2021-07-16T11:12:16,036 Created temporary directory: /tmp/pip-ephem-wheel-cache-qeofu9eo 2021-07-16T11:12:16,039 Created temporary directory: /tmp/pip-req-tracker-vs8pgxbu 2021-07-16T11:12:16,040 Initialized build tracking at /tmp/pip-req-tracker-vs8pgxbu 2021-07-16T11:12:16,040 Created build tracker: /tmp/pip-req-tracker-vs8pgxbu 2021-07-16T11:12:16,040 Entered build tracker: /tmp/pip-req-tracker-vs8pgxbu 2021-07-16T11:12:16,041 Created temporary directory: /tmp/pip-wheel-li2wg2am 2021-07-16T11:12:16,073 1 location(s) to search for versions of hapflk: 2021-07-16T11:12:16,073 * https://pypi.org/simple/hapflk/ 2021-07-16T11:12:16,074 Fetching project page and analyzing links: https://pypi.org/simple/hapflk/ 2021-07-16T11:12:16,074 Getting page https://pypi.org/simple/hapflk/ 2021-07-16T11:12:16,076 Found index url https://pypi.org/simple 2021-07-16T11:12:16,272 Found link https://files.pythonhosted.org/packages/b2/ad/85999140cbc66853d701f214fd6548aab07dc46fe29c2d8632c332e97689/hapflk-1.3.2.tar.gz#sha256=762e84e00cafa571fff57a3b4d3e1629c8ae5fe4993db5fe01e661260bea478b (from https://pypi.org/simple/hapflk/), version: 1.3.2 2021-07-16T11:12:16,272 Found link https://files.pythonhosted.org/packages/ca/fa/51a8f51e01fbc13e8f4b36acbdb6d31188481f4c1ce440b8797ec769d910/hapflk-1.3.3.tar.gz#sha256=8e25c697cc9011b6f24fa1e6a717e826b32f859f2ea1c4ea31b45b59637747a4 (from https://pypi.org/simple/hapflk/), version: 1.3.3 2021-07-16T11:12:16,273 Found link https://files.pythonhosted.org/packages/63/d9/33d91f8a3376ab13ffc0a102caa32a2332fccda2db96009f7cf317593e1b/hapflk-1.3.4.tar.gz#sha256=94978b55fb4524edfc6c8323462ac1eaf642d82877f4a989ad91fdef488cd9b3 (from https://pypi.org/simple/hapflk/), version: 1.3.4 2021-07-16T11:12:16,273 Found link https://files.pythonhosted.org/packages/65/21/a92bba282c49dcacbdb002ed60a7a9b2bddfb98f7eedc382a3d0c134abe7/hapflk-1.3.5.dev0.tar.gz#sha256=b8a820ff6c1decd86dd5da4b51af53e87bbd4c10863578b850744ee6bf6ad8ce (from https://pypi.org/simple/hapflk/), version: 1.3.5.dev0 2021-07-16T11:12:16,273 Found link https://files.pythonhosted.org/packages/6b/81/cc8f04f774e8728b5167bc58ae12eb4fb2125b784a395fdfefb3e78f7733/hapflk-1.3.5.dev1.tar.gz#sha256=a9f1c95349696779a5c5b08ca3cdcc19528958e38ff8e52caff9101b3fc1f03c (from https://pypi.org/simple/hapflk/), version: 1.3.5.dev1 2021-07-16T11:12:16,273 Found link https://files.pythonhosted.org/packages/f8/34/1bd9c49ea13e6be4afec643acfe9f960ae6714fea4d5499a75988e81663e/hapflk-1.3.5.dev2.tar.gz#sha256=bb1897647df2aea1c49041732a6c401ca4bf006c4e20e0eefd135e55c3aad2c4 (from https://pypi.org/simple/hapflk/), version: 1.3.5.dev2 2021-07-16T11:12:16,274 Found link https://files.pythonhosted.org/packages/96/14/256f0eda9b570de3b48a7fcff1d062ab7694bd32e7f2ad7ef8bd483b926f/hapflk-1.3.5.dev3.tar.gz#sha256=95144c003c0d193ed76deaa5a4ad07161e71859e65fa4d60954306a3bf0c4754 (from https://pypi.org/simple/hapflk/), version: 1.3.5.dev3 2021-07-16T11:12:16,274 Found link https://files.pythonhosted.org/packages/aa/c6/c72917e6d4492061b47104c7922b0368c38be20b87bf3e0553d8824a9cfe/hapflk-1.3.5.dev4.tar.gz#sha256=9387bff556d37ced3f0ef3d368f76281226496af14a39499560cb51158d6d520 (from https://pypi.org/simple/hapflk/), version: 1.3.5.dev4 2021-07-16T11:12:16,274 Found link https://files.pythonhosted.org/packages/a4/96/4b534230ad9ea961235c5841bde1054bacbb574f88fe19324a776d4b0992/hapflk-1.3.5.dev5.tar.gz#sha256=c76e80a664b5d2b2778b02ba9b2e263a55dcd4f0281e48ab90a5c11c97ed9bb6 (from https://pypi.org/simple/hapflk/), version: 1.3.5.dev5 2021-07-16T11:12:16,275 Found link https://files.pythonhosted.org/packages/5c/f9/f5bd0ea0712da4d11795fda5b40c44be0421a85d6b05f8e9687ce30b8089/hapflk-1.3.5.tar.gz#sha256=e49a28deb1d52470c6b6c5c27d85ad81d5076953c0ba80cac1cadd81733e2831 (from https://pypi.org/simple/hapflk/), version: 1.3.5 2021-07-16T11:12:16,275 Found link https://files.pythonhosted.org/packages/51/c4/ed7b823aa136185d750d60f53268cfb6804dcc87183dbe216135e63aa583/hapflk-1.4.tar.gz#sha256=ac2591a80b4ca382b520344a1b47c3b950e68b7d32d9662fc2a88c136de72823 (from https://pypi.org/simple/hapflk/), version: 1.4 2021-07-16T11:12:16,275 Found link https://files.pythonhosted.org/packages/c6/a6/ed1b0c03bdb79de6f288c5e982af3afcaae7a26cdd00ff75dd98bf81a13e/hapflk-2.0.dev0.tar.gz#sha256=f9d6270cf2b80d00edfbdbaa1e26d112c92bfa73938616dde9d7c6d1a239980e (from https://pypi.org/simple/hapflk/), version: 2.0.dev0 2021-07-16T11:12:16,275 Found link https://files.pythonhosted.org/packages/30/60/1dab8e6a54e7ef2c19a62114527d5512da17a09a590d5551610b2fce8195/hapflk-2.0.dev1.tar.gz#sha256=742d022fcdc7e3ddd5330748065c2b6c2ae314880a6845234ff08c1d8f692c90 (from https://pypi.org/simple/hapflk/), version: 2.0.dev1 2021-07-16T11:12:16,276 Found link https://files.pythonhosted.org/packages/89/5d/fa3af0a5d868d5154d1516696a317c13bcb686706143ec2052f789e17017/hapflk-2.0.dev2.tar.gz#sha256=bcac5a28ccec7e4daa1a216ce19717bca5e7686a42cd99ee5114be8ba03c2ef6 (from https://pypi.org/simple/hapflk/), version: 2.0.dev2 2021-07-16T11:12:16,276 Skipping link: not a file: https://pypi.org/simple/hapflk/ 2021-07-16T11:12:16,296 Given no hashes to check 1 links for project 'hapflk': discarding no candidates 2021-07-16T11:12:16,315 Collecting hapflk==2.0.dev0 2021-07-16T11:12:16,317 Created temporary directory: /tmp/pip-unpack-c17uy40h 2021-07-16T11:12:16,681 Downloading hapflk-2.0.dev0.tar.gz (512 kB) 2021-07-16T11:12:16,995 Added hapflk==2.0.dev0 from https://files.pythonhosted.org/packages/c6/a6/ed1b0c03bdb79de6f288c5e982af3afcaae7a26cdd00ff75dd98bf81a13e/hapflk-2.0.dev0.tar.gz#sha256=f9d6270cf2b80d00edfbdbaa1e26d112c92bfa73938616dde9d7c6d1a239980e to build tracker '/tmp/pip-req-tracker-vs8pgxbu' 2021-07-16T11:12:16,996 Running setup.py (path:/tmp/pip-wheel-li2wg2am/hapflk_5f00ead384f14e648f816beb633fccc3/setup.py) egg_info for package hapflk 2021-07-16T11:12:16,997 Created temporary directory: /tmp/pip-pip-egg-info-ch1mamwg 2021-07-16T11:12:16,997 Running command python setup.py egg_info 2021-07-16T11:12:22,068 warning: fastphase/fastphase.pyx:486:12: local variable 'k1' referenced before assignment 2021-07-16T11:12:22,069 warning: fastphase/fastphase.pyx:486:18: local variable 'kp1' referenced before assignment 2021-07-16T11:12:22,069 warning: fastphase/fastphase.pyx:487:16: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,069 warning: fastphase/fastphase.pyx:487:22: local variable 'kp2' referenced before assignment 2021-07-16T11:12:22,070 warning: fastphase/fastphase.pyx:488:23: local variable 'k1' referenced before assignment 2021-07-16T11:12:22,070 warning: fastphase/fastphase.pyx:488:27: local variable 'kp1' referenced before assignment 2021-07-16T11:12:22,070 warning: fastphase/fastphase.pyx:489:23: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,070 warning: fastphase/fastphase.pyx:489:27: local variable 'kp2' referenced before assignment 2021-07-16T11:12:22,070 warning: fastphase/fastphase.pyx:491:23: local variable 'k1' referenced before assignment 2021-07-16T11:12:22,070 warning: fastphase/fastphase.pyx:491:27: local variable 'kp1' referenced before assignment 2021-07-16T11:12:22,070 warning: fastphase/fastphase.pyx:492:23: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,070 warning: fastphase/fastphase.pyx:492:27: local variable 'kp2' referenced before assignment 2021-07-16T11:12:22,070 warning: fastphase/fastphase.pyx:493:15: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,071 warning: fastphase/fastphase.pyx:493:21: local variable 'kp2' referenced before assignment 2021-07-16T11:12:22,071 warning: fastphase/fastphase.pyx:494:19: local variable 'k1' referenced before assignment 2021-07-16T11:12:22,071 warning: fastphase/fastphase.pyx:494:23: local variable 'kp1' referenced before assignment 2021-07-16T11:12:22,071 warning: fastphase/fastphase.pyx:495:19: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,071 warning: fastphase/fastphase.pyx:495:23: local variable 'kp2' referenced before assignment 2021-07-16T11:12:22,071 warning: fastphase/fastphase.pyx:496:15: local variable 'k1' referenced before assignment 2021-07-16T11:12:22,071 warning: fastphase/fastphase.pyx:496:21: local variable 'kp2' referenced before assignment 2021-07-16T11:12:22,072 warning: fastphase/fastphase.pyx:496:31: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,072 warning: fastphase/fastphase.pyx:496:37: local variable 'kp1' referenced before assignment 2021-07-16T11:12:22,072 warning: fastphase/fastphase.pyx:497:19: local variable 'k1' referenced before assignment 2021-07-16T11:12:22,072 warning: fastphase/fastphase.pyx:497:23: local variable 'kp2' referenced before assignment 2021-07-16T11:12:22,072 warning: fastphase/fastphase.pyx:498:19: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,072 warning: fastphase/fastphase.pyx:498:23: local variable 'kp1' referenced before assignment 2021-07-16T11:12:22,072 warning: fastphase/fastphase.pyx:499:15: local variable 'k1' referenced before assignment 2021-07-16T11:12:22,072 warning: fastphase/fastphase.pyx:499:21: local variable 'kp2' referenced before assignment 2021-07-16T11:12:22,072 warning: fastphase/fastphase.pyx:499:31: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,073 warning: fastphase/fastphase.pyx:499:37: local variable 'kp1' referenced before assignment 2021-07-16T11:12:22,073 warning: fastphase/fastphase.pyx:500:19: local variable 'k1' referenced before assignment 2021-07-16T11:12:22,073 warning: fastphase/fastphase.pyx:500:23: local variable 'kp2' referenced before assignment 2021-07-16T11:12:22,073 warning: fastphase/fastphase.pyx:501:16: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,073 warning: fastphase/fastphase.pyx:501:20: local variable 'kp1' referenced before assignment 2021-07-16T11:12:22,073 warning: fastphase/fastphase.pyx:503:19: local variable 'k1' referenced before assignment 2021-07-16T11:12:22,073 warning: fastphase/fastphase.pyx:503:23: local variable 'kp1' referenced before assignment 2021-07-16T11:12:22,073 warning: fastphase/fastphase.pyx:504:19: local variable 'k1' referenced before assignment 2021-07-16T11:12:22,074 warning: fastphase/fastphase.pyx:504:23: local variable 'kp2' referenced before assignment 2021-07-16T11:12:22,074 warning: fastphase/fastphase.pyx:505:19: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,074 warning: fastphase/fastphase.pyx:505:23: local variable 'kp1' referenced before assignment 2021-07-16T11:12:22,074 warning: fastphase/fastphase.pyx:506:19: local variable 'k2' referenced before assignment 2021-07-16T11:12:22,074 warning: fastphase/fastphase.pyx:506:23: local variable 'kp2' referenced before assignment 2021-07-16T11:12:24,296 /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-li2wg2am/hapflk_5f00ead384f14e648f816beb633fccc3/pgenlib/_pgenlib.pyx 2021-07-16T11:12:24,296 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-16T11:12:29,524 Compiling fastphase/fastphase.pyx because it depends on /home/piwheels/.local/lib/python3.9/site-packages/numpy/__init__.pxd. 2021-07-16T11:12:29,525 Compiling pgenlib/_pgenlib.pyx because it depends on /home/piwheels/.local/lib/python3.9/site-packages/numpy/__init__.pxd. 2021-07-16T11:12:29,525 [1/2] Cythonizing fastphase/fastphase.pyx 2021-07-16T11:12:29,525 [2/2] Cythonizing pgenlib/_pgenlib.pyx 2021-07-16T11:12:29,716 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0-dev0' to '2.0.dev0' 2021-07-16T11:12:29,716 warnings.warn(tmpl.format(**locals())) 2021-07-16T11:12:29,735 running egg_info 2021-07-16T11:12:29,737 creating /tmp/pip-pip-egg-info-ch1mamwg/hapflk.egg-info 2021-07-16T11:12:29,739 writing /tmp/pip-pip-egg-info-ch1mamwg/hapflk.egg-info/PKG-INFO 2021-07-16T11:12:29,741 writing dependency_links to /tmp/pip-pip-egg-info-ch1mamwg/hapflk.egg-info/dependency_links.txt 2021-07-16T11:12:29,744 writing top-level names to /tmp/pip-pip-egg-info-ch1mamwg/hapflk.egg-info/top_level.txt 2021-07-16T11:12:29,745 writing manifest file '/tmp/pip-pip-egg-info-ch1mamwg/hapflk.egg-info/SOURCES.txt' 2021-07-16T11:12:29,943 reading manifest file '/tmp/pip-pip-egg-info-ch1mamwg/hapflk.egg-info/SOURCES.txt' 2021-07-16T11:12:29,945 reading manifest template 'MANIFEST.in' 2021-07-16T11:12:29,947 warning: no files found matching '*' under directory 'utils' 2021-07-16T11:12:29,950 adding license file 'LICENSE.txt' 2021-07-16T11:12:29,950 adding license file 'COPYING.txt' 2021-07-16T11:12:29,954 writing manifest file '/tmp/pip-pip-egg-info-ch1mamwg/hapflk.egg-info/SOURCES.txt' 2021-07-16T11:12:30,257 Source in /tmp/pip-wheel-li2wg2am/hapflk_5f00ead384f14e648f816beb633fccc3 has version 2.0.dev0, which satisfies requirement hapflk==2.0.dev0 from https://files.pythonhosted.org/packages/c6/a6/ed1b0c03bdb79de6f288c5e982af3afcaae7a26cdd00ff75dd98bf81a13e/hapflk-2.0.dev0.tar.gz#sha256=f9d6270cf2b80d00edfbdbaa1e26d112c92bfa73938616dde9d7c6d1a239980e 2021-07-16T11:12:30,258 Removed hapflk==2.0.dev0 from https://files.pythonhosted.org/packages/c6/a6/ed1b0c03bdb79de6f288c5e982af3afcaae7a26cdd00ff75dd98bf81a13e/hapflk-2.0.dev0.tar.gz#sha256=f9d6270cf2b80d00edfbdbaa1e26d112c92bfa73938616dde9d7c6d1a239980e from build tracker '/tmp/pip-req-tracker-vs8pgxbu' 2021-07-16T11:12:30,263 Created temporary directory: /tmp/pip-unpack-2pogzuq_ 2021-07-16T11:12:30,263 Building wheels for collected packages: hapflk 2021-07-16T11:12:30,268 Created temporary directory: /tmp/pip-wheel-r7g78i1v 2021-07-16T11:12:30,269 Building wheel for hapflk (setup.py): started 2021-07-16T11:12:30,269 Destination directory: /tmp/pip-wheel-r7g78i1v 2021-07-16T11:12:30,270 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-li2wg2am/hapflk_5f00ead384f14e648f816beb633fccc3/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-li2wg2am/hapflk_5f00ead384f14e648f816beb633fccc3/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-r7g78i1v 2021-07-16T11:12:32,582 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0-dev0' to '2.0.dev0' 2021-07-16T11:12:32,583 warnings.warn(tmpl.format(**locals())) 2021-07-16T11:12:32,617 running bdist_wheel 2021-07-16T11:12:32,623 running build 2021-07-16T11:12:32,624 running build_py 2021-07-16T11:12:32,760 creating build 2021-07-16T11:12:32,760 creating build/lib.linux-armv7l-3.9 2021-07-16T11:12:32,761 creating build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:12:32,762 copying hapflk/utils.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:12:32,765 copying hapflk/hapflk.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:12:32,767 copying hapflk/hapflkadapt.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:12:32,771 copying hapflk/data.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:12:32,775 copying hapflk/InputOutput.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:12:32,778 copying hapflk/__init__.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:12:32,780 copying hapflk/popgen.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:12:32,783 copying hapflk/nj.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:12:32,787 running build_ext 2021-07-16T11:12:32,793 building 'hapflk.fastphase' extension 2021-07-16T11:12:32,793 creating build/temp.linux-armv7l-3.9 2021-07-16T11:12:32,794 creating build/temp.linux-armv7l-3.9/fastphase 2021-07-16T11:12:32,795 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c fastphase/fastphase.c -o build/temp.linux-armv7l-3.9/fastphase/fastphase.o 2021-07-16T11:12:33,245 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-16T11:12:33,245 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-16T11:12:33,245 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-16T11:12:33,245 from fastphase/fastphase.c:635: 2021-07-16T11:12:33,246 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-16T11:12:33,246 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-16T11:12:33,246 | ^~~~~~~ 2021-07-16T11:12:46,573 fastphase/fastphase.c: In function ‘__pyx_pw_6hapflk_9fastphase_11calc_cost_matrix_geno_tot’: 2021-07-16T11:12:46,583 fastphase/fastphase.c:15557:38: warning: ‘__pyx_v_k1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:12:46,584 15557 | if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_res.diminfo[1].shape; 2021-07-16T11:12:46,584 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:12:46,593 fastphase/fastphase.c:15137:7: note: ‘__pyx_v_k1’ was declared here 2021-07-16T11:12:46,594 15137 | int __pyx_v_k1; 2021-07-16T11:12:46,594 | ^~~~~~~~~~ 2021-07-16T11:12:46,602 fastphase/fastphase.c:15558:38: warning: ‘__pyx_v_kp1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:12:46,602 15558 | if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_res.diminfo[2].shape; 2021-07-16T11:12:46,602 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:12:46,612 fastphase/fastphase.c:15139:7: note: ‘__pyx_v_kp1’ was declared here 2021-07-16T11:12:46,612 15139 | int __pyx_v_kp1; 2021-07-16T11:12:46,613 | ^~~~~~~~~~~ 2021-07-16T11:12:46,621 fastphase/fastphase.c:15573:38: warning: ‘__pyx_v_kp2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:12:46,621 15573 | if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_pybuffernd_res.diminfo[2].shape; 2021-07-16T11:12:46,621 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:12:46,631 fastphase/fastphase.c:15140:7: note: ‘__pyx_v_kp2’ was declared here 2021-07-16T11:12:46,631 15140 | int __pyx_v_kp2; 2021-07-16T11:12:46,631 | ^~~~~~~~~~~ 2021-07-16T11:12:46,640 fastphase/fastphase.c:15587:38: warning: ‘__pyx_v_k2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:12:46,640 15587 | if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_res.diminfo[1].shape; 2021-07-16T11:12:46,640 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:12:46,652 fastphase/fastphase.c:15138:7: note: ‘__pyx_v_k2’ was declared here 2021-07-16T11:12:46,652 15138 | int __pyx_v_k2; 2021-07-16T11:12:46,652 | ^~~~~~~~~~ 2021-07-16T11:13:04,411 fastphase/fastphase.c: In function ‘__pyx_f_6hapflk_9fastphase_genViterbi.constprop’: 2021-07-16T11:13:04,412 fastphase/fastphase.c:1728:91: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:13:04,412 1728 | #define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1) 2021-07-16T11:13:04,412 | ^ 2021-07-16T11:13:04,423 fastphase/fastphase.c:17490:7: note: ‘__pyx_v_k’ was declared here 2021-07-16T11:13:04,423 17490 | int __pyx_v_k; 2021-07-16T11:13:04,423 | ^~~~~~~~~ 2021-07-16T11:13:04,424 fastphase/fastphase.c:548:40: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:13:04,424 548 | #define PyInt_FromLong PyLong_FromLong 2021-07-16T11:13:04,424 | ^~~~~~~~~~~~~~~ 2021-07-16T11:13:04,435 fastphase/fastphase.c:17491:7: note: ‘__pyx_v_l’ was declared here 2021-07-16T11:13:04,435 17491 | int __pyx_v_l; 2021-07-16T11:13:04,435 | ^~~~~~~~~ 2021-07-16T11:13:04,435 fastphase/fastphase.c:548:40: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:13:04,435 548 | #define PyInt_FromLong PyLong_FromLong 2021-07-16T11:13:04,435 | ^~~~~~~~~~~~~~~ 2021-07-16T11:13:04,446 fastphase/fastphase.c:17490:7: note: ‘__pyx_v_k’ was declared here 2021-07-16T11:13:04,446 17490 | int __pyx_v_k; 2021-07-16T11:13:04,446 | ^~~~~~~~~ 2021-07-16T11:13:04,455 fastphase/fastphase.c:18567:12: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:13:04,456 18567 | if (!__pyx_t_34) { 2021-07-16T11:13:04,456 | ^ 2021-07-16T11:13:04,465 fastphase/fastphase.c:18575:12: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:13:04,466 18575 | if (__pyx_t_33) { 2021-07-16T11:13:04,466 | ^ 2021-07-16T11:13:04,466 fastphase/fastphase.c:18575:12: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:13:21,690 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/fastphase/fastphase.o -o build/lib.linux-armv7l-3.9/hapflk/fastphase.cpython-39-arm-linux-gnueabihf.so 2021-07-16T11:13:21,945 building 'hapflk._pgenlib' extension 2021-07-16T11:13:21,946 creating build/temp.linux-armv7l-3.9/pgenlib 2021-07-16T11:13:21,947 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 -Ipgenlib -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c pgenlib/_pgenlib.cpp -o build/temp.linux-armv7l-3.9/pgenlib/_pgenlib.o -std=c++98 -Wno-unused-function 2021-07-16T11:13:22,287 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-16T11:13:22,287 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-16T11:13:22,287 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-16T11:13:22,287 from pgenlib/_pgenlib.cpp:662: 2021-07-16T11:13:22,288 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-16T11:13:22,288 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-16T11:13:22,288 | ^~~~~~~ 2021-07-16T11:13:23,353 pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_6hapflk_8_pgenlib_10PgenReader_read_range_internal8(__pyx_obj_6hapflk_8_pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, __pyx_opt_args_6hapflk_8_pgenlib_10PgenReader_read_range_internal8*)’: 2021-07-16T11:13:23,354 pgenlib/_pgenlib.cpp:6982:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,354 6982 | __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,354 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,357 pgenlib/_pgenlib.cpp:7038:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,357 7038 | __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,358 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,368 pgenlib/_pgenlib.cpp:7263:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,368 7263 | __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,369 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,372 pgenlib/_pgenlib.cpp:7319:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,372 7319 | __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,372 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,389 pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_6hapflk_8_pgenlib_10PgenReader_read_range_internal32(__pyx_obj_6hapflk_8_pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, __pyx_opt_args_6hapflk_8_pgenlib_10PgenReader_read_range_internal32*)’: 2021-07-16T11:13:23,389 pgenlib/_pgenlib.cpp:7974:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,389 7974 | __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,389 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,392 pgenlib/_pgenlib.cpp:8030:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,393 8030 | __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,393 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,401 pgenlib/_pgenlib.cpp:8255:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,401 8255 | __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,402 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,405 pgenlib/_pgenlib.cpp:8311:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,405 8311 | __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,405 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,422 pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_6hapflk_8_pgenlib_10PgenReader_read_range_internal64(__pyx_obj_6hapflk_8_pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, __pyx_opt_args_6hapflk_8_pgenlib_10PgenReader_read_range_internal64*)’: 2021-07-16T11:13:23,422 pgenlib/_pgenlib.cpp:8966:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,422 8966 | __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,422 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,426 pgenlib/_pgenlib.cpp:9022:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,426 9022 | __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,426 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,434 pgenlib/_pgenlib.cpp:9247:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,435 9247 | __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,435 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,438 pgenlib/_pgenlib.cpp:9303:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,438 9303 | __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,438 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,476 pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_6hapflk_8_pgenlib_10PgenReader_read_list_internal8(__pyx_obj_6hapflk_8_pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_6hapflk_8_pgenlib_10PgenReader_read_list_internal8*)’: 2021-07-16T11:13:23,477 pgenlib/_pgenlib.cpp:10399:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,477 10399 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,477 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,480 pgenlib/_pgenlib.cpp:10455:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,480 10455 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,480 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,489 pgenlib/_pgenlib.cpp:10696:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,490 10696 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,490 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,493 pgenlib/_pgenlib.cpp:10752:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,493 10752 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,493 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,512 pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_6hapflk_8_pgenlib_10PgenReader_read_list_internal32(__pyx_obj_6hapflk_8_pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_6hapflk_8_pgenlib_10PgenReader_read_list_internal32*)’: 2021-07-16T11:13:23,512 pgenlib/_pgenlib.cpp:11447:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,512 11447 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,512 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,515 pgenlib/_pgenlib.cpp:11503:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,516 11503 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,516 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,525 pgenlib/_pgenlib.cpp:11744:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,525 11744 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,525 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,528 pgenlib/_pgenlib.cpp:11800:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,528 11800 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,528 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,547 pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_6hapflk_8_pgenlib_10PgenReader_read_list_internal64(__pyx_obj_6hapflk_8_pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_6hapflk_8_pgenlib_10PgenReader_read_list_internal64*)’: 2021-07-16T11:13:23,547 pgenlib/_pgenlib.cpp:12495:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,547 12495 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,547 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,551 pgenlib/_pgenlib.cpp:12551:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,551 12551 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,551 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,560 pgenlib/_pgenlib.cpp:12792:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,560 12792 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:13:23,561 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,563 pgenlib/_pgenlib.cpp:12848:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,564 12848 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,564 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,621 pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_6hapflk_8_pgenlib_10PgenReader_read_alleles_range(__pyx_obj_6hapflk_8_pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, int, __pyx_opt_args_6hapflk_8_pgenlib_10PgenReader_read_alleles_range*)’: 2021-07-16T11:13:23,621 pgenlib/_pgenlib.cpp:14192:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,621 14192 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,621 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,624 pgenlib/_pgenlib.cpp:14248:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,624 14248 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2021-07-16T11:13:23,624 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,632 pgenlib/_pgenlib.cpp:14473:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,632 14473 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0); 2021-07-16T11:13:23,633 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,635 pgenlib/_pgenlib.cpp:14529:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,635 14529 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,636 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,673 pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_6hapflk_8_pgenlib_10PgenReader_read_alleles_list(__pyx_obj_6hapflk_8_pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, int, __pyx_opt_args_6hapflk_8_pgenlib_10PgenReader_read_alleles_list*)’: 2021-07-16T11:13:23,673 pgenlib/_pgenlib.cpp:15576:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,673 15576 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,673 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,676 pgenlib/_pgenlib.cpp:15632:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,676 15632 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2021-07-16T11:13:23,676 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,684 pgenlib/_pgenlib.cpp:15873:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,685 15873 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0); 2021-07-16T11:13:23,685 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:23,687 pgenlib/_pgenlib.cpp:15929:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T11:13:23,687 15929 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:13:23,688 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:13:48,120 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 -Ipgenlib -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c pgenlib/pgenlib_internal.cpp -o build/temp.linux-armv7l-3.9/pgenlib/pgenlib_internal.o -std=c++98 -Wno-unused-function 2021-07-16T11:13:48,272 pgenlib/pgenlib_internal.cpp:710:4: error: #error "Unaligned accesses in small_genoarr_count_3freq_incr()." 2021-07-16T11:13:48,273 710 | #error "Unaligned accesses in small_genoarr_count_3freq_incr()." 2021-07-16T11:13:48,273 | ^~~~~ 2021-07-16T11:13:48,273 pgenlib/pgenlib_internal.cpp:752:4: error: #error "Unaligned accesses in genoarr_count_subset_freqs()." 2021-07-16T11:13:48,273 752 | #error "Unaligned accesses in genoarr_count_subset_freqs()." 2021-07-16T11:13:48,273 | ^~~~~ 2021-07-16T11:13:48,276 pgenlib/pgenlib_internal.cpp:1911:4: error: #error "Unaligned accesses in pgfi_init_phase2()." 2021-07-16T11:13:48,277 1911 | #error "Unaligned accesses in pgfi_init_phase2()." 2021-07-16T11:13:48,277 | ^~~~~ 2021-07-16T11:13:48,281 pgenlib/pgenlib_internal.cpp:3145:4: error: #error "Unaligned accesses in parse_onebit_unsafe()." 2021-07-16T11:13:48,281 3145 | #error "Unaligned accesses in parse_onebit_unsafe()." 2021-07-16T11:13:48,281 | ^~~~~ 2021-07-16T11:13:48,282 pgenlib/pgenlib_internal.cpp:3178:4: error: #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)." 2021-07-16T11:13:48,282 3178 | #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)." 2021-07-16T11:13:48,283 | ^~~~~ 2021-07-16T11:13:48,287 pgenlib/pgenlib_internal.cpp:3761:4: error: #error "Unaligned accesses in bytesum_arr()." 2021-07-16T11:13:48,288 3761 | #error "Unaligned accesses in bytesum_arr()." 2021-07-16T11:13:48,288 | ^~~~~ 2021-07-16T11:13:48,289 pgenlib/pgenlib_internal.cpp:3814:4: error: #error "Unaligned accesses in skip_difflist_ids()." 2021-07-16T11:13:48,289 3814 | #error "Unaligned accesses in skip_difflist_ids()." 2021-07-16T11:13:48,290 | ^~~~~ 2021-07-16T11:13:48,292 pgenlib/pgenlib_internal.cpp:3940:4: error: #error "Unaligned accesses in countparse_onebit_subset()." 2021-07-16T11:13:48,292 3940 | #error "Unaligned accesses in countparse_onebit_subset()." 2021-07-16T11:13:48,292 | ^~~~~ 2021-07-16T11:13:48,297 pgenlib/pgenlib_internal.cpp:4923:4: error: #error "Unaligned accesses in parse_just_ambig_ids()." 2021-07-16T11:13:48,297 4923 | #error "Unaligned accesses in parse_just_ambig_ids()." 2021-07-16T11:13:48,297 | ^~~~~ 2021-07-16T11:13:48,301 pgenlib/pgenlib_internal.cpp:5454:4: error: #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()." 2021-07-16T11:13:48,302 5454 | #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()." 2021-07-16T11:13:48,302 | ^~~~~ 2021-07-16T11:13:48,305 pgenlib/pgenlib_internal.cpp:5670:4: error: #error "Unaligned accesses in parse_dosage16()." 2021-07-16T11:13:48,305 5670 | #error "Unaligned accesses in parse_dosage16()." 2021-07-16T11:13:48,305 | ^~~~~ 2021-07-16T11:13:48,308 pgenlib/pgenlib_internal.cpp:5889:4: error: #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()." 2021-07-16T11:13:48,309 5889 | #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()." 2021-07-16T11:13:48,309 | ^~~~~ 2021-07-16T11:13:48,313 pgenlib/pgenlib_internal.cpp:6294:4: error: #error "Unaligned accesses in pgr_read_missingness_dosage()." 2021-07-16T11:13:48,313 6294 | #error "Unaligned accesses in pgr_read_missingness_dosage()." 2021-07-16T11:13:48,313 | ^~~~~ 2021-07-16T11:13:48,317 pgenlib/pgenlib_internal.cpp:6542:4: error: #error "Unaligned accesses in validate_onebit()." 2021-07-16T11:13:48,317 6542 | #error "Unaligned accesses in validate_onebit()." 2021-07-16T11:13:48,317 | ^~~~~ 2021-07-16T11:13:48,321 pgenlib/pgenlib_internal.cpp:6760:4: error: #error "Unaligned accesses in validate_dosage16()." 2021-07-16T11:13:48,321 6760 | #error "Unaligned accesses in validate_dosage16()." 2021-07-16T11:13:48,321 | ^~~~~ 2021-07-16T11:13:48,327 pgenlib/pgenlib_internal.cpp:7651:4: error: #error "Unaligned accesses in save_ld_difflist()." 2021-07-16T11:13:48,327 7651 | #error "Unaligned accesses in save_ld_difflist()." 2021-07-16T11:13:48,328 | ^~~~~ 2021-07-16T11:13:48,332 pgenlib/pgenlib_internal.cpp:7793:4: error: #error "Unaligned accesses in save_onebit()." 2021-07-16T11:13:48,332 7793 | #error "Unaligned accesses in save_onebit()." 2021-07-16T11:13:48,332 | ^~~~~ 2021-07-16T11:13:48,337 pgenlib/pgenlib_internal.cpp:8025:4: error: #error "Unaligned accesses in save_ld_two_list_delta()." 2021-07-16T11:13:48,337 8025 | #error "Unaligned accesses in save_ld_two_list_delta()." 2021-07-16T11:13:48,337 | ^~~~~ 2021-07-16T11:13:48,342 pgenlib/pgenlib_internal.cpp:8295:4: error: #error "Unaligned accesses in append_hphase()." 2021-07-16T11:13:48,342 8295 | #error "Unaligned accesses in append_hphase()." 2021-07-16T11:13:48,342 | ^~~~~ 2021-07-16T11:13:48,801 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-16T11:13:48,946 Building wheel for hapflk (setup.py): finished with status 'error' 2021-07-16T11:13:48,946 ERROR: Failed building wheel for hapflk 2021-07-16T11:13:48,947 Running setup.py clean for hapflk 2021-07-16T11:13:48,947 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-li2wg2am/hapflk_5f00ead384f14e648f816beb633fccc3/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-li2wg2am/hapflk_5f00ead384f14e648f816beb633fccc3/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 2021-07-16T11:13:51,417 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0-dev0' to '2.0.dev0' 2021-07-16T11:13:51,418 warnings.warn(tmpl.format(**locals())) 2021-07-16T11:13:51,425 running clean 2021-07-16T11:13:51,429 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-16T11:13:51,435 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-16T11:13:51,441 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-16T11:13:51,442 'build/scripts-3.9' does not exist -- can't clean it 2021-07-16T11:13:51,442 removing 'build' 2021-07-16T11:13:51,565 Failed to build hapflk 2021-07-16T11:13:51,566 ERROR: Failed to build one or more wheels 2021-07-16T11:13:51,567 Exception information: 2021-07-16T11:13:51,567 Traceback (most recent call last): 2021-07-16T11:13:51,567 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-16T11:13:51,567 status = self.run(options, args) 2021-07-16T11:13:51,567 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-16T11:13:51,567 return func(self, options, args) 2021-07-16T11:13:51,567 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-16T11:13:51,567 raise CommandError( 2021-07-16T11:13:51,567 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-16T11:13:51,571 Removed build tracker: '/tmp/pip-req-tracker-vs8pgxbu'