2021-07-16T11:14:41,245 Created temporary directory: /tmp/pip-ephem-wheel-cache-8l68i503
2021-07-16T11:14:41,248 Created temporary directory: /tmp/pip-req-tracker-8ije0pwt
2021-07-16T11:14:41,248 Initialized build tracking at /tmp/pip-req-tracker-8ije0pwt
2021-07-16T11:14:41,248 Created build tracker: /tmp/pip-req-tracker-8ije0pwt
2021-07-16T11:14:41,249 Entered build tracker: /tmp/pip-req-tracker-8ije0pwt
2021-07-16T11:14:41,249 Created temporary directory: /tmp/pip-wheel-tl09av76
2021-07-16T11:14:41,276 1 location(s) to search for versions of hapflk:
2021-07-16T11:14:41,276 * https://pypi.org/simple/hapflk/
2021-07-16T11:14:41,276 Fetching project page and analyzing links: https://pypi.org/simple/hapflk/
2021-07-16T11:14:41,277 Getting page https://pypi.org/simple/hapflk/
2021-07-16T11:14:41,278 Found index url https://pypi.org/simple
2021-07-16T11:14:41,367   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
2021-07-16T11:14:41,368   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
2021-07-16T11:14:41,368   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
2021-07-16T11:14:41,369   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
2021-07-16T11:14:41,369   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
2021-07-16T11:14:41,369   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
2021-07-16T11:14:41,369   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
2021-07-16T11:14:41,370   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
2021-07-16T11:14:41,370   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
2021-07-16T11:14:41,370   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
2021-07-16T11:14:41,370   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
2021-07-16T11:14:41,371   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
2021-07-16T11:14:41,371   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
2021-07-16T11:14:41,371   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
2021-07-16T11:14:41,372 Skipping link: not a file: https://pypi.org/simple/hapflk/
2021-07-16T11:14:41,391 Given no hashes to check 1 links for project 'hapflk': discarding no candidates
2021-07-16T11:14:41,410 Collecting hapflk==2.0.dev1
2021-07-16T11:14:41,411   Created temporary directory: /tmp/pip-unpack-aebmyg0f
2021-07-16T11:14:41,587   Downloading hapflk-2.0.dev1.tar.gz (515 kB)
2021-07-16T11:14:41,889   Added hapflk==2.0.dev1 from https://files.pythonhosted.org/packages/30/60/1dab8e6a54e7ef2c19a62114527d5512da17a09a590d5551610b2fce8195/hapflk-2.0.dev1.tar.gz#sha256=742d022fcdc7e3ddd5330748065c2b6c2ae314880a6845234ff08c1d8f692c90 to build tracker '/tmp/pip-req-tracker-8ije0pwt'
2021-07-16T11:14:41,890     Running setup.py (path:/tmp/pip-wheel-tl09av76/hapflk_fdfe281e4a5a44e29740bc50919a98ed/setup.py) egg_info for package hapflk
2021-07-16T11:14:41,891     Created temporary directory: /tmp/pip-pip-egg-info-cita_o8m
2021-07-16T11:14:41,891     Running command python setup.py egg_info
2021-07-16T11:14:46,517     warning: fastphase/fastphase.pyx:486:12: local variable 'k1' referenced before assignment
2021-07-16T11:14:46,518     warning: fastphase/fastphase.pyx:486:18: local variable 'kp1' referenced before assignment
2021-07-16T11:14:46,518     warning: fastphase/fastphase.pyx:487:16: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,518     warning: fastphase/fastphase.pyx:487:22: local variable 'kp2' referenced before assignment
2021-07-16T11:14:46,518     warning: fastphase/fastphase.pyx:488:23: local variable 'k1' referenced before assignment
2021-07-16T11:14:46,519     warning: fastphase/fastphase.pyx:488:27: local variable 'kp1' referenced before assignment
2021-07-16T11:14:46,519     warning: fastphase/fastphase.pyx:489:23: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,519     warning: fastphase/fastphase.pyx:489:27: local variable 'kp2' referenced before assignment
2021-07-16T11:14:46,519     warning: fastphase/fastphase.pyx:491:23: local variable 'k1' referenced before assignment
2021-07-16T11:14:46,519     warning: fastphase/fastphase.pyx:491:27: local variable 'kp1' referenced before assignment
2021-07-16T11:14:46,519     warning: fastphase/fastphase.pyx:492:23: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,519     warning: fastphase/fastphase.pyx:492:27: local variable 'kp2' referenced before assignment
2021-07-16T11:14:46,519     warning: fastphase/fastphase.pyx:493:15: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,520     warning: fastphase/fastphase.pyx:493:21: local variable 'kp2' referenced before assignment
2021-07-16T11:14:46,520     warning: fastphase/fastphase.pyx:494:19: local variable 'k1' referenced before assignment
2021-07-16T11:14:46,520     warning: fastphase/fastphase.pyx:494:23: local variable 'kp1' referenced before assignment
2021-07-16T11:14:46,520     warning: fastphase/fastphase.pyx:495:19: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,520     warning: fastphase/fastphase.pyx:495:23: local variable 'kp2' referenced before assignment
2021-07-16T11:14:46,520     warning: fastphase/fastphase.pyx:496:15: local variable 'k1' referenced before assignment
2021-07-16T11:14:46,520     warning: fastphase/fastphase.pyx:496:21: local variable 'kp2' referenced before assignment
2021-07-16T11:14:46,520     warning: fastphase/fastphase.pyx:496:31: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,520     warning: fastphase/fastphase.pyx:496:37: local variable 'kp1' referenced before assignment
2021-07-16T11:14:46,521     warning: fastphase/fastphase.pyx:497:19: local variable 'k1' referenced before assignment
2021-07-16T11:14:46,521     warning: fastphase/fastphase.pyx:497:23: local variable 'kp2' referenced before assignment
2021-07-16T11:14:46,521     warning: fastphase/fastphase.pyx:498:19: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,521     warning: fastphase/fastphase.pyx:498:23: local variable 'kp1' referenced before assignment
2021-07-16T11:14:46,521     warning: fastphase/fastphase.pyx:499:15: local variable 'k1' referenced before assignment
2021-07-16T11:14:46,521     warning: fastphase/fastphase.pyx:499:21: local variable 'kp2' referenced before assignment
2021-07-16T11:14:46,521     warning: fastphase/fastphase.pyx:499:31: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,521     warning: fastphase/fastphase.pyx:499:37: local variable 'kp1' referenced before assignment
2021-07-16T11:14:46,521     warning: fastphase/fastphase.pyx:500:19: local variable 'k1' referenced before assignment
2021-07-16T11:14:46,522     warning: fastphase/fastphase.pyx:500:23: local variable 'kp2' referenced before assignment
2021-07-16T11:14:46,522     warning: fastphase/fastphase.pyx:501:16: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,522     warning: fastphase/fastphase.pyx:501:20: local variable 'kp1' referenced before assignment
2021-07-16T11:14:46,522     warning: fastphase/fastphase.pyx:503:19: local variable 'k1' referenced before assignment
2021-07-16T11:14:46,522     warning: fastphase/fastphase.pyx:503:23: local variable 'kp1' referenced before assignment
2021-07-16T11:14:46,522     warning: fastphase/fastphase.pyx:504:19: local variable 'k1' referenced before assignment
2021-07-16T11:14:46,522     warning: fastphase/fastphase.pyx:504:23: local variable 'kp2' referenced before assignment
2021-07-16T11:14:46,522     warning: fastphase/fastphase.pyx:505:19: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,522     warning: fastphase/fastphase.pyx:505:23: local variable 'kp1' referenced before assignment
2021-07-16T11:14:46,523     warning: fastphase/fastphase.pyx:506:19: local variable 'k2' referenced before assignment
2021-07-16T11:14:46,523     warning: fastphase/fastphase.pyx:506:23: local variable 'kp2' referenced before assignment
2021-07-16T11:14:48,833     /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-tl09av76/hapflk_fdfe281e4a5a44e29740bc50919a98ed/pgenlib/_pgenlib.pyx
2021-07-16T11:14:48,833       tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-16T11:14:54,092     Compiling fastphase/fastphase.pyx because it depends on /home/piwheels/.local/lib/python3.9/site-packages/numpy/__init__.pxd.
2021-07-16T11:14:54,093     Compiling pgenlib/_pgenlib.pyx because it depends on /home/piwheels/.local/lib/python3.9/site-packages/numpy/__init__.pxd.
2021-07-16T11:14:54,093     [1/2] Cythonizing fastphase/fastphase.pyx
2021-07-16T11:14:54,093     [2/2] Cythonizing pgenlib/_pgenlib.pyx
2021-07-16T11:14:54,256     /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0-dev1' to '2.0.dev1'
2021-07-16T11:14:54,256       warnings.warn(tmpl.format(**locals()))
2021-07-16T11:14:54,276     running egg_info
2021-07-16T11:14:54,278     creating /tmp/pip-pip-egg-info-cita_o8m/hapflk.egg-info
2021-07-16T11:14:54,279     writing /tmp/pip-pip-egg-info-cita_o8m/hapflk.egg-info/PKG-INFO
2021-07-16T11:14:54,281     writing dependency_links to /tmp/pip-pip-egg-info-cita_o8m/hapflk.egg-info/dependency_links.txt
2021-07-16T11:14:54,283     writing requirements to /tmp/pip-pip-egg-info-cita_o8m/hapflk.egg-info/requires.txt
2021-07-16T11:14:54,284     writing top-level names to /tmp/pip-pip-egg-info-cita_o8m/hapflk.egg-info/top_level.txt
2021-07-16T11:14:54,285     writing manifest file '/tmp/pip-pip-egg-info-cita_o8m/hapflk.egg-info/SOURCES.txt'
2021-07-16T11:14:54,469     reading manifest file '/tmp/pip-pip-egg-info-cita_o8m/hapflk.egg-info/SOURCES.txt'
2021-07-16T11:14:54,471     reading manifest template 'MANIFEST.in'
2021-07-16T11:14:54,473     warning: no files found matching '*' under directory 'utils'
2021-07-16T11:14:54,475     adding license file 'LICENSE.txt'
2021-07-16T11:14:54,475     adding license file 'COPYING.txt'
2021-07-16T11:14:54,478     writing manifest file '/tmp/pip-pip-egg-info-cita_o8m/hapflk.egg-info/SOURCES.txt'
2021-07-16T11:14:54,765   Source in /tmp/pip-wheel-tl09av76/hapflk_fdfe281e4a5a44e29740bc50919a98ed has version 2.0.dev1, which satisfies requirement hapflk==2.0.dev1 from https://files.pythonhosted.org/packages/30/60/1dab8e6a54e7ef2c19a62114527d5512da17a09a590d5551610b2fce8195/hapflk-2.0.dev1.tar.gz#sha256=742d022fcdc7e3ddd5330748065c2b6c2ae314880a6845234ff08c1d8f692c90
2021-07-16T11:14:54,766   Removed hapflk==2.0.dev1 from https://files.pythonhosted.org/packages/30/60/1dab8e6a54e7ef2c19a62114527d5512da17a09a590d5551610b2fce8195/hapflk-2.0.dev1.tar.gz#sha256=742d022fcdc7e3ddd5330748065c2b6c2ae314880a6845234ff08c1d8f692c90 from build tracker '/tmp/pip-req-tracker-8ije0pwt'
2021-07-16T11:14:54,770 Created temporary directory: /tmp/pip-unpack-d6i011ll
2021-07-16T11:14:54,771 Building wheels for collected packages: hapflk
2021-07-16T11:14:54,775   Created temporary directory: /tmp/pip-wheel-43f_0vff
2021-07-16T11:14:54,775   Building wheel for hapflk (setup.py): started
2021-07-16T11:14:54,776   Destination directory: /tmp/pip-wheel-43f_0vff
2021-07-16T11:14:54,776   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-tl09av76/hapflk_fdfe281e4a5a44e29740bc50919a98ed/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-tl09av76/hapflk_fdfe281e4a5a44e29740bc50919a98ed/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-43f_0vff
2021-07-16T11:14:56,692   /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0-dev1' to '2.0.dev1'
2021-07-16T11:14:56,692     warnings.warn(tmpl.format(**locals()))
2021-07-16T11:14:56,723   running bdist_wheel
2021-07-16T11:14:56,729   running build
2021-07-16T11:14:56,729   running build_py
2021-07-16T11:14:56,863   creating build
2021-07-16T11:14:56,864   creating build/lib.linux-armv7l-3.9
2021-07-16T11:14:56,865   creating build/lib.linux-armv7l-3.9/hapflk
2021-07-16T11:14:56,866   copying hapflk/hapflk.py -> build/lib.linux-armv7l-3.9/hapflk
2021-07-16T11:14:56,869   copying hapflk/data.py -> build/lib.linux-armv7l-3.9/hapflk
2021-07-16T11:14:56,872   copying hapflk/nj.py -> build/lib.linux-armv7l-3.9/hapflk
2021-07-16T11:14:56,874   copying hapflk/InputOutput.py -> build/lib.linux-armv7l-3.9/hapflk
2021-07-16T11:14:56,877   copying hapflk/__init__.py -> build/lib.linux-armv7l-3.9/hapflk
2021-07-16T11:14:56,878   copying hapflk/popgen.py -> build/lib.linux-armv7l-3.9/hapflk
2021-07-16T11:14:56,881   copying hapflk/hapflkadapt.py -> build/lib.linux-armv7l-3.9/hapflk
2021-07-16T11:14:56,884   copying hapflk/utils.py -> build/lib.linux-armv7l-3.9/hapflk
2021-07-16T11:14:56,886   running build_ext
2021-07-16T11:14:56,892   building 'hapflk.fastphase' extension
2021-07-16T11:14:56,893   creating build/temp.linux-armv7l-3.9
2021-07-16T11:14:56,893   creating build/temp.linux-armv7l-3.9/fastphase
2021-07-16T11:14:56,894   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
2021-07-16T11:14:57,280   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T11:14:57,281                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T11:14:57,281                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T11:14:57,281                    from fastphase/fastphase.c:635:
2021-07-16T11:14:57,281   /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]
2021-07-16T11:14:57,281      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T11:14:57,282         |  ^~~~~~~
2021-07-16T11:15:10,609   fastphase/fastphase.c: In function ‘__pyx_pw_6hapflk_9fastphase_11calc_cost_matrix_geno_tot’:
2021-07-16T11:15:10,618   fastphase/fastphase.c:15557:38: warning: ‘__pyx_v_k1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T11:15:10,619   15557 |       if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_res.diminfo[1].shape;
2021-07-16T11:15:10,619         |                           ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:10,628   fastphase/fastphase.c:15137:7: note: ‘__pyx_v_k1’ was declared here
2021-07-16T11:15:10,628   15137 |   int __pyx_v_k1;
2021-07-16T11:15:10,628         |       ^~~~~~~~~~
2021-07-16T11:15:10,636   fastphase/fastphase.c:15558:38: warning: ‘__pyx_v_kp1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T11:15:10,636   15558 |       if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_pybuffernd_res.diminfo[2].shape;
2021-07-16T11:15:10,636         |                           ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:10,645   fastphase/fastphase.c:15139:7: note: ‘__pyx_v_kp1’ was declared here
2021-07-16T11:15:10,646   15139 |   int __pyx_v_kp1;
2021-07-16T11:15:10,646         |       ^~~~~~~~~~~
2021-07-16T11:15:10,654   fastphase/fastphase.c:15573:38: warning: ‘__pyx_v_kp2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T11:15:10,654   15573 |       if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_pybuffernd_res.diminfo[2].shape;
2021-07-16T11:15:10,654         |                           ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:10,663   fastphase/fastphase.c:15140:7: note: ‘__pyx_v_kp2’ was declared here
2021-07-16T11:15:10,663   15140 |   int __pyx_v_kp2;
2021-07-16T11:15:10,663         |       ^~~~~~~~~~~
2021-07-16T11:15:10,671   fastphase/fastphase.c:15587:38: warning: ‘__pyx_v_k2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T11:15:10,671   15587 |       if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_res.diminfo[1].shape;
2021-07-16T11:15:10,671         |                           ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:10,680   fastphase/fastphase.c:15138:7: note: ‘__pyx_v_k2’ was declared here
2021-07-16T11:15:10,681   15138 |   int __pyx_v_k2;
2021-07-16T11:15:10,681         |       ^~~~~~~~~~
2021-07-16T11:15:28,416   fastphase/fastphase.c: In function ‘__pyx_f_6hapflk_9fastphase_genViterbi.constprop’:
2021-07-16T11:15:28,416   fastphase/fastphase.c:1728:91: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T11:15:28,416    1728 | #define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1)
2021-07-16T11:15:28,417         |                                                                                           ^
2021-07-16T11:15:28,427   fastphase/fastphase.c:17490:7: note: ‘__pyx_v_k’ was declared here
2021-07-16T11:15:28,427   17490 |   int __pyx_v_k;
2021-07-16T11:15:28,427         |       ^~~~~~~~~
2021-07-16T11:15:28,428   fastphase/fastphase.c:548:40: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T11:15:28,429     548 |   #define PyInt_FromLong               PyLong_FromLong
2021-07-16T11:15:28,429         |                                        ^~~~~~~~~~~~~~~
2021-07-16T11:15:28,439   fastphase/fastphase.c:17491:7: note: ‘__pyx_v_l’ was declared here
2021-07-16T11:15:28,439   17491 |   int __pyx_v_l;
2021-07-16T11:15:28,439         |       ^~~~~~~~~
2021-07-16T11:15:28,440   fastphase/fastphase.c:548:40: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T11:15:28,440     548 |   #define PyInt_FromLong               PyLong_FromLong
2021-07-16T11:15:28,440         |                                        ^~~~~~~~~~~~~~~
2021-07-16T11:15:28,450   fastphase/fastphase.c:17490:7: note: ‘__pyx_v_k’ was declared here
2021-07-16T11:15:28,450   17490 |   int __pyx_v_k;
2021-07-16T11:15:28,451         |       ^~~~~~~~~
2021-07-16T11:15:28,460   fastphase/fastphase.c:18567:12: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T11:15:28,460   18567 |         if (!__pyx_t_34) {
2021-07-16T11:15:28,460         |            ^
2021-07-16T11:15:28,470   fastphase/fastphase.c:18575:12: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T11:15:28,470   18575 |         if (__pyx_t_33) {
2021-07-16T11:15:28,470         |            ^
2021-07-16T11:15:28,471   fastphase/fastphase.c:18575:12: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T11:15:45,705   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
2021-07-16T11:15:45,936   building 'hapflk._pgenlib' extension
2021-07-16T11:15:45,936   creating build/temp.linux-armv7l-3.9/pgenlib
2021-07-16T11:15:45,937   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
2021-07-16T11:15:46,212   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T11:15:46,212                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T11:15:46,212                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T11:15:46,213                    from pgenlib/_pgenlib.cpp:662:
2021-07-16T11:15:46,213   /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]
2021-07-16T11:15:46,213      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T11:15:46,213         |  ^~~~~~~
2021-07-16T11:15:47,248   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*)’:
2021-07-16T11:15:47,248   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]
2021-07-16T11:15:47,249    6982 |     __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,249         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,251   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]
2021-07-16T11:15:47,251    7038 |     __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,252         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,262   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]
2021-07-16T11:15:47,262    7263 |   __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,262         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,265   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]
2021-07-16T11:15:47,265    7319 |   __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,265         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,281   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*)’:
2021-07-16T11:15:47,281   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]
2021-07-16T11:15:47,281    7974 |     __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,282         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,284   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]
2021-07-16T11:15:47,284    8030 |     __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,284         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,292   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]
2021-07-16T11:15:47,292    8255 |   __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,292         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,295   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]
2021-07-16T11:15:47,295    8311 |   __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,295         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,311   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*)’:
2021-07-16T11:15:47,312   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]
2021-07-16T11:15:47,312    8966 |     __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,312         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,314   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]
2021-07-16T11:15:47,315    9022 |     __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,315         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,322   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]
2021-07-16T11:15:47,323    9247 |   __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,323         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,325   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]
2021-07-16T11:15:47,325    9303 |   __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,326         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,363   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*)’:
2021-07-16T11:15:47,363   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]
2021-07-16T11:15:47,363   10399 |     __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,364         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,366   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]
2021-07-16T11:15:47,366   10455 |     __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,366         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,375   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]
2021-07-16T11:15:47,375   10696 |   __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,375         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,377   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]
2021-07-16T11:15:47,378   10752 |   __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,378         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,395   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*)’:
2021-07-16T11:15:47,396   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]
2021-07-16T11:15:47,396   11447 |     __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,396         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,398   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]
2021-07-16T11:15:47,399   11503 |     __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,399         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,407   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]
2021-07-16T11:15:47,407   11744 |   __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,408         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,410   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]
2021-07-16T11:15:47,410   11800 |   __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,410         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,428   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*)’:
2021-07-16T11:15:47,428   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]
2021-07-16T11:15:47,429   12495 |     __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,429         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,431   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]
2021-07-16T11:15:47,431   12551 |     __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,432         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,440   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]
2021-07-16T11:15:47,440   12792 |   __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2021-07-16T11:15:47,440         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,443   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]
2021-07-16T11:15:47,443   12848 |   __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,443         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,493   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*)’:
2021-07-16T11:15:47,493   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]
2021-07-16T11:15:47,493   14192 |     __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,493         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,496   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]
2021-07-16T11:15:47,496   14248 |     __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2021-07-16T11:15:47,496         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,504   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]
2021-07-16T11:15:47,505   14473 |   __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2021-07-16T11:15:47,505         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,507   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]
2021-07-16T11:15:47,507   14529 |   __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,508         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,545   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*)’:
2021-07-16T11:15:47,545   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]
2021-07-16T11:15:47,545   15576 |     __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,545         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,547   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]
2021-07-16T11:15:47,548   15632 |     __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2021-07-16T11:15:47,548         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,556   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]
2021-07-16T11:15:47,556   15873 |   __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2021-07-16T11:15:47,557         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:15:47,559   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]
2021-07-16T11:15:47,559   15929 |   __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2021-07-16T11:15:47,559         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T11:16:12,099   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
2021-07-16T11:16:12,225   pgenlib/pgenlib_internal.cpp:710:4: error: #error "Unaligned accesses in small_genoarr_count_3freq_incr()."
2021-07-16T11:16:12,225     710 |   #error "Unaligned accesses in small_genoarr_count_3freq_incr()."
2021-07-16T11:16:12,225         |    ^~~~~
2021-07-16T11:16:12,225   pgenlib/pgenlib_internal.cpp:752:4: error: #error "Unaligned accesses in genoarr_count_subset_freqs()."
2021-07-16T11:16:12,226     752 |   #error "Unaligned accesses in genoarr_count_subset_freqs()."
2021-07-16T11:16:12,226         |    ^~~~~
2021-07-16T11:16:12,229   pgenlib/pgenlib_internal.cpp:1911:4: error: #error "Unaligned accesses in pgfi_init_phase2()."
2021-07-16T11:16:12,229    1911 |   #error "Unaligned accesses in pgfi_init_phase2()."
2021-07-16T11:16:12,230         |    ^~~~~
2021-07-16T11:16:12,234   pgenlib/pgenlib_internal.cpp:3145:4: error: #error "Unaligned accesses in parse_onebit_unsafe()."
2021-07-16T11:16:12,234    3145 |   #error "Unaligned accesses in parse_onebit_unsafe()."
2021-07-16T11:16:12,234         |    ^~~~~
2021-07-16T11:16:12,235   pgenlib/pgenlib_internal.cpp:3178:4: error: #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)."
2021-07-16T11:16:12,235    3178 |   #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)."
2021-07-16T11:16:12,235         |    ^~~~~
2021-07-16T11:16:12,240   pgenlib/pgenlib_internal.cpp:3761:4: error: #error "Unaligned accesses in bytesum_arr()."
2021-07-16T11:16:12,240    3761 |   #error "Unaligned accesses in bytesum_arr()."
2021-07-16T11:16:12,240         |    ^~~~~
2021-07-16T11:16:12,242   pgenlib/pgenlib_internal.cpp:3814:4: error: #error "Unaligned accesses in skip_difflist_ids()."
2021-07-16T11:16:12,242    3814 |   #error "Unaligned accesses in skip_difflist_ids()."
2021-07-16T11:16:12,242         |    ^~~~~
2021-07-16T11:16:12,244   pgenlib/pgenlib_internal.cpp:3940:4: error: #error "Unaligned accesses in countparse_onebit_subset()."
2021-07-16T11:16:12,245    3940 |   #error "Unaligned accesses in countparse_onebit_subset()."
2021-07-16T11:16:12,245         |    ^~~~~
2021-07-16T11:16:12,250   pgenlib/pgenlib_internal.cpp:4923:4: error: #error "Unaligned accesses in parse_just_ambig_ids()."
2021-07-16T11:16:12,251    4923 |   #error "Unaligned accesses in parse_just_ambig_ids()."
2021-07-16T11:16:12,251         |    ^~~~~
2021-07-16T11:16:12,255   pgenlib/pgenlib_internal.cpp:5454:4: error: #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()."
2021-07-16T11:16:12,255    5454 |   #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()."
2021-07-16T11:16:12,255         |    ^~~~~
2021-07-16T11:16:12,258   pgenlib/pgenlib_internal.cpp:5670:4: error: #error "Unaligned accesses in parse_dosage16()."
2021-07-16T11:16:12,259    5670 |   #error "Unaligned accesses in parse_dosage16()."
2021-07-16T11:16:12,259         |    ^~~~~
2021-07-16T11:16:12,263   pgenlib/pgenlib_internal.cpp:5889:4: error: #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()."
2021-07-16T11:16:12,263    5889 |   #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()."
2021-07-16T11:16:12,263         |    ^~~~~
2021-07-16T11:16:12,267   pgenlib/pgenlib_internal.cpp:6294:4: error: #error "Unaligned accesses in pgr_read_missingness_dosage()."
2021-07-16T11:16:12,267    6294 |   #error "Unaligned accesses in pgr_read_missingness_dosage()."
2021-07-16T11:16:12,267         |    ^~~~~
2021-07-16T11:16:12,271   pgenlib/pgenlib_internal.cpp:6542:4: error: #error "Unaligned accesses in validate_onebit()."
2021-07-16T11:16:12,271    6542 |   #error "Unaligned accesses in validate_onebit()."
2021-07-16T11:16:12,271         |    ^~~~~
2021-07-16T11:16:12,275   pgenlib/pgenlib_internal.cpp:6760:4: error: #error "Unaligned accesses in validate_dosage16()."
2021-07-16T11:16:12,275    6760 |   #error "Unaligned accesses in validate_dosage16()."
2021-07-16T11:16:12,275         |    ^~~~~
2021-07-16T11:16:12,281   pgenlib/pgenlib_internal.cpp:7651:4: error: #error "Unaligned accesses in save_ld_difflist()."
2021-07-16T11:16:12,281    7651 |   #error "Unaligned accesses in save_ld_difflist()."
2021-07-16T11:16:12,282         |    ^~~~~
2021-07-16T11:16:12,286   pgenlib/pgenlib_internal.cpp:7793:4: error: #error "Unaligned accesses in save_onebit()."
2021-07-16T11:16:12,286    7793 |   #error "Unaligned accesses in save_onebit()."
2021-07-16T11:16:12,286         |    ^~~~~
2021-07-16T11:16:12,290   pgenlib/pgenlib_internal.cpp:8025:4: error: #error "Unaligned accesses in save_ld_two_list_delta()."
2021-07-16T11:16:12,291    8025 |   #error "Unaligned accesses in save_ld_two_list_delta()."
2021-07-16T11:16:12,291         |    ^~~~~
2021-07-16T11:16:12,295   pgenlib/pgenlib_internal.cpp:8295:4: error: #error "Unaligned accesses in append_hphase()."
2021-07-16T11:16:12,296    8295 |   #error "Unaligned accesses in append_hphase()."
2021-07-16T11:16:12,296         |    ^~~~~
2021-07-16T11:16:12,751   error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1
2021-07-16T11:16:12,895   Building wheel for hapflk (setup.py): finished with status 'error'
2021-07-16T11:16:12,895   ERROR: Failed building wheel for hapflk
2021-07-16T11:16:12,896   Running setup.py clean for hapflk
2021-07-16T11:16:12,896   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-tl09av76/hapflk_fdfe281e4a5a44e29740bc50919a98ed/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-tl09av76/hapflk_fdfe281e4a5a44e29740bc50919a98ed/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
2021-07-16T11:16:14,955   /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0-dev1' to '2.0.dev1'
2021-07-16T11:16:14,956     warnings.warn(tmpl.format(**locals()))
2021-07-16T11:16:14,967   running clean
2021-07-16T11:16:14,970   removing 'build/temp.linux-armv7l-3.9' (and everything under it)
2021-07-16T11:16:14,977   removing 'build/lib.linux-armv7l-3.9' (and everything under it)
2021-07-16T11:16:14,983   'build/bdist.linux-armv7l' does not exist -- can't clean it
2021-07-16T11:16:14,983   'build/scripts-3.9' does not exist -- can't clean it
2021-07-16T11:16:14,984   removing 'build'
2021-07-16T11:16:15,104 Failed to build hapflk
2021-07-16T11:16:15,105 ERROR: Failed to build one or more wheels
2021-07-16T11:16:15,105 Exception information:
2021-07-16T11:16:15,105 Traceback (most recent call last):
2021-07-16T11:16:15,105   File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in _main
2021-07-16T11:16:15,105     status = self.run(options, args)
2021-07-16T11:16:15,105   File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 205, in wrapper
2021-07-16T11:16:15,105     return func(self, options, args)
2021-07-16T11:16:15,105   File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 174, in run
2021-07-16T11:16:15,105     raise CommandError(
2021-07-16T11:16:15,105 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2021-07-16T11:16:15,109 Removed build tracker: '/tmp/pip-req-tracker-8ije0pwt'