2021-07-12T08:16:20,671 ------------------------------------------------------------ 2021-07-12T08:16:20,671 gat/PositionList.pyx:170:53: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,671 Error compiling Cython file: 2021-07-12T08:16:20,671 ------------------------------------------------------------ 2021-07-12T08:16:20,671 ... 2021-07-12T08:16:20,672 # clone from another list 2021-07-12T08:16:20,672 elif clone != None: 2021-07-12T08:16:20,672 self.npositions = self.allocated = clone.npositions 2021-07-12T08:16:20,672 self.positions = calloc(clone.npositions, sizeof(Position)) 2021-07-12T08:16:20,672 memcpy(self.positions, 2021-07-12T08:16:20,672 ^ 2021-07-12T08:16:20,672 ------------------------------------------------------------ 2021-07-12T08:16:20,673 gat/PositionList.pyx:168:23: Cannot convert Python object to 'void *' 2021-07-12T08:16:20,673 Error compiling Cython file: 2021-07-12T08:16:20,673 ------------------------------------------------------------ 2021-07-12T08:16:20,673 ... 2021-07-12T08:16:20,673 # clone from another list 2021-07-12T08:16:20,673 elif clone != None: 2021-07-12T08:16:20,673 self.npositions = self.allocated = clone.npositions 2021-07-12T08:16:20,674 self.positions = calloc(clone.npositions, sizeof(Position)) 2021-07-12T08:16:20,674 memcpy(self.positions, 2021-07-12T08:16:20,674 clone.positions, 2021-07-12T08:16:20,674 ^ 2021-07-12T08:16:20,674 ------------------------------------------------------------ 2021-07-12T08:16:20,674 gat/PositionList.pyx:169:24: Cannot convert Python object to 'const void *' 2021-07-12T08:16:20,674 Error compiling Cython file: 2021-07-12T08:16:20,675 ------------------------------------------------------------ 2021-07-12T08:16:20,675 ... 2021-07-12T08:16:20,675 # create from an iterable 2021-07-12T08:16:20,675 elif iter: 2021-07-12T08:16:20,675 a = tuple(iter) 2021-07-12T08:16:20,675 self.npositions = self.allocated = len(a) 2021-07-12T08:16:20,675 self.positions = calloc(self.npositions, sizeof(Position)) 2021-07-12T08:16:20,675 ^ 2021-07-12T08:16:20,676 ------------------------------------------------------------ 2021-07-12T08:16:20,676 gat/PositionList.pyx:178:30: 'Position' is not a type identifier 2021-07-12T08:16:20,676 Error compiling Cython file: 2021-07-12T08:16:20,676 ------------------------------------------------------------ 2021-07-12T08:16:20,676 ... 2021-07-12T08:16:20,676 # create from an iterable 2021-07-12T08:16:20,677 elif iter: 2021-07-12T08:16:20,677 a = tuple(iter) 2021-07-12T08:16:20,677 self.npositions = self.allocated = len(a) 2021-07-12T08:16:20,677 self.positions = calloc(self.npositions, sizeof(Position)) 2021-07-12T08:16:20,677 ^ 2021-07-12T08:16:20,677 ------------------------------------------------------------ 2021-07-12T08:16:20,677 gat/PositionList.pyx:178:79: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,678 Error compiling Cython file: 2021-07-12T08:16:20,678 ------------------------------------------------------------ 2021-07-12T08:16:20,678 ... 2021-07-12T08:16:20,678 self.is_sorted = False 2021-07-12T08:16:20,678 # allocated memory only, list remains empty 2021-07-12T08:16:20,678 elif allocate: 2021-07-12T08:16:20,678 self.allocated = allocate 2021-07-12T08:16:20,678 self.positions = calloc(allocate, sizeof(Position)) 2021-07-12T08:16:20,679 ^ 2021-07-12T08:16:20,679 ------------------------------------------------------------ 2021-07-12T08:16:20,679 gat/PositionList.pyx:189:30: 'Position' is not a type identifier 2021-07-12T08:16:20,679 Error compiling Cython file: 2021-07-12T08:16:20,679 ------------------------------------------------------------ 2021-07-12T08:16:20,679 ... 2021-07-12T08:16:20,679 self.is_sorted = False 2021-07-12T08:16:20,680 # allocated memory only, list remains empty 2021-07-12T08:16:20,680 elif allocate: 2021-07-12T08:16:20,680 self.allocated = allocate 2021-07-12T08:16:20,680 self.positions = calloc(allocate, sizeof(Position)) 2021-07-12T08:16:20,680 ^ 2021-07-12T08:16:20,680 ------------------------------------------------------------ 2021-07-12T08:16:20,681 gat/PositionList.pyx:189:72: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,681 Error compiling Cython file: 2021-07-12T08:16:20,681 ------------------------------------------------------------ 2021-07-12T08:16:20,681 ... 2021-07-12T08:16:20,681 self.shared_fd)) 2021-07-12T08:16:20,681 else: 2021-07-12T08:16:20,681 data = PyBytes_FromStringAndSize( 2021-07-12T08:16:20,682 self.positions, \ 2021-07-12T08:16:20,682 self.npositions * cython.sizeof(Position) * 2) 2021-07-12T08:16:20,682 ^ 2021-07-12T08:16:20,682 ------------------------------------------------------------ 2021-07-12T08:16:20,682 gat/PositionList.pyx:214:48: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,682 Error compiling Cython file: 2021-07-12T08:16:20,683 ------------------------------------------------------------ 2021-07-12T08:16:20,683 ... 2021-07-12T08:16:20,683 The list will not be normalized automatically - call 2021-07-12T08:16:20,683 :meth:`PositionList.normalize`. 2021-07-12T08:16:20,683 ''' 2021-07-12T08:16:20,683 if self.allocated == 0: 2021-07-12T08:16:20,683 self.positions = malloc(self.chunk_size * sizeof(Position)) 2021-07-12T08:16:20,683 ^ 2021-07-12T08:16:20,684 ------------------------------------------------------------ 2021-07-12T08:16:20,684 gat/PositionList.pyx:261:30: 'Position' is not a type identifier 2021-07-12T08:16:20,684 Error compiling Cython file: 2021-07-12T08:16:20,684 ------------------------------------------------------------ 2021-07-12T08:16:20,684 ... 2021-07-12T08:16:20,684 The list will not be normalized automatically - call 2021-07-12T08:16:20,684 :meth:`PositionList.normalize`. 2021-07-12T08:16:20,685 ''' 2021-07-12T08:16:20,685 if self.allocated == 0: 2021-07-12T08:16:20,685 self.positions = malloc(self.chunk_size * sizeof(Position)) 2021-07-12T08:16:20,685 ^ 2021-07-12T08:16:20,685 ------------------------------------------------------------ 2021-07-12T08:16:20,685 gat/PositionList.pyx:261:80: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,686 Error compiling Cython file: 2021-07-12T08:16:20,686 ------------------------------------------------------------ 2021-07-12T08:16:20,686 ... 2021-07-12T08:16:20,686 if self.allocated == 0: 2021-07-12T08:16:20,686 self.positions = malloc(self.chunk_size * sizeof(Position)) 2021-07-12T08:16:20,686 if not self.positions: 2021-07-12T08:16:20,686 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:20,686 sizeof( self.chunk_size * sizeof(Position))) 2021-07-12T08:16:20,687 ^ 2021-07-12T08:16:20,687 ------------------------------------------------------------ 2021-07-12T08:16:20,687 gat/PositionList.pyx:264:75: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,687 Error compiling Cython file: 2021-07-12T08:16:20,687 ------------------------------------------------------------ 2021-07-12T08:16:20,687 ... 2021-07-12T08:16:20,687 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:20,688 sizeof( self.chunk_size * sizeof(Position))) 2021-07-12T08:16:20,688 self.allocated = self.chunk_size 2021-07-12T08:16:20,688 elif self.npositions == self.allocated: 2021-07-12T08:16:20,688 self.allocated *= 2 2021-07-12T08:16:20,688 self.positions = realloc(self.positions, 2021-07-12T08:16:20,688 ^ 2021-07-12T08:16:20,688 ------------------------------------------------------------ 2021-07-12T08:16:20,688 gat/PositionList.pyx:268:30: 'Position' is not a type identifier 2021-07-12T08:16:20,689 Error compiling Cython file: 2021-07-12T08:16:20,689 ------------------------------------------------------------ 2021-07-12T08:16:20,689 ... 2021-07-12T08:16:20,689 sizeof( self.chunk_size * sizeof(Position))) 2021-07-12T08:16:20,689 self.allocated = self.chunk_size 2021-07-12T08:16:20,689 elif self.npositions == self.allocated: 2021-07-12T08:16:20,689 self.allocated *= 2 2021-07-12T08:16:20,689 self.positions = realloc(self.positions, 2021-07-12T08:16:20,690 self.allocated * sizeof(Position)) 2021-07-12T08:16:20,690 ^ 2021-07-12T08:16:20,690 ------------------------------------------------------------ 2021-07-12T08:16:20,690 gat/PositionList.pyx:269:80: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,690 Error compiling Cython file: 2021-07-12T08:16:20,690 ------------------------------------------------------------ 2021-07-12T08:16:20,690 ... 2021-07-12T08:16:20,691 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:20,691 sizeof( self.chunk_size * sizeof(Position))) 2021-07-12T08:16:20,691 self.allocated = self.chunk_size 2021-07-12T08:16:20,691 elif self.npositions == self.allocated: 2021-07-12T08:16:20,691 self.allocated *= 2 2021-07-12T08:16:20,691 self.positions = realloc(self.positions, 2021-07-12T08:16:20,691 ^ 2021-07-12T08:16:20,691 ------------------------------------------------------------ 2021-07-12T08:16:20,692 gat/PositionList.pyx:268:52: Cannot convert Python object to 'void *' 2021-07-12T08:16:20,692 Error compiling Cython file: 2021-07-12T08:16:20,692 ------------------------------------------------------------ 2021-07-12T08:16:20,692 ... 2021-07-12T08:16:20,692 self.positions = realloc(self.positions, 2021-07-12T08:16:20,692 self.allocated * sizeof(Position)) 2021-07-12T08:16:20,692 if not self.positions: 2021-07-12T08:16:20,692 raise MemoryError( 2021-07-12T08:16:20,693 "out of memory when allocation %i bytes" % 2021-07-12T08:16:20,693 sizeof(self.allocated * sizeof(Position))) 2021-07-12T08:16:20,693 ^ 2021-07-12T08:16:20,693 ------------------------------------------------------------ 2021-07-12T08:16:20,693 gat/PositionList.pyx:273:59: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,693 Error compiling Cython file: 2021-07-12T08:16:20,693 ------------------------------------------------------------ 2021-07-12T08:16:20,694 ... 2021-07-12T08:16:20,694 self.clear() 2021-07-12T08:16:20,694 cdef int idx 2021-07-12T08:16:20,694 self.npositions = self.allocated = len(segments) 2021-07-12T08:16:20,694 self.positions = calloc(self.npositions, sizeof(Position)) 2021-07-12T08:16:20,694 ^ 2021-07-12T08:16:20,694 ------------------------------------------------------------ 2021-07-12T08:16:20,695 gat/PositionList.pyx:305:26: 'Position' is not a type identifier 2021-07-12T08:16:20,695 Error compiling Cython file: 2021-07-12T08:16:20,695 ------------------------------------------------------------ 2021-07-12T08:16:20,695 ... 2021-07-12T08:16:20,695 self.clear() 2021-07-12T08:16:20,695 cdef int idx 2021-07-12T08:16:20,696 self.npositions = self.allocated = len(segments) 2021-07-12T08:16:20,696 self.positions = calloc(self.npositions, sizeof(Position)) 2021-07-12T08:16:20,696 ^ 2021-07-12T08:16:20,696 ------------------------------------------------------------ 2021-07-12T08:16:20,696 gat/PositionList.pyx:305:75: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,696 Error compiling Cython file: 2021-07-12T08:16:20,697 ------------------------------------------------------------ 2021-07-12T08:16:20,697 ... 2021-07-12T08:16:20,697 self.is_sorted = True 2021-07-12T08:16:20,697 return 2021-07-12T08:16:20,697 qsort(self.positions, 2021-07-12T08:16:20,697 self.npositions, 2021-07-12T08:16:20,697 sizeof(Position), 2021-07-12T08:16:20,697 ^ 2021-07-12T08:16:20,698 ------------------------------------------------------------ 2021-07-12T08:16:20,698 gat/PositionList.pyx:345:29: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,698 Error compiling Cython file: 2021-07-12T08:16:20,698 ------------------------------------------------------------ 2021-07-12T08:16:20,698 ... 2021-07-12T08:16:20,698 npositions = 1 2021-07-12T08:16:20,699 assert npositions >= self.npositions, "resizing will loose positions" 2021-07-12T08:16:20,699 if self.allocated == 0: 2021-07-12T08:16:20,699 self.positions = malloc(npositions * sizeof(Position)) 2021-07-12T08:16:20,699 ^ 2021-07-12T08:16:20,699 ------------------------------------------------------------ 2021-07-12T08:16:20,699 gat/PositionList.pyx:385:30: 'Position' is not a type identifier 2021-07-12T08:16:20,700 Error compiling Cython file: 2021-07-12T08:16:20,700 ------------------------------------------------------------ 2021-07-12T08:16:20,700 ... 2021-07-12T08:16:20,700 npositions = 1 2021-07-12T08:16:20,700 assert npositions >= self.npositions, "resizing will loose positions" 2021-07-12T08:16:20,700 if self.allocated == 0: 2021-07-12T08:16:20,701 self.positions = malloc(npositions * sizeof(Position)) 2021-07-12T08:16:20,701 ^ 2021-07-12T08:16:20,701 ------------------------------------------------------------ 2021-07-12T08:16:20,701 gat/PositionList.pyx:385:75: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,701 Error compiling Cython file: 2021-07-12T08:16:20,701 ------------------------------------------------------------ 2021-07-12T08:16:20,701 ... 2021-07-12T08:16:20,702 if self.allocated == 0: 2021-07-12T08:16:20,702 self.positions = malloc(npositions * sizeof(Position)) 2021-07-12T08:16:20,702 if not self.positions: 2021-07-12T08:16:20,702 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:20,702 sizeof(npositions * sizeof(Position))) 2021-07-12T08:16:20,702 ^ 2021-07-12T08:16:20,702 ------------------------------------------------------------ 2021-07-12T08:16:20,703 gat/PositionList.pyx:388:69: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,703 Error compiling Cython file: 2021-07-12T08:16:20,703 ------------------------------------------------------------ 2021-07-12T08:16:20,703 ... 2021-07-12T08:16:20,703 self.positions = malloc(npositions * sizeof(Position)) 2021-07-12T08:16:20,703 if not self.positions: 2021-07-12T08:16:20,703 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:20,703 sizeof(npositions * sizeof(Position))) 2021-07-12T08:16:20,704 else: 2021-07-12T08:16:20,704 self.positions = realloc(self.positions, 2021-07-12T08:16:20,704 ^ 2021-07-12T08:16:20,704 ------------------------------------------------------------ 2021-07-12T08:16:20,704 gat/PositionList.pyx:390:30: 'Position' is not a type identifier 2021-07-12T08:16:20,704 Error compiling Cython file: 2021-07-12T08:16:20,704 ------------------------------------------------------------ 2021-07-12T08:16:20,705 ... 2021-07-12T08:16:20,705 if not self.positions: 2021-07-12T08:16:20,705 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:20,705 sizeof(npositions * sizeof(Position))) 2021-07-12T08:16:20,705 else: 2021-07-12T08:16:20,705 self.positions = realloc(self.positions, 2021-07-12T08:16:20,705 npositions * sizeof(Position)) 2021-07-12T08:16:20,705 ^ 2021-07-12T08:16:20,705 ------------------------------------------------------------ 2021-07-12T08:16:20,706 gat/PositionList.pyx:391:75: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,706 Error compiling Cython file: 2021-07-12T08:16:20,706 ------------------------------------------------------------ 2021-07-12T08:16:20,706 ... 2021-07-12T08:16:20,706 self.positions = malloc(npositions * sizeof(Position)) 2021-07-12T08:16:20,706 if not self.positions: 2021-07-12T08:16:20,706 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:20,707 sizeof(npositions * sizeof(Position))) 2021-07-12T08:16:20,707 else: 2021-07-12T08:16:20,707 self.positions = realloc(self.positions, 2021-07-12T08:16:20,707 ^ 2021-07-12T08:16:20,707 ------------------------------------------------------------ 2021-07-12T08:16:20,707 gat/PositionList.pyx:390:52: Cannot convert Python object to 'void *' 2021-07-12T08:16:20,707 Error compiling Cython file: 2021-07-12T08:16:20,708 ------------------------------------------------------------ 2021-07-12T08:16:20,708 ... 2021-07-12T08:16:20,708 else: 2021-07-12T08:16:20,708 self.positions = realloc(self.positions, 2021-07-12T08:16:20,708 npositions * sizeof(Position)) 2021-07-12T08:16:20,708 if not self.positions: 2021-07-12T08:16:20,708 raise MemoryError("out of memory when allocation %i bytes" % 2021-07-12T08:16:20,708 sizeof(self.npositions * sizeof(Position))) 2021-07-12T08:16:20,708 ^ 2021-07-12T08:16:20,709 ------------------------------------------------------------ 2021-07-12T08:16:20,709 gat/PositionList.pyx:394:74: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,709 Error compiling Cython file: 2021-07-12T08:16:20,709 ------------------------------------------------------------ 2021-07-12T08:16:20,709 ... 2021-07-12T08:16:20,709 if other < self.positions[0]: 2021-07-12T08:16:20,710 return -1 2021-07-12T08:16:20,710 if other >= self.positions[self.npositions-1]: 2021-07-12T08:16:20,710 return self.npositions 2021-07-12T08:16:20,710 return searchsorted(self.positions, 2021-07-12T08:16:20,710 ^ 2021-07-12T08:16:20,710 ------------------------------------------------------------ 2021-07-12T08:16:20,710 gat/PositionList.pyx:426:15: undeclared name not builtin: searchsorted 2021-07-12T08:16:20,711 Error compiling Cython file: 2021-07-12T08:16:20,711 ------------------------------------------------------------ 2021-07-12T08:16:20,711 ... 2021-07-12T08:16:20,711 if other >= self.positions[self.npositions-1]: 2021-07-12T08:16:20,711 return self.npositions 2021-07-12T08:16:20,711 return searchsorted(self.positions, 2021-07-12T08:16:20,711 self.npositions, 2021-07-12T08:16:20,711 sizeof(Position), 2021-07-12T08:16:20,712 ^ 2021-07-12T08:16:20,712 ------------------------------------------------------------ 2021-07-12T08:16:20,712 gat/PositionList.pyx:428:43: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,712 Error compiling Cython file: 2021-07-12T08:16:20,712 ------------------------------------------------------------ 2021-07-12T08:16:20,712 ... 2021-07-12T08:16:20,713 return searchsorted(self.positions, 2021-07-12T08:16:20,713 self.npositions, 2021-07-12T08:16:20,713 sizeof(Position), 2021-07-12T08:16:20,713 &other, 2021-07-12T08:16:20,713 &cmpPosition) 2021-07-12T08:16:20,713 ^ 2021-07-12T08:16:20,713 ------------------------------------------------------------ 2021-07-12T08:16:20,713 gat/PositionList.pyx:430:28: Cannot convert 'int (*)(const_void_ptr, const_void_ptr) nogil' to Python object 2021-07-12T08:16:20,714 Error compiling Cython file: 2021-07-12T08:16:20,714 ------------------------------------------------------------ 2021-07-12T08:16:20,714 ... 2021-07-12T08:16:20,714 overlap : int 2021-07-12T08:16:20,714 Number of residues overlapping 2021-07-12T08:16:20,714 """ 2021-07-12T08:16:20,714 cdef Segment s 2021-07-12T08:16:20,715 s = Segment(start, end) 2021-07-12T08:16:20,715 ^ 2021-07-12T08:16:20,715 ------------------------------------------------------------ 2021-07-12T08:16:20,715 gat/PositionList.pyx:487:12: 'Segment' is not a constant, variable or function identifier 2021-07-12T08:16:20,715 Error compiling Cython file: 2021-07-12T08:16:20,715 ------------------------------------------------------------ 2021-07-12T08:16:20,716 ... 2021-07-12T08:16:20,716 cdef int this_idx, other_idx, last_this_idx, last_other_idx 2021-07-12T08:16:20,716 this_idx = other_idx = 0 2021-07-12T08:16:20,716 last_this_idx = last_other_idx = -1 2021-07-12T08:16:20,716 cdef Position this_position = -1 2021-07-12T08:16:20,716 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:20,716 ^ 2021-07-12T08:16:20,716 ------------------------------------------------------------ 2021-07-12T08:16:20,717 gat/PositionList.pyx:519:37: 'Segment' is not a constant, variable or function identifier 2021-07-12T08:16:20,717 Error compiling Cython file: 2021-07-12T08:16:20,717 ------------------------------------------------------------ 2021-07-12T08:16:20,717 ... 2021-07-12T08:16:20,717 cdef int this_idx, other_idx, last_this_idx, last_other_idx, working_idx 2021-07-12T08:16:20,717 this_idx = other_idx = working_idx = 0 2021-07-12T08:16:20,718 last_this_idx = last_other_idx = -1 2021-07-12T08:16:20,718 cdef Position this_position = -1 2021-07-12T08:16:20,718 cdef Segment other_segment = Segment(0,0) 2021-07-12T08:16:20,718 ^ 2021-07-12T08:16:20,718 ------------------------------------------------------------ 2021-07-12T08:16:20,718 gat/PositionList.pyx:563:37: 'Segment' is not a constant, variable or function identifier 2021-07-12T08:16:20,723 Error compiling Cython file: 2021-07-12T08:16:20,723 ------------------------------------------------------------ 2021-07-12T08:16:20,723 ... 2021-07-12T08:16:20,723 cpdef PositionList clone(self): 2021-07-12T08:16:20,723 """return a copy of self.""" 2021-07-12T08:16:20,724 clone = PositionList(allocate=self.npositions) 2021-07-12T08:16:20,724 memcpy(clone.positions, 2021-07-12T08:16:20,724 self.positions, 2021-07-12T08:16:20,724 self.npositions * sizeof(Position)) 2021-07-12T08:16:20,724 ^ 2021-07-12T08:16:20,724 ------------------------------------------------------------ 2021-07-12T08:16:20,724 gat/PositionList.pyx:603:48: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,725 Error compiling Cython file: 2021-07-12T08:16:20,725 ------------------------------------------------------------ 2021-07-12T08:16:20,725 ... 2021-07-12T08:16:20,725 return result 2021-07-12T08:16:20,725 cpdef PositionList clone(self): 2021-07-12T08:16:20,725 """return a copy of self.""" 2021-07-12T08:16:20,725 clone = PositionList(allocate=self.npositions) 2021-07-12T08:16:20,725 memcpy(clone.positions, 2021-07-12T08:16:20,726 ^ 2021-07-12T08:16:20,726 ------------------------------------------------------------ 2021-07-12T08:16:20,726 gat/PositionList.pyx:601:20: Cannot convert Python object to 'void *' 2021-07-12T08:16:20,726 Error compiling Cython file: 2021-07-12T08:16:20,726 ------------------------------------------------------------ 2021-07-12T08:16:20,726 ... 2021-07-12T08:16:20,727 cpdef PositionList clone(self): 2021-07-12T08:16:20,727 """return a copy of self.""" 2021-07-12T08:16:20,727 clone = PositionList(allocate=self.npositions) 2021-07-12T08:16:20,727 memcpy(clone.positions, 2021-07-12T08:16:20,727 self.positions, 2021-07-12T08:16:20,727 ^ 2021-07-12T08:16:20,727 ------------------------------------------------------------ 2021-07-12T08:16:20,727 gat/PositionList.pyx:602:19: Cannot convert Python object to 'const void *' 2021-07-12T08:16:20,728 Error compiling Cython file: 2021-07-12T08:16:20,728 ------------------------------------------------------------ 2021-07-12T08:16:20,728 ... 2021-07-12T08:16:20,728 return clone 2021-07-12T08:16:20,728 def __dealloc__(self): 2021-07-12T08:16:20,728 cdef int fd 2021-07-12T08:16:20,729 if self.positions != NULL: 2021-07-12T08:16:20,729 ^ 2021-07-12T08:16:20,729 ------------------------------------------------------------ 2021-07-12T08:16:20,729 gat/PositionList.pyx:612:26: Invalid types for '!=' (Python object, void *) 2021-07-12T08:16:20,729 Error compiling Cython file: 2021-07-12T08:16:20,729 ------------------------------------------------------------ 2021-07-12T08:16:20,730 ... 2021-07-12T08:16:20,730 if self.is_slave: 2021-07-12T08:16:20,730 pass 2021-07-12T08:16:20,730 else: 2021-07-12T08:16:20,730 # free shared memory as master 2021-07-12T08:16:20,730 munmap(self.positions, 2021-07-12T08:16:20,730 self.npositions * sizeof(Position)) 2021-07-12T08:16:20,730 ^ 2021-07-12T08:16:20,730 ------------------------------------------------------------ 2021-07-12T08:16:20,731 gat/PositionList.pyx:620:60: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,731 Error compiling Cython file: 2021-07-12T08:16:20,731 ------------------------------------------------------------ 2021-07-12T08:16:20,731 ... 2021-07-12T08:16:20,731 if self.is_shared: 2021-07-12T08:16:20,731 if self.is_slave: 2021-07-12T08:16:20,731 pass 2021-07-12T08:16:20,732 else: 2021-07-12T08:16:20,732 # free shared memory as master 2021-07-12T08:16:20,732 munmap(self.positions, 2021-07-12T08:16:20,732 ^ 2021-07-12T08:16:20,732 ------------------------------------------------------------ 2021-07-12T08:16:20,732 gat/PositionList.pyx:619:31: Cannot convert Python object to 'void *' 2021-07-12T08:16:20,732 Error compiling Cython file: 2021-07-12T08:16:20,733 ------------------------------------------------------------ 2021-07-12T08:16:20,733 ... 2021-07-12T08:16:20,733 # free shared memory as master 2021-07-12T08:16:20,733 munmap(self.positions, 2021-07-12T08:16:20,733 self.npositions * sizeof(Position)) 2021-07-12T08:16:20,733 else: 2021-07-12T08:16:20,733 # free private copy 2021-07-12T08:16:20,733 free(self.positions) 2021-07-12T08:16:20,733 ^ 2021-07-12T08:16:20,734 ------------------------------------------------------------ 2021-07-12T08:16:20,734 gat/PositionList.pyx:623:25: Cannot convert Python object to 'void *' 2021-07-12T08:16:20,734 Error compiling Cython file: 2021-07-12T08:16:20,734 ------------------------------------------------------------ 2021-07-12T08:16:20,734 ... 2021-07-12T08:16:20,734 cdef void fromMMAP(self): 2021-07-12T08:16:20,734 '''retrieve data from mmapped location to private copy. 2021-07-12T08:16:20,735 ''' 2021-07-12T08:16:20,735 # copy data back to unshared memory 2021-07-12T08:16:20,735 cdef Position * s 2021-07-12T08:16:20,735 cdef off_t nbytes = sizeof(Position) * self.npositions 2021-07-12T08:16:20,735 ^ 2021-07-12T08:16:20,735 ------------------------------------------------------------ 2021-07-12T08:16:20,735 gat/PositionList.pyx:635:43: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,736 Error compiling Cython file: 2021-07-12T08:16:20,736 ------------------------------------------------------------ 2021-07-12T08:16:20,736 ... 2021-07-12T08:16:20,736 cdef off_t nbytes = sizeof(Position) * self.npositions 2021-07-12T08:16:20,736 if self.npositions == 0: 2021-07-12T08:16:20,736 return 2021-07-12T08:16:20,736 s = malloc(nbytes) 2021-07-12T08:16:20,737 ^ 2021-07-12T08:16:20,737 ------------------------------------------------------------ 2021-07-12T08:16:20,737 gat/PositionList.pyx:640:13: 'Position' is not a type identifier 2021-07-12T08:16:20,737 Error compiling Cython file: 2021-07-12T08:16:20,737 ------------------------------------------------------------ 2021-07-12T08:16:20,737 ... 2021-07-12T08:16:20,737 s = malloc(nbytes) 2021-07-12T08:16:20,738 if s == NULL: 2021-07-12T08:16:20,738 raise ValueError( "could not allocate memory when unsharing" ) 2021-07-12T08:16:20,738 memcpy(s, self.positions, nbytes) 2021-07-12T08:16:20,738 ^ 2021-07-12T08:16:20,738 ------------------------------------------------------------ 2021-07-12T08:16:20,738 gat/PositionList.pyx:644:22: Cannot convert Python object to 'const void *' 2021-07-12T08:16:20,739 Error compiling Cython file: 2021-07-12T08:16:20,739 ------------------------------------------------------------ 2021-07-12T08:16:20,739 ... 2021-07-12T08:16:20,739 if self.npositions == 0: 2021-07-12T08:16:20,739 # do not move empty position lists 2021-07-12T08:16:20,739 return offset 2021-07-12T08:16:20,739 cdef off_t nbytes = sizeof(Position) * self.npositions 2021-07-12T08:16:20,739 ^ 2021-07-12T08:16:20,740 ------------------------------------------------------------ 2021-07-12T08:16:20,740 gat/PositionList.pyx:665:43: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:20,740 Error compiling Cython file: 2021-07-12T08:16:20,740 ------------------------------------------------------------ 2021-07-12T08:16:20,740 ... 2021-07-12T08:16:20,740 if self.npositions == 0: 2021-07-12T08:16:20,740 # do not move empty position lists 2021-07-12T08:16:20,741 return offset 2021-07-12T08:16:20,741 cdef off_t nbytes = sizeof(Position) * self.npositions 2021-07-12T08:16:20,741 cdef Position * p = mmap + offset 2021-07-12T08:16:20,741 ^ 2021-07-12T08:16:20,741 ------------------------------------------------------------ 2021-07-12T08:16:20,741 gat/PositionList.pyx:666:29: 'Position' is not a type identifier 2021-07-12T08:16:20,741 Error compiling Cython file: 2021-07-12T08:16:20,742 ------------------------------------------------------------ 2021-07-12T08:16:20,742 ... 2021-07-12T08:16:20,742 cdef off_t nbytes = sizeof(Position) * self.npositions 2021-07-12T08:16:20,742 cdef Position * p = mmap + offset 2021-07-12T08:16:20,742 # copy data 2021-07-12T08:16:20,742 memcpy(p, self.positions, nbytes) 2021-07-12T08:16:20,742 ^ 2021-07-12T08:16:20,743 ------------------------------------------------------------ 2021-07-12T08:16:20,743 gat/PositionList.pyx:669:22: Cannot convert Python object to 'const void *' 2021-07-12T08:16:20,743 Error compiling Cython file: 2021-07-12T08:16:20,743 ------------------------------------------------------------ 2021-07-12T08:16:20,743 ... 2021-07-12T08:16:20,743 # copy data 2021-07-12T08:16:20,743 memcpy(p, self.positions, nbytes) 2021-07-12T08:16:20,744 # free allocated private memory 2021-07-12T08:16:20,744 self.allocated = 0 2021-07-12T08:16:20,744 free(self.positions) 2021-07-12T08:16:20,744 ^ 2021-07-12T08:16:20,744 ------------------------------------------------------------ 2021-07-12T08:16:20,744 gat/PositionList.pyx:673:17: Cannot convert Python object to 'void *' 2021-07-12T08:16:20,959 cythoning gat/Engine.pyx to gat/Engine.c 2021-07-12T08:16:20,965 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-sammuaxk/gat_98fddb3111d94ae9bf647f384bede459/gat/Engine.pyx 2021-07-12T08:16:20,966 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T08:16:23,576 Error compiling Cython file: 2021-07-12T08:16:23,577 ------------------------------------------------------------ 2021-07-12T08:16:23,577 ... 2021-07-12T08:16:23,577 from posix.stat cimport S_IRUSR, S_IWUSR 2021-07-12T08:16:23,577 from posix.fcntl cimport O_CREAT, O_RDWR, O_RDONLY 2021-07-12T08:16:23,577 from posix.unistd cimport ftruncate 2021-07-12T08:16:23,577 # import SegmentList and PositionList 2021-07-12T08:16:23,577 from CoordinateList cimport CoordinateList 2021-07-12T08:16:23,578 ^ 2021-07-12T08:16:23,578 ------------------------------------------------------------ 2021-07-12T08:16:23,578 gat/Engine.pyx:29:0: 'CoordinateList.pxd' not found 2021-07-12T08:16:23,584 Error compiling Cython file: 2021-07-12T08:16:23,584 ------------------------------------------------------------ 2021-07-12T08:16:23,584 ... 2021-07-12T08:16:23,584 from posix.stat cimport S_IRUSR, S_IWUSR 2021-07-12T08:16:23,584 from posix.fcntl cimport O_CREAT, O_RDWR, O_RDONLY 2021-07-12T08:16:23,584 from posix.unistd cimport ftruncate 2021-07-12T08:16:23,585 # import SegmentList and PositionList 2021-07-12T08:16:23,585 from CoordinateList cimport CoordinateList 2021-07-12T08:16:23,585 ^ 2021-07-12T08:16:23,585 ------------------------------------------------------------ 2021-07-12T08:16:23,585 gat/Engine.pyx:29:0: 'CoordinateList/CoordinateList.pxd' not found 2021-07-12T08:16:23,586 Error compiling Cython file: 2021-07-12T08:16:23,586 ------------------------------------------------------------ 2021-07-12T08:16:23,586 ... 2021-07-12T08:16:23,586 from posix.unistd cimport ftruncate 2021-07-12T08:16:23,587 # import SegmentList and PositionList 2021-07-12T08:16:23,587 from CoordinateList cimport CoordinateList 2021-07-12T08:16:23,587 cimport SegmentList 2021-07-12T08:16:23,587 ^ 2021-07-12T08:16:23,587 ------------------------------------------------------------ 2021-07-12T08:16:23,587 gat/Engine.pyx:31:8: 'SegmentList.pxd' not found 2021-07-12T08:16:23,588 Error compiling Cython file: 2021-07-12T08:16:23,588 ------------------------------------------------------------ 2021-07-12T08:16:23,588 ... 2021-07-12T08:16:23,588 # import SegmentList and PositionList 2021-07-12T08:16:23,588 from CoordinateList cimport CoordinateList 2021-07-12T08:16:23,589 cimport SegmentList 2021-07-12T08:16:23,589 import SegmentList 2021-07-12T08:16:23,589 from SegmentList cimport SegmentList, PositionDifference, Segment, Position, force_bytes, force_str 2021-07-12T08:16:23,589 ^ 2021-07-12T08:16:23,589 ------------------------------------------------------------ 2021-07-12T08:16:23,589 gat/Engine.pyx:33:0: 'SegmentList/SegmentList.pxd' not found 2021-07-12T08:16:23,592 Error compiling Cython file: 2021-07-12T08:16:23,592 ------------------------------------------------------------ 2021-07-12T08:16:23,592 ... 2021-07-12T08:16:23,592 # import SegmentList and PositionList 2021-07-12T08:16:23,592 from CoordinateList cimport CoordinateList 2021-07-12T08:16:23,593 cimport SegmentList 2021-07-12T08:16:23,593 import SegmentList 2021-07-12T08:16:23,593 from SegmentList cimport SegmentList, PositionDifference, Segment, Position, force_bytes, force_str 2021-07-12T08:16:23,593 ^ 2021-07-12T08:16:23,593 ------------------------------------------------------------ 2021-07-12T08:16:23,594 gat/Engine.pyx:33:0: 'SegmentList/PositionDifference.pxd' not found 2021-07-12T08:16:23,594 Error compiling Cython file: 2021-07-12T08:16:23,594 ------------------------------------------------------------ 2021-07-12T08:16:23,594 ... 2021-07-12T08:16:23,594 # import SegmentList and PositionList 2021-07-12T08:16:23,594 from CoordinateList cimport CoordinateList 2021-07-12T08:16:23,595 cimport SegmentList 2021-07-12T08:16:23,595 import SegmentList 2021-07-12T08:16:23,595 from SegmentList cimport SegmentList, PositionDifference, Segment, Position, force_bytes, force_str 2021-07-12T08:16:23,595 ^ 2021-07-12T08:16:23,595 ------------------------------------------------------------ 2021-07-12T08:16:23,595 gat/Engine.pyx:33:0: 'SegmentList/Segment.pxd' not found 2021-07-12T08:16:23,596 Error compiling Cython file: 2021-07-12T08:16:23,596 ------------------------------------------------------------ 2021-07-12T08:16:23,596 ... 2021-07-12T08:16:23,596 # import SegmentList and PositionList 2021-07-12T08:16:23,596 from CoordinateList cimport CoordinateList 2021-07-12T08:16:23,596 cimport SegmentList 2021-07-12T08:16:23,597 import SegmentList 2021-07-12T08:16:23,597 from SegmentList cimport SegmentList, PositionDifference, Segment, Position, force_bytes, force_str 2021-07-12T08:16:23,597 ^ 2021-07-12T08:16:23,597 ------------------------------------------------------------ 2021-07-12T08:16:23,597 gat/Engine.pyx:33:0: 'SegmentList/Position.pxd' not found 2021-07-12T08:16:23,599 Error compiling Cython file: 2021-07-12T08:16:23,599 ------------------------------------------------------------ 2021-07-12T08:16:23,599 ... 2021-07-12T08:16:23,599 # import SegmentList and PositionList 2021-07-12T08:16:23,599 from CoordinateList cimport CoordinateList 2021-07-12T08:16:23,600 cimport SegmentList 2021-07-12T08:16:23,600 import SegmentList 2021-07-12T08:16:23,600 from SegmentList cimport SegmentList, PositionDifference, Segment, Position, force_bytes, force_str 2021-07-12T08:16:23,600 ^ 2021-07-12T08:16:23,600 ------------------------------------------------------------ 2021-07-12T08:16:23,600 gat/Engine.pyx:33:0: 'SegmentList/force_bytes.pxd' not found 2021-07-12T08:16:23,603 Error compiling Cython file: 2021-07-12T08:16:23,603 ------------------------------------------------------------ 2021-07-12T08:16:23,603 ... 2021-07-12T08:16:23,603 # import SegmentList and PositionList 2021-07-12T08:16:23,604 from CoordinateList cimport CoordinateList 2021-07-12T08:16:23,604 cimport SegmentList 2021-07-12T08:16:23,604 import SegmentList 2021-07-12T08:16:23,604 from SegmentList cimport SegmentList, PositionDifference, Segment, Position, force_bytes, force_str 2021-07-12T08:16:23,604 ^ 2021-07-12T08:16:23,604 ------------------------------------------------------------ 2021-07-12T08:16:23,605 gat/Engine.pyx:33:0: 'SegmentList/force_str.pxd' not found 2021-07-12T08:16:23,611 Error compiling Cython file: 2021-07-12T08:16:23,611 ------------------------------------------------------------ 2021-07-12T08:16:23,611 ... 2021-07-12T08:16:23,611 cimport SegmentList 2021-07-12T08:16:23,612 import SegmentList 2021-07-12T08:16:23,612 from SegmentList cimport SegmentList, PositionDifference, Segment, Position, force_bytes, force_str 2021-07-12T08:16:23,612 from PositionList cimport PositionList 2021-07-12T08:16:23,612 ^ 2021-07-12T08:16:23,612 ------------------------------------------------------------ 2021-07-12T08:16:23,612 gat/Engine.pyx:35:0: 'PositionList.pxd' not found 2021-07-12T08:16:23,616 Error compiling Cython file: 2021-07-12T08:16:23,617 ------------------------------------------------------------ 2021-07-12T08:16:23,617 ... 2021-07-12T08:16:23,617 cimport SegmentList 2021-07-12T08:16:23,617 import SegmentList 2021-07-12T08:16:23,617 from SegmentList cimport SegmentList, PositionDifference, Segment, Position, force_bytes, force_str 2021-07-12T08:16:23,617 from PositionList cimport PositionList 2021-07-12T08:16:23,618 ^ 2021-07-12T08:16:23,618 ------------------------------------------------------------ 2021-07-12T08:16:23,618 gat/Engine.pyx:35:0: 'PositionList/PositionList.pxd' not found 2021-07-12T08:16:24,611 Error compiling Cython file: 2021-07-12T08:16:24,611 ------------------------------------------------------------ 2021-07-12T08:16:24,611 ... 2021-07-12T08:16:24,611 HAS_SCIPY = False 2021-07-12T08:16:24,612 # min/max are not optimized, so declare them as C functions 2021-07-12T08:16:24,612 # declare as signed comparisons as a Position might be negative 2021-07-12T08:16:24,612 @cython.profile(False) 2021-07-12T08:16:24,612 cdef inline PositionDifference lmin(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:24,612 ^ 2021-07-12T08:16:24,612 ------------------------------------------------------------ 2021-07-12T08:16:24,613 gat/Engine.pyx:59:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,613 Error compiling Cython file: 2021-07-12T08:16:24,613 ------------------------------------------------------------ 2021-07-12T08:16:24,613 ... 2021-07-12T08:16:24,613 HAS_SCIPY = False 2021-07-12T08:16:24,613 # min/max are not optimized, so declare them as C functions 2021-07-12T08:16:24,614 # declare as signed comparisons as a Position might be negative 2021-07-12T08:16:24,614 @cython.profile(False) 2021-07-12T08:16:24,614 cdef inline PositionDifference lmin(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:24,614 ^ 2021-07-12T08:16:24,614 ------------------------------------------------------------ 2021-07-12T08:16:24,614 gat/Engine.pyx:59:36: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,614 Error compiling Cython file: 2021-07-12T08:16:24,615 ------------------------------------------------------------ 2021-07-12T08:16:24,615 ... 2021-07-12T08:16:24,615 HAS_SCIPY = False 2021-07-12T08:16:24,615 # min/max are not optimized, so declare them as C functions 2021-07-12T08:16:24,615 # declare as signed comparisons as a Position might be negative 2021-07-12T08:16:24,615 @cython.profile(False) 2021-07-12T08:16:24,615 cdef inline PositionDifference lmin(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:24,615 ^ 2021-07-12T08:16:24,616 ------------------------------------------------------------ 2021-07-12T08:16:24,616 gat/Engine.pyx:59:58: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,616 Error compiling Cython file: 2021-07-12T08:16:24,616 ------------------------------------------------------------ 2021-07-12T08:16:24,616 ... 2021-07-12T08:16:24,616 if a < b: 2021-07-12T08:16:24,617 return a 2021-07-12T08:16:24,617 return b 2021-07-12T08:16:24,617 @cython.profile(False) 2021-07-12T08:16:24,617 cdef inline PositionDifference lmax(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:24,617 ^ 2021-07-12T08:16:24,617 ------------------------------------------------------------ 2021-07-12T08:16:24,617 gat/Engine.pyx:65:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,618 Error compiling Cython file: 2021-07-12T08:16:24,618 ------------------------------------------------------------ 2021-07-12T08:16:24,618 ... 2021-07-12T08:16:24,618 if a < b: 2021-07-12T08:16:24,618 return a 2021-07-12T08:16:24,618 return b 2021-07-12T08:16:24,618 @cython.profile(False) 2021-07-12T08:16:24,619 cdef inline PositionDifference lmax(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:24,619 ^ 2021-07-12T08:16:24,619 ------------------------------------------------------------ 2021-07-12T08:16:24,619 gat/Engine.pyx:65:36: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,619 Error compiling Cython file: 2021-07-12T08:16:24,619 ------------------------------------------------------------ 2021-07-12T08:16:24,619 ... 2021-07-12T08:16:24,620 if a < b: 2021-07-12T08:16:24,620 return a 2021-07-12T08:16:24,620 return b 2021-07-12T08:16:24,620 @cython.profile(False) 2021-07-12T08:16:24,620 cdef inline PositionDifference lmax(PositionDifference a, PositionDifference b) nogil: 2021-07-12T08:16:24,620 ^ 2021-07-12T08:16:24,620 ------------------------------------------------------------ 2021-07-12T08:16:24,621 gat/Engine.pyx:65:58: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,621 Error compiling Cython file: 2021-07-12T08:16:24,621 ------------------------------------------------------------ 2021-07-12T08:16:24,621 ... 2021-07-12T08:16:24,621 if a > b: 2021-07-12T08:16:24,621 return a 2021-07-12T08:16:24,621 return b 2021-07-12T08:16:24,622 @cython.profile(False) 2021-07-12T08:16:24,622 cdef inline PositionDifference segment_overlap( Segment a, Segment b) nogil: 2021-07-12T08:16:24,622 ^ 2021-07-12T08:16:24,622 ------------------------------------------------------------ 2021-07-12T08:16:24,622 gat/Engine.pyx:83:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,623 Error compiling Cython file: 2021-07-12T08:16:24,623 ------------------------------------------------------------ 2021-07-12T08:16:24,623 ... 2021-07-12T08:16:24,623 if a > b: 2021-07-12T08:16:24,623 return a 2021-07-12T08:16:24,623 return b 2021-07-12T08:16:24,623 @cython.profile(False) 2021-07-12T08:16:24,623 cdef inline PositionDifference segment_overlap( Segment a, Segment b) nogil: 2021-07-12T08:16:24,624 ^ 2021-07-12T08:16:24,624 ------------------------------------------------------------ 2021-07-12T08:16:24,624 gat/Engine.pyx:83:48: 'Segment' is not a type identifier 2021-07-12T08:16:24,624 Error compiling Cython file: 2021-07-12T08:16:24,624 ------------------------------------------------------------ 2021-07-12T08:16:24,624 ... 2021-07-12T08:16:24,624 if a > b: 2021-07-12T08:16:24,625 return a 2021-07-12T08:16:24,625 return b 2021-07-12T08:16:24,625 @cython.profile(False) 2021-07-12T08:16:24,625 cdef inline PositionDifference segment_overlap( Segment a, Segment b) nogil: 2021-07-12T08:16:24,625 ^ 2021-07-12T08:16:24,625 ------------------------------------------------------------ 2021-07-12T08:16:24,625 gat/Engine.pyx:83:59: 'Segment' is not a type identifier 2021-07-12T08:16:24,626 Error compiling Cython file: 2021-07-12T08:16:24,626 ------------------------------------------------------------ 2021-07-12T08:16:24,626 ... 2021-07-12T08:16:24,626 cdef inline PositionDifference segment_overlap( Segment a, Segment b) nogil: 2021-07-12T08:16:24,626 return lmax(0, lmin( a.end, b.end) - \ 2021-07-12T08:16:24,626 lmax(a.start, b.start)) 2021-07-12T08:16:24,627 @cython.profile(False) 2021-07-12T08:16:24,627 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:24,627 ^ 2021-07-12T08:16:24,627 ------------------------------------------------------------ 2021-07-12T08:16:24,627 gat/Engine.pyx:88:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,628 Error compiling Cython file: 2021-07-12T08:16:24,628 ------------------------------------------------------------ 2021-07-12T08:16:24,628 ... 2021-07-12T08:16:24,628 return lmax(0, lmin( a.end, b.end) - \ 2021-07-12T08:16:24,628 lmax(a.start, b.start)) 2021-07-12T08:16:24,629 @cython.profile(False) 2021-07-12T08:16:24,629 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:24,629 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:24,629 ^ 2021-07-12T08:16:24,629 ------------------------------------------------------------ 2021-07-12T08:16:24,630 gat/Engine.pyx:89:4: 'Position' is not a type identifier 2021-07-12T08:16:24,630 Error compiling Cython file: 2021-07-12T08:16:24,630 ------------------------------------------------------------ 2021-07-12T08:16:24,630 ... 2021-07-12T08:16:24,630 return lmax(0, lmin( a.end, b.end) - \ 2021-07-12T08:16:24,630 lmax(a.start, b.start)) 2021-07-12T08:16:24,631 @cython.profile(False) 2021-07-12T08:16:24,631 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:24,631 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:24,631 ^ 2021-07-12T08:16:24,631 ------------------------------------------------------------ 2021-07-12T08:16:24,631 gat/Engine.pyx:89:21: 'Position' is not a type identifier 2021-07-12T08:16:24,632 Error compiling Cython file: 2021-07-12T08:16:24,632 ------------------------------------------------------------ 2021-07-12T08:16:24,632 ... 2021-07-12T08:16:24,632 return lmax(0, lmin( a.end, b.end) - \ 2021-07-12T08:16:24,632 lmax(a.start, b.start)) 2021-07-12T08:16:24,632 @cython.profile(False) 2021-07-12T08:16:24,633 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:24,633 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:24,633 ^ 2021-07-12T08:16:24,633 ------------------------------------------------------------ 2021-07-12T08:16:24,633 gat/Engine.pyx:89:36: 'Position' is not a type identifier 2021-07-12T08:16:24,633 Error compiling Cython file: 2021-07-12T08:16:24,633 ------------------------------------------------------------ 2021-07-12T08:16:24,634 ... 2021-07-12T08:16:24,634 return lmax(0, lmin( a.end, b.end) - \ 2021-07-12T08:16:24,634 lmax(a.start, b.start)) 2021-07-12T08:16:24,634 @cython.profile(False) 2021-07-12T08:16:24,634 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:24,634 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:24,634 ^ 2021-07-12T08:16:24,634 ------------------------------------------------------------ 2021-07-12T08:16:24,635 gat/Engine.pyx:89:53: 'Position' is not a type identifier 2021-07-12T08:16:24,635 Error compiling Cython file: 2021-07-12T08:16:24,635 ------------------------------------------------------------ 2021-07-12T08:16:24,635 ... 2021-07-12T08:16:24,635 return lmax(0, 2021-07-12T08:16:24,635 lmin( aend, bend) - 2021-07-12T08:16:24,635 lmax(astart, bstart)) 2021-07-12T08:16:24,636 @cython.profile(False) 2021-07-12T08:16:24,636 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:24,636 ^ 2021-07-12T08:16:24,636 ------------------------------------------------------------ 2021-07-12T08:16:24,636 gat/Engine.pyx:95:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,636 Error compiling Cython file: 2021-07-12T08:16:24,637 ------------------------------------------------------------ 2021-07-12T08:16:24,637 ... 2021-07-12T08:16:24,637 return lmax(0, 2021-07-12T08:16:24,637 lmin( aend, bend) - 2021-07-12T08:16:24,637 lmax(astart, bstart)) 2021-07-12T08:16:24,637 @cython.profile(False) 2021-07-12T08:16:24,637 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:24,637 ^ 2021-07-12T08:16:24,638 ------------------------------------------------------------ 2021-07-12T08:16:24,638 gat/Engine.pyx:95:51: 'Segment' is not a type identifier 2021-07-12T08:16:24,638 Error compiling Cython file: 2021-07-12T08:16:24,638 ------------------------------------------------------------ 2021-07-12T08:16:24,638 ... 2021-07-12T08:16:24,638 return lmax(0, 2021-07-12T08:16:24,638 lmin( aend, bend) - 2021-07-12T08:16:24,639 lmax(astart, bstart)) 2021-07-12T08:16:24,639 @cython.profile(False) 2021-07-12T08:16:24,639 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:24,639 ^ 2021-07-12T08:16:24,639 ------------------------------------------------------------ 2021-07-12T08:16:24,639 gat/Engine.pyx:95:62: 'Segment' is not a type identifier 2021-07-12T08:16:24,640 Error compiling Cython file: 2021-07-12T08:16:24,640 ------------------------------------------------------------ 2021-07-12T08:16:24,640 ... 2021-07-12T08:16:24,640 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:24,640 return lmin(a.end, b.end) - \ 2021-07-12T08:16:24,640 lmax(a.start, b.start) 2021-07-12T08:16:24,640 @cython.profile(False) 2021-07-12T08:16:24,641 cdef inline PositionDifference segment_length( Segment a) nogil: 2021-07-12T08:16:24,641 ^ 2021-07-12T08:16:24,641 ------------------------------------------------------------ 2021-07-12T08:16:24,641 gat/Engine.pyx:100:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,641 Error compiling Cython file: 2021-07-12T08:16:24,641 ------------------------------------------------------------ 2021-07-12T08:16:24,641 ... 2021-07-12T08:16:24,642 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:24,642 return lmin(a.end, b.end) - \ 2021-07-12T08:16:24,642 lmax(a.start, b.start) 2021-07-12T08:16:24,642 @cython.profile(False) 2021-07-12T08:16:24,642 cdef inline PositionDifference segment_length( Segment a) nogil: 2021-07-12T08:16:24,642 ^ 2021-07-12T08:16:24,642 ------------------------------------------------------------ 2021-07-12T08:16:24,643 gat/Engine.pyx:100:47: 'Segment' is not a type identifier 2021-07-12T08:16:24,643 Error compiling Cython file: 2021-07-12T08:16:24,643 ------------------------------------------------------------ 2021-07-12T08:16:24,643 ... 2021-07-12T08:16:24,643 cdef double db = (s2)[0] 2021-07-12T08:16:24,643 return (da > db) - (da < db) 2021-07-12T08:16:24,644 cdef class SegmentListSamplerSlow: 2021-07-12T08:16:24,644 cdef SegmentList segment_list 2021-07-12T08:16:24,644 ^ 2021-07-12T08:16:24,644 ------------------------------------------------------------ 2021-07-12T08:16:24,644 gat/Engine.pyx:131:9: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,644 Error compiling Cython file: 2021-07-12T08:16:24,645 ------------------------------------------------------------ 2021-07-12T08:16:24,645 ... 2021-07-12T08:16:24,645 cdef class SegmentListSamplerSlow: 2021-07-12T08:16:24,645 cdef SegmentList segment_list 2021-07-12T08:16:24,645 cdef numpy.ndarray cdf 2021-07-12T08:16:24,645 cdef Position total_size 2021-07-12T08:16:24,645 ^ 2021-07-12T08:16:24,645 ------------------------------------------------------------ 2021-07-12T08:16:24,646 gat/Engine.pyx:133:9: 'Position' is not a type identifier 2021-07-12T08:16:24,646 Error compiling Cython file: 2021-07-12T08:16:24,646 ------------------------------------------------------------ 2021-07-12T08:16:24,646 ... 2021-07-12T08:16:24,646 cdef SegmentList segment_list 2021-07-12T08:16:24,646 cdef numpy.ndarray cdf 2021-07-12T08:16:24,647 cdef Position total_size 2021-07-12T08:16:24,647 def __init__(self, SegmentList segment_list ): 2021-07-12T08:16:24,647 ^ 2021-07-12T08:16:24,647 ------------------------------------------------------------ 2021-07-12T08:16:24,647 gat/Engine.pyx:135:23: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,647 Error compiling Cython file: 2021-07-12T08:16:24,648 ------------------------------------------------------------ 2021-07-12T08:16:24,648 ... 2021-07-12T08:16:24,648 self.segment_list = segment_list 2021-07-12T08:16:24,648 self.cdf = numpy.cumsum( [x[1] - x[0] for x in self.segment_list ] ) 2021-07-12T08:16:24,648 self.total_size = self.cdf[-1] 2021-07-12T08:16:24,648 cpdef sample(self, Position length): 2021-07-12T08:16:24,648 ^ 2021-07-12T08:16:24,649 ------------------------------------------------------------ 2021-07-12T08:16:24,649 gat/Engine.pyx:143:23: 'Position' is not a type identifier 2021-07-12T08:16:24,649 Error compiling Cython file: 2021-07-12T08:16:24,649 ------------------------------------------------------------ 2021-07-12T08:16:24,649 ... 2021-07-12T08:16:24,649 return pos, overlap 2021-07-12T08:16:24,650 cdef class SegmentListSamplerWithEdgeEffects: 2021-07-12T08:16:24,650 cdef SegmentList segment_list 2021-07-12T08:16:24,650 ^ 2021-07-12T08:16:24,650 ------------------------------------------------------------ 2021-07-12T08:16:24,650 gat/Engine.pyx:170:9: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,651 Error compiling Cython file: 2021-07-12T08:16:24,651 ------------------------------------------------------------ 2021-07-12T08:16:24,651 ... 2021-07-12T08:16:24,651 return pos, overlap 2021-07-12T08:16:24,651 cdef class SegmentListSamplerWithEdgeEffects: 2021-07-12T08:16:24,651 cdef SegmentList segment_list 2021-07-12T08:16:24,651 cdef Position * cdf 2021-07-12T08:16:24,652 ^ 2021-07-12T08:16:24,652 ------------------------------------------------------------ 2021-07-12T08:16:24,652 gat/Engine.pyx:171:9: 'Position' is not a type identifier 2021-07-12T08:16:24,652 Error compiling Cython file: 2021-07-12T08:16:24,652 ------------------------------------------------------------ 2021-07-12T08:16:24,652 ... 2021-07-12T08:16:24,653 cdef class SegmentListSamplerWithEdgeEffects: 2021-07-12T08:16:24,653 cdef SegmentList segment_list 2021-07-12T08:16:24,653 cdef Position * cdf 2021-07-12T08:16:24,653 cdef Position total_size 2021-07-12T08:16:24,653 ^ 2021-07-12T08:16:24,653 ------------------------------------------------------------ 2021-07-12T08:16:24,654 gat/Engine.pyx:172:9: 'Position' is not a type identifier 2021-07-12T08:16:24,654 Error compiling Cython file: 2021-07-12T08:16:24,654 ------------------------------------------------------------ 2021-07-12T08:16:24,654 ... 2021-07-12T08:16:24,654 cdef class SegmentListSamplerWithEdgeEffects: 2021-07-12T08:16:24,654 cdef SegmentList segment_list 2021-07-12T08:16:24,654 cdef Position * cdf 2021-07-12T08:16:24,655 cdef Position total_size 2021-07-12T08:16:24,655 cdef Position nsegments 2021-07-12T08:16:24,655 ^ 2021-07-12T08:16:24,655 ------------------------------------------------------------ 2021-07-12T08:16:24,655 gat/Engine.pyx:173:9: 'Position' is not a type identifier 2021-07-12T08:16:24,655 Error compiling Cython file: 2021-07-12T08:16:24,655 ------------------------------------------------------------ 2021-07-12T08:16:24,656 ... 2021-07-12T08:16:24,656 cdef SegmentList segment_list 2021-07-12T08:16:24,656 cdef Position * cdf 2021-07-12T08:16:24,656 cdef Position total_size 2021-07-12T08:16:24,656 cdef Position nsegments 2021-07-12T08:16:24,656 def __init__(self, SegmentList segment_list): 2021-07-12T08:16:24,656 ^ 2021-07-12T08:16:24,656 ------------------------------------------------------------ 2021-07-12T08:16:24,657 gat/Engine.pyx:175:23: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,657 Error compiling Cython file: 2021-07-12T08:16:24,657 ------------------------------------------------------------ 2021-07-12T08:16:24,657 ... 2021-07-12T08:16:24,657 self.total_size = 0 2021-07-12T08:16:24,657 for i from 0 <= i < len(segment_list): 2021-07-12T08:16:24,657 self.total_size += segment_length(segment_list.segments[i]) 2021-07-12T08:16:24,658 self.cdf[i] = self.total_size 2021-07-12T08:16:24,658 cpdef sample(self, Position length): 2021-07-12T08:16:24,658 ^ 2021-07-12T08:16:24,658 ------------------------------------------------------------ 2021-07-12T08:16:24,658 gat/Engine.pyx:191:23: 'Position' is not a type identifier 2021-07-12T08:16:24,658 Error compiling Cython file: 2021-07-12T08:16:24,659 ------------------------------------------------------------ 2021-07-12T08:16:24,659 ... 2021-07-12T08:16:24,659 In order to avoid edge effects the position 2021-07-12T08:16:24,659 of the sample within a workspace segment is 2021-07-12T08:16:24,659 sampled again. 2021-07-12T08:16:24,659 ''' 2021-07-12T08:16:24,659 cdef SegmentList segment_list 2021-07-12T08:16:24,659 ^ 2021-07-12T08:16:24,660 ------------------------------------------------------------ 2021-07-12T08:16:24,660 gat/Engine.pyx:256:9: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,660 Error compiling Cython file: 2021-07-12T08:16:24,660 ------------------------------------------------------------ 2021-07-12T08:16:24,660 ... 2021-07-12T08:16:24,660 of the sample within a workspace segment is 2021-07-12T08:16:24,660 sampled again. 2021-07-12T08:16:24,661 ''' 2021-07-12T08:16:24,661 cdef SegmentList segment_list 2021-07-12T08:16:24,661 cdef Position * cdf 2021-07-12T08:16:24,661 ^ 2021-07-12T08:16:24,661 ------------------------------------------------------------ 2021-07-12T08:16:24,661 gat/Engine.pyx:257:9: 'Position' is not a type identifier 2021-07-12T08:16:24,662 Error compiling Cython file: 2021-07-12T08:16:24,662 ------------------------------------------------------------ 2021-07-12T08:16:24,662 ... 2021-07-12T08:16:24,662 sampled again. 2021-07-12T08:16:24,662 ''' 2021-07-12T08:16:24,662 cdef SegmentList segment_list 2021-07-12T08:16:24,662 cdef Position * cdf 2021-07-12T08:16:24,663 cdef Position total_size 2021-07-12T08:16:24,663 ^ 2021-07-12T08:16:24,663 ------------------------------------------------------------ 2021-07-12T08:16:24,663 gat/Engine.pyx:258:9: 'Position' is not a type identifier 2021-07-12T08:16:24,663 Error compiling Cython file: 2021-07-12T08:16:24,663 ------------------------------------------------------------ 2021-07-12T08:16:24,663 ... 2021-07-12T08:16:24,664 cdef SegmentList segment_list 2021-07-12T08:16:24,664 cdef Position * cdf 2021-07-12T08:16:24,664 cdef Position total_size 2021-07-12T08:16:24,664 cdef int nsegments 2021-07-12T08:16:24,664 def __init__(self, SegmentList segment_list ): 2021-07-12T08:16:24,664 ^ 2021-07-12T08:16:24,664 ------------------------------------------------------------ 2021-07-12T08:16:24,665 gat/Engine.pyx:261:23: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,665 Error compiling Cython file: 2021-07-12T08:16:24,665 ------------------------------------------------------------ 2021-07-12T08:16:24,665 ... 2021-07-12T08:16:24,665 for i from 0 <= i < len(segment_list): 2021-07-12T08:16:24,665 self.total_size += segment_length( segment_list.segments[i] ) 2021-07-12T08:16:24,665 # -1, as searchsorted inserts on left 2021-07-12T08:16:24,665 self.cdf[i] = self.total_size -1 2021-07-12T08:16:24,666 cpdef sample( self, Position sample_length ): 2021-07-12T08:16:24,666 ^ 2021-07-12T08:16:24,666 ------------------------------------------------------------ 2021-07-12T08:16:24,666 gat/Engine.pyx:279:24: 'Position' is not a type identifier 2021-07-12T08:16:24,666 Error compiling Cython file: 2021-07-12T08:16:24,666 ------------------------------------------------------------ 2021-07-12T08:16:24,667 ... 2021-07-12T08:16:24,667 self.cdf = NULL 2021-07-12T08:16:24,667 cdef class HistogramSamplerSlow: 2021-07-12T08:16:24,667 cdef numpy.ndarray cdf 2021-07-12T08:16:24,667 cdef Position bucket_size 2021-07-12T08:16:24,667 ^ 2021-07-12T08:16:24,667 ------------------------------------------------------------ 2021-07-12T08:16:24,668 gat/Engine.pyx:358:9: 'Position' is not a type identifier 2021-07-12T08:16:24,668 Error compiling Cython file: 2021-07-12T08:16:24,668 ------------------------------------------------------------ 2021-07-12T08:16:24,668 ... 2021-07-12T08:16:24,668 cdef numpy.ndarray cdf 2021-07-12T08:16:24,668 cdef Position bucket_size 2021-07-12T08:16:24,668 def __init__(self, 2021-07-12T08:16:24,669 numpy.ndarray histogram, 2021-07-12T08:16:24,669 Position bucket_size): 2021-07-12T08:16:24,669 ^ 2021-07-12T08:16:24,669 ------------------------------------------------------------ 2021-07-12T08:16:24,669 gat/Engine.pyx:362:17: 'Position' is not a type identifier 2021-07-12T08:16:24,669 Error compiling Cython file: 2021-07-12T08:16:24,669 ------------------------------------------------------------ 2021-07-12T08:16:24,670 ... 2021-07-12T08:16:24,670 self.cdf = numpy.cumsum(histogram, dtype = numpy.float) 2021-07-12T08:16:24,670 self.cdf /= self.cdf[-1] 2021-07-12T08:16:24,670 self.bucket_size = bucket_size 2021-07-12T08:16:24,670 cpdef Position sample( self ): 2021-07-12T08:16:24,670 ^ 2021-07-12T08:16:24,670 ------------------------------------------------------------ 2021-07-12T08:16:24,671 gat/Engine.pyx:370:10: 'Position' is not a type identifier 2021-07-12T08:16:24,671 Error compiling Cython file: 2021-07-12T08:16:24,671 ------------------------------------------------------------ 2021-07-12T08:16:24,671 ... 2021-07-12T08:16:24,671 return base 2021-07-12T08:16:24,672 cdef class HistogramSampler: 2021-07-12T08:16:24,672 cdef Position * cdf 2021-07-12T08:16:24,672 ^ 2021-07-12T08:16:24,672 ------------------------------------------------------------ 2021-07-12T08:16:24,672 gat/Engine.pyx:389:9: 'Position' is not a type identifier 2021-07-12T08:16:24,673 Error compiling Cython file: 2021-07-12T08:16:24,673 ------------------------------------------------------------ 2021-07-12T08:16:24,673 ... 2021-07-12T08:16:24,673 return base 2021-07-12T08:16:24,673 cdef class HistogramSampler: 2021-07-12T08:16:24,673 cdef Position * cdf 2021-07-12T08:16:24,673 cdef Position bucket_size 2021-07-12T08:16:24,674 ^ 2021-07-12T08:16:24,674 ------------------------------------------------------------ 2021-07-12T08:16:24,674 gat/Engine.pyx:390:9: 'Position' is not a type identifier 2021-07-12T08:16:24,674 Error compiling Cython file: 2021-07-12T08:16:24,674 ------------------------------------------------------------ 2021-07-12T08:16:24,674 ... 2021-07-12T08:16:24,674 cdef class HistogramSampler: 2021-07-12T08:16:24,675 cdef Position * cdf 2021-07-12T08:16:24,675 cdef Position bucket_size 2021-07-12T08:16:24,675 cdef Position nbuckets 2021-07-12T08:16:24,675 ^ 2021-07-12T08:16:24,675 ------------------------------------------------------------ 2021-07-12T08:16:24,675 gat/Engine.pyx:391:9: 'Position' is not a type identifier 2021-07-12T08:16:24,676 Error compiling Cython file: 2021-07-12T08:16:24,676 ------------------------------------------------------------ 2021-07-12T08:16:24,676 ... 2021-07-12T08:16:24,676 cdef class HistogramSampler: 2021-07-12T08:16:24,676 cdef Position * cdf 2021-07-12T08:16:24,677 cdef Position bucket_size 2021-07-12T08:16:24,677 cdef Position nbuckets 2021-07-12T08:16:24,677 cdef Position total_size 2021-07-12T08:16:24,677 ^ 2021-07-12T08:16:24,677 ------------------------------------------------------------ 2021-07-12T08:16:24,677 gat/Engine.pyx:392:9: 'Position' is not a type identifier 2021-07-12T08:16:24,678 Error compiling Cython file: 2021-07-12T08:16:24,678 ------------------------------------------------------------ 2021-07-12T08:16:24,678 ... 2021-07-12T08:16:24,678 cdef Position total_size 2021-07-12T08:16:24,678 @cython.boundscheck(False) 2021-07-12T08:16:24,679 def __init__(self, 2021-07-12T08:16:24,679 numpy.ndarray[DTYPE_INT_t, ndim=1] histogram, 2021-07-12T08:16:24,679 Position bucket_size ): 2021-07-12T08:16:24,679 ^ 2021-07-12T08:16:24,679 ------------------------------------------------------------ 2021-07-12T08:16:24,679 gat/Engine.pyx:397:17: 'Position' is not a type identifier 2021-07-12T08:16:24,679 Error compiling Cython file: 2021-07-12T08:16:24,680 ------------------------------------------------------------ 2021-07-12T08:16:24,680 ... 2021-07-12T08:16:24,680 self.total_size += histogram[i] 2021-07-12T08:16:24,680 self.cdf[i] = self.total_size 2021-07-12T08:16:24,680 self.bucket_size = bucket_size 2021-07-12T08:16:24,680 cpdef Position sample( self ): 2021-07-12T08:16:24,680 ^ 2021-07-12T08:16:24,681 ------------------------------------------------------------ 2021-07-12T08:16:24,681 gat/Engine.pyx:413:10: 'Position' is not a type identifier 2021-07-12T08:16:24,681 Error compiling Cython file: 2021-07-12T08:16:24,681 ------------------------------------------------------------ 2021-07-12T08:16:24,681 ... 2021-07-12T08:16:24,681 returns a SegmentList of sampled segments. 2021-07-12T08:16:24,682 ''' 2021-07-12T08:16:24,682 cdef Position bucket_size 2021-07-12T08:16:24,682 ^ 2021-07-12T08:16:24,682 ------------------------------------------------------------ 2021-07-12T08:16:24,682 gat/Engine.pyx:498:9: 'Position' is not a type identifier 2021-07-12T08:16:24,683 Error compiling Cython file: 2021-07-12T08:16:24,683 ------------------------------------------------------------ 2021-07-12T08:16:24,683 ... 2021-07-12T08:16:24,683 def __reduce__(self): 2021-07-12T08:16:24,683 return (buildSamplerAnnotator, (self.bucket_size, 2021-07-12T08:16:24,684 self.nbuckets, 2021-07-12T08:16:24,684 self.nunsuccessful_rounds)) 2021-07-12T08:16:24,684 cpdef SegmentList sample(self, 2021-07-12T08:16:24,684 ^ 2021-07-12T08:16:24,685 ------------------------------------------------------------ 2021-07-12T08:16:24,685 gat/Engine.pyx:515:10: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,685 Error compiling Cython file: 2021-07-12T08:16:24,686 ------------------------------------------------------------ 2021-07-12T08:16:24,686 ... 2021-07-12T08:16:24,686 return (buildSamplerAnnotator, (self.bucket_size, 2021-07-12T08:16:24,686 self.nbuckets, 2021-07-12T08:16:24,686 self.nunsuccessful_rounds)) 2021-07-12T08:16:24,687 cpdef SegmentList sample(self, 2021-07-12T08:16:24,687 SegmentList segments, 2021-07-12T08:16:24,687 ^ 2021-07-12T08:16:24,687 ------------------------------------------------------------ 2021-07-12T08:16:24,687 gat/Engine.pyx:516:29: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,688 Error compiling Cython file: 2021-07-12T08:16:24,688 ------------------------------------------------------------ 2021-07-12T08:16:24,688 ... 2021-07-12T08:16:24,688 self.nbuckets, 2021-07-12T08:16:24,688 self.nunsuccessful_rounds)) 2021-07-12T08:16:24,689 cpdef SegmentList sample(self, 2021-07-12T08:16:24,689 SegmentList segments, 2021-07-12T08:16:24,689 SegmentList workspace): 2021-07-12T08:16:24,689 ^ 2021-07-12T08:16:24,689 ------------------------------------------------------------ 2021-07-12T08:16:24,690 gat/Engine.pyx:517:29: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,690 Error compiling Cython file: 2021-07-12T08:16:24,690 ------------------------------------------------------------ 2021-07-12T08:16:24,690 ... 2021-07-12T08:16:24,690 the largest segment in the input set. 2021-07-12T08:16:24,691 returns a SegmentList of sampled segments. 2021-07-12T08:16:24,691 ''' 2021-07-12T08:16:24,691 cdef Position bucket_size 2021-07-12T08:16:24,691 ^ 2021-07-12T08:16:24,691 ------------------------------------------------------------ 2021-07-12T08:16:24,692 gat/Engine.pyx:685:9: 'Position' is not a type identifier 2021-07-12T08:16:24,692 Error compiling Cython file: 2021-07-12T08:16:24,692 ------------------------------------------------------------ 2021-07-12T08:16:24,692 ... 2021-07-12T08:16:24,693 returns a SegmentList of sampled segments. 2021-07-12T08:16:24,693 ''' 2021-07-12T08:16:24,693 cdef Position bucket_size 2021-07-12T08:16:24,693 cdef Position nbuckets 2021-07-12T08:16:24,694 ^ 2021-07-12T08:16:24,694 ------------------------------------------------------------ 2021-07-12T08:16:24,694 gat/Engine.pyx:686:9: 'Position' is not a type identifier 2021-07-12T08:16:24,695 Error compiling Cython file: 2021-07-12T08:16:24,695 ------------------------------------------------------------ 2021-07-12T08:16:24,695 ... 2021-07-12T08:16:24,696 def __reduce__(self): 2021-07-12T08:16:24,696 return (buildSamplerSegments, (self.bucket_size, 2021-07-12T08:16:24,696 self.nbuckets )) 2021-07-12T08:16:24,696 cpdef SegmentList sample( self, 2021-07-12T08:16:24,696 ^ 2021-07-12T08:16:24,697 ------------------------------------------------------------ 2021-07-12T08:16:24,697 gat/Engine.pyx:697:10: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,698 Error compiling Cython file: 2021-07-12T08:16:24,698 ------------------------------------------------------------ 2021-07-12T08:16:24,698 ... 2021-07-12T08:16:24,698 def __reduce__(self): 2021-07-12T08:16:24,698 return (buildSamplerSegments, (self.bucket_size, 2021-07-12T08:16:24,699 self.nbuckets )) 2021-07-12T08:16:24,699 cpdef SegmentList sample( self, 2021-07-12T08:16:24,699 SegmentList segments, 2021-07-12T08:16:24,699 ^ 2021-07-12T08:16:24,700 ------------------------------------------------------------ 2021-07-12T08:16:24,700 gat/Engine.pyx:698:43: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,700 Error compiling Cython file: 2021-07-12T08:16:24,701 ------------------------------------------------------------ 2021-07-12T08:16:24,701 ... 2021-07-12T08:16:24,701 return (buildSamplerSegments, (self.bucket_size, 2021-07-12T08:16:24,701 self.nbuckets )) 2021-07-12T08:16:24,702 cpdef SegmentList sample( self, 2021-07-12T08:16:24,702 SegmentList segments, 2021-07-12T08:16:24,702 SegmentList workspace ): 2021-07-12T08:16:24,702 ^ 2021-07-12T08:16:24,703 ------------------------------------------------------------ 2021-07-12T08:16:24,703 gat/Engine.pyx:699:43: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,704 Error compiling Cython file: 2021-07-12T08:16:24,704 ------------------------------------------------------------ 2021-07-12T08:16:24,704 ... 2021-07-12T08:16:24,705 returns a SegmentList of sampled segments. 2021-07-12T08:16:24,705 ''' 2021-07-12T08:16:24,705 cdef Position bucket_size 2021-07-12T08:16:24,705 ^ 2021-07-12T08:16:24,706 ------------------------------------------------------------ 2021-07-12T08:16:24,706 gat/Engine.pyx:771:9: 'Position' is not a type identifier 2021-07-12T08:16:24,706 Error compiling Cython file: 2021-07-12T08:16:24,706 ------------------------------------------------------------ 2021-07-12T08:16:24,706 ... 2021-07-12T08:16:24,706 returns a SegmentList of sampled segments. 2021-07-12T08:16:24,707 ''' 2021-07-12T08:16:24,707 cdef Position bucket_size 2021-07-12T08:16:24,707 cdef Position nbuckets 2021-07-12T08:16:24,707 ^ 2021-07-12T08:16:24,707 ------------------------------------------------------------ 2021-07-12T08:16:24,708 gat/Engine.pyx:772:9: 'Position' is not a type identifier 2021-07-12T08:16:24,708 Error compiling Cython file: 2021-07-12T08:16:24,708 ------------------------------------------------------------ 2021-07-12T08:16:24,709 ... 2021-07-12T08:16:24,709 return (buildSamplerBruteForce, (self.bucket_size, 2021-07-12T08:16:24,709 self.nbuckets, 2021-07-12T08:16:24,709 self.ntries_inner, 2021-07-12T08:16:24,710 self.ntries_outer)) 2021-07-12T08:16:24,710 cpdef SegmentList sample(self, 2021-07-12T08:16:24,710 ^ 2021-07-12T08:16:24,710 ------------------------------------------------------------ 2021-07-12T08:16:24,711 gat/Engine.pyx:793:10: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,711 Error compiling Cython file: 2021-07-12T08:16:24,711 ------------------------------------------------------------ 2021-07-12T08:16:24,711 ... 2021-07-12T08:16:24,711 self.nbuckets, 2021-07-12T08:16:24,712 self.ntries_inner, 2021-07-12T08:16:24,712 self.ntries_outer)) 2021-07-12T08:16:24,712 cpdef SegmentList sample(self, 2021-07-12T08:16:24,712 SegmentList segments, 2021-07-12T08:16:24,713 ^ 2021-07-12T08:16:24,713 ------------------------------------------------------------ 2021-07-12T08:16:24,713 gat/Engine.pyx:794:29: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,714 Error compiling Cython file: 2021-07-12T08:16:24,714 ------------------------------------------------------------ 2021-07-12T08:16:24,714 ... 2021-07-12T08:16:24,714 self.ntries_inner, 2021-07-12T08:16:24,714 self.ntries_outer)) 2021-07-12T08:16:24,715 cpdef SegmentList sample(self, 2021-07-12T08:16:24,715 SegmentList segments, 2021-07-12T08:16:24,715 SegmentList workspace): 2021-07-12T08:16:24,715 ^ 2021-07-12T08:16:24,715 ------------------------------------------------------------ 2021-07-12T08:16:24,716 gat/Engine.pyx:795:29: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,716 Error compiling Cython file: 2021-07-12T08:16:24,716 ------------------------------------------------------------ 2021-07-12T08:16:24,716 ... 2021-07-12T08:16:24,717 The product of *bucket_size* and *nbuckets* needs to be larger than 2021-07-12T08:16:24,717 the largest segment in the input set. 2021-07-12T08:16:24,717 ''' 2021-07-12T08:16:24,717 cdef Position bucket_size 2021-07-12T08:16:24,717 ^ 2021-07-12T08:16:24,718 ------------------------------------------------------------ 2021-07-12T08:16:24,718 gat/Engine.pyx:897:9: 'Position' is not a type identifier 2021-07-12T08:16:24,718 Error compiling Cython file: 2021-07-12T08:16:24,718 ------------------------------------------------------------ 2021-07-12T08:16:24,718 ... 2021-07-12T08:16:24,719 The product of *bucket_size* and *nbuckets* needs to be larger than 2021-07-12T08:16:24,719 the largest segment in the input set. 2021-07-12T08:16:24,719 ''' 2021-07-12T08:16:24,719 cdef Position bucket_size 2021-07-12T08:16:24,720 cdef Position nbuckets 2021-07-12T08:16:24,720 ^ 2021-07-12T08:16:24,720 ------------------------------------------------------------ 2021-07-12T08:16:24,720 gat/Engine.pyx:898:9: 'Position' is not a type identifier 2021-07-12T08:16:24,720 Error compiling Cython file: 2021-07-12T08:16:24,721 ------------------------------------------------------------ 2021-07-12T08:16:24,721 ... 2021-07-12T08:16:24,721 the largest segment in the input set. 2021-07-12T08:16:24,721 ''' 2021-07-12T08:16:24,721 cdef Position bucket_size 2021-07-12T08:16:24,722 cdef Position nbuckets 2021-07-12T08:16:24,722 cdef Position increment 2021-07-12T08:16:24,722 ^ 2021-07-12T08:16:24,722 ------------------------------------------------------------ 2021-07-12T08:16:24,723 gat/Engine.pyx:899:9: 'Position' is not a type identifier 2021-07-12T08:16:24,723 Error compiling Cython file: 2021-07-12T08:16:24,723 ------------------------------------------------------------ 2021-07-12T08:16:24,723 ... 2021-07-12T08:16:24,724 ''' 2021-07-12T08:16:24,724 cdef Position bucket_size 2021-07-12T08:16:24,724 cdef Position nbuckets 2021-07-12T08:16:24,724 cdef Position increment 2021-07-12T08:16:24,724 cdef Position current_workspace 2021-07-12T08:16:24,725 ^ 2021-07-12T08:16:24,725 ------------------------------------------------------------ 2021-07-12T08:16:24,725 gat/Engine.pyx:900:9: 'Position' is not a type identifier 2021-07-12T08:16:24,726 Error compiling Cython file: 2021-07-12T08:16:24,726 ------------------------------------------------------------ 2021-07-12T08:16:24,726 ... 2021-07-12T08:16:24,726 cdef Position bucket_size 2021-07-12T08:16:24,727 cdef Position nbuckets 2021-07-12T08:16:24,727 cdef Position increment 2021-07-12T08:16:24,727 cdef Position current_workspace 2021-07-12T08:16:24,727 cdef Position current_position 2021-07-12T08:16:24,727 ^ 2021-07-12T08:16:24,728 ------------------------------------------------------------ 2021-07-12T08:16:24,728 gat/Engine.pyx:901:9: 'Position' is not a type identifier 2021-07-12T08:16:24,728 Error compiling Cython file: 2021-07-12T08:16:24,729 ------------------------------------------------------------ 2021-07-12T08:16:24,729 ... 2021-07-12T08:16:24,729 self.nbuckets, 2021-07-12T08:16:24,729 self.current_orientation, 2021-07-12T08:16:24,730 self.current_workspace, 2021-07-12T08:16:24,730 self.current_position) ) 2021-07-12T08:16:24,730 cpdef SegmentList sample( self, 2021-07-12T08:16:24,730 ^ 2021-07-12T08:16:24,731 ------------------------------------------------------------ 2021-07-12T08:16:24,731 gat/Engine.pyx:927:10: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,731 Error compiling Cython file: 2021-07-12T08:16:24,732 ------------------------------------------------------------ 2021-07-12T08:16:24,732 ... 2021-07-12T08:16:24,732 self.current_orientation, 2021-07-12T08:16:24,732 self.current_workspace, 2021-07-12T08:16:24,733 self.current_position) ) 2021-07-12T08:16:24,733 cpdef SegmentList sample( self, 2021-07-12T08:16:24,733 SegmentList segments, 2021-07-12T08:16:24,733 ^ 2021-07-12T08:16:24,734 ------------------------------------------------------------ 2021-07-12T08:16:24,734 gat/Engine.pyx:928:43: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,734 Error compiling Cython file: 2021-07-12T08:16:24,735 ------------------------------------------------------------ 2021-07-12T08:16:24,735 ... 2021-07-12T08:16:24,735 self.current_workspace, 2021-07-12T08:16:24,735 self.current_position) ) 2021-07-12T08:16:24,735 cpdef SegmentList sample( self, 2021-07-12T08:16:24,736 SegmentList segments, 2021-07-12T08:16:24,736 SegmentList workspace ): 2021-07-12T08:16:24,736 ^ 2021-07-12T08:16:24,736 ------------------------------------------------------------ 2021-07-12T08:16:24,736 gat/Engine.pyx:929:43: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,736 Error compiling Cython file: 2021-07-12T08:16:24,737 ------------------------------------------------------------ 2021-07-12T08:16:24,737 ... 2021-07-12T08:16:24,737 def __reduce__(self): 2021-07-12T08:16:24,737 return (buildSamplerShift, (self.radius, 2021-07-12T08:16:24,737 self.extension)), 2021-07-12T08:16:24,738 cpdef SegmentList sample(self, 2021-07-12T08:16:24,738 ^ 2021-07-12T08:16:24,738 ------------------------------------------------------------ 2021-07-12T08:16:24,738 gat/Engine.pyx:1032:10: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,738 Error compiling Cython file: 2021-07-12T08:16:24,739 ------------------------------------------------------------ 2021-07-12T08:16:24,739 ... 2021-07-12T08:16:24,739 def __reduce__(self): 2021-07-12T08:16:24,739 return (buildSamplerShift, (self.radius, 2021-07-12T08:16:24,739 self.extension)), 2021-07-12T08:16:24,739 cpdef SegmentList sample(self, 2021-07-12T08:16:24,739 SegmentList segments, 2021-07-12T08:16:24,740 ^ 2021-07-12T08:16:24,740 ------------------------------------------------------------ 2021-07-12T08:16:24,740 gat/Engine.pyx:1033:29: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,740 Error compiling Cython file: 2021-07-12T08:16:24,740 ------------------------------------------------------------ 2021-07-12T08:16:24,741 ... 2021-07-12T08:16:24,741 return (buildSamplerShift, (self.radius, 2021-07-12T08:16:24,741 self.extension)), 2021-07-12T08:16:24,741 cpdef SegmentList sample(self, 2021-07-12T08:16:24,741 SegmentList segments, 2021-07-12T08:16:24,741 SegmentList workspace): 2021-07-12T08:16:24,742 ^ 2021-07-12T08:16:24,742 ------------------------------------------------------------ 2021-07-12T08:16:24,742 gat/Engine.pyx:1034:29: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,742 Error compiling Cython file: 2021-07-12T08:16:24,743 ------------------------------------------------------------ 2021-07-12T08:16:24,743 ... 2021-07-12T08:16:24,743 ''' 2021-07-12T08:16:24,743 def __init__( self ): 2021-07-12T08:16:24,743 pass 2021-07-12T08:16:24,744 cpdef SegmentList sample( self, 2021-07-12T08:16:24,744 ^ 2021-07-12T08:16:24,744 ------------------------------------------------------------ 2021-07-12T08:16:24,744 gat/Engine.pyx:1148:10: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,745 Error compiling Cython file: 2021-07-12T08:16:24,745 ------------------------------------------------------------ 2021-07-12T08:16:24,745 ... 2021-07-12T08:16:24,745 def __init__( self ): 2021-07-12T08:16:24,745 pass 2021-07-12T08:16:24,746 cpdef SegmentList sample( self, 2021-07-12T08:16:24,746 SegmentList segments, 2021-07-12T08:16:24,746 ^ 2021-07-12T08:16:24,746 ------------------------------------------------------------ 2021-07-12T08:16:24,746 gat/Engine.pyx:1149:43: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,747 Error compiling Cython file: 2021-07-12T08:16:24,747 ------------------------------------------------------------ 2021-07-12T08:16:24,747 ... 2021-07-12T08:16:24,747 def __init__( self ): 2021-07-12T08:16:24,748 pass 2021-07-12T08:16:24,748 cpdef SegmentList sample( self, 2021-07-12T08:16:24,748 SegmentList segments, 2021-07-12T08:16:24,748 SegmentList workspace ): 2021-07-12T08:16:24,748 ^ 2021-07-12T08:16:24,749 ------------------------------------------------------------ 2021-07-12T08:16:24,749 gat/Engine.pyx:1150:43: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,749 Error compiling Cython file: 2021-07-12T08:16:24,749 ------------------------------------------------------------ 2021-07-12T08:16:24,750 ... 2021-07-12T08:16:24,750 ''' 2021-07-12T08:16:24,750 def __init__( self ): 2021-07-12T08:16:24,750 pass 2021-07-12T08:16:24,750 cpdef SegmentList sample( self, 2021-07-12T08:16:24,751 ^ 2021-07-12T08:16:24,751 ------------------------------------------------------------ 2021-07-12T08:16:24,751 gat/Engine.pyx:1264:10: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,751 Error compiling Cython file: 2021-07-12T08:16:24,751 ------------------------------------------------------------ 2021-07-12T08:16:24,752 ... 2021-07-12T08:16:24,752 def __init__( self ): 2021-07-12T08:16:24,752 pass 2021-07-12T08:16:24,752 cpdef SegmentList sample( self, 2021-07-12T08:16:24,752 SegmentList segments, 2021-07-12T08:16:24,753 ^ 2021-07-12T08:16:24,753 ------------------------------------------------------------ 2021-07-12T08:16:24,753 gat/Engine.pyx:1265:43: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,753 Error compiling Cython file: 2021-07-12T08:16:24,754 ------------------------------------------------------------ 2021-07-12T08:16:24,754 ... 2021-07-12T08:16:24,754 def __init__( self ): 2021-07-12T08:16:24,754 pass 2021-07-12T08:16:24,754 cpdef SegmentList sample( self, 2021-07-12T08:16:24,754 SegmentList segments, 2021-07-12T08:16:24,755 SegmentList workspace ): 2021-07-12T08:16:24,755 ^ 2021-07-12T08:16:24,755 ------------------------------------------------------------ 2021-07-12T08:16:24,755 gat/Engine.pyx:1266:43: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,755 Error compiling Cython file: 2021-07-12T08:16:24,756 ------------------------------------------------------------ 2021-07-12T08:16:24,756 ... 2021-07-12T08:16:24,756 def __init__( self ): 2021-07-12T08:16:24,756 ''' 2021-07-12T08:16:24,756 returns a copy of the observed data. 2021-07-12T08:16:24,756 ''' 2021-07-12T08:16:24,757 cpdef SegmentList sample( self, 2021-07-12T08:16:24,757 ^ 2021-07-12T08:16:24,757 ------------------------------------------------------------ 2021-07-12T08:16:24,757 gat/Engine.pyx:1398:10: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,757 Error compiling Cython file: 2021-07-12T08:16:24,758 ------------------------------------------------------------ 2021-07-12T08:16:24,758 ... 2021-07-12T08:16:24,758 ''' 2021-07-12T08:16:24,758 returns a copy of the observed data. 2021-07-12T08:16:24,758 ''' 2021-07-12T08:16:24,758 cpdef SegmentList sample( self, 2021-07-12T08:16:24,759 SegmentList segments, 2021-07-12T08:16:24,759 ^ 2021-07-12T08:16:24,759 ------------------------------------------------------------ 2021-07-12T08:16:24,759 gat/Engine.pyx:1399:30: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,760 Error compiling Cython file: 2021-07-12T08:16:24,760 ------------------------------------------------------------ 2021-07-12T08:16:24,760 ... 2021-07-12T08:16:24,760 returns a copy of the observed data. 2021-07-12T08:16:24,760 ''' 2021-07-12T08:16:24,761 cpdef SegmentList sample( self, 2021-07-12T08:16:24,761 SegmentList segments, 2021-07-12T08:16:24,761 SegmentList workspace ): 2021-07-12T08:16:24,761 ^ 2021-07-12T08:16:24,762 ------------------------------------------------------------ 2021-07-12T08:16:24,762 gat/Engine.pyx:1400:30: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,762 Error compiling Cython file: 2021-07-12T08:16:24,762 ------------------------------------------------------------ 2021-07-12T08:16:24,763 ... 2021-07-12T08:16:24,763 """return number of nucleotides overlapping between segments and 2021-07-12T08:16:24,763 annotations.""" 2021-07-12T08:16:24,763 name = "nucleotide-overlap" 2021-07-12T08:16:24,764 def __call__(self, SegmentList segments, 2021-07-12T08:16:24,764 ^ 2021-07-12T08:16:24,764 ------------------------------------------------------------ 2021-07-12T08:16:24,764 gat/Engine.pyx:1423:23: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,764 Error compiling Cython file: 2021-07-12T08:16:24,765 ------------------------------------------------------------ 2021-07-12T08:16:24,765 ... 2021-07-12T08:16:24,765 annotations.""" 2021-07-12T08:16:24,765 name = "nucleotide-overlap" 2021-07-12T08:16:24,765 def __call__(self, SegmentList segments, 2021-07-12T08:16:24,766 SegmentList annotations, 2021-07-12T08:16:24,766 ^ 2021-07-12T08:16:24,766 ------------------------------------------------------------ 2021-07-12T08:16:24,766 gat/Engine.pyx:1424:17: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,767 Error compiling Cython file: 2021-07-12T08:16:24,767 ------------------------------------------------------------ 2021-07-12T08:16:24,767 ... 2021-07-12T08:16:24,767 name = "nucleotide-overlap" 2021-07-12T08:16:24,767 def __call__(self, SegmentList segments, 2021-07-12T08:16:24,767 SegmentList annotations, 2021-07-12T08:16:24,768 SegmentList workspace=None): 2021-07-12T08:16:24,768 ^ 2021-07-12T08:16:24,768 ------------------------------------------------------------ 2021-07-12T08:16:24,768 gat/Engine.pyx:1425:17: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,769 Error compiling Cython file: 2021-07-12T08:16:24,769 ------------------------------------------------------------ 2021-07-12T08:16:24,769 ... 2021-07-12T08:16:24,770 return annotations.overlapWithSegments(segments) 2021-07-12T08:16:24,770 cdef class CounterNucleotideDensity(Counter): 2021-07-12T08:16:24,770 name = "nucleotide-density" 2021-07-12T08:16:24,771 def __call__(self, SegmentList segments, 2021-07-12T08:16:24,771 ^ 2021-07-12T08:16:24,771 ------------------------------------------------------------ 2021-07-12T08:16:24,772 gat/Engine.pyx:1431:23: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,772 Error compiling Cython file: 2021-07-12T08:16:24,772 ------------------------------------------------------------ 2021-07-12T08:16:24,773 ... 2021-07-12T08:16:24,773 cdef class CounterNucleotideDensity(Counter): 2021-07-12T08:16:24,773 name = "nucleotide-density" 2021-07-12T08:16:24,774 def __call__(self, SegmentList segments, 2021-07-12T08:16:24,774 SegmentList annotations, 2021-07-12T08:16:24,774 ^ 2021-07-12T08:16:24,774 ------------------------------------------------------------ 2021-07-12T08:16:24,775 gat/Engine.pyx:1432:17: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,775 Error compiling Cython file: 2021-07-12T08:16:24,775 ------------------------------------------------------------ 2021-07-12T08:16:24,776 ... 2021-07-12T08:16:24,776 cdef class CounterNucleotideDensity(Counter): 2021-07-12T08:16:24,776 name = "nucleotide-density" 2021-07-12T08:16:24,777 def __call__(self, SegmentList segments, 2021-07-12T08:16:24,777 SegmentList annotations, 2021-07-12T08:16:24,777 SegmentList workspace ): 2021-07-12T08:16:24,777 ^ 2021-07-12T08:16:24,777 ------------------------------------------------------------ 2021-07-12T08:16:24,778 gat/Engine.pyx:1433:17: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,778 Error compiling Cython file: 2021-07-12T08:16:24,779 ------------------------------------------------------------ 2021-07-12T08:16:24,779 ... 2021-07-12T08:16:24,779 double observed 2021-07-12T08:16:24,779 double stddev 2021-07-12T08:16:24,779 double lower95 2021-07-12T08:16:24,780 double upper95 2021-07-12T08:16:24,780 double fold 2021-07-12T08:16:24,780 Position nsamples 2021-07-12T08:16:24,780 ^ 2021-07-12T08:16:24,780 ------------------------------------------------------------ 2021-07-12T08:16:24,781 gat/Engine.pyx:1536:4: 'Position' is not a type identifier 2021-07-12T08:16:24,781 Error compiling Cython file: 2021-07-12T08:16:24,781 ------------------------------------------------------------ 2021-07-12T08:16:24,781 ... 2021-07-12T08:16:24,781 "percent_overlap_nsegments_annotation", 2021-07-12T08:16:24,781 "percent_overlap_size_annotation", 2021-07-12T08:16:24,782 ] 2021-07-12T08:16:24,782 cdef: 2021-07-12T08:16:24,782 Position track_nsegments 2021-07-12T08:16:24,782 ^ 2021-07-12T08:16:24,782 ------------------------------------------------------------ 2021-07-12T08:16:24,783 gat/Engine.pyx:1886:8: 'Position' is not a type identifier 2021-07-12T08:16:24,783 Error compiling Cython file: 2021-07-12T08:16:24,783 ------------------------------------------------------------ 2021-07-12T08:16:24,783 ... 2021-07-12T08:16:24,783 "percent_overlap_size_annotation", 2021-07-12T08:16:24,784 ] 2021-07-12T08:16:24,784 cdef: 2021-07-12T08:16:24,784 Position track_nsegments 2021-07-12T08:16:24,784 Position track_size 2021-07-12T08:16:24,784 ^ 2021-07-12T08:16:24,785 ------------------------------------------------------------ 2021-07-12T08:16:24,785 gat/Engine.pyx:1887:8: 'Position' is not a type identifier 2021-07-12T08:16:24,785 Error compiling Cython file: 2021-07-12T08:16:24,785 ------------------------------------------------------------ 2021-07-12T08:16:24,785 ... 2021-07-12T08:16:24,786 ] 2021-07-12T08:16:24,786 cdef: 2021-07-12T08:16:24,786 Position track_nsegments 2021-07-12T08:16:24,786 Position track_size 2021-07-12T08:16:24,786 Position annotation_nsegments 2021-07-12T08:16:24,786 ^ 2021-07-12T08:16:24,786 ------------------------------------------------------------ 2021-07-12T08:16:24,787 gat/Engine.pyx:1888:8: 'Position' is not a type identifier 2021-07-12T08:16:24,787 Error compiling Cython file: 2021-07-12T08:16:24,787 ------------------------------------------------------------ 2021-07-12T08:16:24,787 ... 2021-07-12T08:16:24,788 cdef: 2021-07-12T08:16:24,788 Position track_nsegments 2021-07-12T08:16:24,788 Position track_size 2021-07-12T08:16:24,788 Position annotation_nsegments 2021-07-12T08:16:24,788 Position annotation_size 2021-07-12T08:16:24,788 ^ 2021-07-12T08:16:24,789 ------------------------------------------------------------ 2021-07-12T08:16:24,789 gat/Engine.pyx:1889:8: 'Position' is not a type identifier 2021-07-12T08:16:24,789 Error compiling Cython file: 2021-07-12T08:16:24,789 ------------------------------------------------------------ 2021-07-12T08:16:24,790 ... 2021-07-12T08:16:24,790 cdef: 2021-07-12T08:16:24,790 Position track_nsegments 2021-07-12T08:16:24,790 Position track_size 2021-07-12T08:16:24,790 Position annotation_nsegments 2021-07-12T08:16:24,790 Position annotation_size 2021-07-12T08:16:24,790 Position overlap_nsegments 2021-07-12T08:16:24,791 ^ 2021-07-12T08:16:24,791 ------------------------------------------------------------ 2021-07-12T08:16:24,791 gat/Engine.pyx:1890:8: 'Position' is not a type identifier 2021-07-12T08:16:24,791 Error compiling Cython file: 2021-07-12T08:16:24,792 ------------------------------------------------------------ 2021-07-12T08:16:24,792 ... 2021-07-12T08:16:24,792 Position track_nsegments 2021-07-12T08:16:24,792 Position track_size 2021-07-12T08:16:24,792 Position annotation_nsegments 2021-07-12T08:16:24,792 Position annotation_size 2021-07-12T08:16:24,793 Position overlap_nsegments 2021-07-12T08:16:24,793 Position overlap_size 2021-07-12T08:16:24,793 ^ 2021-07-12T08:16:24,793 ------------------------------------------------------------ 2021-07-12T08:16:24,793 gat/Engine.pyx:1891:8: 'Position' is not a type identifier 2021-07-12T08:16:24,794 Error compiling Cython file: 2021-07-12T08:16:24,794 ------------------------------------------------------------ 2021-07-12T08:16:24,794 ... 2021-07-12T08:16:24,794 Position track_size 2021-07-12T08:16:24,794 Position annotation_nsegments 2021-07-12T08:16:24,794 Position annotation_size 2021-07-12T08:16:24,794 Position overlap_nsegments 2021-07-12T08:16:24,795 Position overlap_size 2021-07-12T08:16:24,795 Position workspace_size 2021-07-12T08:16:24,795 ^ 2021-07-12T08:16:24,795 ------------------------------------------------------------ 2021-07-12T08:16:24,795 gat/Engine.pyx:1892:8: 'Position' is not a type identifier 2021-07-12T08:16:24,796 Error compiling Cython file: 2021-07-12T08:16:24,796 ------------------------------------------------------------ 2021-07-12T08:16:24,796 ... 2021-07-12T08:16:24,796 ############################################################ 2021-07-12T08:16:24,796 ############################################################ 2021-07-12T08:16:24,796 ## FDR computation - obsolete 2021-07-12T08:16:24,797 ############################################################ 2021-07-12T08:16:24,797 cdef double computeFalsePositiveRate( EnrichmentStatistics ** allstats, 2021-07-12T08:16:24,797 Position nresults, 2021-07-12T08:16:24,797 ^ 2021-07-12T08:16:24,797 ------------------------------------------------------------ 2021-07-12T08:16:24,798 gat/Engine.pyx:3351:38: 'Position' is not a type identifier 2021-07-12T08:16:24,798 Error compiling Cython file: 2021-07-12T08:16:24,798 ------------------------------------------------------------ 2021-07-12T08:16:24,798 ... 2021-07-12T08:16:24,798 ############################################################ 2021-07-12T08:16:24,798 ## FDR computation - obsolete 2021-07-12T08:16:24,799 ############################################################ 2021-07-12T08:16:24,799 cdef double computeFalsePositiveRate( EnrichmentStatistics ** allstats, 2021-07-12T08:16:24,799 Position nresults, 2021-07-12T08:16:24,799 Position nsamples, 2021-07-12T08:16:24,799 ^ 2021-07-12T08:16:24,799 ------------------------------------------------------------ 2021-07-12T08:16:24,800 gat/Engine.pyx:3352:38: 'Position' is not a type identifier 2021-07-12T08:16:24,826 Error compiling Cython file: 2021-07-12T08:16:24,827 ------------------------------------------------------------ 2021-07-12T08:16:24,827 ... 2021-07-12T08:16:24,827 break 2021-07-12T08:16:24,827 @cython.profile(False) 2021-07-12T08:16:24,827 cdef inline int isSampleSignificantAtPvalue( EnrichmentStatistics * stats, 2021-07-12T08:16:24,827 Position sample_id, 2021-07-12T08:16:24,827 ^ 2021-07-12T08:16:24,828 ------------------------------------------------------------ 2021-07-12T08:16:24,828 gat/Engine.pyx:3448:45: 'Position' is not a type identifier 2021-07-12T08:16:24,833 Error compiling Cython file: 2021-07-12T08:16:24,833 ------------------------------------------------------------ 2021-07-12T08:16:24,833 ... 2021-07-12T08:16:24,833 '''return a new position within segment list.''' 2021-07-12T08:16:24,834 # note: could be made quicker by 2021-07-12T08:16:24,834 # - creating a sample random integers once, see numpy.random_integers? 2021-07-12T08:16:24,834 # - avoiding the binary search? 2021-07-12T08:16:24,834 cdef Position r, offset, pos 2021-07-12T08:16:24,834 ^ 2021-07-12T08:16:24,834 ------------------------------------------------------------ 2021-07-12T08:16:24,834 gat/Engine.pyx:149:13: 'Position' is not a type identifier 2021-07-12T08:16:24,835 Error compiling Cython file: 2021-07-12T08:16:24,835 ------------------------------------------------------------ 2021-07-12T08:16:24,835 ... 2021-07-12T08:16:24,835 # note: could be made quicker by 2021-07-12T08:16:24,835 # - creating a sample random integers once, see numpy.random_integers? 2021-07-12T08:16:24,835 # - avoiding the binary search? 2021-07-12T08:16:24,835 cdef Position r, offset, pos 2021-07-12T08:16:24,836 cdef PositionDifference overlap 2021-07-12T08:16:24,836 ^ 2021-07-12T08:16:24,836 ------------------------------------------------------------ 2021-07-12T08:16:24,836 gat/Engine.pyx:150:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,842 Error compiling Cython file: 2021-07-12T08:16:24,842 ------------------------------------------------------------ 2021-07-12T08:16:24,842 ... 2021-07-12T08:16:24,842 cdef Position * cdf 2021-07-12T08:16:24,842 cdef Position total_size 2021-07-12T08:16:24,842 cdef Position nsegments 2021-07-12T08:16:24,842 def __init__(self, SegmentList segment_list): 2021-07-12T08:16:24,842 cdef Position i, totsize 2021-07-12T08:16:24,843 ^ 2021-07-12T08:16:24,843 ------------------------------------------------------------ 2021-07-12T08:16:24,843 gat/Engine.pyx:176:13: 'Position' is not a type identifier 2021-07-12T08:16:24,843 Error compiling Cython file: 2021-07-12T08:16:24,843 ------------------------------------------------------------ 2021-07-12T08:16:24,843 ... 2021-07-12T08:16:24,844 ''' 2021-07-12T08:16:24,844 # note: could be made quicker by 2021-07-12T08:16:24,844 # - creating a sample random integers once, see numpy.random_integers? 2021-07-12T08:16:24,844 # - avoiding the binary search? 2021-07-12T08:16:24,844 cdef Position rpos, rseg, offset, pos, start, end 2021-07-12T08:16:24,844 ^ 2021-07-12T08:16:24,844 ------------------------------------------------------------ 2021-07-12T08:16:24,844 gat/Engine.pyx:201:13: 'Position' is not a type identifier 2021-07-12T08:16:24,845 Error compiling Cython file: 2021-07-12T08:16:24,845 ------------------------------------------------------------ 2021-07-12T08:16:24,845 ... 2021-07-12T08:16:24,845 # note: could be made quicker by 2021-07-12T08:16:24,845 # - creating a sample random integers once, see numpy.random_integers? 2021-07-12T08:16:24,845 # - avoiding the binary search? 2021-07-12T08:16:24,845 cdef Position rpos, rseg, offset, pos, start, end 2021-07-12T08:16:24,846 cdef PositionDifference overlap 2021-07-12T08:16:24,846 ^ 2021-07-12T08:16:24,846 ------------------------------------------------------------ 2021-07-12T08:16:24,846 gat/Engine.pyx:202:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,851 Error compiling Cython file: 2021-07-12T08:16:24,851 ------------------------------------------------------------ 2021-07-12T08:16:24,852 ... 2021-07-12T08:16:24,852 cdef Position * cdf 2021-07-12T08:16:24,852 cdef Position total_size 2021-07-12T08:16:24,852 cdef int nsegments 2021-07-12T08:16:24,852 def __init__(self, SegmentList segment_list ): 2021-07-12T08:16:24,852 cdef Position i, totsize 2021-07-12T08:16:24,852 ^ 2021-07-12T08:16:24,853 ------------------------------------------------------------ 2021-07-12T08:16:24,853 gat/Engine.pyx:262:13: 'Position' is not a type identifier 2021-07-12T08:16:24,853 Error compiling Cython file: 2021-07-12T08:16:24,853 ------------------------------------------------------------ 2021-07-12T08:16:24,853 ... 2021-07-12T08:16:24,853 ''' 2021-07-12T08:16:24,854 # note: could be made quicker by 2021-07-12T08:16:24,854 # - creating a sample random integers once, see numpy.random_integers? 2021-07-12T08:16:24,854 # - avoiding the binary search? 2021-07-12T08:16:24,854 cdef Position start, end 2021-07-12T08:16:24,854 ^ 2021-07-12T08:16:24,854 ------------------------------------------------------------ 2021-07-12T08:16:24,854 gat/Engine.pyx:290:13: 'Position' is not a type identifier 2021-07-12T08:16:24,855 Error compiling Cython file: 2021-07-12T08:16:24,855 ------------------------------------------------------------ 2021-07-12T08:16:24,855 ... 2021-07-12T08:16:24,855 # note: could be made quicker by 2021-07-12T08:16:24,855 # - creating a sample random integers once, see numpy.random_integers? 2021-07-12T08:16:24,855 # - avoiding the binary search? 2021-07-12T08:16:24,855 cdef Position start, end 2021-07-12T08:16:24,855 cdef PositionDifference overlap 2021-07-12T08:16:24,856 ^ 2021-07-12T08:16:24,856 ------------------------------------------------------------ 2021-07-12T08:16:24,856 gat/Engine.pyx:291:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,856 Error compiling Cython file: 2021-07-12T08:16:24,856 ------------------------------------------------------------ 2021-07-12T08:16:24,856 ... 2021-07-12T08:16:24,856 # - creating a sample random integers once, see numpy.random_integers? 2021-07-12T08:16:24,857 # - avoiding the binary search? 2021-07-12T08:16:24,857 cdef Position start, end 2021-07-12T08:16:24,857 cdef PositionDifference overlap 2021-07-12T08:16:24,857 cdef size_t segment_index 2021-07-12T08:16:24,857 cdef Segment chosen_segment 2021-07-12T08:16:24,857 ^ 2021-07-12T08:16:24,857 ------------------------------------------------------------ 2021-07-12T08:16:24,857 gat/Engine.pyx:293:13: 'Segment' is not a type identifier 2021-07-12T08:16:24,858 Error compiling Cython file: 2021-07-12T08:16:24,858 ------------------------------------------------------------ 2021-07-12T08:16:24,858 ... 2021-07-12T08:16:24,858 cdef Position start, end 2021-07-12T08:16:24,858 cdef PositionDifference overlap 2021-07-12T08:16:24,858 cdef size_t segment_index 2021-07-12T08:16:24,858 cdef Segment chosen_segment 2021-07-12T08:16:24,858 cdef Position random_pos_in_workspace 2021-07-12T08:16:24,859 ^ 2021-07-12T08:16:24,859 ------------------------------------------------------------ 2021-07-12T08:16:24,859 gat/Engine.pyx:295:13: 'Position' is not a type identifier 2021-07-12T08:16:24,862 Error compiling Cython file: 2021-07-12T08:16:24,863 ------------------------------------------------------------ 2021-07-12T08:16:24,863 ... 2021-07-12T08:16:24,863 self.bucket_size = bucket_size 2021-07-12T08:16:24,863 cpdef Position sample( self ): 2021-07-12T08:16:24,863 '''return a new position within segment list.''' 2021-07-12T08:16:24,863 cdef Position base, ip 2021-07-12T08:16:24,864 ^ 2021-07-12T08:16:24,864 ------------------------------------------------------------ 2021-07-12T08:16:24,864 gat/Engine.pyx:373:13: 'Position' is not a type identifier 2021-07-12T08:16:24,864 Error compiling Cython file: 2021-07-12T08:16:24,864 ------------------------------------------------------------ 2021-07-12T08:16:24,864 ... 2021-07-12T08:16:24,864 cpdef Position sample( self ): 2021-07-12T08:16:24,865 '''return a new position within segment list.''' 2021-07-12T08:16:24,865 cdef Position base, ip 2021-07-12T08:16:24,865 cdef double r 2021-07-12T08:16:24,865 cdef Position bucket_size 2021-07-12T08:16:24,865 ^ 2021-07-12T08:16:24,865 ------------------------------------------------------------ 2021-07-12T08:16:24,865 gat/Engine.pyx:375:13: 'Position' is not a type identifier 2021-07-12T08:16:24,870 Error compiling Cython file: 2021-07-12T08:16:24,870 ------------------------------------------------------------ 2021-07-12T08:16:24,871 ... 2021-07-12T08:16:24,871 @cython.boundscheck(False) 2021-07-12T08:16:24,871 def __init__(self, 2021-07-12T08:16:24,871 numpy.ndarray[DTYPE_INT_t, ndim=1] histogram, 2021-07-12T08:16:24,871 Position bucket_size ): 2021-07-12T08:16:24,871 cdef Position i 2021-07-12T08:16:24,871 ^ 2021-07-12T08:16:24,871 ------------------------------------------------------------ 2021-07-12T08:16:24,872 gat/Engine.pyx:398:13: 'Position' is not a type identifier 2021-07-12T08:16:24,872 Error compiling Cython file: 2021-07-12T08:16:24,872 ------------------------------------------------------------ 2021-07-12T08:16:24,872 ... 2021-07-12T08:16:24,872 self.bucket_size = bucket_size 2021-07-12T08:16:24,872 cpdef Position sample( self ): 2021-07-12T08:16:24,873 '''return a new position within segment list.''' 2021-07-12T08:16:24,873 cdef Position base, index, r 2021-07-12T08:16:24,873 ^ 2021-07-12T08:16:24,873 ------------------------------------------------------------ 2021-07-12T08:16:24,873 gat/Engine.pyx:416:13: 'Position' is not a type identifier 2021-07-12T08:16:24,907 Error compiling Cython file: 2021-07-12T08:16:24,907 ------------------------------------------------------------ 2021-07-12T08:16:24,907 ... 2021-07-12T08:16:24,908 cpdef SegmentList sample(self, 2021-07-12T08:16:24,908 SegmentList segments, 2021-07-12T08:16:24,908 SegmentList workspace): 2021-07-12T08:16:24,908 '''return a sampled list of segments.''' 2021-07-12T08:16:24,908 cdef PositionDifference remaining 2021-07-12T08:16:24,908 ^ 2021-07-12T08:16:24,908 ------------------------------------------------------------ 2021-07-12T08:16:24,909 gat/Engine.pyx:520:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,909 Error compiling Cython file: 2021-07-12T08:16:24,909 ------------------------------------------------------------ 2021-07-12T08:16:24,909 ... 2021-07-12T08:16:24,909 SegmentList segments, 2021-07-12T08:16:24,909 SegmentList workspace): 2021-07-12T08:16:24,909 '''return a sampled list of segments.''' 2021-07-12T08:16:24,910 cdef PositionDifference remaining 2021-07-12T08:16:24,910 cdef PositionDifference true_remaining 2021-07-12T08:16:24,910 ^ 2021-07-12T08:16:24,910 ------------------------------------------------------------ 2021-07-12T08:16:24,910 gat/Engine.pyx:521:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,910 Error compiling Cython file: 2021-07-12T08:16:24,910 ------------------------------------------------------------ 2021-07-12T08:16:24,911 ... 2021-07-12T08:16:24,911 SegmentList workspace): 2021-07-12T08:16:24,911 '''return a sampled list of segments.''' 2021-07-12T08:16:24,911 cdef PositionDifference remaining 2021-07-12T08:16:24,911 cdef PositionDifference true_remaining 2021-07-12T08:16:24,911 cdef PositionDifference overlap, ltotal, length 2021-07-12T08:16:24,911 ^ 2021-07-12T08:16:24,911 ------------------------------------------------------------ 2021-07-12T08:16:24,912 gat/Engine.pyx:522:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,912 Error compiling Cython file: 2021-07-12T08:16:24,912 ------------------------------------------------------------ 2021-07-12T08:16:24,912 ... 2021-07-12T08:16:24,912 cdef PositionDifference true_remaining 2021-07-12T08:16:24,912 cdef PositionDifference overlap, ltotal, length 2021-07-12T08:16:24,913 cdef int nunsuccessful_rounds 2021-07-12T08:16:24,913 cdef int max_unsuccessful_rounds 2021-07-12T08:16:24,913 cdef Position start, end 2021-07-12T08:16:24,913 ^ 2021-07-12T08:16:24,913 ------------------------------------------------------------ 2021-07-12T08:16:24,913 gat/Engine.pyx:526:13: 'Position' is not a type identifier 2021-07-12T08:16:24,914 Error compiling Cython file: 2021-07-12T08:16:24,914 ------------------------------------------------------------ 2021-07-12T08:16:24,914 ... 2021-07-12T08:16:24,914 cdef PositionDifference overlap, ltotal, length 2021-07-12T08:16:24,914 cdef int nunsuccessful_rounds 2021-07-12T08:16:24,914 cdef int max_unsuccessful_rounds 2021-07-12T08:16:24,914 cdef Position start, end 2021-07-12T08:16:24,914 cdef Segment segment, sampled_segment 2021-07-12T08:16:24,914 ^ 2021-07-12T08:16:24,915 ------------------------------------------------------------ 2021-07-12T08:16:24,915 gat/Engine.pyx:527:13: 'Segment' is not a type identifier 2021-07-12T08:16:24,915 Error compiling Cython file: 2021-07-12T08:16:24,915 ------------------------------------------------------------ 2021-07-12T08:16:24,915 ... 2021-07-12T08:16:24,915 cdef int nunsuccessful_rounds 2021-07-12T08:16:24,916 cdef int max_unsuccessful_rounds 2021-07-12T08:16:24,916 cdef Position start, end 2021-07-12T08:16:24,916 cdef Segment segment, sampled_segment 2021-07-12T08:16:24,916 cdef SegmentList sampled_segments 2021-07-12T08:16:24,916 ^ 2021-07-12T08:16:24,916 ------------------------------------------------------------ 2021-07-12T08:16:24,916 gat/Engine.pyx:528:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,916 Error compiling Cython file: 2021-07-12T08:16:24,917 ------------------------------------------------------------ 2021-07-12T08:16:24,917 ... 2021-07-12T08:16:24,917 cdef int nunsuccessful_rounds 2021-07-12T08:16:24,917 cdef int max_unsuccessful_rounds 2021-07-12T08:16:24,917 cdef Position start, end 2021-07-12T08:16:24,917 cdef Segment segment, sampled_segment 2021-07-12T08:16:24,917 cdef SegmentList sampled_segments 2021-07-12T08:16:24,917 cdef SegmentList unintersected_segments 2021-07-12T08:16:24,917 ^ 2021-07-12T08:16:24,918 ------------------------------------------------------------ 2021-07-12T08:16:24,918 gat/Engine.pyx:529:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,918 Error compiling Cython file: 2021-07-12T08:16:24,918 ------------------------------------------------------------ 2021-07-12T08:16:24,918 ... 2021-07-12T08:16:24,918 cdef int max_unsuccessful_rounds 2021-07-12T08:16:24,918 cdef Position start, end 2021-07-12T08:16:24,919 cdef Segment segment, sampled_segment 2021-07-12T08:16:24,919 cdef SegmentList sampled_segments 2021-07-12T08:16:24,919 cdef SegmentList unintersected_segments 2021-07-12T08:16:24,919 cdef SegmentList intersected_segments 2021-07-12T08:16:24,919 ^ 2021-07-12T08:16:24,919 ------------------------------------------------------------ 2021-07-12T08:16:24,919 gat/Engine.pyx:530:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,920 Error compiling Cython file: 2021-07-12T08:16:24,920 ------------------------------------------------------------ 2021-07-12T08:16:24,920 ... 2021-07-12T08:16:24,920 cdef Position start, end 2021-07-12T08:16:24,920 cdef Segment segment, sampled_segment 2021-07-12T08:16:24,920 cdef SegmentList sampled_segments 2021-07-12T08:16:24,920 cdef SegmentList unintersected_segments 2021-07-12T08:16:24,920 cdef SegmentList intersected_segments 2021-07-12T08:16:24,920 cdef SegmentList working_segments 2021-07-12T08:16:24,920 ^ 2021-07-12T08:16:24,921 ------------------------------------------------------------ 2021-07-12T08:16:24,921 gat/Engine.pyx:531:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,921 Error compiling Cython file: 2021-07-12T08:16:24,921 ------------------------------------------------------------ 2021-07-12T08:16:24,921 ... 2021-07-12T08:16:24,921 cdef Segment segment, sampled_segment 2021-07-12T08:16:24,921 cdef SegmentList sampled_segments 2021-07-12T08:16:24,922 cdef SegmentList unintersected_segments 2021-07-12T08:16:24,922 cdef SegmentList intersected_segments 2021-07-12T08:16:24,922 cdef SegmentList working_segments 2021-07-12T08:16:24,922 cdef SegmentList tmp_segments 2021-07-12T08:16:24,922 ^ 2021-07-12T08:16:24,922 ------------------------------------------------------------ 2021-07-12T08:16:24,922 gat/Engine.pyx:532:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,923 Error compiling Cython file: 2021-07-12T08:16:24,923 ------------------------------------------------------------ 2021-07-12T08:16:24,923 ... 2021-07-12T08:16:24,923 cpdef SegmentList sample( self, 2021-07-12T08:16:24,923 SegmentList segments, 2021-07-12T08:16:24,923 SegmentList workspace ): 2021-07-12T08:16:24,923 '''return a sampled list of segments.''' 2021-07-12T08:16:24,923 cdef Position length 2021-07-12T08:16:24,924 ^ 2021-07-12T08:16:24,924 ------------------------------------------------------------ 2021-07-12T08:16:24,924 gat/Engine.pyx:702:13: 'Position' is not a type identifier 2021-07-12T08:16:24,924 Error compiling Cython file: 2021-07-12T08:16:24,924 ------------------------------------------------------------ 2021-07-12T08:16:24,924 ... 2021-07-12T08:16:24,924 SegmentList workspace ): 2021-07-12T08:16:24,925 '''return a sampled list of segments.''' 2021-07-12T08:16:24,925 cdef Position length 2021-07-12T08:16:24,925 cdef SegmentListSampler sls 2021-07-12T08:16:24,925 cdef SegmentList sample 2021-07-12T08:16:24,925 ^ 2021-07-12T08:16:24,925 ------------------------------------------------------------ 2021-07-12T08:16:24,925 gat/Engine.pyx:704:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,926 Error compiling Cython file: 2021-07-12T08:16:24,926 ------------------------------------------------------------ 2021-07-12T08:16:24,926 ... 2021-07-12T08:16:24,926 cpdef SegmentList sample(self, 2021-07-12T08:16:24,926 SegmentList segments, 2021-07-12T08:16:24,926 SegmentList workspace): 2021-07-12T08:16:24,926 '''return a sampled list of segments.''' 2021-07-12T08:16:24,927 cdef Position start, end, length 2021-07-12T08:16:24,927 ^ 2021-07-12T08:16:24,927 ------------------------------------------------------------ 2021-07-12T08:16:24,927 gat/Engine.pyx:798:13: 'Position' is not a type identifier 2021-07-12T08:16:24,927 Error compiling Cython file: 2021-07-12T08:16:24,927 ------------------------------------------------------------ 2021-07-12T08:16:24,927 ... 2021-07-12T08:16:24,928 SegmentList workspace): 2021-07-12T08:16:24,928 '''return a sampled list of segments.''' 2021-07-12T08:16:24,928 cdef Position start, end, length 2021-07-12T08:16:24,928 cdef SegmentListSampler sls 2021-07-12T08:16:24,928 cdef SegmentList sample 2021-07-12T08:16:24,928 ^ 2021-07-12T08:16:24,928 ------------------------------------------------------------ 2021-07-12T08:16:24,928 gat/Engine.pyx:800:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,929 Error compiling Cython file: 2021-07-12T08:16:24,929 ------------------------------------------------------------ 2021-07-12T08:16:24,929 ... 2021-07-12T08:16:24,929 # create segment sampler 2021-07-12T08:16:24,929 sls = SegmentListSampler(workspace) 2021-07-12T08:16:24,929 cdef int ntries_outer = self.ntries_outer 2021-07-12T08:16:24,929 cdef int ntries_inner 2021-07-12T08:16:24,930 cdef PositionDifference remaining, overlap 2021-07-12T08:16:24,930 ^ 2021-07-12T08:16:24,930 ------------------------------------------------------------ 2021-07-12T08:16:24,930 gat/Engine.pyx:824:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,930 Error compiling Cython file: 2021-07-12T08:16:24,930 ------------------------------------------------------------ 2021-07-12T08:16:24,930 ... 2021-07-12T08:16:24,931 SegmentList segments, 2021-07-12T08:16:24,931 SegmentList workspace ): 2021-07-12T08:16:24,931 '''return a sampled list of segments.''' 2021-07-12T08:16:24,931 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,931 cdef SegmentList sample 2021-07-12T08:16:24,931 ^ 2021-07-12T08:16:24,931 ------------------------------------------------------------ 2021-07-12T08:16:24,932 gat/Engine.pyx:933:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,932 Error compiling Cython file: 2021-07-12T08:16:24,932 ------------------------------------------------------------ 2021-07-12T08:16:24,932 ... 2021-07-12T08:16:24,932 '''return a sampled list of segments.''' 2021-07-12T08:16:24,932 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,932 cdef SegmentList sample 2021-07-12T08:16:24,933 cdef SegmentListSampler sls 2021-07-12T08:16:24,933 cdef Position increment = self.increment 2021-07-12T08:16:24,933 ^ 2021-07-12T08:16:24,933 ------------------------------------------------------------ 2021-07-12T08:16:24,933 gat/Engine.pyx:935:13: 'Position' is not a type identifier 2021-07-12T08:16:24,933 Error compiling Cython file: 2021-07-12T08:16:24,933 ------------------------------------------------------------ 2021-07-12T08:16:24,934 ... 2021-07-12T08:16:24,934 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,934 cdef SegmentList sample 2021-07-12T08:16:24,934 cdef SegmentListSampler sls 2021-07-12T08:16:24,934 cdef Position increment = self.increment 2021-07-12T08:16:24,934 cdef Position start, end, x, length, i, added, nsegments, nworkspaces 2021-07-12T08:16:24,934 ^ 2021-07-12T08:16:24,935 ------------------------------------------------------------ 2021-07-12T08:16:24,935 gat/Engine.pyx:936:13: 'Position' is not a type identifier 2021-07-12T08:16:24,935 Error compiling Cython file: 2021-07-12T08:16:24,935 ------------------------------------------------------------ 2021-07-12T08:16:24,935 ... 2021-07-12T08:16:24,935 cdef SegmentList sample 2021-07-12T08:16:24,936 cdef SegmentListSampler sls 2021-07-12T08:16:24,936 cdef Position increment = self.increment 2021-07-12T08:16:24,936 cdef Position start, end, x, length, i, added, nsegments, nworkspaces 2021-07-12T08:16:24,936 cdef Position current_offset, current_workspace 2021-07-12T08:16:24,936 ^ 2021-07-12T08:16:24,936 ------------------------------------------------------------ 2021-07-12T08:16:24,936 gat/Engine.pyx:937:13: 'Position' is not a type identifier 2021-07-12T08:16:24,937 Error compiling Cython file: 2021-07-12T08:16:24,937 ------------------------------------------------------------ 2021-07-12T08:16:24,937 ... 2021-07-12T08:16:24,937 returns: a list of sampled segments. 2021-07-12T08:16:24,937 ''' 2021-07-12T08:16:24,937 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,938 cdef Segment segment 2021-07-12T08:16:24,938 ^ 2021-07-12T08:16:24,938 ------------------------------------------------------------ 2021-07-12T08:16:24,938 gat/Engine.pyx:1046:13: 'Segment' is not a type identifier 2021-07-12T08:16:24,938 Error compiling Cython file: 2021-07-12T08:16:24,938 ------------------------------------------------------------ 2021-07-12T08:16:24,938 ... 2021-07-12T08:16:24,939 ''' 2021-07-12T08:16:24,939 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,939 cdef Segment segment 2021-07-12T08:16:24,939 cdef SegmentList sample, working_segments 2021-07-12T08:16:24,939 ^ 2021-07-12T08:16:24,939 ------------------------------------------------------------ 2021-07-12T08:16:24,939 gat/Engine.pyx:1047:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,940 Error compiling Cython file: 2021-07-12T08:16:24,940 ------------------------------------------------------------ 2021-07-12T08:16:24,940 ... 2021-07-12T08:16:24,940 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,940 cdef Segment segment 2021-07-12T08:16:24,940 cdef SegmentList sample, working_segments 2021-07-12T08:16:24,941 cdef Position length, direction, extended_length 2021-07-12T08:16:24,941 ^ 2021-07-12T08:16:24,941 ------------------------------------------------------------ 2021-07-12T08:16:24,941 gat/Engine.pyx:1048:13: 'Position' is not a type identifier 2021-07-12T08:16:24,941 Error compiling Cython file: 2021-07-12T08:16:24,941 ------------------------------------------------------------ 2021-07-12T08:16:24,941 ... 2021-07-12T08:16:24,942 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,942 cdef Segment segment 2021-07-12T08:16:24,942 cdef SegmentList sample, working_segments 2021-07-12T08:16:24,942 cdef Position length, direction, extended_length 2021-07-12T08:16:24,942 cdef Position x, midpoint 2021-07-12T08:16:24,942 ^ 2021-07-12T08:16:24,942 ------------------------------------------------------------ 2021-07-12T08:16:24,943 gat/Engine.pyx:1049:13: 'Position' is not a type identifier 2021-07-12T08:16:24,943 Error compiling Cython file: 2021-07-12T08:16:24,943 ------------------------------------------------------------ 2021-07-12T08:16:24,943 ... 2021-07-12T08:16:24,943 cdef Segment segment 2021-07-12T08:16:24,943 cdef SegmentList sample, working_segments 2021-07-12T08:16:24,943 cdef Position length, direction, extended_length 2021-07-12T08:16:24,944 cdef Position x, midpoint 2021-07-12T08:16:24,944 cdef PositionDifference shift, start, end, ws_start, ws_end, shift_area 2021-07-12T08:16:24,944 ^ 2021-07-12T08:16:24,944 ------------------------------------------------------------ 2021-07-12T08:16:24,944 gat/Engine.pyx:1050:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,944 Error compiling Cython file: 2021-07-12T08:16:24,944 ------------------------------------------------------------ 2021-07-12T08:16:24,945 ... 2021-07-12T08:16:24,945 cdef Segment segment 2021-07-12T08:16:24,945 cdef SegmentList sample, working_segments 2021-07-12T08:16:24,945 cdef Position length, direction, extended_length 2021-07-12T08:16:24,945 cdef Position x, midpoint 2021-07-12T08:16:24,945 cdef PositionDifference shift, start, end, ws_start, ws_end, shift_area 2021-07-12T08:16:24,945 cdef PositionDifference remainder, remainder_left, remainder_right 2021-07-12T08:16:24,945 ^ 2021-07-12T08:16:24,945 ------------------------------------------------------------ 2021-07-12T08:16:24,946 gat/Engine.pyx:1051:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,946 Error compiling Cython file: 2021-07-12T08:16:24,946 ------------------------------------------------------------ 2021-07-12T08:16:24,946 ... 2021-07-12T08:16:24,946 cdef Position length, direction, extended_length 2021-07-12T08:16:24,946 cdef Position x, midpoint 2021-07-12T08:16:24,946 cdef PositionDifference shift, start, end, ws_start, ws_end, shift_area 2021-07-12T08:16:24,946 cdef PositionDifference remainder, remainder_left, remainder_right 2021-07-12T08:16:24,947 cdef double half_radius = self.radius / 2 2021-07-12T08:16:24,947 cdef PositionDifference half_extension = self.extension // 2 2021-07-12T08:16:24,947 ^ 2021-07-12T08:16:24,947 ------------------------------------------------------------ 2021-07-12T08:16:24,947 gat/Engine.pyx:1053:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,947 Error compiling Cython file: 2021-07-12T08:16:24,947 ------------------------------------------------------------ 2021-07-12T08:16:24,948 ... 2021-07-12T08:16:24,948 cdef Position x, midpoint 2021-07-12T08:16:24,948 cdef PositionDifference shift, start, end, ws_start, ws_end, shift_area 2021-07-12T08:16:24,948 cdef PositionDifference remainder, remainder_left, remainder_right 2021-07-12T08:16:24,948 cdef double half_radius = self.radius / 2 2021-07-12T08:16:24,948 cdef PositionDifference half_extension = self.extension // 2 2021-07-12T08:16:24,948 cdef Segment * _working_segments 2021-07-12T08:16:24,948 ^ 2021-07-12T08:16:24,948 ------------------------------------------------------------ 2021-07-12T08:16:24,949 gat/Engine.pyx:1054:13: 'Segment' is not a type identifier 2021-07-12T08:16:24,949 Error compiling Cython file: 2021-07-12T08:16:24,949 ------------------------------------------------------------ 2021-07-12T08:16:24,949 ... 2021-07-12T08:16:24,949 cdef PositionDifference shift, start, end, ws_start, ws_end, shift_area 2021-07-12T08:16:24,949 cdef PositionDifference remainder, remainder_left, remainder_right 2021-07-12T08:16:24,949 cdef double half_radius = self.radius / 2 2021-07-12T08:16:24,950 cdef PositionDifference half_extension = self.extension // 2 2021-07-12T08:16:24,950 cdef Segment * _working_segments 2021-07-12T08:16:24,950 cdef SegmentList ws 2021-07-12T08:16:24,950 ^ 2021-07-12T08:16:24,950 ------------------------------------------------------------ 2021-07-12T08:16:24,950 gat/Engine.pyx:1055:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,950 Error compiling Cython file: 2021-07-12T08:16:24,951 ------------------------------------------------------------ 2021-07-12T08:16:24,951 ... 2021-07-12T08:16:24,951 returns: a list of sampled segments. 2021-07-12T08:16:24,951 ''' 2021-07-12T08:16:24,951 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,951 cdef Segment segment 2021-07-12T08:16:24,951 ^ 2021-07-12T08:16:24,952 ------------------------------------------------------------ 2021-07-12T08:16:24,952 gat/Engine.pyx:1166:13: 'Segment' is not a type identifier 2021-07-12T08:16:24,952 Error compiling Cython file: 2021-07-12T08:16:24,952 ------------------------------------------------------------ 2021-07-12T08:16:24,952 ... 2021-07-12T08:16:24,952 ''' 2021-07-12T08:16:24,953 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,953 cdef Segment segment 2021-07-12T08:16:24,953 cdef SegmentList working_segments 2021-07-12T08:16:24,953 ^ 2021-07-12T08:16:24,953 ------------------------------------------------------------ 2021-07-12T08:16:24,953 gat/Engine.pyx:1167:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,954 Error compiling Cython file: 2021-07-12T08:16:24,954 ------------------------------------------------------------ 2021-07-12T08:16:24,954 ... 2021-07-12T08:16:24,954 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,954 cdef Segment segment 2021-07-12T08:16:24,954 cdef SegmentList working_segments 2021-07-12T08:16:24,954 cdef PositionDifference work_start, work_end, start, end, last 2021-07-12T08:16:24,955 ^ 2021-07-12T08:16:24,955 ------------------------------------------------------------ 2021-07-12T08:16:24,955 gat/Engine.pyx:1168:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,955 Error compiling Cython file: 2021-07-12T08:16:24,955 ------------------------------------------------------------ 2021-07-12T08:16:24,955 ... 2021-07-12T08:16:24,955 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,956 cdef Segment segment 2021-07-12T08:16:24,956 cdef SegmentList working_segments 2021-07-12T08:16:24,956 cdef PositionDifference work_start, work_end, start, end, last 2021-07-12T08:16:24,956 cdef PositionDifference total_length, free_length 2021-07-12T08:16:24,956 ^ 2021-07-12T08:16:24,956 ------------------------------------------------------------ 2021-07-12T08:16:24,956 gat/Engine.pyx:1169:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,957 Error compiling Cython file: 2021-07-12T08:16:24,957 ------------------------------------------------------------ 2021-07-12T08:16:24,957 ... 2021-07-12T08:16:24,957 cdef Segment segment 2021-07-12T08:16:24,957 cdef SegmentList working_segments 2021-07-12T08:16:24,957 cdef PositionDifference work_start, work_end, start, end, last 2021-07-12T08:16:24,957 cdef PositionDifference total_length, free_length 2021-07-12T08:16:24,957 cdef Segment* _working_segments 2021-07-12T08:16:24,958 ^ 2021-07-12T08:16:24,958 ------------------------------------------------------------ 2021-07-12T08:16:24,958 gat/Engine.pyx:1170:13: 'Segment' is not a type identifier 2021-07-12T08:16:24,958 Error compiling Cython file: 2021-07-12T08:16:24,958 ------------------------------------------------------------ 2021-07-12T08:16:24,958 ... 2021-07-12T08:16:24,958 cdef Segment segment 2021-07-12T08:16:24,958 cdef SegmentList working_segments 2021-07-12T08:16:24,959 cdef PositionDifference work_start, work_end, start, end, last 2021-07-12T08:16:24,959 cdef PositionDifference total_length, free_length 2021-07-12T08:16:24,959 cdef Segment* _working_segments 2021-07-12T08:16:24,959 cdef PositionDifference shift 2021-07-12T08:16:24,959 ^ 2021-07-12T08:16:24,959 ------------------------------------------------------------ 2021-07-12T08:16:24,959 gat/Engine.pyx:1171:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,960 Error compiling Cython file: 2021-07-12T08:16:24,960 ------------------------------------------------------------ 2021-07-12T08:16:24,960 ... 2021-07-12T08:16:24,960 cdef SegmentList working_segments 2021-07-12T08:16:24,960 cdef PositionDifference work_start, work_end, start, end, last 2021-07-12T08:16:24,960 cdef PositionDifference total_length, free_length 2021-07-12T08:16:24,960 cdef Segment* _working_segments 2021-07-12T08:16:24,960 cdef PositionDifference shift 2021-07-12T08:16:24,960 cdef SegmentList sample = SegmentList() 2021-07-12T08:16:24,961 ^ 2021-07-12T08:16:24,961 ------------------------------------------------------------ 2021-07-12T08:16:24,961 gat/Engine.pyx:1172:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,965 Error compiling Cython file: 2021-07-12T08:16:24,965 ------------------------------------------------------------ 2021-07-12T08:16:24,965 ... 2021-07-12T08:16:24,965 returns: a list of sampled segments. 2021-07-12T08:16:24,965 ''' 2021-07-12T08:16:24,966 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,966 cdef Segment segment 2021-07-12T08:16:24,966 ^ 2021-07-12T08:16:24,966 ------------------------------------------------------------ 2021-07-12T08:16:24,966 gat/Engine.pyx:1281:13: 'Segment' is not a type identifier 2021-07-12T08:16:24,967 Error compiling Cython file: 2021-07-12T08:16:24,967 ------------------------------------------------------------ 2021-07-12T08:16:24,967 ... 2021-07-12T08:16:24,967 ''' 2021-07-12T08:16:24,967 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,967 cdef Segment segment 2021-07-12T08:16:24,967 cdef SegmentList working_segments, working_workspace 2021-07-12T08:16:24,968 ^ 2021-07-12T08:16:24,968 ------------------------------------------------------------ 2021-07-12T08:16:24,968 gat/Engine.pyx:1282:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,968 Error compiling Cython file: 2021-07-12T08:16:24,968 ------------------------------------------------------------ 2021-07-12T08:16:24,968 ... 2021-07-12T08:16:24,969 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,969 cdef Segment segment 2021-07-12T08:16:24,969 cdef SegmentList working_segments, working_workspace 2021-07-12T08:16:24,969 cdef PositionDifference work_start, work_end, start, end, last_end 2021-07-12T08:16:24,969 ^ 2021-07-12T08:16:24,969 ------------------------------------------------------------ 2021-07-12T08:16:24,969 gat/Engine.pyx:1283:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,970 Error compiling Cython file: 2021-07-12T08:16:24,970 ------------------------------------------------------------ 2021-07-12T08:16:24,970 ... 2021-07-12T08:16:24,970 assert workspace.isNormalized, "workspace is not normalized" 2021-07-12T08:16:24,970 cdef Segment segment 2021-07-12T08:16:24,970 cdef SegmentList working_segments, working_workspace 2021-07-12T08:16:24,970 cdef PositionDifference work_start, work_end, start, end, last_end 2021-07-12T08:16:24,970 cdef PositionDifference total_length, free_length 2021-07-12T08:16:24,971 ^ 2021-07-12T08:16:24,971 ------------------------------------------------------------ 2021-07-12T08:16:24,971 gat/Engine.pyx:1284:13: 'PositionDifference' is not a type identifier 2021-07-12T08:16:24,971 Error compiling Cython file: 2021-07-12T08:16:24,971 ------------------------------------------------------------ 2021-07-12T08:16:24,971 ... 2021-07-12T08:16:24,971 cdef Segment segment 2021-07-12T08:16:24,972 cdef SegmentList working_segments, working_workspace 2021-07-12T08:16:24,972 cdef PositionDifference work_start, work_end, start, end, last_end 2021-07-12T08:16:24,972 cdef PositionDifference total_length, free_length 2021-07-12T08:16:24,972 cdef SegmentList sample = SegmentList() 2021-07-12T08:16:24,972 ^ 2021-07-12T08:16:24,972 ------------------------------------------------------------ 2021-07-12T08:16:24,972 gat/Engine.pyx:1286:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:24,998 Error compiling Cython file: 2021-07-12T08:16:24,998 ------------------------------------------------------------ 2021-07-12T08:16:24,998 ... 2021-07-12T08:16:24,998 cpdef SegmentList sample( self, 2021-07-12T08:16:24,998 SegmentList segments, 2021-07-12T08:16:24,998 SegmentList workspace ): 2021-07-12T08:16:24,999 '''return a sampled list of segments.''' 2021-07-12T08:16:24,999 cdef SegmentList sample 2021-07-12T08:16:24,999 ^ 2021-07-12T08:16:24,999 ------------------------------------------------------------ 2021-07-12T08:16:24,999 gat/Engine.pyx:1403:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:25,085 Error compiling Cython file: 2021-07-12T08:16:25,085 ------------------------------------------------------------ 2021-07-12T08:16:25,085 ... 2021-07-12T08:16:25,085 SegmentList annotations, 2021-07-12T08:16:25,085 SegmentList workspace ): 2021-07-12T08:16:25,085 '''return number of nucleotides overlapping between segments and annotations. 2021-07-12T08:16:25,085 divided by the size of the workspace 2021-07-12T08:16:25,086 ''' 2021-07-12T08:16:25,086 cdef Position l 2021-07-12T08:16:25,086 ^ 2021-07-12T08:16:25,086 ------------------------------------------------------------ 2021-07-12T08:16:25,086 gat/Engine.pyx:1437:13: 'Position' is not a type identifier 2021-07-12T08:16:25,226 Error compiling Cython file: 2021-07-12T08:16:25,227 ------------------------------------------------------------ 2021-07-12T08:16:25,227 ... 2021-07-12T08:16:25,227 double mean): 2021-07-12T08:16:25,227 '''return a two-sided pvalue. 2021-07-12T08:16:25,227 Fast if val is small or large. 2021-07-12T08:16:25,227 ''' 2021-07-12T08:16:25,227 cdef Position l, x 2021-07-12T08:16:25,227 ^ 2021-07-12T08:16:25,228 ------------------------------------------------------------ 2021-07-12T08:16:25,228 gat/Engine.pyx:1507:9: 'Position' is not a type identifier 2021-07-12T08:16:25,229 Error compiling Cython file: 2021-07-12T08:16:25,229 ------------------------------------------------------------ 2021-07-12T08:16:25,230 ... 2021-07-12T08:16:25,230 cdef void compressSampleIndex( EnrichmentStatistics * stats ): 2021-07-12T08:16:25,230 '''compress indices in stats.''' 2021-07-12T08:16:25,230 cdef int x, refidx, observed_idx 2021-07-12T08:16:25,230 cdef double lastval, thisval 2021-07-12T08:16:25,230 cdef Position l 2021-07-12T08:16:25,230 ^ 2021-07-12T08:16:25,230 ------------------------------------------------------------ 2021-07-12T08:16:25,231 gat/Engine.pyx:1583:9: 'Position' is not a type identifier 2021-07-12T08:16:25,231 Error compiling Cython file: 2021-07-12T08:16:25,231 ------------------------------------------------------------ 2021-07-12T08:16:25,231 ... 2021-07-12T08:16:25,231 samples, 2021-07-12T08:16:25,231 reference, 2021-07-12T08:16:25,232 pseudo_count): 2021-07-12T08:16:25,232 cdef EnrichmentStatistics * stats 2021-07-12T08:16:25,232 cdef Position offset, i, l 2021-07-12T08:16:25,232 ^ 2021-07-12T08:16:25,232 ------------------------------------------------------------ 2021-07-12T08:16:25,232 gat/Engine.pyx:1641:9: 'Position' is not a type identifier 2021-07-12T08:16:25,238 Error compiling Cython file: 2021-07-12T08:16:25,238 ------------------------------------------------------------ 2021-07-12T08:16:25,238 ... 2021-07-12T08:16:25,238 property nsamples: 2021-07-12T08:16:25,239 def __get__(self): return self.stats.nsamples 2021-07-12T08:16:25,239 property samples: 2021-07-12T08:16:25,239 def __get__(self): 2021-07-12T08:16:25,239 cdef Position x 2021-07-12T08:16:25,239 ^ 2021-07-12T08:16:25,239 ------------------------------------------------------------ 2021-07-12T08:16:25,239 gat/Engine.pyx:1836:17: 'Position' is not a type identifier 2021-07-12T08:16:25,290 Error compiling Cython file: 2021-07-12T08:16:25,290 ------------------------------------------------------------ 2021-07-12T08:16:25,291 ... 2021-07-12T08:16:25,291 ignore_tracks : bool 2021-07-12T08:16:25,291 If True, ignore track information. There will only 2021-07-12T08:16:25,291 be a single track called "merged". 2021-07-12T08:16:25,291 ''' 2021-07-12T08:16:25,291 cdef SegmentList l 2021-07-12T08:16:25,291 ^ 2021-07-12T08:16:25,292 ------------------------------------------------------------ 2021-07-12T08:16:25,292 gat/Engine.pyx:2503:9: 'SegmentList' is not a type identifier 2021-07-12T08:16:25,292 Error compiling Cython file: 2021-07-12T08:16:25,292 ------------------------------------------------------------ 2021-07-12T08:16:25,292 ... 2021-07-12T08:16:25,292 be a single track called "merged". 2021-07-12T08:16:25,293 ''' 2021-07-12T08:16:25,293 cdef SegmentList l 2021-07-12T08:16:25,293 cdef BedProxy bed 2021-07-12T08:16:25,293 cdef Position lineno 2021-07-12T08:16:25,293 ^ 2021-07-12T08:16:25,293 ------------------------------------------------------------ 2021-07-12T08:16:25,293 gat/Engine.pyx:2505:9: 'Position' is not a type identifier 2021-07-12T08:16:25,306 Error compiling Cython file: 2021-07-12T08:16:25,306 ------------------------------------------------------------ 2021-07-12T08:16:25,306 ... 2021-07-12T08:16:25,306 if mm == -1: 2021-07-12T08:16:25,307 raise ValueError("could not create memory mapped file") 2021-07-12T08:16:25,307 # copy all segment lists to shared memory 2021-07-12T08:16:25,307 cdef off_t offset = 0 2021-07-12T08:16:25,307 cdef CoordinateList clist 2021-07-12T08:16:25,307 ^ 2021-07-12T08:16:25,307 ------------------------------------------------------------ 2021-07-12T08:16:25,307 gat/Engine.pyx:2640:13: 'CoordinateList' is not a type identifier 2021-07-12T08:16:25,308 Error compiling Cython file: 2021-07-12T08:16:25,308 ------------------------------------------------------------ 2021-07-12T08:16:25,308 ... 2021-07-12T08:16:25,308 offset = clist.toMMAP(mm, fd, offset) 2021-07-12T08:16:25,308 def __dealloc__(self): 2021-07-12T08:16:25,308 cdef int error 2021-07-12T08:16:25,309 cdef CoordinateList clist 2021-07-12T08:16:25,309 ^ 2021-07-12T08:16:25,309 ------------------------------------------------------------ 2021-07-12T08:16:25,309 gat/Engine.pyx:2647:13: 'CoordinateList' is not a type identifier 2021-07-12T08:16:25,309 Error compiling Cython file: 2021-07-12T08:16:25,309 ------------------------------------------------------------ 2021-07-12T08:16:25,310 ... 2021-07-12T08:16:25,310 E.debug("IntervalCollection.__dealloc__(): freeing shared memory " 2021-07-12T08:16:25,310 "at %s" % self.shared_fn) 2021-07-12T08:16:25,310 def unshare(self): 2021-07-12T08:16:25,310 '''revert sharing.''' 2021-07-12T08:16:25,310 cdef CoordinateList clist 2021-07-12T08:16:25,310 ^ 2021-07-12T08:16:25,310 ------------------------------------------------------------ 2021-07-12T08:16:25,311 gat/Engine.pyx:2677:13: 'CoordinateList' is not a type identifier 2021-07-12T08:16:25,311 Error compiling Cython file: 2021-07-12T08:16:25,311 ------------------------------------------------------------ 2021-07-12T08:16:25,311 ... 2021-07-12T08:16:25,311 for segmentlist in self.getSegmentLists(): 2021-07-12T08:16:25,311 segmentlist.sort() 2021-07-12T08:16:25,312 def extend(self, extension): 2021-07-12T08:16:25,312 '''extend each interval by a certain amount.''' 2021-07-12T08:16:25,312 cdef SegmentList segmentlist 2021-07-12T08:16:25,312 ^ 2021-07-12T08:16:25,312 ------------------------------------------------------------ 2021-07-12T08:16:25,312 gat/Engine.pyx:2722:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:25,313 Error compiling Cython file: 2021-07-12T08:16:25,313 ------------------------------------------------------------ 2021-07-12T08:16:25,313 ... 2021-07-12T08:16:25,313 for segmentlist in self.getSegmentLists(): 2021-07-12T08:16:25,313 segmentlist.extend_segments(extension) 2021-07-12T08:16:25,313 def expand(self, expansion): 2021-07-12T08:16:25,313 '''expand each interval by a certain amount.''' 2021-07-12T08:16:25,313 cdef SegmentList segmentlist 2021-07-12T08:16:25,314 ^ 2021-07-12T08:16:25,314 ------------------------------------------------------------ 2021-07-12T08:16:25,314 gat/Engine.pyx:2728:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:25,355 Error compiling Cython file: 2021-07-12T08:16:25,355 ------------------------------------------------------------ 2021-07-12T08:16:25,356 ... 2021-07-12T08:16:25,356 def outputStats(self, outfile): 2021-07-12T08:16:25,356 '''output segment statistics.''' 2021-07-12T08:16:25,356 outfile.write( "section\ttrack\tcontig\tnsegments\tlength\n" ) 2021-07-12T08:16:25,356 cdef Position total_length = 0 2021-07-12T08:16:25,356 ^ 2021-07-12T08:16:25,356 ------------------------------------------------------------ 2021-07-12T08:16:25,357 gat/Engine.pyx:2953:13: 'Position' is not a type identifier 2021-07-12T08:16:25,357 Error compiling Cython file: 2021-07-12T08:16:25,357 ------------------------------------------------------------ 2021-07-12T08:16:25,357 ... 2021-07-12T08:16:25,357 '''output segment statistics.''' 2021-07-12T08:16:25,358 outfile.write( "section\ttrack\tcontig\tnsegments\tlength\n" ) 2021-07-12T08:16:25,358 cdef Position total_length = 0 2021-07-12T08:16:25,358 cdef Position total_segments = 0 2021-07-12T08:16:25,358 ^ 2021-07-12T08:16:25,358 ------------------------------------------------------------ 2021-07-12T08:16:25,358 gat/Engine.pyx:2954:13: 'Position' is not a type identifier 2021-07-12T08:16:25,359 Error compiling Cython file: 2021-07-12T08:16:25,359 ------------------------------------------------------------ 2021-07-12T08:16:25,359 ... 2021-07-12T08:16:25,359 outfile.write( "section\ttrack\tcontig\tnsegments\tlength\n" ) 2021-07-12T08:16:25,359 cdef Position total_length = 0 2021-07-12T08:16:25,359 cdef Position total_segments = 0 2021-07-12T08:16:25,359 cdef Position length, segments 2021-07-12T08:16:25,360 ^ 2021-07-12T08:16:25,360 ------------------------------------------------------------ 2021-07-12T08:16:25,360 gat/Engine.pyx:2955:13: 'Position' is not a type identifier 2021-07-12T08:16:25,430 Error compiling Cython file: 2021-07-12T08:16:25,430 ------------------------------------------------------------ 2021-07-12T08:16:25,430 ... 2021-07-12T08:16:25,431 def add( self, track, sample_id, isochore, segmentlist): 2021-07-12T08:16:25,431 '''add a new *sample* for *track* and *isochore*, giving it *sample_id*.''' 2021-07-12T08:16:25,431 Samples.add( self, track, sample_id, isochore, segmentlist ) 2021-07-12T08:16:25,431 cdef SegmentList seglist 2021-07-12T08:16:25,431 ^ 2021-07-12T08:16:25,431 ------------------------------------------------------------ 2021-07-12T08:16:25,431 gat/Engine.pyx:3284:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:25,433 Error compiling Cython file: 2021-07-12T08:16:25,433 ------------------------------------------------------------ 2021-07-12T08:16:25,433 ... 2021-07-12T08:16:25,433 fclose( self.findex) 2021-07-12T08:16:25,433 def load(self, track, sample_id, isochore): 2021-07-12T08:16:25,433 '''load data into memory''' 2021-07-12T08:16:25,434 cdef off_t pos 2021-07-12T08:16:25,434 cdef SegmentList seglist 2021-07-12T08:16:25,434 ^ 2021-07-12T08:16:25,434 ------------------------------------------------------------ 2021-07-12T08:16:25,434 gat/Engine.pyx:3330:13: 'SegmentList' is not a type identifier 2021-07-12T08:16:25,434 Error compiling Cython file: 2021-07-12T08:16:25,434 ------------------------------------------------------------ 2021-07-12T08:16:25,435 ... 2021-07-12T08:16:25,435 def load(self, track, sample_id, isochore): 2021-07-12T08:16:25,435 '''load data into memory''' 2021-07-12T08:16:25,435 cdef off_t pos 2021-07-12T08:16:25,435 cdef SegmentList seglist 2021-07-12T08:16:25,435 cdef Position nsegments 2021-07-12T08:16:25,435 ^ 2021-07-12T08:16:25,435 ------------------------------------------------------------ 2021-07-12T08:16:25,436 gat/Engine.pyx:3331:13: 'Position' is not a type identifier 2021-07-12T08:16:25,440 Error compiling Cython file: 2021-07-12T08:16:25,441 ------------------------------------------------------------ 2021-07-12T08:16:25,441 ... 2021-07-12T08:16:25,441 double pvalue ): 2021-07-12T08:16:25,441 '''return the number of expected number of false positives 2021-07-12T08:16:25,441 for less than or equal to *pvalue*. 2021-07-12T08:16:25,441 ''' 2021-07-12T08:16:25,441 cdef Position y, nsample, nfp, total_nfp 2021-07-12T08:16:25,442 ^ 2021-07-12T08:16:25,442 ------------------------------------------------------------ 2021-07-12T08:16:25,442 gat/Engine.pyx:3358:9: 'Position' is not a type identifier 2021-07-12T08:16:25,442 Error compiling Cython file: 2021-07-12T08:16:25,442 ------------------------------------------------------------ 2021-07-12T08:16:25,442 ... 2021-07-12T08:16:25,443 The results are added to annotator_results. 2021-07-12T08:16:25,443 ''' 2021-07-12T08:16:25,443 fdr_cache = {} 2021-07-12T08:16:25,443 cdef Position nresults 2021-07-12T08:16:25,443 ^ 2021-07-12T08:16:25,443 ------------------------------------------------------------ 2021-07-12T08:16:25,444 gat/Engine.pyx:3396:9: 'Position' is not a type identifier 2021-07-12T08:16:25,444 Error compiling Cython file: 2021-07-12T08:16:25,444 ------------------------------------------------------------ 2021-07-12T08:16:25,444 ... 2021-07-12T08:16:25,444 cdef Position nresults 2021-07-12T08:16:25,444 cdef AnnotatorResult r 2021-07-12T08:16:25,444 cdef EnrichmentStatistics * r1 2021-07-12T08:16:25,445 cdef EnrichmentStatistics ** allstats 2021-07-12T08:16:25,445 cdef Position nsample, nfp, R, x,y, total_nfp 2021-07-12T08:16:25,445 ^ 2021-07-12T08:16:25,445 ------------------------------------------------------------ 2021-07-12T08:16:25,445 gat/Engine.pyx:3400:9: 'Position' is not a type identifier 2021-07-12T08:16:25,445 Error compiling Cython file: 2021-07-12T08:16:25,445 ------------------------------------------------------------ 2021-07-12T08:16:25,446 ... 2021-07-12T08:16:25,446 cdef Position nresults 2021-07-12T08:16:25,446 cdef AnnotatorResult r 2021-07-12T08:16:25,446 cdef EnrichmentStatistics * r1 2021-07-12T08:16:25,446 cdef EnrichmentStatistics ** allstats 2021-07-12T08:16:25,446 cdef Position nsample, nfp, R, x,y, total_nfp 2021-07-12T08:16:25,446 cdef Position * nfps 2021-07-12T08:16:25,446 ^ 2021-07-12T08:16:25,446 ------------------------------------------------------------ 2021-07-12T08:16:25,447 gat/Engine.pyx:3401:9: 'Position' is not a type identifier 2021-07-12T08:16:25,447 Error compiling Cython file: 2021-07-12T08:16:25,447 ------------------------------------------------------------ 2021-07-12T08:16:25,447 ... 2021-07-12T08:16:25,447 This method works by scanning the first/last samples 2021-07-12T08:16:25,447 until one is found that is larger/smaller than the 2021-07-12T08:16:25,447 value of samples[sample_id]. 2021-07-12T08:16:25,447 ''' 2021-07-12T08:16:25,448 cdef double pval, min_pval, val 2021-07-12T08:16:25,448 cdef Position l 2021-07-12T08:16:25,448 ^ 2021-07-12T08:16:25,448 ------------------------------------------------------------ 2021-07-12T08:16:25,448 gat/Engine.pyx:3461:9: 'Position' is not a type identifier 2021-07-12T08:16:26,503 Error compiling Cython file: 2021-07-12T08:16:26,503 ------------------------------------------------------------ 2021-07-12T08:16:26,503 ... 2021-07-12T08:16:26,503 return a 2021-07-12T08:16:26,504 return b 2021-07-12T08:16:26,504 @cython.profile(False) 2021-07-12T08:16:26,504 cdef inline PositionDifference segment_overlap( Segment a, Segment b) nogil: 2021-07-12T08:16:26,504 return lmax(0, lmin( a.end, b.end) - \ 2021-07-12T08:16:26,504 ^ 2021-07-12T08:16:26,504 ------------------------------------------------------------ 2021-07-12T08:16:26,505 gat/Engine.pyx:84:20: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,505 Error compiling Cython file: 2021-07-12T08:16:26,505 ------------------------------------------------------------ 2021-07-12T08:16:26,505 ... 2021-07-12T08:16:26,505 return b 2021-07-12T08:16:26,505 @cython.profile(False) 2021-07-12T08:16:26,505 cdef inline PositionDifference segment_overlap( Segment a, Segment b) nogil: 2021-07-12T08:16:26,506 return lmax(0, lmin( a.end, b.end) - \ 2021-07-12T08:16:26,506 lmax(a.start, b.start)) 2021-07-12T08:16:26,506 ^ 2021-07-12T08:16:26,506 ------------------------------------------------------------ 2021-07-12T08:16:26,506 gat/Engine.pyx:85:17: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,506 Error compiling Cython file: 2021-07-12T08:16:26,507 ------------------------------------------------------------ 2021-07-12T08:16:26,507 ... 2021-07-12T08:16:26,507 @cython.profile(False) 2021-07-12T08:16:26,507 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:26,507 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:26,507 return lmax(0, 2021-07-12T08:16:26,507 lmin( aend, bend) - 2021-07-12T08:16:26,507 ^ 2021-07-12T08:16:26,508 ------------------------------------------------------------ 2021-07-12T08:16:26,508 gat/Engine.pyx:91:17: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,508 Error compiling Cython file: 2021-07-12T08:16:26,508 ------------------------------------------------------------ 2021-07-12T08:16:26,508 ... 2021-07-12T08:16:26,508 @cython.profile(False) 2021-07-12T08:16:26,508 cdef inline PositionDifference range_overlap( 2021-07-12T08:16:26,509 Position astart, Position aend, Position bstart, Position bend) nogil: 2021-07-12T08:16:26,509 return lmax(0, 2021-07-12T08:16:26,509 lmin( aend, bend) - 2021-07-12T08:16:26,509 lmax(astart, bstart)) 2021-07-12T08:16:26,509 ^ 2021-07-12T08:16:26,509 ------------------------------------------------------------ 2021-07-12T08:16:26,509 gat/Engine.pyx:92:17: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,510 Error compiling Cython file: 2021-07-12T08:16:26,510 ------------------------------------------------------------ 2021-07-12T08:16:26,510 ... 2021-07-12T08:16:26,510 lmin( aend, bend) - 2021-07-12T08:16:26,510 lmax(astart, bstart)) 2021-07-12T08:16:26,510 @cython.profile(False) 2021-07-12T08:16:26,511 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:26,511 return lmin(a.end, b.end) - \ 2021-07-12T08:16:26,511 ^ 2021-07-12T08:16:26,511 ------------------------------------------------------------ 2021-07-12T08:16:26,511 gat/Engine.pyx:96:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,511 Error compiling Cython file: 2021-07-12T08:16:26,511 ------------------------------------------------------------ 2021-07-12T08:16:26,512 ... 2021-07-12T08:16:26,512 lmax(astart, bstart)) 2021-07-12T08:16:26,512 @cython.profile(False) 2021-07-12T08:16:26,512 cdef inline PositionDifference segment_overlap_raw(Segment a, Segment b) nogil: 2021-07-12T08:16:26,512 return lmin(a.end, b.end) - \ 2021-07-12T08:16:26,512 lmax(a.start, b.start) 2021-07-12T08:16:26,512 ^ 2021-07-12T08:16:26,513 ------------------------------------------------------------ 2021-07-12T08:16:26,513 gat/Engine.pyx:97:9: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,513 Error compiling Cython file: 2021-07-12T08:16:26,513 ------------------------------------------------------------ 2021-07-12T08:16:26,513 ... 2021-07-12T08:16:26,513 return lmin(a.end, b.end) - \ 2021-07-12T08:16:26,513 lmax(a.start, b.start) 2021-07-12T08:16:26,514 @cython.profile(False) 2021-07-12T08:16:26,514 cdef inline PositionDifference segment_length( Segment a) nogil: 2021-07-12T08:16:26,514 return a.end - a.start 2021-07-12T08:16:26,514 ^ 2021-07-12T08:16:26,514 ------------------------------------------------------------ 2021-07-12T08:16:26,514 gat/Engine.pyx:101:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,515 Error compiling Cython file: 2021-07-12T08:16:26,515 ------------------------------------------------------------ 2021-07-12T08:16:26,515 ... 2021-07-12T08:16:26,515 return lmin(a.end, b.end) - \ 2021-07-12T08:16:26,515 lmax(a.start, b.start) 2021-07-12T08:16:26,515 @cython.profile(False) 2021-07-12T08:16:26,515 cdef inline PositionDifference segment_length( Segment a) nogil: 2021-07-12T08:16:26,515 return a.end - a.start 2021-07-12T08:16:26,516 ^ 2021-07-12T08:16:26,516 ------------------------------------------------------------ 2021-07-12T08:16:26,516 gat/Engine.pyx:101:40: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,516 Error compiling Cython file: 2021-07-12T08:16:26,516 ------------------------------------------------------------ 2021-07-12T08:16:26,516 ... 2021-07-12T08:16:26,516 cdef extern from *: 2021-07-12T08:16:26,517 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:26,517 @cython.profile(False) 2021-07-12T08:16:26,517 cdef int cmpSegments( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,517 return (s1).start - (s2).start 2021-07-12T08:16:26,517 ^ 2021-07-12T08:16:26,517 ------------------------------------------------------------ 2021-07-12T08:16:26,517 gat/Engine.pyx:109:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,518 Error compiling Cython file: 2021-07-12T08:16:26,518 ------------------------------------------------------------ 2021-07-12T08:16:26,518 ... 2021-07-12T08:16:26,518 cdef extern from *: 2021-07-12T08:16:26,518 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:26,518 @cython.profile(False) 2021-07-12T08:16:26,518 cdef int cmpSegments( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,519 return (s1).start - (s2).start 2021-07-12T08:16:26,519 ^ 2021-07-12T08:16:26,519 ------------------------------------------------------------ 2021-07-12T08:16:26,519 gat/Engine.pyx:109:33: 'Segment' is not a type identifier 2021-07-12T08:16:26,519 Error compiling Cython file: 2021-07-12T08:16:26,519 ------------------------------------------------------------ 2021-07-12T08:16:26,519 ... 2021-07-12T08:16:26,519 cdef extern from *: 2021-07-12T08:16:26,520 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:26,520 @cython.profile(False) 2021-07-12T08:16:26,520 cdef int cmpSegments( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,520 return (s1).start - (s2).start 2021-07-12T08:16:26,520 ^ 2021-07-12T08:16:26,520 ------------------------------------------------------------ 2021-07-12T08:16:26,520 gat/Engine.pyx:109:56: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,521 Error compiling Cython file: 2021-07-12T08:16:26,521 ------------------------------------------------------------ 2021-07-12T08:16:26,521 ... 2021-07-12T08:16:26,521 cdef extern from *: 2021-07-12T08:16:26,521 ctypedef void * const_void_ptr "const void*" 2021-07-12T08:16:26,521 @cython.profile(False) 2021-07-12T08:16:26,521 cdef int cmpSegments( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,522 return (s1).start - (s2).start 2021-07-12T08:16:26,522 ^ 2021-07-12T08:16:26,522 ------------------------------------------------------------ 2021-07-12T08:16:26,522 gat/Engine.pyx:109:77: 'Segment' is not a type identifier 2021-07-12T08:16:26,522 Error compiling Cython file: 2021-07-12T08:16:26,522 ------------------------------------------------------------ 2021-07-12T08:16:26,523 ... 2021-07-12T08:16:26,523 return (s1).start - (s2).start 2021-07-12T08:16:26,523 @cython.profile(False) 2021-07-12T08:16:26,523 cdef int cmpSegmentsStartAndEnd( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,523 cdef int x 2021-07-12T08:16:26,523 x = (s1).start - (s2).start 2021-07-12T08:16:26,523 ^ 2021-07-12T08:16:26,523 ------------------------------------------------------------ 2021-07-12T08:16:26,524 gat/Engine.pyx:114:9: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,524 Error compiling Cython file: 2021-07-12T08:16:26,524 ------------------------------------------------------------ 2021-07-12T08:16:26,524 ... 2021-07-12T08:16:26,524 return (s1).start - (s2).start 2021-07-12T08:16:26,524 @cython.profile(False) 2021-07-12T08:16:26,525 cdef int cmpSegmentsStartAndEnd( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,525 cdef int x 2021-07-12T08:16:26,525 x = (s1).start - (s2).start 2021-07-12T08:16:26,525 ^ 2021-07-12T08:16:26,525 ------------------------------------------------------------ 2021-07-12T08:16:26,525 gat/Engine.pyx:114:30: 'Segment' is not a type identifier 2021-07-12T08:16:26,525 Error compiling Cython file: 2021-07-12T08:16:26,526 ------------------------------------------------------------ 2021-07-12T08:16:26,526 ... 2021-07-12T08:16:26,526 return (s1).start - (s2).start 2021-07-12T08:16:26,526 @cython.profile(False) 2021-07-12T08:16:26,526 cdef int cmpSegmentsStartAndEnd( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,526 cdef int x 2021-07-12T08:16:26,526 x = (s1).start - (s2).start 2021-07-12T08:16:26,526 ^ 2021-07-12T08:16:26,527 ------------------------------------------------------------ 2021-07-12T08:16:26,527 gat/Engine.pyx:114:53: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,527 Error compiling Cython file: 2021-07-12T08:16:26,527 ------------------------------------------------------------ 2021-07-12T08:16:26,527 ... 2021-07-12T08:16:26,527 return (s1).start - (s2).start 2021-07-12T08:16:26,528 @cython.profile(False) 2021-07-12T08:16:26,528 cdef int cmpSegmentsStartAndEnd( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,528 cdef int x 2021-07-12T08:16:26,528 x = (s1).start - (s2).start 2021-07-12T08:16:26,528 ^ 2021-07-12T08:16:26,529 ------------------------------------------------------------ 2021-07-12T08:16:26,529 gat/Engine.pyx:114:74: 'Segment' is not a type identifier 2021-07-12T08:16:26,529 Error compiling Cython file: 2021-07-12T08:16:26,529 ------------------------------------------------------------ 2021-07-12T08:16:26,529 ... 2021-07-12T08:16:26,529 @cython.profile(False) 2021-07-12T08:16:26,530 cdef int cmpSegmentsStartAndEnd( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,530 cdef int x 2021-07-12T08:16:26,530 x = (s1).start - (s2).start 2021-07-12T08:16:26,530 if x != 0: return x 2021-07-12T08:16:26,530 return (s1).end - (s2).end 2021-07-12T08:16:26,530 ^ 2021-07-12T08:16:26,530 ------------------------------------------------------------ 2021-07-12T08:16:26,530 gat/Engine.pyx:116:12: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,531 Error compiling Cython file: 2021-07-12T08:16:26,531 ------------------------------------------------------------ 2021-07-12T08:16:26,531 ... 2021-07-12T08:16:26,531 @cython.profile(False) 2021-07-12T08:16:26,531 cdef int cmpSegmentsStartAndEnd( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,531 cdef int x 2021-07-12T08:16:26,531 x = (s1).start - (s2).start 2021-07-12T08:16:26,531 if x != 0: return x 2021-07-12T08:16:26,532 return (s1).end - (s2).end 2021-07-12T08:16:26,532 ^ 2021-07-12T08:16:26,532 ------------------------------------------------------------ 2021-07-12T08:16:26,532 gat/Engine.pyx:116:33: 'Segment' is not a type identifier 2021-07-12T08:16:26,532 Error compiling Cython file: 2021-07-12T08:16:26,532 ------------------------------------------------------------ 2021-07-12T08:16:26,532 ... 2021-07-12T08:16:26,533 @cython.profile(False) 2021-07-12T08:16:26,533 cdef int cmpSegmentsStartAndEnd( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,533 cdef int x 2021-07-12T08:16:26,533 x = (s1).start - (s2).start 2021-07-12T08:16:26,533 if x != 0: return x 2021-07-12T08:16:26,533 return (s1).end - (s2).end 2021-07-12T08:16:26,533 ^ 2021-07-12T08:16:26,533 ------------------------------------------------------------ 2021-07-12T08:16:26,534 gat/Engine.pyx:116:54: 'PositionDifference' is not a type identifier 2021-07-12T08:16:26,534 Error compiling Cython file: 2021-07-12T08:16:26,534 ------------------------------------------------------------ 2021-07-12T08:16:26,534 ... 2021-07-12T08:16:26,534 @cython.profile(False) 2021-07-12T08:16:26,534 cdef int cmpSegmentsStartAndEnd( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,534 cdef int x 2021-07-12T08:16:26,535 x = (s1).start - (s2).start 2021-07-12T08:16:26,535 if x != 0: return x 2021-07-12T08:16:26,535 return (s1).end - (s2).end 2021-07-12T08:16:26,535 ^ 2021-07-12T08:16:26,535 ------------------------------------------------------------ 2021-07-12T08:16:26,535 gat/Engine.pyx:116:75: 'Segment' is not a type identifier 2021-07-12T08:16:26,535 Error compiling Cython file: 2021-07-12T08:16:26,536 ------------------------------------------------------------ 2021-07-12T08:16:26,536 ... 2021-07-12T08:16:26,536 if x != 0: return x 2021-07-12T08:16:26,536 return (s1).end - (s2).end 2021-07-12T08:16:26,536 @cython.profile(False) 2021-07-12T08:16:26,536 cdef int cmpPosition( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,536 return (s1)[0] - (s2)[0] 2021-07-12T08:16:26,536 ^ 2021-07-12T08:16:26,537 ------------------------------------------------------------ 2021-07-12T08:16:26,537 gat/Engine.pyx:120:13: 'Position' is not a type identifier 2021-07-12T08:16:26,537 Error compiling Cython file: 2021-07-12T08:16:26,537 ------------------------------------------------------------ 2021-07-12T08:16:26,537 ... 2021-07-12T08:16:26,537 if x != 0: return x 2021-07-12T08:16:26,537 return (s1).end - (s2).end 2021-07-12T08:16:26,538 @cython.profile(False) 2021-07-12T08:16:26,538 cdef int cmpPosition( const_void_ptr s1, const_void_ptr s2 ): 2021-07-12T08:16:26,538 return (s1)[0] - (s2)[0] 2021-07-12T08:16:26,538 ^ 2021-07-12T08:16:26,538 ------------------------------------------------------------ 2021-07-12T08:16:26,538 gat/Engine.pyx:120:34: 'Position' is not a type identifier 2021-07-12T08:16:26,539 Error compiling Cython file: 2021-07-12T08:16:26,539 ------------------------------------------------------------ 2021-07-12T08:16:26,539 ... 2021-07-12T08:16:26,539 cdef Position i, totsize 2021-07-12T08:16:26,539 assert len(segment_list) > 0, "sampling from empty segment list" 2021-07-12T08:16:26,539 self.segment_list = segment_list 2021-07-12T08:16:26,539 self.nsegments = len(segment_list) 2021-07-12T08:16:26,539 self.cdf = malloc(sizeof(Position) * self.nsegments) 2021-07-12T08:16:26,540 ^ 2021-07-12T08:16:26,540 ------------------------------------------------------------ 2021-07-12T08:16:26,540 gat/Engine.pyx:181:20: 'Position' is not a type identifier 2021-07-12T08:16:26,540 Error compiling Cython file: 2021-07-12T08:16:26,540 ------------------------------------------------------------ 2021-07-12T08:16:26,540 ... 2021-07-12T08:16:26,540 cdef Position i, totsize 2021-07-12T08:16:26,540 assert len(segment_list) > 0, "sampling from empty segment list" 2021-07-12T08:16:26,541 self.segment_list = segment_list 2021-07-12T08:16:26,541 self.nsegments = len(segment_list) 2021-07-12T08:16:26,541 self.cdf = malloc(sizeof(Position) * self.nsegments) 2021-07-12T08:16:26,541 ^ 2021-07-12T08:16:26,541 ------------------------------------------------------------ 2021-07-12T08:16:26,541 gat/Engine.pyx:181:52: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:26,542 Error compiling Cython file: 2021-07-12T08:16:26,542 ------------------------------------------------------------ 2021-07-12T08:16:26,542 ... 2021-07-12T08:16:26,542 self.nsegments = len(segment_list) 2021-07-12T08:16:26,542 self.cdf = malloc(sizeof(Position) * self.nsegments) 2021-07-12T08:16:26,542 if not self.cdf: 2021-07-12T08:16:26,542 raise MemoryError( 2021-07-12T08:16:26,542 "out of memory when allocation %i bytes" % 2021-07-12T08:16:26,543 sizeof( sizeof(Position) * self.nsegments)) 2021-07-12T08:16:26,543 ^ 2021-07-12T08:16:26,543 ------------------------------------------------------------ 2021-07-12T08:16:26,543 gat/Engine.pyx:185:39: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:26,543 Error compiling Cython file: 2021-07-12T08:16:26,543 ------------------------------------------------------------ 2021-07-12T08:16:26,543 ... 2021-07-12T08:16:26,544 if not self.cdf: 2021-07-12T08:16:26,544 raise MemoryError( 2021-07-12T08:16:26,544 "out of memory when allocation %i bytes" % 2021-07-12T08:16:26,544 sizeof( sizeof(Position) * self.nsegments)) 2021-07-12T08:16:26,544 self.total_size = 0 2021-07-12T08:16:26,544 for i from 0 <= i < len(segment_list): 2021-07-12T08:16:26,544 ^ 2021-07-12T08:16:26,544 ------------------------------------------------------------ 2021-07-12T08:16:26,545 gat/Engine.pyx:187:12: for-from loop variable must be c numeric type or Python object 2021-07-12T08:16:26,545 Error compiling Cython file: 2021-07-12T08:16:26,545 ------------------------------------------------------------ 2021-07-12T08:16:26,545 ... 2021-07-12T08:16:26,545 cdef PositionDifference overlap 2021-07-12T08:16:26,545 cdef size_t segment_index 2021-07-12T08:16:26,545 # r = rand() / (RAND_MAX / total_size + 1) 2021-07-12T08:16:26,546 rpos = numpy.random.randint( 0, self.total_size ) 2021-07-12T08:16:26,546 segment_index = searchsorted( self.cdf, 2021-07-12T08:16:26,546 ^ 2021-07-12T08:16:26,546 ------------------------------------------------------------ 2021-07-12T08:16:26,546 gat/Engine.pyx:207:24: undeclared name not builtin: searchsorted 2021-07-12T08:16:26,546 Error compiling Cython file: 2021-07-12T08:16:26,546 ------------------------------------------------------------ 2021-07-12T08:16:26,547 ... 2021-07-12T08:16:26,547 # r = rand() / (RAND_MAX / total_size + 1) 2021-07-12T08:16:26,547 rpos = numpy.random.randint( 0, self.total_size ) 2021-07-12T08:16:26,547 segment_index = searchsorted( self.cdf, 2021-07-12T08:16:26,547 self.nsegments, 2021-07-12T08:16:26,547 sizeof(Position), 2021-07-12T08:16:26,547 ^ 2021-07-12T08:16:26,547 ------------------------------------------------------------ 2021-07-12T08:16:26,548 gat/Engine.pyx:209:53: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:26,548 Error compiling Cython file: 2021-07-12T08:16:26,548 ------------------------------------------------------------ 2021-07-12T08:16:26,548 ... 2021-07-12T08:16:26,548 rpos = numpy.random.randint( 0, self.total_size ) 2021-07-12T08:16:26,548 segment_index = searchsorted( self.cdf, 2021-07-12T08:16:26,548 self.nsegments, 2021-07-12T08:16:26,548 sizeof(Position), 2021-07-12T08:16:26,549 &rpos, 2021-07-12T08:16:26,549 &cmpPosition, 2021-07-12T08:16:26,549 ^ 2021-07-12T08:16:26,549 ------------------------------------------------------------ 2021-07-12T08:16:26,549 gat/Engine.pyx:211:38: Cannot convert 'int (*)(const_void_ptr, const_void_ptr)' to Python object 2021-07-12T08:16:26,549 Error compiling Cython file: 2021-07-12T08:16:26,550 ------------------------------------------------------------ 2021-07-12T08:16:26,550 ... 2021-07-12T08:16:26,550 assert len(segment_list) > 0, "sampling from empty segment list" 2021-07-12T08:16:26,550 assert segment_list.isNormalized 2021-07-12T08:16:26,550 self.segment_list = segment_list 2021-07-12T08:16:26,550 self.nsegments = len(segment_list) 2021-07-12T08:16:26,550 self.cdf = malloc( sizeof(Position) * self.nsegments ) 2021-07-12T08:16:26,550 ^ 2021-07-12T08:16:26,551 ------------------------------------------------------------ 2021-07-12T08:16:26,551 gat/Engine.pyx:268:20: 'Position' is not a type identifier 2021-07-12T08:16:26,551 Error compiling Cython file: 2021-07-12T08:16:26,551 ------------------------------------------------------------ 2021-07-12T08:16:26,551 ... 2021-07-12T08:16:26,551 assert len(segment_list) > 0, "sampling from empty segment list" 2021-07-12T08:16:26,551 assert segment_list.isNormalized 2021-07-12T08:16:26,552 self.segment_list = segment_list 2021-07-12T08:16:26,552 self.nsegments = len(segment_list) 2021-07-12T08:16:26,552 self.cdf = malloc( sizeof(Position) * self.nsegments ) 2021-07-12T08:16:26,552 ^ 2021-07-12T08:16:26,552 ------------------------------------------------------------ 2021-07-12T08:16:26,552 gat/Engine.pyx:268:53: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:26,553 Error compiling Cython file: 2021-07-12T08:16:26,553 ------------------------------------------------------------ 2021-07-12T08:16:26,553 ... 2021-07-12T08:16:26,553 self.nsegments = len(segment_list) 2021-07-12T08:16:26,553 self.cdf = malloc( sizeof(Position) * self.nsegments ) 2021-07-12T08:16:26,553 if not self.cdf: 2021-07-12T08:16:26,553 raise MemoryError( 2021-07-12T08:16:26,553 "out of memory when allocation %i bytes" % 2021-07-12T08:16:26,553 sizeof(sizeof(Position) * self.nsegments)) 2021-07-12T08:16:26,554 ^ 2021-07-12T08:16:26,554 ------------------------------------------------------------ 2021-07-12T08:16:26,554 gat/Engine.pyx:272:38: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:26,554 Error compiling Cython file: 2021-07-12T08:16:26,554 ------------------------------------------------------------ 2021-07-12T08:16:26,554 ... 2021-07-12T08:16:26,554 if not self.cdf: 2021-07-12T08:16:26,555 raise MemoryError( 2021-07-12T08:16:26,555 "out of memory when allocation %i bytes" % 2021-07-12T08:16:26,555 sizeof(sizeof(Position) * self.nsegments)) 2021-07-12T08:16:26,555 self.total_size = 0 2021-07-12T08:16:26,555 for i from 0 <= i < len(segment_list): 2021-07-12T08:16:26,555 ^ 2021-07-12T08:16:26,555 ------------------------------------------------------------ 2021-07-12T08:16:26,555 gat/Engine.pyx:274:12: for-from loop variable must be c numeric type or Python object 2021-07-12T08:16:26,556 Error compiling Cython file: 2021-07-12T08:16:26,556 ------------------------------------------------------------ 2021-07-12T08:16:26,556 ... 2021-07-12T08:16:26,556 # sample a position 2021-07-12T08:16:26,556 # r = rand() / (RAND_MAX / total_size + 1) 2021-07-12T08:16:26,556 random_pos_in_workspace = numpy.random.randint(0, self.total_size) 2021-07-12T08:16:26,556 segment_index = searchsorted( self.cdf, 2021-07-12T08:16:26,556 self.nsegments, 2021-07-12T08:16:26,557 sizeof(Position), 2021-07-12T08:16:26,557 ^ 2021-07-12T08:16:26,557 ------------------------------------------------------------ 2021-07-12T08:16:26,557 gat/Engine.pyx:302:53: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:26,557 Error compiling Cython file: 2021-07-12T08:16:26,557 ------------------------------------------------------------ 2021-07-12T08:16:26,558 ... 2021-07-12T08:16:26,558 random_pos_in_workspace = numpy.random.randint(0, self.total_size) 2021-07-12T08:16:26,558 segment_index = searchsorted( self.cdf, 2021-07-12T08:16:26,558 self.nsegments, 2021-07-12T08:16:26,558 sizeof(Position), 2021-07-12T08:16:26,558 &random_pos_in_workspace, 2021-07-12T08:16:26,558 &cmpPosition, 2021-07-12T08:16:26,558 ^ 2021-07-12T08:16:26,558 ------------------------------------------------------------ 2021-07-12T08:16:26,559 gat/Engine.pyx:304:38: Cannot convert 'int (*)(const_void_ptr, const_void_ptr)' to Python object 2021-07-12T08:16:26,559 Error compiling Cython file: 2021-07-12T08:16:26,559 ------------------------------------------------------------ 2021-07-12T08:16:26,559 ... 2021-07-12T08:16:26,559 self.cdf = NULL 2021-07-12T08:16:26,559 self.nbuckets = len(histogram) 2021-07-12T08:16:26,560 assert self.nbuckets > 0, "sampling from empty histogram" 2021-07-12T08:16:26,560 self.cdf = malloc( sizeof(Position) * self.nbuckets ) 2021-07-12T08:16:26,560 ^ 2021-07-12T08:16:26,560 ------------------------------------------------------------ 2021-07-12T08:16:26,560 gat/Engine.pyx:404:20: 'Position' is not a type identifier 2021-07-12T08:16:26,560 Error compiling Cython file: 2021-07-12T08:16:26,560 ------------------------------------------------------------ 2021-07-12T08:16:26,561 ... 2021-07-12T08:16:26,561 self.cdf = NULL 2021-07-12T08:16:26,561 self.nbuckets = len(histogram) 2021-07-12T08:16:26,561 assert self.nbuckets > 0, "sampling from empty histogram" 2021-07-12T08:16:26,561 self.cdf = malloc( sizeof(Position) * self.nbuckets ) 2021-07-12T08:16:26,561 ^ 2021-07-12T08:16:26,561 ------------------------------------------------------------ 2021-07-12T08:16:26,562 gat/Engine.pyx:404:53: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:26,562 Error compiling Cython file: 2021-07-12T08:16:26,562 ------------------------------------------------------------ 2021-07-12T08:16:26,562 ... 2021-07-12T08:16:26,562 self.nbuckets = len(histogram) 2021-07-12T08:16:26,563 assert self.nbuckets > 0, "sampling from empty histogram" 2021-07-12T08:16:26,563 self.cdf = malloc( sizeof(Position) * self.nbuckets ) 2021-07-12T08:16:26,563 if not self.cdf: raise MemoryError( "out of memory when allocation %i bytes" % sizeof( sizeof(Position) * self.nbuckets )) 2021-07-12T08:16:26,563 ^ 2021-07-12T08:16:26,563 ------------------------------------------------------------ 2021-07-12T08:16:26,563 gat/Engine.pyx:405:110: 'Position' is not a constant, variable or function identifier 2021-07-12T08:16:26,594 Error compiling Cython file: 2021-07-12T08:16:26,594 ------------------------------------------------------------ 2021-07-12T08:16:26,594 ... 2021-07-12T08:16:26,594 assert self.nbuckets > 0, "sampling from empty histogram" 2021-07-12T08:16:26,594 self.cdf = malloc( sizeof(Position) * self.nbuckets ) 2021-07-12T08:16:26,594 if not self.cdf: raise MemoryError( "out of memory when allocation %i bytes" % sizeof( sizeof(Position) * self.nbuckets )) 2021-07-12T08:16:26,595 self.total_size = 0 2021-07-12T08:16:26,595 for i from 0 <= i < self.nbuckets: 2021-07-12T08:16:26,595 ^ 2021-07-12T08:16:26,595 ------------------------------------------------------------ 2021-07-12T08:16:26,595 gat/Engine.pyx:407:8: Compiler crash in AnalyseExpressionsTransform 2021-07-12T08:16:26,596 ModuleNode.body = StatListNode(Engine.pyx:4:0) 2021-07-12T08:16:26,596 StatListNode.stats[50] = StatListNode(Engine.pyx:387:5) 2021-07-12T08:16:26,596 StatListNode.stats[0] = CClassDefNode(Engine.pyx:387:5, 2021-07-12T08:16:26,596 as_name = 'HistogramSampler', 2021-07-12T08:16:26,596 class_name = 'HistogramSampler', 2021-07-12T08:16:26,596 module_name = '', 2021-07-12T08:16:26,596 visibility = 'private') 2021-07-12T08:16:26,597 CClassDefNode.body = StatListNode(Engine.pyx:389:4) 2021-07-12T08:16:26,597 StatListNode.stats[0] = CompilerDirectivesNode(Engine.pyx:395:4) 2021-07-12T08:16:26,597 CompilerDirectivesNode.body = StatListNode(Engine.pyx:395:4) 2021-07-12T08:16:26,597 StatListNode.stats[0] = DefNode(Engine.pyx:395:4, 2021-07-12T08:16:26,597 modifiers = [...]/0, 2021-07-12T08:16:26,597 name = '__init__', 2021-07-12T08:16:26,597 np_args_idx = [...]/0, 2021-07-12T08:16:26,598 num_required_args = 3, 2021-07-12T08:16:26,598 outer_attrs = [...]/2, 2021-07-12T08:16:26,598 py_wrapper_required = True, 2021-07-12T08:16:26,598 reqd_kw_flags_cname = '0', 2021-07-12T08:16:26,598 used = True) 2021-07-12T08:16:26,598 File 'Nodes.py', line 435, in analyse_expressions: StatListNode(Engine.pyx:398:8) 2021-07-12T08:16:26,598 File 'Nodes.py', line 6839, in analyse_expressions: ForFromStatNode(Engine.pyx:407:8, 2021-07-12T08:16:26,599 relation1 = '<=', 2021-07-12T08:16:26,599 relation2 = '<') 2021-07-12T08:16:26,599 File 'Nodes.py', line 6863, in set_up_loop: ForFromStatNode(Engine.pyx:407:8, 2021-07-12T08:16:26,599 relation1 = '<=', 2021-07-12T08:16:26,599 relation2 = '<') 2021-07-12T08:16:26,599 Compiler crash traceback from this point on: 2021-07-12T08:16:26,600 File "/usr/local/lib/python3.9/dist-packages/Cython/Compiler/Nodes.py", line 6863, in set_up_loop 2021-07-12T08:16:26,600 loop_type = PyrexTypes.widest_numeric_type(loop_type, self.bound2.type) 2021-07-12T08:16:26,600 File "/usr/local/lib/python3.9/dist-packages/Cython/Compiler/PyrexTypes.py", line 4475, in widest_numeric_type 2021-07-12T08:16:26,600 elif type1.rank < type2.rank: 2021-07-12T08:16:26,600 AttributeError: 'ErrorType' object has no attribute 'rank' 2021-07-12T08:16:26,600 building 'gat.CoordinateList' extension 2021-07-12T08:16:26,601 creating build/temp.linux-armv7l-3.9 2021-07-12T08:16:26,601 creating build/temp.linux-armv7l-3.9/gat 2021-07-12T08:16:26,601 creating build/temp.linux-armv7l-3.9/utils 2021-07-12T08:16:26,601 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I./utils -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c gat/CoordinateList.c -o build/temp.linux-armv7l-3.9/gat/CoordinateList.o 2021-07-12T08:16:29,132 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I./utils -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c utils/gat_utils.c -o build/temp.linux-armv7l-3.9/utils/gat_utils.o 2021-07-12T08:16:29,274 utils/gat_utils.c: In function ‘fromCompressedFile’: 2021-07-12T08:16:29,275 utils/gat_utils.c:110:33: warning: passing argument 2 of ‘uncompress’ from incompatible pointer type [-Wincompatible-pointer-types] 2021-07-12T08:16:29,275 110 | int zok = uncompress (buffer, &uncompressed_size, compressed, compressed_size); 2021-07-12T08:16:29,275 | ^~~~~~~~~~~~~~~~~~ 2021-07-12T08:16:29,275 | | 2021-07-12T08:16:29,275 | size_t * {aka unsigned int *} 2021-07-12T08:16:29,276 In file included from /usr/include/zlib.h:34, 2021-07-12T08:16:29,276 from utils/gat_utils.c:2: 2021-07-12T08:16:29,277 /usr/include/zlib.h:1265:32: note: expected ‘uLongf *’ {aka ‘long unsigned int *’} but argument is of type ‘size_t *’ {aka ‘unsigned int *’} 2021-07-12T08:16:29,277 1265 | ZEXTERN int ZEXPORT uncompress OF((Bytef *dest, uLongf *destLen, 2021-07-12T08:16:29,277 | ^~ 2021-07-12T08:16:29,393 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/gat/CoordinateList.o build/temp.linux-armv7l-3.9/utils/gat_utils.o -lz -lrt -o build/lib.linux-armv7l-3.9/gat/CoordinateList.cpython-39-arm-linux-gnueabihf.so 2021-07-12T08:16:29,528 building 'gat.SegmentList' extension 2021-07-12T08:16:29,528 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I./utils -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c gat/SegmentList.c -o build/temp.linux-armv7l-3.9/gat/SegmentList.o 2021-07-12T08:16:29,585 gat/SegmentList.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation. 2021-07-12T08:16:29,585 1 | #error Do not use this file, it is the result of a failed Cython compilation. 2021-07-12T08:16:29,585 | ^~~~~ 2021-07-12T08:16:29,589 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-12T08:16:29,998 Building wheel for gat (setup.py): finished with status 'error' 2021-07-12T08:16:29,998 ERROR: Failed building wheel for gat 2021-07-12T08:16:30,000 Running setup.py clean for gat 2021-07-12T08:16:30,000 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-sammuaxk/gat_98fddb3111d94ae9bf647f384bede459/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-sammuaxk/gat_98fddb3111d94ae9bf647f384bede459/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2021-07-12T08:16:31,232 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'distribution-name' will not be supported in future versions. Please use the underscore name 'distribution_name' instead 2021-07-12T08:16:31,232 warnings.warn( 2021-07-12T08:16:31,349 running clean 2021-07-12T08:16:31,352 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-12T08:16:31,355 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-12T08:16:31,358 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-12T08:16:31,358 'build/scripts-3.9' does not exist -- can't clean it 2021-07-12T08:16:31,359 removing 'build' 2021-07-12T08:16:31,448 Failed to build gat 2021-07-12T08:16:31,448 ERROR: Failed to build one or more wheels 2021-07-12T08:16:31,449 Exception information: 2021-07-12T08:16:31,449 Traceback (most recent call last): 2021-07-12T08:16:31,449 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-12T08:16:31,449 status = self.run(options, args) 2021-07-12T08:16:31,449 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-12T08:16:31,449 return func(self, options, args) 2021-07-12T08:16:31,449 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-12T08:16:31,449 raise CommandError( 2021-07-12T08:16:31,449 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-12T08:16:31,452 Removed build tracker: '/tmp/pip-req-tracker-nj0p_fwh'