2020-07-08T07:03:03,817 Created temporary directory: /tmp/pip-ephem-wheel-cache-o79v61u3
2020-07-08T07:03:03,821 Created temporary directory: /tmp/pip-req-tracker-k_32dl3y
2020-07-08T07:03:03,822 Initialized build tracking at /tmp/pip-req-tracker-k_32dl3y
2020-07-08T07:03:03,822 Created build tracker: /tmp/pip-req-tracker-k_32dl3y
2020-07-08T07:03:03,823 Entered build tracker: /tmp/pip-req-tracker-k_32dl3y
2020-07-08T07:03:03,824 Created temporary directory: /tmp/pip-wheel-2fiqjbom
2020-07-08T07:03:03,841 1 location(s) to search for versions of hapflk:
2020-07-08T07:03:03,841 * https://pypi.org/simple/hapflk/
2020-07-08T07:03:03,842 Fetching project page and analyzing links: https://pypi.org/simple/hapflk/
2020-07-08T07:03:03,842 Getting page https://pypi.org/simple/hapflk/
2020-07-08T07:03:03,845 Found index url https://pypi.org/simple
2020-07-08T07:03:04,053   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
2020-07-08T07:03:04,054   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
2020-07-08T07:03:04,055   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
2020-07-08T07:03:04,056   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
2020-07-08T07:03:04,056   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
2020-07-08T07:03:04,057   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
2020-07-08T07:03:04,058   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
2020-07-08T07:03:04,058   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
2020-07-08T07:03:04,059   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
2020-07-08T07:03:04,059   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
2020-07-08T07:03:04,060   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
2020-07-08T07:03:04,061   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
2020-07-08T07:03:04,061   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
2020-07-08T07:03:04,062   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
2020-07-08T07:03:04,074 Given no hashes to check 1 links for project 'hapflk': discarding no candidates
2020-07-08T07:03:04,080 Using version 2.0.dev2 (newest of versions: 2.0.dev2)
2020-07-08T07:03:04,085 Collecting hapflk==2.0.dev2
2020-07-08T07:03:04,089   Created temporary directory: /tmp/pip-unpack-fs5tqwo0
2020-07-08T07:03:04,324   Downloading hapflk-2.0.dev2.tar.gz (511 kB)
2020-07-08T07:03:05,217   Added hapflk==2.0.dev2 from https://files.pythonhosted.org/packages/89/5d/fa3af0a5d868d5154d1516696a317c13bcb686706143ec2052f789e17017/hapflk-2.0.dev2.tar.gz#sha256=bcac5a28ccec7e4daa1a216ce19717bca5e7686a42cd99ee5114be8ba03c2ef6 to build tracker '/tmp/pip-req-tracker-k_32dl3y'
2020-07-08T07:03:05,219     Running setup.py (path:/tmp/pip-wheel-2fiqjbom/hapflk/setup.py) egg_info for package hapflk
2020-07-08T07:03:05,221     Created temporary directory: /tmp/pip-pip-egg-info-nwc1b_lk
2020-07-08T07:03:05,221     Running command python setup.py egg_info
2020-07-08T07:03:10,674     running egg_info
2020-07-08T07:03:10,678     creating /tmp/pip-pip-egg-info-nwc1b_lk/hapflk.egg-info
2020-07-08T07:03:10,680     writing /tmp/pip-pip-egg-info-nwc1b_lk/hapflk.egg-info/PKG-INFO
2020-07-08T07:03:10,685     writing dependency_links to /tmp/pip-pip-egg-info-nwc1b_lk/hapflk.egg-info/dependency_links.txt
2020-07-08T07:03:10,689     writing requirements to /tmp/pip-pip-egg-info-nwc1b_lk/hapflk.egg-info/requires.txt
2020-07-08T07:03:10,691     writing top-level names to /tmp/pip-pip-egg-info-nwc1b_lk/hapflk.egg-info/top_level.txt
2020-07-08T07:03:10,695     writing manifest file '/tmp/pip-pip-egg-info-nwc1b_lk/hapflk.egg-info/SOURCES.txt'
2020-07-08T07:03:10,983     reading manifest file '/tmp/pip-pip-egg-info-nwc1b_lk/hapflk.egg-info/SOURCES.txt'
2020-07-08T07:03:10,986     reading manifest template 'MANIFEST.in'
2020-07-08T07:03:10,990     /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:458: UserWarning: Normalizing '2.0-dev2' to '2.0.dev2'
2020-07-08T07:03:10,990       warnings.warn(tmpl.format(**locals()))
2020-07-08T07:03:10,991     warning: no files found matching '*' under directory 'utils'
2020-07-08T07:03:10,998     writing manifest file '/tmp/pip-pip-egg-info-nwc1b_lk/hapflk.egg-info/SOURCES.txt'
2020-07-08T07:03:11,282   Source in /tmp/pip-wheel-2fiqjbom/hapflk has version 2.0.dev2, which satisfies requirement hapflk==2.0.dev2 from https://files.pythonhosted.org/packages/89/5d/fa3af0a5d868d5154d1516696a317c13bcb686706143ec2052f789e17017/hapflk-2.0.dev2.tar.gz#sha256=bcac5a28ccec7e4daa1a216ce19717bca5e7686a42cd99ee5114be8ba03c2ef6
2020-07-08T07:03:11,284   Removed hapflk==2.0.dev2 from https://files.pythonhosted.org/packages/89/5d/fa3af0a5d868d5154d1516696a317c13bcb686706143ec2052f789e17017/hapflk-2.0.dev2.tar.gz#sha256=bcac5a28ccec7e4daa1a216ce19717bca5e7686a42cd99ee5114be8ba03c2ef6 from build tracker '/tmp/pip-req-tracker-k_32dl3y'
2020-07-08T07:03:11,287 Building wheels for collected packages: hapflk
2020-07-08T07:03:11,296   Created temporary directory: /tmp/pip-wheel-uwcc35tq
2020-07-08T07:03:11,297   Building wheel for hapflk (setup.py): started
2020-07-08T07:03:11,298   Destination directory: /tmp/pip-wheel-uwcc35tq
2020-07-08T07:03:11,298   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-2fiqjbom/hapflk/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-2fiqjbom/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-uwcc35tq
2020-07-08T07:03:14,858   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:458: UserWarning: Normalizing '2.0-dev2' to '2.0.dev2'
2020-07-08T07:03:14,859     warnings.warn(tmpl.format(**locals()))
2020-07-08T07:03:14,911   running bdist_wheel
2020-07-08T07:03:14,919   running build
2020-07-08T07:03:14,920   running build_py
2020-07-08T07:03:15,172   creating build
2020-07-08T07:03:15,173   creating build/lib.linux-armv7l-3.7
2020-07-08T07:03:15,174   creating build/lib.linux-armv7l-3.7/hapflk
2020-07-08T07:03:15,177   copying hapflk/__init__.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-08T07:03:15,182   copying hapflk/InputOutput.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-08T07:03:15,189   copying hapflk/utils.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-08T07:03:15,194   copying hapflk/popgen.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-08T07:03:15,202   copying hapflk/data.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-08T07:03:15,210   copying hapflk/hapflkadapt.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-08T07:03:15,217   copying hapflk/hapflk.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-08T07:03:15,223   copying hapflk/nj.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-08T07:03:15,230   running build_ext
2020-07-08T07:03:15,247   building 'hapflk.fastphase' extension
2020-07-08T07:03:15,249   creating build/temp.linux-armv7l-3.7
2020-07-08T07:03:15,250   creating build/temp.linux-armv7l-3.7/fastphase
2020-07-08T07:03:15,251   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
2020-07-08T07:03:15,989   In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
2020-07-08T07:03:15,990                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2020-07-08T07:03:15,991                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2020-07-08T07:03:15,993                    from fastphase/fastphase.c:618:
2020-07-08T07:03:15,993   /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]
2020-07-08T07:03:15,994    #warning "Using deprecated NumPy API, disable it with " \
2020-07-08T07:03:15,995     ^~~~~~~
2020-07-08T07:03:56,298   fastphase/fastphase.c: In function ‘__pyx_pw_6hapflk_9fastphase_11calc_cost_matrix_geno_tot’:
2020-07-08T07:03:56,303   fastphase/fastphase.c:15442:38: warning: ‘__pyx_v_k1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-08T07:03:56,304          if (__pyx_t_40 < 0) __pyx_t_40 += __pyx_pybuffernd_res.diminfo[1].shape;
2020-07-08T07:03:56,304                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:03:56,309   fastphase/fastphase.c:14989:7: note: ‘__pyx_v_k1’ was declared here
2020-07-08T07:03:56,309      int __pyx_v_k1;
2020-07-08T07:03:56,310          ^~~~~~~~~~
2020-07-08T07:03:56,312   fastphase/fastphase.c:15443:38: warning: ‘__pyx_v_kp1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-08T07:03:56,312          if (__pyx_t_41 < 0) __pyx_t_41 += __pyx_pybuffernd_res.diminfo[2].shape;
2020-07-08T07:03:56,312                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:03:56,317   fastphase/fastphase.c:14991:7: note: ‘__pyx_v_kp1’ was declared here
2020-07-08T07:03:56,318      int __pyx_v_kp1;
2020-07-08T07:03:56,318          ^~~~~~~~~~~
2020-07-08T07:03:56,320   fastphase/fastphase.c:15458:38: warning: ‘__pyx_v_kp2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-08T07:03:56,320          if (__pyx_t_44 < 0) __pyx_t_44 += __pyx_pybuffernd_res.diminfo[2].shape;
2020-07-08T07:03:56,321                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:03:56,325   fastphase/fastphase.c:14992:7: note: ‘__pyx_v_kp2’ was declared here
2020-07-08T07:03:56,326      int __pyx_v_kp2;
2020-07-08T07:03:56,326          ^~~~~~~~~~~
2020-07-08T07:03:56,328   fastphase/fastphase.c:15472:38: warning: ‘__pyx_v_k2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-08T07:03:56,329          if (__pyx_t_46 < 0) __pyx_t_46 += __pyx_pybuffernd_res.diminfo[1].shape;
2020-07-08T07:03:56,329                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:03:56,334   fastphase/fastphase.c:14990:7: note: ‘__pyx_v_k2’ was declared here
2020-07-08T07:03:56,334      int __pyx_v_k2;
2020-07-08T07:03:56,335          ^~~~~~~~~~
2020-07-08T07:04:42,586   fastphase/fastphase.c: In function ‘__pyx_f_6hapflk_9fastphase_genViterbi.isra.67’:
2020-07-08T07:04:42,590   fastphase/fastphase.c:17359:7: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-08T07:04:42,591      int __pyx_v_k;
2020-07-08T07:04:42,591          ^~~~~~~~~
2020-07-08T07:04:42,596   fastphase/fastphase.c:530:40: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-08T07:04:42,597      #define PyInt_FromLong               PyLong_FromLong
2020-07-08T07:04:42,597                                           ^~~~~~~~~~~~~~~
2020-07-08T07:04:42,603   fastphase/fastphase.c:17360:7: note: ‘__pyx_v_l’ was declared here
2020-07-08T07:04:42,604      int __pyx_v_l;
2020-07-08T07:04:42,604          ^~~~~~~~~
2020-07-08T07:04:42,605   fastphase/fastphase.c:530:40: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-08T07:04:42,605      #define PyInt_FromLong               PyLong_FromLong
2020-07-08T07:04:42,606                                           ^~~~~~~~~~~~~~~
2020-07-08T07:04:42,610   fastphase/fastphase.c:17359:7: note: ‘__pyx_v_k’ was declared here
2020-07-08T07:04:42,611      int __pyx_v_k;
2020-07-08T07:04:42,611          ^~~~~~~~~
2020-07-08T07:04:42,614   fastphase/fastphase.c:18496:12: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-08T07:04:42,614            if (!__pyx_t_64) {
2020-07-08T07:04:42,615               ^
2020-07-08T07:04:42,617   fastphase/fastphase.c:18504:12: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-08T07:04:42,618            if (__pyx_t_44) {
2020-07-08T07:04:42,618               ^
2020-07-08T07:04:42,621   fastphase/fastphase.c:18603:38: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-08T07:04:42,621          if (__pyx_t_89 < 0) __pyx_t_89 += __pyx_pybuffernd_theta.diminfo[1].shape;
2020-07-08T07:04:42,622                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:20,310   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
2020-07-08T07:05:20,875   building 'hapflk._pgenlib' extension
2020-07-08T07:05:20,876   creating build/temp.linux-armv7l-3.7/pgenlib
2020-07-08T07:05:20,877   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
2020-07-08T07:05:21,447   In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
2020-07-08T07:05:21,448                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2020-07-08T07:05:21,449                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2020-07-08T07:05:21,449                    from pgenlib/_pgenlib.cpp:572:
2020-07-08T07:05:21,449   /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]
2020-07-08T07:05:21,450    #warning "Using deprecated NumPy API, disable it with " \
2020-07-08T07:05:21,450     ^~~~~~~
2020-07-08T07:05:23,312   pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_8_pgenlib_10PgenReader_read_range_internal8(__pyx_obj_8_pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, __pyx_opt_args_8_pgenlib_10PgenReader_read_range_internal8*)’:
2020-07-08T07:05:23,313   pgenlib/_pgenlib.cpp:6777:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,313        __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,314                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,320   pgenlib/_pgenlib.cpp:6848:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,321        __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,321                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,337   pgenlib/_pgenlib.cpp:7112:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,337      __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,338                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,343   pgenlib/_pgenlib.cpp:7183:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,344      __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,344                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,378   pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_8_pgenlib_10PgenReader_read_range_internal32(__pyx_obj_8_pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, __pyx_opt_args_8_pgenlib_10PgenReader_read_range_internal32*)’:
2020-07-08T07:05:23,378   pgenlib/_pgenlib.cpp:7869:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,379        __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,380                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,384   pgenlib/_pgenlib.cpp:7940:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,385        __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,386                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,401   pgenlib/_pgenlib.cpp:8204:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,401      __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,402                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,408   pgenlib/_pgenlib.cpp:8275:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,408      __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,409                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,442   pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_8_pgenlib_10PgenReader_read_range_internal64(__pyx_obj_8_pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, __pyx_opt_args_8_pgenlib_10PgenReader_read_range_internal64*)’:
2020-07-08T07:05:23,442   pgenlib/_pgenlib.cpp:8961:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,443        __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,444                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,448   pgenlib/_pgenlib.cpp:9032:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,449        __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,450                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,465   pgenlib/_pgenlib.cpp:9296:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,466      __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,467                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,472   pgenlib/_pgenlib.cpp:9367:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,472      __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,473                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,539   pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_8_pgenlib_10PgenReader_read_list_internal8(__pyx_obj_8_pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_8_pgenlib_10PgenReader_read_list_internal8*)’:
2020-07-08T07:05:23,539   pgenlib/_pgenlib.cpp:10457:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,540        __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,541                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,545   pgenlib/_pgenlib.cpp:10528:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,546        __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,547                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,563   pgenlib/_pgenlib.cpp:10808:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,564      __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,564                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,570   pgenlib/_pgenlib.cpp:10879:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,570      __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,571                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,607   pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_8_pgenlib_10PgenReader_read_list_internal32(__pyx_obj_8_pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_8_pgenlib_10PgenReader_read_list_internal32*)’:
2020-07-08T07:05:23,608   pgenlib/_pgenlib.cpp:11607:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,608        __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,609                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,614   pgenlib/_pgenlib.cpp:11678:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,614        __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,615                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,631   pgenlib/_pgenlib.cpp:11958:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,632      __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,633                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,638   pgenlib/_pgenlib.cpp:12029:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,638      __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,639                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,688   pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_8_pgenlib_10PgenReader_read_list_internal64(__pyx_obj_8_pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_8_pgenlib_10PgenReader_read_list_internal64*)’:
2020-07-08T07:05:23,689   pgenlib/_pgenlib.cpp:12757:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,690        __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,690                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,695   pgenlib/_pgenlib.cpp:12828:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,696        __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,696                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,712   pgenlib/_pgenlib.cpp:13108:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,713      __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-08T07:05:23,714                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,719   pgenlib/_pgenlib.cpp:13179:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,719      __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,720                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,804   pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_8_pgenlib_10PgenReader_read_alleles_range(__pyx_obj_8_pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, int, __pyx_opt_args_8_pgenlib_10PgenReader_read_alleles_range*)’:
2020-07-08T07:05:23,805   pgenlib/_pgenlib.cpp:14533:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,805        __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,806                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,811   pgenlib/_pgenlib.cpp:14604:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,811        __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-08T07:05:23,812                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,827   pgenlib/_pgenlib.cpp:14868:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,828      __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-08T07:05:23,829                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,834   pgenlib/_pgenlib.cpp:14939:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,834      __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,835                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,888   pgenlib/_pgenlib.cpp: In function ‘PyObject* __pyx_f_8_pgenlib_10PgenReader_read_alleles_list(__pyx_obj_8_pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, int, __pyx_opt_args_8_pgenlib_10PgenReader_read_alleles_list*)’:
2020-07-08T07:05:23,888   pgenlib/_pgenlib.cpp:15986:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,889        __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,890                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,894   pgenlib/_pgenlib.cpp:16057:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,895        __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-08T07:05:23,895                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,912   pgenlib/_pgenlib.cpp:16337:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,912      __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-08T07:05:23,913                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:05:23,918   pgenlib/_pgenlib.cpp:16408:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-07-08T07:05:23,919      __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-08T07:05:23,919                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-08T07:06:23,639   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
2020-07-08T07:06:24,981   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
2020-07-08T07:06:25,200   pgenlib/pgenlib_internal.cpp:710:4: error: #error "Unaligned accesses in small_genoarr_count_3freq_incr()."
2020-07-08T07:06:25,200      #error "Unaligned accesses in small_genoarr_count_3freq_incr()."
2020-07-08T07:06:25,201       ^~~~~
2020-07-08T07:06:25,201   pgenlib/pgenlib_internal.cpp:752:4: error: #error "Unaligned accesses in genoarr_count_subset_freqs()."
2020-07-08T07:06:25,201      #error "Unaligned accesses in genoarr_count_subset_freqs()."
2020-07-08T07:06:25,202       ^~~~~
2020-07-08T07:06:25,206   pgenlib/pgenlib_internal.cpp:1911:4: error: #error "Unaligned accesses in pgfi_init_phase2()."
2020-07-08T07:06:25,207      #error "Unaligned accesses in pgfi_init_phase2()."
2020-07-08T07:06:25,207       ^~~~~
2020-07-08T07:06:25,212   pgenlib/pgenlib_internal.cpp:3145:4: error: #error "Unaligned accesses in parse_onebit_unsafe()."
2020-07-08T07:06:25,213      #error "Unaligned accesses in parse_onebit_unsafe()."
2020-07-08T07:06:25,213       ^~~~~
2020-07-08T07:06:25,214   pgenlib/pgenlib_internal.cpp:3178:4: error: #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)."
2020-07-08T07:06:25,214      #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)."
2020-07-08T07:06:25,214       ^~~~~
2020-07-08T07:06:25,218   pgenlib/pgenlib_internal.cpp:3761:4: error: #error "Unaligned accesses in bytesum_arr()."
2020-07-08T07:06:25,219      #error "Unaligned accesses in bytesum_arr()."
2020-07-08T07:06:25,219       ^~~~~
2020-07-08T07:06:25,219   pgenlib/pgenlib_internal.cpp:3814:4: error: #error "Unaligned accesses in skip_difflist_ids()."
2020-07-08T07:06:25,220      #error "Unaligned accesses in skip_difflist_ids()."
2020-07-08T07:06:25,220       ^~~~~
2020-07-08T07:06:25,220   pgenlib/pgenlib_internal.cpp:3940:4: error: #error "Unaligned accesses in countparse_onebit_subset()."
2020-07-08T07:06:25,221      #error "Unaligned accesses in countparse_onebit_subset()."
2020-07-08T07:06:25,221       ^~~~~
2020-07-08T07:06:25,229   pgenlib/pgenlib_internal.cpp:4923:4: error: #error "Unaligned accesses in parse_just_ambig_ids()."
2020-07-08T07:06:25,229      #error "Unaligned accesses in parse_just_ambig_ids()."
2020-07-08T07:06:25,230       ^~~~~
2020-07-08T07:06:25,231   pgenlib/pgenlib_internal.cpp:5454:4: error: #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()."
2020-07-08T07:06:25,232      #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()."
2020-07-08T07:06:25,232       ^~~~~
2020-07-08T07:06:25,234   pgenlib/pgenlib_internal.cpp:5670:4: error: #error "Unaligned accesses in parse_dosage16()."
2020-07-08T07:06:25,235      #error "Unaligned accesses in parse_dosage16()."
2020-07-08T07:06:25,235       ^~~~~
2020-07-08T07:06:25,237   pgenlib/pgenlib_internal.cpp:5889:4: error: #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()."
2020-07-08T07:06:25,238      #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()."
2020-07-08T07:06:25,239       ^~~~~
2020-07-08T07:06:25,241   pgenlib/pgenlib_internal.cpp:6294:4: error: #error "Unaligned accesses in pgr_read_missingness_dosage()."
2020-07-08T07:06:25,242      #error "Unaligned accesses in pgr_read_missingness_dosage()."
2020-07-08T07:06:25,243       ^~~~~
2020-07-08T07:06:25,247   pgenlib/pgenlib_internal.cpp:6542:4: error: #error "Unaligned accesses in validate_onebit()."
2020-07-08T07:06:25,248      #error "Unaligned accesses in validate_onebit()."
2020-07-08T07:06:25,248       ^~~~~
2020-07-08T07:06:25,249   pgenlib/pgenlib_internal.cpp:6760:4: error: #error "Unaligned accesses in validate_dosage16()."
2020-07-08T07:06:25,249      #error "Unaligned accesses in validate_dosage16()."
2020-07-08T07:06:25,250       ^~~~~
2020-07-08T07:06:25,254   pgenlib/pgenlib_internal.cpp:7651:4: error: #error "Unaligned accesses in save_ld_difflist()."
2020-07-08T07:06:25,255      #error "Unaligned accesses in save_ld_difflist()."
2020-07-08T07:06:25,255       ^~~~~
2020-07-08T07:06:25,256   pgenlib/pgenlib_internal.cpp:7793:4: error: #error "Unaligned accesses in save_onebit()."
2020-07-08T07:06:25,257      #error "Unaligned accesses in save_onebit()."
2020-07-08T07:06:25,257       ^~~~~
2020-07-08T07:06:25,259   pgenlib/pgenlib_internal.cpp:8025:4: error: #error "Unaligned accesses in save_ld_two_list_delta()."
2020-07-08T07:06:25,260      #error "Unaligned accesses in save_ld_two_list_delta()."
2020-07-08T07:06:25,260       ^~~~~
2020-07-08T07:06:25,262   pgenlib/pgenlib_internal.cpp:8295:4: error: #error "Unaligned accesses in append_hphase()."
2020-07-08T07:06:25,263      #error "Unaligned accesses in append_hphase()."
2020-07-08T07:06:25,263       ^~~~~
2020-07-08T07:06:25,996   error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1
2020-07-08T07:06:26,236   Building wheel for hapflk (setup.py): finished with status 'error'
2020-07-08T07:06:26,237   ERROR: Failed building wheel for hapflk
2020-07-08T07:06:26,238   Running setup.py clean for hapflk
2020-07-08T07:06:26,239   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-2fiqjbom/hapflk/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-2fiqjbom/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
2020-07-08T07:06:30,163   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:458: UserWarning: Normalizing '2.0-dev2' to '2.0.dev2'
2020-07-08T07:06:30,163     warnings.warn(tmpl.format(**locals()))
2020-07-08T07:06:30,181   running clean
2020-07-08T07:06:30,186   removing 'build/temp.linux-armv7l-3.7' (and everything under it)
2020-07-08T07:06:30,196   removing 'build/lib.linux-armv7l-3.7' (and everything under it)
2020-07-08T07:06:30,206   'build/bdist.linux-armv7l' does not exist -- can't clean it
2020-07-08T07:06:30,207   'build/scripts-3.7' does not exist -- can't clean it
2020-07-08T07:06:30,207   removing 'build'
2020-07-08T07:06:30,431 Failed to build hapflk
2020-07-08T07:06:30,432 ERROR: Failed to build one or more wheels
2020-07-08T07:06:30,433 Exception information:
2020-07-08T07:06:30,433 Traceback (most recent call last):
2020-07-08T07:06:30,433   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 188, in _main
2020-07-08T07:06:30,433     status = self.run(options, args)
2020-07-08T07:06:30,433   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/req_command.py", line 185, in wrapper
2020-07-08T07:06:30,433     return func(self, options, args)
2020-07-08T07:06:30,433   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 189, in run
2020-07-08T07:06:30,433     "Failed to build one or more wheels"
2020-07-08T07:06:30,433 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2020-07-08T07:06:30,441 Removed build tracker: '/tmp/pip-req-tracker-k_32dl3y'