2020-07-07T09:55:27,957 Created temporary directory: /tmp/pip-ephem-wheel-cache-tsgrmtsl
2020-07-07T09:55:27,961 Created temporary directory: /tmp/pip-req-tracker-vzssvtyu
2020-07-07T09:55:27,962 Initialized build tracking at /tmp/pip-req-tracker-vzssvtyu
2020-07-07T09:55:27,963 Created build tracker: /tmp/pip-req-tracker-vzssvtyu
2020-07-07T09:55:27,963 Entered build tracker: /tmp/pip-req-tracker-vzssvtyu
2020-07-07T09:55:27,964 Created temporary directory: /tmp/pip-wheel-z_8vts67
2020-07-07T09:55:27,981 1 location(s) to search for versions of hapflk:
2020-07-07T09:55:27,981 * https://pypi.org/simple/hapflk/
2020-07-07T09:55:27,982 Fetching project page and analyzing links: https://pypi.org/simple/hapflk/
2020-07-07T09:55:27,983 Getting page https://pypi.org/simple/hapflk/
2020-07-07T09:55:27,985 Found index url https://pypi.org/simple
2020-07-07T09:55:28,193   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
2020-07-07T09:55:28,194   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
2020-07-07T09:55:28,194   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
2020-07-07T09:55:28,195   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
2020-07-07T09:55:28,196   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
2020-07-07T09:55:28,196   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
2020-07-07T09:55:28,197   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
2020-07-07T09:55:28,198   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
2020-07-07T09:55:28,198   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
2020-07-07T09:55:28,199   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
2020-07-07T09:55:28,199   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
2020-07-07T09:55:28,200   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
2020-07-07T09:55:28,211 Given no hashes to check 1 links for project 'hapflk': discarding no candidates
2020-07-07T09:55:28,213 Using version 2.0.dev0 (newest of versions: 2.0.dev0)
2020-07-07T09:55:28,218 Collecting hapflk==2.0.dev0
2020-07-07T09:55:28,222   Created temporary directory: /tmp/pip-unpack-c7blotlz
2020-07-07T09:55:28,309   Downloading hapflk-2.0.dev0.tar.gz (512 kB)
2020-07-07T09:55:29,209   Added hapflk==2.0.dev0 from https://files.pythonhosted.org/packages/c6/a6/ed1b0c03bdb79de6f288c5e982af3afcaae7a26cdd00ff75dd98bf81a13e/hapflk-2.0.dev0.tar.gz#sha256=f9d6270cf2b80d00edfbdbaa1e26d112c92bfa73938616dde9d7c6d1a239980e to build tracker '/tmp/pip-req-tracker-vzssvtyu'
2020-07-07T09:55:29,212     Running setup.py (path:/tmp/pip-wheel-z_8vts67/hapflk/setup.py) egg_info for package hapflk
2020-07-07T09:55:29,214     Created temporary directory: /tmp/pip-pip-egg-info-3gzbawjy
2020-07-07T09:55:29,215     Running command python setup.py egg_info
2020-07-07T09:55:46,393     Compiling fastphase/fastphase.pyx because it depends on /usr/local/lib/python3.7/dist-packages/Cython/Includes/numpy/__init__.pxd.
2020-07-07T09:55:46,395     [1/1] Cythonizing fastphase/fastphase.pyx
2020-07-07T09:55:46,658     running egg_info
2020-07-07T09:55:46,663     creating /tmp/pip-pip-egg-info-3gzbawjy/hapflk.egg-info
2020-07-07T09:55:46,665     writing /tmp/pip-pip-egg-info-3gzbawjy/hapflk.egg-info/PKG-INFO
2020-07-07T09:55:46,670     writing dependency_links to /tmp/pip-pip-egg-info-3gzbawjy/hapflk.egg-info/dependency_links.txt
2020-07-07T09:55:46,675     writing top-level names to /tmp/pip-pip-egg-info-3gzbawjy/hapflk.egg-info/top_level.txt
2020-07-07T09:55:46,679     writing manifest file '/tmp/pip-pip-egg-info-3gzbawjy/hapflk.egg-info/SOURCES.txt'
2020-07-07T09:55:46,965     reading manifest file '/tmp/pip-pip-egg-info-3gzbawjy/hapflk.egg-info/SOURCES.txt'
2020-07-07T09:55:46,968     reading manifest template 'MANIFEST.in'
2020-07-07T09:55:46,972     warning: fastphase/fastphase.pyx:486:12: local variable 'k1' referenced before assignment
2020-07-07T09:55:46,972     warning: fastphase/fastphase.pyx:486:18: local variable 'kp1' referenced before assignment
2020-07-07T09:55:46,973     warning: fastphase/fastphase.pyx:487:16: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,974     warning: fastphase/fastphase.pyx:487:22: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,974     warning: fastphase/fastphase.pyx:488:23: local variable 'k1' referenced before assignment
2020-07-07T09:55:46,975     warning: fastphase/fastphase.pyx:488:27: local variable 'kp1' referenced before assignment
2020-07-07T09:55:46,975     warning: fastphase/fastphase.pyx:489:23: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,975     warning: fastphase/fastphase.pyx:489:27: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,976     warning: fastphase/fastphase.pyx:491:23: local variable 'k1' referenced before assignment
2020-07-07T09:55:46,976     warning: fastphase/fastphase.pyx:491:27: local variable 'kp1' referenced before assignment
2020-07-07T09:55:46,977     warning: fastphase/fastphase.pyx:492:23: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,977     warning: fastphase/fastphase.pyx:492:27: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,977     warning: fastphase/fastphase.pyx:493:15: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,978     warning: fastphase/fastphase.pyx:493:21: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,978     warning: fastphase/fastphase.pyx:494:19: local variable 'k1' referenced before assignment
2020-07-07T09:55:46,978     warning: fastphase/fastphase.pyx:494:23: local variable 'kp1' referenced before assignment
2020-07-07T09:55:46,979     warning: fastphase/fastphase.pyx:495:19: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,979     warning: fastphase/fastphase.pyx:495:23: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,979     warning: fastphase/fastphase.pyx:496:15: local variable 'k1' referenced before assignment
2020-07-07T09:55:46,980     warning: fastphase/fastphase.pyx:496:21: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,980     warning: fastphase/fastphase.pyx:496:31: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,980     warning: fastphase/fastphase.pyx:496:37: local variable 'kp1' referenced before assignment
2020-07-07T09:55:46,981     warning: fastphase/fastphase.pyx:497:19: local variable 'k1' referenced before assignment
2020-07-07T09:55:46,981     warning: fastphase/fastphase.pyx:497:23: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,981     warning: fastphase/fastphase.pyx:498:19: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,982     warning: fastphase/fastphase.pyx:498:23: local variable 'kp1' referenced before assignment
2020-07-07T09:55:46,982     warning: fastphase/fastphase.pyx:499:15: local variable 'k1' referenced before assignment
2020-07-07T09:55:46,983     warning: fastphase/fastphase.pyx:499:21: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,984     warning: fastphase/fastphase.pyx:499:31: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,984     warning: fastphase/fastphase.pyx:499:37: local variable 'kp1' referenced before assignment
2020-07-07T09:55:46,985     warning: fastphase/fastphase.pyx:500:19: local variable 'k1' referenced before assignment
2020-07-07T09:55:46,985     warning: fastphase/fastphase.pyx:500:23: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,986     warning: fastphase/fastphase.pyx:501:16: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,986     warning: fastphase/fastphase.pyx:501:20: local variable 'kp1' referenced before assignment
2020-07-07T09:55:46,987     warning: fastphase/fastphase.pyx:503:19: local variable 'k1' referenced before assignment
2020-07-07T09:55:46,987     warning: fastphase/fastphase.pyx:503:23: local variable 'kp1' referenced before assignment
2020-07-07T09:55:46,988     warning: fastphase/fastphase.pyx:504:19: local variable 'k1' referenced before assignment
2020-07-07T09:55:46,988     warning: fastphase/fastphase.pyx:504:23: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,989     warning: fastphase/fastphase.pyx:505:19: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,989     warning: fastphase/fastphase.pyx:505:23: local variable 'kp1' referenced before assignment
2020-07-07T09:55:46,990     warning: fastphase/fastphase.pyx:506:19: local variable 'k2' referenced before assignment
2020-07-07T09:55:46,990     warning: fastphase/fastphase.pyx:506:23: local variable 'kp2' referenced before assignment
2020-07-07T09:55:46,990     /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:454: UserWarning: Normalizing '2.0-dev0' to '2.0.dev0'
2020-07-07T09:55:46,991       warnings.warn(tmpl.format(**locals()))
2020-07-07T09:55:46,991     warning: no files found matching '*' under directory 'utils'
2020-07-07T09:55:46,991     writing manifest file '/tmp/pip-pip-egg-info-3gzbawjy/hapflk.egg-info/SOURCES.txt'
2020-07-07T09:55:47,459   Source in /tmp/pip-wheel-z_8vts67/hapflk has version 2.0.dev0, which satisfies requirement hapflk==2.0.dev0 from https://files.pythonhosted.org/packages/c6/a6/ed1b0c03bdb79de6f288c5e982af3afcaae7a26cdd00ff75dd98bf81a13e/hapflk-2.0.dev0.tar.gz#sha256=f9d6270cf2b80d00edfbdbaa1e26d112c92bfa73938616dde9d7c6d1a239980e
2020-07-07T09:55:47,460   Removed hapflk==2.0.dev0 from https://files.pythonhosted.org/packages/c6/a6/ed1b0c03bdb79de6f288c5e982af3afcaae7a26cdd00ff75dd98bf81a13e/hapflk-2.0.dev0.tar.gz#sha256=f9d6270cf2b80d00edfbdbaa1e26d112c92bfa73938616dde9d7c6d1a239980e from build tracker '/tmp/pip-req-tracker-vzssvtyu'
2020-07-07T09:55:47,464 Building wheels for collected packages: hapflk
2020-07-07T09:55:47,473   Created temporary directory: /tmp/pip-wheel-uk6spl85
2020-07-07T09:55:47,474   Building wheel for hapflk (setup.py): started
2020-07-07T09:55:47,474   Destination directory: /tmp/pip-wheel-uk6spl85
2020-07-07T09:55:47,474   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-z_8vts67/hapflk/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-z_8vts67/hapflk/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-uk6spl85
2020-07-07T09:55:51,068   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:454: UserWarning: Normalizing '2.0-dev0' to '2.0.dev0'
2020-07-07T09:55:51,069     warnings.warn(tmpl.format(**locals()))
2020-07-07T09:55:51,113   running bdist_wheel
2020-07-07T09:55:51,123   running build
2020-07-07T09:55:51,123   running build_py
2020-07-07T09:55:51,373   creating build
2020-07-07T09:55:51,374   creating build/lib.linux-armv7l-3.7
2020-07-07T09:55:51,376   creating build/lib.linux-armv7l-3.7/hapflk
2020-07-07T09:55:51,380   copying hapflk/hapflkadapt.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T09:55:51,388   copying hapflk/data.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T09:55:51,395   copying hapflk/hapflk.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T09:55:51,403   copying hapflk/popgen.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T09:55:51,411   copying hapflk/__init__.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T09:55:51,417   copying hapflk/utils.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T09:55:51,422   copying hapflk/InputOutput.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T09:55:51,428   copying hapflk/nj.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T09:55:51,435   running build_ext
2020-07-07T09:55:51,446   building 'hapflk.fastphase' extension
2020-07-07T09:55:51,448   creating build/temp.linux-armv7l-3.7
2020-07-07T09:55:51,449   creating build/temp.linux-armv7l-3.7/fastphase
2020-07-07T09:55:51,451   arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c fastphase/fastphase.c -o build/temp.linux-armv7l-3.7/fastphase/fastphase.o
2020-07-07T09:55:52,212   In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
2020-07-07T09:55:52,213                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2020-07-07T09:55:52,214                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2020-07-07T09:55:52,215                    from fastphase/fastphase.c:626:
2020-07-07T09:55:52,216   /usr/lib/python3/dist-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]
2020-07-07T09:55:52,217    #warning "Using deprecated NumPy API, disable it with " \
2020-07-07T09:55:52,218     ^~~~~~~
2020-07-07T09:56:44,090   fastphase/fastphase.c: In function ‘__pyx_pw_6hapflk_9fastphase_11calc_cost_matrix_geno_tot’:
2020-07-07T09:56:44,095   fastphase/fastphase.c:15600:38: warning: ‘__pyx_v_k1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T09:56:44,096          if (__pyx_t_40 < 0) __pyx_t_40 += __pyx_pybuffernd_res.diminfo[1].shape;
2020-07-07T09:56:44,096                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:56:44,100   fastphase/fastphase.c:15144:7: note: ‘__pyx_v_k1’ was declared here
2020-07-07T09:56:44,101      int __pyx_v_k1;
2020-07-07T09:56:44,101          ^~~~~~~~~~
2020-07-07T09:56:44,103   fastphase/fastphase.c:15601:38: warning: ‘__pyx_v_kp1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T09:56:44,104          if (__pyx_t_41 < 0) __pyx_t_41 += __pyx_pybuffernd_res.diminfo[2].shape;
2020-07-07T09:56:44,104                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:56:44,109   fastphase/fastphase.c:15146:7: note: ‘__pyx_v_kp1’ was declared here
2020-07-07T09:56:44,109      int __pyx_v_kp1;
2020-07-07T09:56:44,110          ^~~~~~~~~~~
2020-07-07T09:56:44,112   fastphase/fastphase.c:15616:38: warning: ‘__pyx_v_kp2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T09:56:44,112          if (__pyx_t_44 < 0) __pyx_t_44 += __pyx_pybuffernd_res.diminfo[2].shape;
2020-07-07T09:56:44,112                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:56:44,117   fastphase/fastphase.c:15147:7: note: ‘__pyx_v_kp2’ was declared here
2020-07-07T09:56:44,118      int __pyx_v_kp2;
2020-07-07T09:56:44,118          ^~~~~~~~~~~
2020-07-07T09:56:44,120   fastphase/fastphase.c:15630:38: warning: ‘__pyx_v_k2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T09:56:44,120          if (__pyx_t_46 < 0) __pyx_t_46 += __pyx_pybuffernd_res.diminfo[1].shape;
2020-07-07T09:56:44,121                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:56:44,125   fastphase/fastphase.c:15145:7: note: ‘__pyx_v_k2’ was declared here
2020-07-07T09:56:44,126      int __pyx_v_k2;
2020-07-07T09:56:44,127          ^~~~~~~~~~
2020-07-07T09:56:45,467   fastphase/fastphase.c: In function ‘__pyx_f_6hapflk_9fastphase_genViterbi.isra.67’:
2020-07-07T09:56:45,470   fastphase/fastphase.c:17533:7: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T09:56:45,471      int __pyx_v_k;
2020-07-07T09:56:45,471          ^~~~~~~~~
2020-07-07T09:56:45,474   fastphase/fastphase.c:539:40: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T09:56:45,474      #define PyInt_FromLong               PyLong_FromLong
2020-07-07T09:56:45,475                                           ^~~~~~~~~~~~~~~
2020-07-07T09:56:45,477   fastphase/fastphase.c:17534:7: note: ‘__pyx_v_l’ was declared here
2020-07-07T09:56:45,477      int __pyx_v_l;
2020-07-07T09:56:45,478          ^~~~~~~~~
2020-07-07T09:56:45,478   fastphase/fastphase.c:539:40: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T09:56:45,478      #define PyInt_FromLong               PyLong_FromLong
2020-07-07T09:56:45,479                                           ^~~~~~~~~~~~~~~
2020-07-07T09:56:45,483   fastphase/fastphase.c:17533:7: note: ‘__pyx_v_k’ was declared here
2020-07-07T09:56:45,484      int __pyx_v_k;
2020-07-07T09:56:45,484          ^~~~~~~~~
2020-07-07T09:56:45,487   fastphase/fastphase.c:18620:12: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T09:56:45,488            if (!__pyx_t_36) {
2020-07-07T09:56:45,488               ^
2020-07-07T09:56:45,491   fastphase/fastphase.c:18628:12: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T09:56:45,491            if (__pyx_t_35) {
2020-07-07T09:56:45,491               ^
2020-07-07T09:56:45,494   fastphase/fastphase.c:18727:38: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T09:56:45,495          if (__pyx_t_41 < 0) __pyx_t_41 += __pyx_pybuffernd_theta.diminfo[1].shape;
2020-07-07T09:56:45,495                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:39,886   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.7/fastphase/fastphase.o -o build/lib.linux-armv7l-3.7/hapflk/fastphase.cpython-37m-arm-linux-gnueabihf.so
2020-07-07T09:57:40,454   building 'hapflk._pgenlib' extension
2020-07-07T09:57:40,456   creating build/temp.linux-armv7l-3.7/pgenlib
2020-07-07T09:57:40,458   arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipgenlib -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c pgenlib/_pgenlib.cpp -o build/temp.linux-armv7l-3.7/pgenlib/_pgenlib.o -std=c++98 -Wno-unused-function
2020-07-07T09:57:41,011   In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
2020-07-07T09:57:41,012                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2020-07-07T09:57:41,012                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2020-07-07T09:57:41,012                    from pgenlib/_pgenlib.cpp:645:
2020-07-07T09:57:41,013   /usr/lib/python3/dist-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]
2020-07-07T09:57:41,013    #warning "Using deprecated NumPy API, disable it with " \
2020-07-07T09:57:41,013     ^~~~~~~
2020-07-07T09:57:42,892   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*)’:
2020-07-07T09:57:42,893   pgenlib/_pgenlib.cpp:6906:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:42,893        __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:42,893                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:42,899   pgenlib/_pgenlib.cpp:6962:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:42,900        __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:42,900                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:42,915   pgenlib/_pgenlib.cpp:7187:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:42,915      __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:42,916                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:42,921   pgenlib/_pgenlib.cpp:7243:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:42,922      __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:42,923                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:42,952   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*)’:
2020-07-07T09:57:42,953   pgenlib/_pgenlib.cpp:7896:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:42,953        __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:42,954                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:42,957   pgenlib/_pgenlib.cpp:7952:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:42,958        __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:42,959                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:42,972   pgenlib/_pgenlib.cpp:8177:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:42,972      __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:42,973                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:42,977   pgenlib/_pgenlib.cpp:8233:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:42,978      __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:42,979                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,008   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*)’:
2020-07-07T09:57:43,009   pgenlib/_pgenlib.cpp:8886:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,009        __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,010                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,013   pgenlib/_pgenlib.cpp:8942:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,014        __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:43,015                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,028   pgenlib/_pgenlib.cpp:9167:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,029      __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:43,030                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,033   pgenlib/_pgenlib.cpp:9223:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,034      __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,035                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,100   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*)’:
2020-07-07T09:57:43,101   pgenlib/_pgenlib.cpp:10310:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,102        __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,103                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,106   pgenlib/_pgenlib.cpp:10366:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,107        __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:43,108                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,121   pgenlib/_pgenlib.cpp:10607:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,122      __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:43,123                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,127   pgenlib/_pgenlib.cpp:10663:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,128      __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,129                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,161   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*)’:
2020-07-07T09:57:43,162   pgenlib/_pgenlib.cpp:11358:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,162        __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,163                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,166   pgenlib/_pgenlib.cpp:11414:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,167        __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:43,168                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,182   pgenlib/_pgenlib.cpp:11655:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,183      __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:43,183                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,188   pgenlib/_pgenlib.cpp:11711:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,188      __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,189                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,221   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*)’:
2020-07-07T09:57:43,222   pgenlib/_pgenlib.cpp:12406:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,223        __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,223                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,227   pgenlib/_pgenlib.cpp:12462:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,228        __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:43,228                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,243   pgenlib/_pgenlib.cpp:12703:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,243      __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T09:57:43,244                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,261   pgenlib/_pgenlib.cpp:12759:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,262      __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,263                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,346   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*)’:
2020-07-07T09:57:43,347   pgenlib/_pgenlib.cpp:14095:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,348        __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,348                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,352   pgenlib/_pgenlib.cpp:14151:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,353        __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-07T09:57:43,353                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,367   pgenlib/_pgenlib.cpp:14376:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,367      __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-07T09:57:43,368                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,372   pgenlib/_pgenlib.cpp:14432:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,373      __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,373                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,425   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*)’:
2020-07-07T09:57:43,425   pgenlib/_pgenlib.cpp:15476:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,426        __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,427                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,430   pgenlib/_pgenlib.cpp:15532:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,431        __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-07T09:57:43,432                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,445   pgenlib/_pgenlib.cpp:15773:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,446      __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-07T09:57:43,447                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:57:43,451   pgenlib/_pgenlib.cpp:15829:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-07T09:57:43,452      __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T09:57:43,452                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T09:58:40,493   arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipgenlib -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c pgenlib/pgenlib_python_support.cpp -o build/temp.linux-armv7l-3.7/pgenlib/pgenlib_python_support.o -std=c++98 -Wno-unused-function
2020-07-07T09:58:41,838   arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipgenlib -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c pgenlib/pgenlib_internal.cpp -o build/temp.linux-armv7l-3.7/pgenlib/pgenlib_internal.o -std=c++98 -Wno-unused-function
2020-07-07T09:58:42,059   pgenlib/pgenlib_internal.cpp:710:4: error: #error "Unaligned accesses in small_genoarr_count_3freq_incr()."
2020-07-07T09:58:42,060      #error "Unaligned accesses in small_genoarr_count_3freq_incr()."
2020-07-07T09:58:42,060       ^~~~~
2020-07-07T09:58:42,061   pgenlib/pgenlib_internal.cpp:752:4: error: #error "Unaligned accesses in genoarr_count_subset_freqs()."
2020-07-07T09:58:42,061      #error "Unaligned accesses in genoarr_count_subset_freqs()."
2020-07-07T09:58:42,062       ^~~~~
2020-07-07T09:58:42,069   pgenlib/pgenlib_internal.cpp:1911:4: error: #error "Unaligned accesses in pgfi_init_phase2()."
2020-07-07T09:58:42,069      #error "Unaligned accesses in pgfi_init_phase2()."
2020-07-07T09:58:42,069       ^~~~~
2020-07-07T09:58:42,076   pgenlib/pgenlib_internal.cpp:3145:4: error: #error "Unaligned accesses in parse_onebit_unsafe()."
2020-07-07T09:58:42,077      #error "Unaligned accesses in parse_onebit_unsafe()."
2020-07-07T09:58:42,077       ^~~~~
2020-07-07T09:58:42,078   pgenlib/pgenlib_internal.cpp:3178:4: error: #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)."
2020-07-07T09:58:42,079      #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)."
2020-07-07T09:58:42,079       ^~~~~
2020-07-07T09:58:42,085   pgenlib/pgenlib_internal.cpp:3761:4: error: #error "Unaligned accesses in bytesum_arr()."
2020-07-07T09:58:42,085      #error "Unaligned accesses in bytesum_arr()."
2020-07-07T09:58:42,085       ^~~~~
2020-07-07T09:58:42,087   pgenlib/pgenlib_internal.cpp:3814:4: error: #error "Unaligned accesses in skip_difflist_ids()."
2020-07-07T09:58:42,088      #error "Unaligned accesses in skip_difflist_ids()."
2020-07-07T09:58:42,088       ^~~~~
2020-07-07T09:58:42,090   pgenlib/pgenlib_internal.cpp:3940:4: error: #error "Unaligned accesses in countparse_onebit_subset()."
2020-07-07T09:58:42,090      #error "Unaligned accesses in countparse_onebit_subset()."
2020-07-07T09:58:42,091       ^~~~~
2020-07-07T09:58:42,098   pgenlib/pgenlib_internal.cpp:4923:4: error: #error "Unaligned accesses in parse_just_ambig_ids()."
2020-07-07T09:58:42,099      #error "Unaligned accesses in parse_just_ambig_ids()."
2020-07-07T09:58:42,099       ^~~~~
2020-07-07T09:58:42,103   pgenlib/pgenlib_internal.cpp:5454:4: error: #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()."
2020-07-07T09:58:42,104      #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()."
2020-07-07T09:58:42,104       ^~~~~
2020-07-07T09:58:42,107   pgenlib/pgenlib_internal.cpp:5670:4: error: #error "Unaligned accesses in parse_dosage16()."
2020-07-07T09:58:42,108      #error "Unaligned accesses in parse_dosage16()."
2020-07-07T09:58:42,108       ^~~~~
2020-07-07T09:58:42,111   pgenlib/pgenlib_internal.cpp:5889:4: error: #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()."
2020-07-07T09:58:42,112      #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()."
2020-07-07T09:58:42,112       ^~~~~
2020-07-07T09:58:42,116   pgenlib/pgenlib_internal.cpp:6294:4: error: #error "Unaligned accesses in pgr_read_missingness_dosage()."
2020-07-07T09:58:42,117      #error "Unaligned accesses in pgr_read_missingness_dosage()."
2020-07-07T09:58:42,117       ^~~~~
2020-07-07T09:58:42,120   pgenlib/pgenlib_internal.cpp:6542:4: error: #error "Unaligned accesses in validate_onebit()."
2020-07-07T09:58:42,121      #error "Unaligned accesses in validate_onebit()."
2020-07-07T09:58:42,121       ^~~~~
2020-07-07T09:58:42,124   pgenlib/pgenlib_internal.cpp:6760:4: error: #error "Unaligned accesses in validate_dosage16()."
2020-07-07T09:58:42,125      #error "Unaligned accesses in validate_dosage16()."
2020-07-07T09:58:42,125       ^~~~~
2020-07-07T09:58:42,132   pgenlib/pgenlib_internal.cpp:7651:4: error: #error "Unaligned accesses in save_ld_difflist()."
2020-07-07T09:58:42,132      #error "Unaligned accesses in save_ld_difflist()."
2020-07-07T09:58:42,133       ^~~~~
2020-07-07T09:58:42,136   pgenlib/pgenlib_internal.cpp:7793:4: error: #error "Unaligned accesses in save_onebit()."
2020-07-07T09:58:42,136      #error "Unaligned accesses in save_onebit()."
2020-07-07T09:58:42,137       ^~~~~
2020-07-07T09:58:42,139   pgenlib/pgenlib_internal.cpp:8025:4: error: #error "Unaligned accesses in save_ld_two_list_delta()."
2020-07-07T09:58:42,140      #error "Unaligned accesses in save_ld_two_list_delta()."
2020-07-07T09:58:42,140       ^~~~~
2020-07-07T09:58:42,142   pgenlib/pgenlib_internal.cpp:8295:4: error: #error "Unaligned accesses in append_hphase()."
2020-07-07T09:58:42,143      #error "Unaligned accesses in append_hphase()."
2020-07-07T09:58:42,143       ^~~~~
2020-07-07T09:58:42,852   error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1
2020-07-07T09:58:43,088   Building wheel for hapflk (setup.py): finished with status 'error'
2020-07-07T09:58:43,089   ERROR: Failed building wheel for hapflk
2020-07-07T09:58:43,090   Running setup.py clean for hapflk
2020-07-07T09:58:43,091   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-z_8vts67/hapflk/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-z_8vts67/hapflk/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
2020-07-07T09:58:46,964   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:454: UserWarning: Normalizing '2.0-dev0' to '2.0.dev0'
2020-07-07T09:58:46,965     warnings.warn(tmpl.format(**locals()))
2020-07-07T09:58:46,972   running clean
2020-07-07T09:58:46,978   removing 'build/temp.linux-armv7l-3.7' (and everything under it)
2020-07-07T09:58:46,989   removing 'build/lib.linux-armv7l-3.7' (and everything under it)
2020-07-07T09:58:46,1000   'build/bdist.linux-armv7l' does not exist -- can't clean it
2020-07-07T09:58:47,001   'build/scripts-3.7' does not exist -- can't clean it
2020-07-07T09:58:47,001   removing 'build'
2020-07-07T09:58:47,222 Failed to build hapflk
2020-07-07T09:58:47,222 ERROR: Failed to build one or more wheels
2020-07-07T09:58:47,223 Exception information:
2020-07-07T09:58:47,223 Traceback (most recent call last):
2020-07-07T09:58:47,223   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 188, in _main
2020-07-07T09:58:47,223     status = self.run(options, args)
2020-07-07T09:58:47,223   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/req_command.py", line 185, in wrapper
2020-07-07T09:58:47,223     return func(self, options, args)
2020-07-07T09:58:47,223   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 189, in run
2020-07-07T09:58:47,223     "Failed to build one or more wheels"
2020-07-07T09:58:47,223 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2020-07-07T09:58:47,231 Removed build tracker: '/tmp/pip-req-tracker-vzssvtyu'