2021-07-16T11:22:08,731 Created temporary directory: /tmp/pip-ephem-wheel-cache-fxt7b5vy 2021-07-16T11:22:08,736 Created temporary directory: /tmp/pip-req-tracker-6cmxmxe8 2021-07-16T11:22:08,736 Initialized build tracking at /tmp/pip-req-tracker-6cmxmxe8 2021-07-16T11:22:08,737 Created build tracker: /tmp/pip-req-tracker-6cmxmxe8 2021-07-16T11:22:08,737 Entered build tracker: /tmp/pip-req-tracker-6cmxmxe8 2021-07-16T11:22:08,738 Created temporary directory: /tmp/pip-wheel-d3ebdw2u 2021-07-16T11:22:08,789 1 location(s) to search for versions of hapflk: 2021-07-16T11:22:08,789 * https://pypi.org/simple/hapflk/ 2021-07-16T11:22:08,790 Fetching project page and analyzing links: https://pypi.org/simple/hapflk/ 2021-07-16T11:22:08,791 Getting page https://pypi.org/simple/hapflk/ 2021-07-16T11:22:08,794 Found index url https://pypi.org/simple 2021-07-16T11:22:08,919 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 2021-07-16T11:22:08,920 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 2021-07-16T11:22:08,921 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 2021-07-16T11:22:08,922 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 2021-07-16T11:22:08,923 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 2021-07-16T11:22:08,923 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 2021-07-16T11:22:08,924 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 2021-07-16T11:22:08,925 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 2021-07-16T11:22:08,925 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 2021-07-16T11:22:08,926 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 2021-07-16T11:22:08,927 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 2021-07-16T11:22:08,928 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 2021-07-16T11:22:08,928 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 2021-07-16T11:22:08,929 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 2021-07-16T11:22:08,930 Skipping link: not a file: https://pypi.org/simple/hapflk/ 2021-07-16T11:22:08,961 Given no hashes to check 1 links for project 'hapflk': discarding no candidates 2021-07-16T11:22:09,012 Collecting hapflk==2.0.dev2 2021-07-16T11:22:09,025 Created temporary directory: /tmp/pip-unpack-x59cg11w 2021-07-16T11:22:09,433 Downloading hapflk-2.0.dev2.tar.gz (511 kB) 2021-07-16T11:22:09,918 Added hapflk==2.0.dev2 from https://files.pythonhosted.org/packages/89/5d/fa3af0a5d868d5154d1516696a317c13bcb686706143ec2052f789e17017/hapflk-2.0.dev2.tar.gz#sha256=bcac5a28ccec7e4daa1a216ce19717bca5e7686a42cd99ee5114be8ba03c2ef6 to build tracker '/tmp/pip-req-tracker-6cmxmxe8' 2021-07-16T11:22:09,920 Running setup.py (path:/tmp/pip-wheel-d3ebdw2u/hapflk_a8b87c517e9f475aa0c8158c5d029354/setup.py) egg_info for package hapflk 2021-07-16T11:22:09,921 Created temporary directory: /tmp/pip-pip-egg-info-zi5oktr2 2021-07-16T11:22:09,922 Running command python setup.py egg_info 2021-07-16T11:22:19,387 warning: fastphase/fastphase.pyx:486:12: local variable 'k1' referenced before assignment 2021-07-16T11:22:19,388 warning: fastphase/fastphase.pyx:486:18: local variable 'kp1' referenced before assignment 2021-07-16T11:22:19,389 warning: fastphase/fastphase.pyx:487:16: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,389 warning: fastphase/fastphase.pyx:487:22: local variable 'kp2' referenced before assignment 2021-07-16T11:22:19,389 warning: fastphase/fastphase.pyx:488:23: local variable 'k1' referenced before assignment 2021-07-16T11:22:19,390 warning: fastphase/fastphase.pyx:488:27: local variable 'kp1' referenced before assignment 2021-07-16T11:22:19,390 warning: fastphase/fastphase.pyx:489:23: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,390 warning: fastphase/fastphase.pyx:489:27: local variable 'kp2' referenced before assignment 2021-07-16T11:22:19,390 warning: fastphase/fastphase.pyx:491:23: local variable 'k1' referenced before assignment 2021-07-16T11:22:19,391 warning: fastphase/fastphase.pyx:491:27: local variable 'kp1' referenced before assignment 2021-07-16T11:22:19,391 warning: fastphase/fastphase.pyx:492:23: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,391 warning: fastphase/fastphase.pyx:492:27: local variable 'kp2' referenced before assignment 2021-07-16T11:22:19,392 warning: fastphase/fastphase.pyx:493:15: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,392 warning: fastphase/fastphase.pyx:493:21: local variable 'kp2' referenced before assignment 2021-07-16T11:22:19,392 warning: fastphase/fastphase.pyx:494:19: local variable 'k1' referenced before assignment 2021-07-16T11:22:19,393 warning: fastphase/fastphase.pyx:494:23: local variable 'kp1' referenced before assignment 2021-07-16T11:22:19,393 warning: fastphase/fastphase.pyx:495:19: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,393 warning: fastphase/fastphase.pyx:495:23: local variable 'kp2' referenced before assignment 2021-07-16T11:22:19,393 warning: fastphase/fastphase.pyx:496:15: local variable 'k1' referenced before assignment 2021-07-16T11:22:19,394 warning: fastphase/fastphase.pyx:496:21: local variable 'kp2' referenced before assignment 2021-07-16T11:22:19,394 warning: fastphase/fastphase.pyx:496:31: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,394 warning: fastphase/fastphase.pyx:496:37: local variable 'kp1' referenced before assignment 2021-07-16T11:22:19,395 warning: fastphase/fastphase.pyx:497:19: local variable 'k1' referenced before assignment 2021-07-16T11:22:19,395 warning: fastphase/fastphase.pyx:497:23: local variable 'kp2' referenced before assignment 2021-07-16T11:22:19,396 warning: fastphase/fastphase.pyx:498:19: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,396 warning: fastphase/fastphase.pyx:498:23: local variable 'kp1' referenced before assignment 2021-07-16T11:22:19,396 warning: fastphase/fastphase.pyx:499:15: local variable 'k1' referenced before assignment 2021-07-16T11:22:19,397 warning: fastphase/fastphase.pyx:499:21: local variable 'kp2' referenced before assignment 2021-07-16T11:22:19,397 warning: fastphase/fastphase.pyx:499:31: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,397 warning: fastphase/fastphase.pyx:499:37: local variable 'kp1' referenced before assignment 2021-07-16T11:22:19,398 warning: fastphase/fastphase.pyx:500:19: local variable 'k1' referenced before assignment 2021-07-16T11:22:19,398 warning: fastphase/fastphase.pyx:500:23: local variable 'kp2' referenced before assignment 2021-07-16T11:22:19,399 warning: fastphase/fastphase.pyx:501:16: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,399 warning: fastphase/fastphase.pyx:501:20: local variable 'kp1' referenced before assignment 2021-07-16T11:22:19,399 warning: fastphase/fastphase.pyx:503:19: local variable 'k1' referenced before assignment 2021-07-16T11:22:19,400 warning: fastphase/fastphase.pyx:503:23: local variable 'kp1' referenced before assignment 2021-07-16T11:22:19,400 warning: fastphase/fastphase.pyx:504:19: local variable 'k1' referenced before assignment 2021-07-16T11:22:19,401 warning: fastphase/fastphase.pyx:504:23: local variable 'kp2' referenced before assignment 2021-07-16T11:22:19,401 warning: fastphase/fastphase.pyx:505:19: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,402 warning: fastphase/fastphase.pyx:505:23: local variable 'kp1' referenced before assignment 2021-07-16T11:22:19,402 warning: fastphase/fastphase.pyx:506:19: local variable 'k2' referenced before assignment 2021-07-16T11:22:19,403 warning: fastphase/fastphase.pyx:506:23: local variable 'kp2' referenced before assignment 2021-07-16T11:22:24,324 /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-d3ebdw2u/hapflk_a8b87c517e9f475aa0c8158c5d029354/pgenlib/_pgenlib.pyx 2021-07-16T11:22:24,325 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-16T11:22:33,841 Compiling fastphase/fastphase.pyx because it depends on /home/piwheels/.local/lib/python3.9/site-packages/numpy/__init__.pxd. 2021-07-16T11:22:33,842 Compiling pgenlib/_pgenlib.pyx because it depends on /home/piwheels/.local/lib/python3.9/site-packages/numpy/__init__.pxd. 2021-07-16T11:22:33,842 [1/2] Cythonizing fastphase/fastphase.pyx 2021-07-16T11:22:33,842 [2/2] Cythonizing pgenlib/_pgenlib.pyx 2021-07-16T11:22:34,113 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0-dev2' to '2.0.dev2' 2021-07-16T11:22:34,113 warnings.warn(tmpl.format(**locals())) 2021-07-16T11:22:34,151 running egg_info 2021-07-16T11:22:34,157 creating /tmp/pip-pip-egg-info-zi5oktr2/hapflk.egg-info 2021-07-16T11:22:34,159 writing /tmp/pip-pip-egg-info-zi5oktr2/hapflk.egg-info/PKG-INFO 2021-07-16T11:22:34,162 writing dependency_links to /tmp/pip-pip-egg-info-zi5oktr2/hapflk.egg-info/dependency_links.txt 2021-07-16T11:22:34,166 writing requirements to /tmp/pip-pip-egg-info-zi5oktr2/hapflk.egg-info/requires.txt 2021-07-16T11:22:34,168 writing top-level names to /tmp/pip-pip-egg-info-zi5oktr2/hapflk.egg-info/top_level.txt 2021-07-16T11:22:34,170 writing manifest file '/tmp/pip-pip-egg-info-zi5oktr2/hapflk.egg-info/SOURCES.txt' 2021-07-16T11:22:34,417 reading manifest file '/tmp/pip-pip-egg-info-zi5oktr2/hapflk.egg-info/SOURCES.txt' 2021-07-16T11:22:34,420 reading manifest template 'MANIFEST.in' 2021-07-16T11:22:34,423 warning: no files found matching '*' under directory 'utils' 2021-07-16T11:22:34,426 adding license file 'LICENSE.txt' 2021-07-16T11:22:34,426 adding license file 'COPYING.txt' 2021-07-16T11:22:34,429 writing manifest file '/tmp/pip-pip-egg-info-zi5oktr2/hapflk.egg-info/SOURCES.txt' 2021-07-16T11:22:35,061 Source in /tmp/pip-wheel-d3ebdw2u/hapflk_a8b87c517e9f475aa0c8158c5d029354 has version 2.0.dev2, which satisfies requirement hapflk==2.0.dev2 from https://files.pythonhosted.org/packages/89/5d/fa3af0a5d868d5154d1516696a317c13bcb686706143ec2052f789e17017/hapflk-2.0.dev2.tar.gz#sha256=bcac5a28ccec7e4daa1a216ce19717bca5e7686a42cd99ee5114be8ba03c2ef6 2021-07-16T11:22:35,062 Removed hapflk==2.0.dev2 from https://files.pythonhosted.org/packages/89/5d/fa3af0a5d868d5154d1516696a317c13bcb686706143ec2052f789e17017/hapflk-2.0.dev2.tar.gz#sha256=bcac5a28ccec7e4daa1a216ce19717bca5e7686a42cd99ee5114be8ba03c2ef6 from build tracker '/tmp/pip-req-tracker-6cmxmxe8' 2021-07-16T11:22:35,078 Created temporary directory: /tmp/pip-unpack-uwdha174 2021-07-16T11:22:35,079 Building wheels for collected packages: hapflk 2021-07-16T11:22:35,087 Created temporary directory: /tmp/pip-wheel-kzzyz8me 2021-07-16T11:22:35,088 Building wheel for hapflk (setup.py): started 2021-07-16T11:22:35,089 Destination directory: /tmp/pip-wheel-kzzyz8me 2021-07-16T11:22:35,090 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-d3ebdw2u/hapflk_a8b87c517e9f475aa0c8158c5d029354/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-d3ebdw2u/hapflk_a8b87c517e9f475aa0c8158c5d029354/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-kzzyz8me 2021-07-16T11:22:38,834 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0-dev2' to '2.0.dev2' 2021-07-16T11:22:38,835 warnings.warn(tmpl.format(**locals())) 2021-07-16T11:22:38,892 running bdist_wheel 2021-07-16T11:22:38,900 running build 2021-07-16T11:22:38,900 running build_py 2021-07-16T11:22:39,087 creating build 2021-07-16T11:22:39,087 creating build/lib.linux-armv7l-3.9 2021-07-16T11:22:39,088 creating build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:22:39,090 copying hapflk/data.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:22:39,095 copying hapflk/hapflkadapt.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:22:39,099 copying hapflk/hapflk.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:22:39,103 copying hapflk/utils.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:22:39,107 copying hapflk/popgen.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:22:39,111 copying hapflk/InputOutput.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:22:39,115 copying hapflk/nj.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:22:39,119 copying hapflk/__init__.py -> build/lib.linux-armv7l-3.9/hapflk 2021-07-16T11:22:39,123 running build_ext 2021-07-16T11:22:39,130 building 'hapflk.fastphase' extension 2021-07-16T11:22:39,131 creating build/temp.linux-armv7l-3.9 2021-07-16T11:22:39,132 creating build/temp.linux-armv7l-3.9/fastphase 2021-07-16T11:22:39,133 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 2021-07-16T11:22:40,457 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-16T11:22:40,457 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-16T11:22:40,457 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-16T11:22:40,458 from fastphase/fastphase.c:635: 2021-07-16T11:22:40,458 /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] 2021-07-16T11:22:40,458 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-16T11:22:40,459 | ^~~~~~~ 2021-07-16T11:23:02,795 fastphase/fastphase.c: In function ‘__pyx_pw_6hapflk_9fastphase_11calc_cost_matrix_geno_tot’: 2021-07-16T11:23:02,815 fastphase/fastphase.c:15557:38: warning: ‘__pyx_v_k1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:23:02,815 15557 | if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_res.diminfo[1].shape; 2021-07-16T11:23:02,816 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:23:02,824 fastphase/fastphase.c:15137:7: note: ‘__pyx_v_k1’ was declared here 2021-07-16T11:23:02,825 15137 | int __pyx_v_k1; 2021-07-16T11:23:02,825 | ^~~~~~~~~~ 2021-07-16T11:23:02,843 fastphase/fastphase.c:15558:38: warning: ‘__pyx_v_kp1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:23:02,843 15558 | if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_res.diminfo[2].shape; 2021-07-16T11:23:02,843 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:23:02,872 fastphase/fastphase.c:15139:7: note: ‘__pyx_v_kp1’ was declared here 2021-07-16T11:23:02,873 15139 | int __pyx_v_kp1; 2021-07-16T11:23:02,873 | ^~~~~~~~~~~ 2021-07-16T11:23:02,882 fastphase/fastphase.c:15573:38: warning: ‘__pyx_v_kp2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:23:02,883 15573 | if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_pybuffernd_res.diminfo[2].shape; 2021-07-16T11:23:02,883 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:23:02,905 fastphase/fastphase.c:15140:7: note: ‘__pyx_v_kp2’ was declared here 2021-07-16T11:23:02,905 15140 | int __pyx_v_kp2; 2021-07-16T11:23:02,906 | ^~~~~~~~~~~ 2021-07-16T11:23:02,914 fastphase/fastphase.c:15587:38: warning: ‘__pyx_v_k2’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:23:02,915 15587 | if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_res.diminfo[1].shape; 2021-07-16T11:23:02,915 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:23:02,925 fastphase/fastphase.c:15138:7: note: ‘__pyx_v_k2’ was declared here 2021-07-16T11:23:02,926 15138 | int __pyx_v_k2; 2021-07-16T11:23:02,926 | ^~~~~~~~~~ 2021-07-16T11:23:35,546 fastphase/fastphase.c: In function ‘__pyx_f_6hapflk_9fastphase_genViterbi.constprop’: 2021-07-16T11:23:35,556 fastphase/fastphase.c:1728:91: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:23:35,556 1728 | #define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1) 2021-07-16T11:23:35,557 | ^ 2021-07-16T11:23:35,568 fastphase/fastphase.c:17490:7: note: ‘__pyx_v_k’ was declared here 2021-07-16T11:23:35,569 17490 | int __pyx_v_k; 2021-07-16T11:23:35,569 | ^~~~~~~~~ 2021-07-16T11:23:35,577 fastphase/fastphase.c:548:40: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:23:35,577 548 | #define PyInt_FromLong PyLong_FromLong 2021-07-16T11:23:35,578 | ^~~~~~~~~~~~~~~ 2021-07-16T11:23:35,589 fastphase/fastphase.c:17491:7: note: ‘__pyx_v_l’ was declared here 2021-07-16T11:23:35,589 17491 | int __pyx_v_l; 2021-07-16T11:23:35,590 | ^~~~~~~~~ 2021-07-16T11:23:35,606 fastphase/fastphase.c:548:40: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:23:35,606 548 | #define PyInt_FromLong PyLong_FromLong 2021-07-16T11:23:35,606 | ^~~~~~~~~~~~~~~ 2021-07-16T11:23:35,618 fastphase/fastphase.c:17490:7: note: ‘__pyx_v_k’ was declared here 2021-07-16T11:23:35,618 17490 | int __pyx_v_k; 2021-07-16T11:23:35,618 | ^~~~~~~~~ 2021-07-16T11:23:35,645 fastphase/fastphase.c:18567:12: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:23:35,646 18567 | if (!__pyx_t_34) { 2021-07-16T11:23:35,646 | ^ 2021-07-16T11:23:35,666 fastphase/fastphase.c:18575:12: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:23:35,666 18575 | if (__pyx_t_33) { 2021-07-16T11:23:35,667 | ^ 2021-07-16T11:23:35,667 fastphase/fastphase.c:18575:12: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-16T11:24:07,724 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 2021-07-16T11:24:08,077 building 'hapflk._pgenlib' extension 2021-07-16T11:24:08,078 creating build/temp.linux-armv7l-3.9/pgenlib 2021-07-16T11:24:08,079 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 2021-07-16T11:24:08,593 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-16T11:24:08,593 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-16T11:24:08,593 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-16T11:24:08,594 from pgenlib/_pgenlib.cpp:662: 2021-07-16T11:24:08,594 /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] 2021-07-16T11:24:08,594 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-16T11:24:08,595 | ^~~~~~~ 2021-07-16T11:24:10,346 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*)’: 2021-07-16T11:24:10,347 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] 2021-07-16T11:24:10,347 6982 | __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,347 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,353 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] 2021-07-16T11:24:10,353 7038 | __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,354 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,380 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] 2021-07-16T11:24:10,381 7263 | __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,381 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,400 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] 2021-07-16T11:24:10,400 7319 | __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,401 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,435 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*)’: 2021-07-16T11:24:10,435 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] 2021-07-16T11:24:10,435 7974 | __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,436 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,460 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] 2021-07-16T11:24:10,461 8030 | __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,461 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,475 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] 2021-07-16T11:24:10,475 8255 | __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,476 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,480 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] 2021-07-16T11:24:10,481 8311 | __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,481 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,507 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*)’: 2021-07-16T11:24:10,507 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] 2021-07-16T11:24:10,508 8966 | __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,508 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,513 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] 2021-07-16T11:24:10,514 9022 | __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,514 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,526 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] 2021-07-16T11:24:10,527 9247 | __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,527 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,531 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] 2021-07-16T11:24:10,532 9303 | __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,532 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,588 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*)’: 2021-07-16T11:24:10,589 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] 2021-07-16T11:24:10,589 10399 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,589 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,594 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] 2021-07-16T11:24:10,595 10455 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,595 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,610 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] 2021-07-16T11:24:10,610 10696 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,611 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,615 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] 2021-07-16T11:24:10,616 10752 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,616 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,642 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*)’: 2021-07-16T11:24:10,642 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] 2021-07-16T11:24:10,642 11447 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,643 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,648 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] 2021-07-16T11:24:10,649 11503 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,649 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,663 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] 2021-07-16T11:24:10,663 11744 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,663 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,668 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] 2021-07-16T11:24:10,668 11800 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,669 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,694 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*)’: 2021-07-16T11:24:10,695 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] 2021-07-16T11:24:10,695 12495 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,696 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,701 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] 2021-07-16T11:24:10,701 12551 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,701 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,739 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] 2021-07-16T11:24:10,739 12792 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2021-07-16T11:24:10,739 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,744 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] 2021-07-16T11:24:10,745 12848 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,745 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,897 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*)’: 2021-07-16T11:24:10,897 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] 2021-07-16T11:24:10,898 14192 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,898 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,902 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] 2021-07-16T11:24:10,902 14248 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2021-07-16T11:24:10,902 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,914 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] 2021-07-16T11:24:10,914 14473 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0); 2021-07-16T11:24:10,915 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,919 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] 2021-07-16T11:24:10,919 14529 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,920 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,975 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*)’: 2021-07-16T11:24:10,975 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] 2021-07-16T11:24:10,975 15576 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,976 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,979 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] 2021-07-16T11:24:10,979 15632 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2021-07-16T11:24:10,980 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,992 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] 2021-07-16T11:24:10,992 15873 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0); 2021-07-16T11:24:10,993 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:10,996 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] 2021-07-16T11:24:10,997 15929 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2021-07-16T11:24:10,997 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T11:24:57,393 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 2021-07-16T11:24:57,653 pgenlib/pgenlib_internal.cpp:710:4: error: #error "Unaligned accesses in small_genoarr_count_3freq_incr()." 2021-07-16T11:24:57,653 710 | #error "Unaligned accesses in small_genoarr_count_3freq_incr()." 2021-07-16T11:24:57,654 | ^~~~~ 2021-07-16T11:24:57,654 pgenlib/pgenlib_internal.cpp:752:4: error: #error "Unaligned accesses in genoarr_count_subset_freqs()." 2021-07-16T11:24:57,654 752 | #error "Unaligned accesses in genoarr_count_subset_freqs()." 2021-07-16T11:24:57,654 | ^~~~~ 2021-07-16T11:24:57,658 pgenlib/pgenlib_internal.cpp:1911:4: error: #error "Unaligned accesses in pgfi_init_phase2()." 2021-07-16T11:24:57,658 1911 | #error "Unaligned accesses in pgfi_init_phase2()." 2021-07-16T11:24:57,659 | ^~~~~ 2021-07-16T11:24:57,664 pgenlib/pgenlib_internal.cpp:3145:4: error: #error "Unaligned accesses in parse_onebit_unsafe()." 2021-07-16T11:24:57,664 3145 | #error "Unaligned accesses in parse_onebit_unsafe()." 2021-07-16T11:24:57,664 | ^~~~~ 2021-07-16T11:24:57,666 pgenlib/pgenlib_internal.cpp:3178:4: error: #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)." 2021-07-16T11:24:57,666 3178 | #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)." 2021-07-16T11:24:57,666 | ^~~~~ 2021-07-16T11:24:57,672 pgenlib/pgenlib_internal.cpp:3761:4: error: #error "Unaligned accesses in bytesum_arr()." 2021-07-16T11:24:57,673 3761 | #error "Unaligned accesses in bytesum_arr()." 2021-07-16T11:24:57,673 | ^~~~~ 2021-07-16T11:24:57,675 pgenlib/pgenlib_internal.cpp:3814:4: error: #error "Unaligned accesses in skip_difflist_ids()." 2021-07-16T11:24:57,675 3814 | #error "Unaligned accesses in skip_difflist_ids()." 2021-07-16T11:24:57,675 | ^~~~~ 2021-07-16T11:24:57,677 pgenlib/pgenlib_internal.cpp:3940:4: error: #error "Unaligned accesses in countparse_onebit_subset()." 2021-07-16T11:24:57,678 3940 | #error "Unaligned accesses in countparse_onebit_subset()." 2021-07-16T11:24:57,678 | ^~~~~ 2021-07-16T11:24:57,683 pgenlib/pgenlib_internal.cpp:4923:4: error: #error "Unaligned accesses in parse_just_ambig_ids()." 2021-07-16T11:24:57,684 4923 | #error "Unaligned accesses in parse_just_ambig_ids()." 2021-07-16T11:24:57,684 | ^~~~~ 2021-07-16T11:24:57,689 pgenlib/pgenlib_internal.cpp:5454:4: error: #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()." 2021-07-16T11:24:57,690 5454 | #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()." 2021-07-16T11:24:57,690 | ^~~~~ 2021-07-16T11:24:57,694 pgenlib/pgenlib_internal.cpp:5670:4: error: #error "Unaligned accesses in parse_dosage16()." 2021-07-16T11:24:57,694 5670 | #error "Unaligned accesses in parse_dosage16()." 2021-07-16T11:24:57,695 | ^~~~~ 2021-07-16T11:24:57,699 pgenlib/pgenlib_internal.cpp:5889:4: error: #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()." 2021-07-16T11:24:57,699 5889 | #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()." 2021-07-16T11:24:57,699 | ^~~~~ 2021-07-16T11:24:57,704 pgenlib/pgenlib_internal.cpp:6294:4: error: #error "Unaligned accesses in pgr_read_missingness_dosage()." 2021-07-16T11:24:57,704 6294 | #error "Unaligned accesses in pgr_read_missingness_dosage()." 2021-07-16T11:24:57,704 | ^~~~~ 2021-07-16T11:24:57,708 pgenlib/pgenlib_internal.cpp:6542:4: error: #error "Unaligned accesses in validate_onebit()." 2021-07-16T11:24:57,708 6542 | #error "Unaligned accesses in validate_onebit()." 2021-07-16T11:24:57,709 | ^~~~~ 2021-07-16T11:24:57,712 pgenlib/pgenlib_internal.cpp:6760:4: error: #error "Unaligned accesses in validate_dosage16()." 2021-07-16T11:24:57,712 6760 | #error "Unaligned accesses in validate_dosage16()." 2021-07-16T11:24:57,713 | ^~~~~ 2021-07-16T11:24:57,719 pgenlib/pgenlib_internal.cpp:7651:4: error: #error "Unaligned accesses in save_ld_difflist()." 2021-07-16T11:24:57,719 7651 | #error "Unaligned accesses in save_ld_difflist()." 2021-07-16T11:24:57,720 | ^~~~~ 2021-07-16T11:24:57,724 pgenlib/pgenlib_internal.cpp:7793:4: error: #error "Unaligned accesses in save_onebit()." 2021-07-16T11:24:57,724 7793 | #error "Unaligned accesses in save_onebit()." 2021-07-16T11:24:57,724 | ^~~~~ 2021-07-16T11:24:57,729 pgenlib/pgenlib_internal.cpp:8025:4: error: #error "Unaligned accesses in save_ld_two_list_delta()." 2021-07-16T11:24:57,729 8025 | #error "Unaligned accesses in save_ld_two_list_delta()." 2021-07-16T11:24:57,729 | ^~~~~ 2021-07-16T11:24:57,734 pgenlib/pgenlib_internal.cpp:8295:4: error: #error "Unaligned accesses in append_hphase()." 2021-07-16T11:24:57,734 8295 | #error "Unaligned accesses in append_hphase()." 2021-07-16T11:24:57,735 | ^~~~~ 2021-07-16T11:24:58,485 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-16T11:24:58,797 Building wheel for hapflk (setup.py): finished with status 'error' 2021-07-16T11:24:58,798 ERROR: Failed building wheel for hapflk 2021-07-16T11:24:58,799 Running setup.py clean for hapflk 2021-07-16T11:24:58,800 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-d3ebdw2u/hapflk_a8b87c517e9f475aa0c8158c5d029354/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-d3ebdw2u/hapflk_a8b87c517e9f475aa0c8158c5d029354/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 2021-07-16T11:25:02,919 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0-dev2' to '2.0.dev2' 2021-07-16T11:25:02,920 warnings.warn(tmpl.format(**locals())) 2021-07-16T11:25:02,953 running clean 2021-07-16T11:25:02,978 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-16T11:25:02,989 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-16T11:25:03,001 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-16T11:25:03,001 'build/scripts-3.9' does not exist -- can't clean it 2021-07-16T11:25:03,002 removing 'build' 2021-07-16T11:25:03,318 Failed to build hapflk 2021-07-16T11:25:03,318 ERROR: Failed to build one or more wheels 2021-07-16T11:25:03,319 Exception information: 2021-07-16T11:25:03,319 Traceback (most recent call last): 2021-07-16T11:25:03,319 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-16T11:25:03,319 status = self.run(options, args) 2021-07-16T11:25:03,319 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-16T11:25:03,319 return func(self, options, args) 2021-07-16T11:25:03,319 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-16T11:25:03,319 raise CommandError( 2021-07-16T11:25:03,319 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-16T11:25:03,326 Removed build tracker: '/tmp/pip-req-tracker-6cmxmxe8'