2020-07-07T15:10:27,800 Created temporary directory: /tmp/pip-ephem-wheel-cache-41zod3do
2020-07-07T15:10:27,804 Created temporary directory: /tmp/pip-req-tracker-opjfmqu8
2020-07-07T15:10:27,805 Initialized build tracking at /tmp/pip-req-tracker-opjfmqu8
2020-07-07T15:10:27,806 Created build tracker: /tmp/pip-req-tracker-opjfmqu8
2020-07-07T15:10:27,806 Entered build tracker: /tmp/pip-req-tracker-opjfmqu8
2020-07-07T15:10:27,808 Created temporary directory: /tmp/pip-wheel-vyvsi6_h
2020-07-07T15:10:27,821 1 location(s) to search for versions of hapflk:
2020-07-07T15:10:27,821 * https://pypi.org/simple/hapflk/
2020-07-07T15:10:27,822 Fetching project page and analyzing links: https://pypi.org/simple/hapflk/
2020-07-07T15:10:27,823 Getting page https://pypi.org/simple/hapflk/
2020-07-07T15:10:27,825 Found index url https://pypi.org/simple
2020-07-07T15:10:28,030   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
2020-07-07T15:10:28,031   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
2020-07-07T15:10:28,031   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
2020-07-07T15:10:28,032   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
2020-07-07T15:10:28,033   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
2020-07-07T15:10:28,033   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
2020-07-07T15:10:28,034   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
2020-07-07T15:10:28,035   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
2020-07-07T15:10:28,035   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
2020-07-07T15:10:28,036   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
2020-07-07T15:10:28,036   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
2020-07-07T15:10:28,037   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
2020-07-07T15:10:28,037   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
2020-07-07T15:10:28,049 Given no hashes to check 1 links for project 'hapflk': discarding no candidates
2020-07-07T15:10:28,051 Using version 2.0.dev1 (newest of versions: 2.0.dev1)
2020-07-07T15:10:28,056 Collecting hapflk==2.0.dev1
2020-07-07T15:10:28,060   Created temporary directory: /tmp/pip-unpack-e3bsj6l2
2020-07-07T15:10:28,297   Downloading hapflk-2.0.dev1.tar.gz (515 kB)
2020-07-07T15:10:29,213   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-opjfmqu8'
2020-07-07T15:10:29,216     Running setup.py (path:/tmp/pip-wheel-vyvsi6_h/hapflk/setup.py) egg_info for package hapflk
2020-07-07T15:10:29,218     Created temporary directory: /tmp/pip-pip-egg-info-6sxdd3dh
2020-07-07T15:10:29,219     Running command python setup.py egg_info
2020-07-07T15:10:33,027     running egg_info
2020-07-07T15:10:33,034     creating /tmp/pip-pip-egg-info-6sxdd3dh/hapflk.egg-info
2020-07-07T15:10:33,036     writing /tmp/pip-pip-egg-info-6sxdd3dh/hapflk.egg-info/PKG-INFO
2020-07-07T15:10:33,040     writing dependency_links to /tmp/pip-pip-egg-info-6sxdd3dh/hapflk.egg-info/dependency_links.txt
2020-07-07T15:10:33,045     writing requirements to /tmp/pip-pip-egg-info-6sxdd3dh/hapflk.egg-info/requires.txt
2020-07-07T15:10:33,047     writing top-level names to /tmp/pip-pip-egg-info-6sxdd3dh/hapflk.egg-info/top_level.txt
2020-07-07T15:10:33,051     writing manifest file '/tmp/pip-pip-egg-info-6sxdd3dh/hapflk.egg-info/SOURCES.txt'
2020-07-07T15:10:33,326     reading manifest file '/tmp/pip-pip-egg-info-6sxdd3dh/hapflk.egg-info/SOURCES.txt'
2020-07-07T15:10:33,329     reading manifest template 'MANIFEST.in'
2020-07-07T15:10:33,333     /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:454: UserWarning: Normalizing '2.0-dev1' to '2.0.dev1'
2020-07-07T15:10:33,333       warnings.warn(tmpl.format(**locals()))
2020-07-07T15:10:33,334     warning: no files found matching '*' under directory 'utils'
2020-07-07T15:10:33,341     writing manifest file '/tmp/pip-pip-egg-info-6sxdd3dh/hapflk.egg-info/SOURCES.txt'
2020-07-07T15:10:33,578   Source in /tmp/pip-wheel-vyvsi6_h/hapflk 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
2020-07-07T15:10:33,580   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-opjfmqu8'
2020-07-07T15:10:33,583 Building wheels for collected packages: hapflk
2020-07-07T15:10:33,592   Created temporary directory: /tmp/pip-wheel-l1qhizzq
2020-07-07T15:10:33,593   Building wheel for hapflk (setup.py): started
2020-07-07T15:10:33,594   Destination directory: /tmp/pip-wheel-l1qhizzq
2020-07-07T15:10:33,594   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-vyvsi6_h/hapflk/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-vyvsi6_h/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-l1qhizzq
2020-07-07T15:10:37,214   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:454: UserWarning: Normalizing '2.0-dev1' to '2.0.dev1'
2020-07-07T15:10:37,214     warnings.warn(tmpl.format(**locals()))
2020-07-07T15:10:37,268   running bdist_wheel
2020-07-07T15:10:37,277   running build
2020-07-07T15:10:37,278   running build_py
2020-07-07T15:10:37,528   creating build
2020-07-07T15:10:37,529   creating build/lib.linux-armv7l-3.7
2020-07-07T15:10:37,530   creating build/lib.linux-armv7l-3.7/hapflk
2020-07-07T15:10:37,533   copying hapflk/hapflkadapt.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T15:10:37,541   copying hapflk/data.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T15:10:37,549   copying hapflk/hapflk.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T15:10:37,556   copying hapflk/popgen.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T15:10:37,563   copying hapflk/__init__.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T15:10:37,568   copying hapflk/utils.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T15:10:37,571   copying hapflk/InputOutput.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T15:10:37,577   copying hapflk/nj.py -> build/lib.linux-armv7l-3.7/hapflk
2020-07-07T15:10:37,584   running build_ext
2020-07-07T15:10:37,594   building 'hapflk.fastphase' extension
2020-07-07T15:10:37,595   creating build/temp.linux-armv7l-3.7
2020-07-07T15:10:37,596   creating build/temp.linux-armv7l-3.7/fastphase
2020-07-07T15:10:37,598   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
2020-07-07T15:10:38,269   In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
2020-07-07T15:10:38,270                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2020-07-07T15:10:38,270                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2020-07-07T15:10:38,271                    from fastphase/fastphase.c:618:
2020-07-07T15:10:38,271   /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]
2020-07-07T15:10:38,272    #warning "Using deprecated NumPy API, disable it with " \
2020-07-07T15:10:38,272     ^~~~~~~
2020-07-07T15:11:18,352   fastphase/fastphase.c: In function ‘__pyx_pw_6hapflk_9fastphase_11calc_cost_matrix_geno_tot’:
2020-07-07T15:11:18,358   fastphase/fastphase.c:15442:38: warning: ‘__pyx_v_k1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T15:11:18,358          if (__pyx_t_40 < 0) __pyx_t_40 += __pyx_pybuffernd_res.diminfo[1].shape;
2020-07-07T15:11:18,359                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:11:18,363   fastphase/fastphase.c:14989:7: note: ‘__pyx_v_k1’ was declared here
2020-07-07T15:11:18,364      int __pyx_v_k1;
2020-07-07T15:11:18,364          ^~~~~~~~~~
2020-07-07T15:11:18,366   fastphase/fastphase.c:15443:38: warning: ‘__pyx_v_kp1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T15:11:18,366          if (__pyx_t_41 < 0) __pyx_t_41 += __pyx_pybuffernd_res.diminfo[2].shape;
2020-07-07T15:11:18,367                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:11:18,371   fastphase/fastphase.c:14991:7: note: ‘__pyx_v_kp1’ was declared here
2020-07-07T15:11:18,372      int __pyx_v_kp1;
2020-07-07T15:11:18,372          ^~~~~~~~~~~
2020-07-07T15:11:18,374   fastphase/fastphase.c:15458:38: warning: ‘__pyx_v_kp2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T15:11:18,375          if (__pyx_t_44 < 0) __pyx_t_44 += __pyx_pybuffernd_res.diminfo[2].shape;
2020-07-07T15:11:18,375                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:11:18,380   fastphase/fastphase.c:14992:7: note: ‘__pyx_v_kp2’ was declared here
2020-07-07T15:11:18,380      int __pyx_v_kp2;
2020-07-07T15:11:18,381          ^~~~~~~~~~~
2020-07-07T15:11:18,382   fastphase/fastphase.c:15472:38: warning: ‘__pyx_v_k2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T15:11:18,383          if (__pyx_t_46 < 0) __pyx_t_46 += __pyx_pybuffernd_res.diminfo[1].shape;
2020-07-07T15:11:18,383                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:11:18,388   fastphase/fastphase.c:14990:7: note: ‘__pyx_v_k2’ was declared here
2020-07-07T15:11:18,389      int __pyx_v_k2;
2020-07-07T15:11:18,389          ^~~~~~~~~~
2020-07-07T15:12:04,243   fastphase/fastphase.c: In function ‘__pyx_f_6hapflk_9fastphase_genViterbi.isra.67’:
2020-07-07T15:12:04,247   fastphase/fastphase.c:17359:7: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T15:12:04,247      int __pyx_v_k;
2020-07-07T15:12:04,248          ^~~~~~~~~
2020-07-07T15:12:04,251   fastphase/fastphase.c:530:40: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T15:12:04,252      #define PyInt_FromLong               PyLong_FromLong
2020-07-07T15:12:04,252                                           ^~~~~~~~~~~~~~~
2020-07-07T15:12:04,257   fastphase/fastphase.c:17360:7: note: ‘__pyx_v_l’ was declared here
2020-07-07T15:12:04,258      int __pyx_v_l;
2020-07-07T15:12:04,258          ^~~~~~~~~
2020-07-07T15:12:04,259   fastphase/fastphase.c:530:40: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T15:12:04,259      #define PyInt_FromLong               PyLong_FromLong
2020-07-07T15:12:04,259                                           ^~~~~~~~~~~~~~~
2020-07-07T15:12:04,264   fastphase/fastphase.c:17359:7: note: ‘__pyx_v_k’ was declared here
2020-07-07T15:12:04,264      int __pyx_v_k;
2020-07-07T15:12:04,265          ^~~~~~~~~
2020-07-07T15:12:04,267   fastphase/fastphase.c:18496:12: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T15:12:04,268            if (!__pyx_t_64) {
2020-07-07T15:12:04,268               ^
2020-07-07T15:12:04,271   fastphase/fastphase.c:18504:12: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T15:12:04,272            if (__pyx_t_44) {
2020-07-07T15:12:04,272               ^
2020-07-07T15:12:04,274   fastphase/fastphase.c:18603:38: warning: ‘__pyx_v_l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-07-07T15:12:04,275          if (__pyx_t_89 < 0) __pyx_t_89 += __pyx_pybuffernd_theta.diminfo[1].shape;
2020-07-07T15:12:04,276                              ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:40,874   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
2020-07-07T15:12:41,453   building 'hapflk._pgenlib' extension
2020-07-07T15:12:41,456   creating build/temp.linux-armv7l-3.7/pgenlib
2020-07-07T15:12:41,457   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
2020-07-07T15:12:42,005   In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
2020-07-07T15:12:42,006                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2020-07-07T15:12:42,006                    from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2020-07-07T15:12:42,007                    from pgenlib/_pgenlib.cpp:645:
2020-07-07T15:12:42,007   /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]
2020-07-07T15:12:42,007    #warning "Using deprecated NumPy API, disable it with " \
2020-07-07T15:12:42,007     ^~~~~~~
2020-07-07T15:12:43,780   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*)’:
2020-07-07T15:12:43,780   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]
2020-07-07T15:12:43,781        __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:43,781                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,787   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]
2020-07-07T15:12:43,788        __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:43,788                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,802   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]
2020-07-07T15:12:43,803      __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:43,803                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,809   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]
2020-07-07T15:12:43,810      __pyx_t_1 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:43,810                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,841   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*)’:
2020-07-07T15:12:43,841   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]
2020-07-07T15:12:43,842        __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:43,842                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,848   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]
2020-07-07T15:12:43,848        __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:43,849                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,863   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]
2020-07-07T15:12:43,864      __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:43,864                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,870   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]
2020-07-07T15:12:43,871      __pyx_t_1 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:43,871                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,902   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*)’:
2020-07-07T15:12:43,903   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]
2020-07-07T15:12:43,903        __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:43,904                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,908   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]
2020-07-07T15:12:43,908        __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:43,909                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,923   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]
2020-07-07T15:12:43,923      __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:43,924                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,928   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]
2020-07-07T15:12:43,929      __pyx_t_1 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:43,930                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:43,996   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*)’:
2020-07-07T15:12:43,997   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]
2020-07-07T15:12:43,998        __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:43,998                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,002   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]
2020-07-07T15:12:44,003        __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:44,004                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,018   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]
2020-07-07T15:12:44,019      __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:44,019                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,024   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]
2020-07-07T15:12:44,024      __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:44,025                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,058   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*)’:
2020-07-07T15:12:44,059   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]
2020-07-07T15:12:44,060        __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:44,060                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,064   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]
2020-07-07T15:12:44,065        __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:44,065                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,080   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]
2020-07-07T15:12:44,081      __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:44,081                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,086   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]
2020-07-07T15:12:44,086      __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:44,087                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,120   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*)’:
2020-07-07T15:12:44,121   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]
2020-07-07T15:12:44,121        __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:44,122                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,126   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]
2020-07-07T15:12:44,127        __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:44,127                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,142   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]
2020-07-07T15:12:44,143      __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2020-07-07T15:12:44,143                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,161   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]
2020-07-07T15:12:44,161      __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:44,162                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,248   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*)’:
2020-07-07T15:12:44,249   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]
2020-07-07T15:12:44,249        __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:44,250                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,254   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]
2020-07-07T15:12:44,254        __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-07T15:12:44,255                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,269   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]
2020-07-07T15:12:44,269      __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-07T15:12:44,270                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,274   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]
2020-07-07T15:12:44,275      __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:44,276                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,328   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*)’:
2020-07-07T15:12:44,329   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]
2020-07-07T15:12:44,330        __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:44,330                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,334   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]
2020-07-07T15:12:44,335        __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-07T15:12:44,335                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,350   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]
2020-07-07T15:12:44,350      __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2020-07-07T15:12:44,351                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:12:44,355   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]
2020-07-07T15:12:44,356      __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2020-07-07T15:12:44,357                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2020-07-07T15:13:41,638   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
2020-07-07T15:13:42,945   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
2020-07-07T15:13:43,154   pgenlib/pgenlib_internal.cpp:710:4: error: #error "Unaligned accesses in small_genoarr_count_3freq_incr()."
2020-07-07T15:13:43,154      #error "Unaligned accesses in small_genoarr_count_3freq_incr()."
2020-07-07T15:13:43,155       ^~~~~
2020-07-07T15:13:43,155   pgenlib/pgenlib_internal.cpp:752:4: error: #error "Unaligned accesses in genoarr_count_subset_freqs()."
2020-07-07T15:13:43,155      #error "Unaligned accesses in genoarr_count_subset_freqs()."
2020-07-07T15:13:43,156       ^~~~~
2020-07-07T15:13:43,160   pgenlib/pgenlib_internal.cpp:1911:4: error: #error "Unaligned accesses in pgfi_init_phase2()."
2020-07-07T15:13:43,161      #error "Unaligned accesses in pgfi_init_phase2()."
2020-07-07T15:13:43,161       ^~~~~
2020-07-07T15:13:43,166   pgenlib/pgenlib_internal.cpp:3145:4: error: #error "Unaligned accesses in parse_onebit_unsafe()."
2020-07-07T15:13:43,167      #error "Unaligned accesses in parse_onebit_unsafe()."
2020-07-07T15:13:43,167       ^~~~~
2020-07-07T15:13:43,168   pgenlib/pgenlib_internal.cpp:3178:4: error: #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)."
2020-07-07T15:13:43,168      #error "Unaligned accesses in extract_genoarr_ambig_ids() (genoarr may not be aligned)."
2020-07-07T15:13:43,168       ^~~~~
2020-07-07T15:13:43,172   pgenlib/pgenlib_internal.cpp:3761:4: error: #error "Unaligned accesses in bytesum_arr()."
2020-07-07T15:13:43,172      #error "Unaligned accesses in bytesum_arr()."
2020-07-07T15:13:43,173       ^~~~~
2020-07-07T15:13:43,173   pgenlib/pgenlib_internal.cpp:3814:4: error: #error "Unaligned accesses in skip_difflist_ids()."
2020-07-07T15:13:43,174      #error "Unaligned accesses in skip_difflist_ids()."
2020-07-07T15:13:43,174       ^~~~~
2020-07-07T15:13:43,174   pgenlib/pgenlib_internal.cpp:3940:4: error: #error "Unaligned accesses in countparse_onebit_subset()."
2020-07-07T15:13:43,175      #error "Unaligned accesses in countparse_onebit_subset()."
2020-07-07T15:13:43,175       ^~~~~
2020-07-07T15:13:43,181   pgenlib/pgenlib_internal.cpp:4923:4: error: #error "Unaligned accesses in parse_just_ambig_ids()."
2020-07-07T15:13:43,181      #error "Unaligned accesses in parse_just_ambig_ids()."
2020-07-07T15:13:43,182       ^~~~~
2020-07-07T15:13:43,184   pgenlib/pgenlib_internal.cpp:5454:4: error: #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()."
2020-07-07T15:13:43,185      #error "Unaligned accesses in read_refalt1_genovec_hphase_subset_unsafe()."
2020-07-07T15:13:43,185       ^~~~~
2020-07-07T15:13:43,187   pgenlib/pgenlib_internal.cpp:5670:4: error: #error "Unaligned accesses in parse_dosage16()."
2020-07-07T15:13:43,187      #error "Unaligned accesses in parse_dosage16()."
2020-07-07T15:13:43,188       ^~~~~
2020-07-07T15:13:43,189   pgenlib/pgenlib_internal.cpp:5889:4: error: #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()."
2020-07-07T15:13:43,190      #error "Unaligned accesses in get_ref_nonref_genotype_counts_and_dosage16s()."
2020-07-07T15:13:43,190       ^~~~~
2020-07-07T15:13:43,193   pgenlib/pgenlib_internal.cpp:6294:4: error: #error "Unaligned accesses in pgr_read_missingness_dosage()."
2020-07-07T15:13:43,194      #error "Unaligned accesses in pgr_read_missingness_dosage()."
2020-07-07T15:13:43,194       ^~~~~
2020-07-07T15:13:43,196   pgenlib/pgenlib_internal.cpp:6542:4: error: #error "Unaligned accesses in validate_onebit()."
2020-07-07T15:13:43,196      #error "Unaligned accesses in validate_onebit()."
2020-07-07T15:13:43,197       ^~~~~
2020-07-07T15:13:43,198   pgenlib/pgenlib_internal.cpp:6760:4: error: #error "Unaligned accesses in validate_dosage16()."
2020-07-07T15:13:43,198      #error "Unaligned accesses in validate_dosage16()."
2020-07-07T15:13:43,199       ^~~~~
2020-07-07T15:13:43,204   pgenlib/pgenlib_internal.cpp:7651:4: error: #error "Unaligned accesses in save_ld_difflist()."
2020-07-07T15:13:43,205      #error "Unaligned accesses in save_ld_difflist()."
2020-07-07T15:13:43,205       ^~~~~
2020-07-07T15:13:43,207   pgenlib/pgenlib_internal.cpp:7793:4: error: #error "Unaligned accesses in save_onebit()."
2020-07-07T15:13:43,207      #error "Unaligned accesses in save_onebit()."
2020-07-07T15:13:43,207       ^~~~~
2020-07-07T15:13:43,210   pgenlib/pgenlib_internal.cpp:8025:4: error: #error "Unaligned accesses in save_ld_two_list_delta()."
2020-07-07T15:13:43,210      #error "Unaligned accesses in save_ld_two_list_delta()."
2020-07-07T15:13:43,210       ^~~~~
2020-07-07T15:13:43,213   pgenlib/pgenlib_internal.cpp:8295:4: error: #error "Unaligned accesses in append_hphase()."
2020-07-07T15:13:43,213      #error "Unaligned accesses in append_hphase()."
2020-07-07T15:13:43,214       ^~~~~
2020-07-07T15:13:43,934   error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1
2020-07-07T15:13:44,170   Building wheel for hapflk (setup.py): finished with status 'error'
2020-07-07T15:13:44,171   ERROR: Failed building wheel for hapflk
2020-07-07T15:13:44,172   Running setup.py clean for hapflk
2020-07-07T15:13:44,172   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-vyvsi6_h/hapflk/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-vyvsi6_h/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
2020-07-07T15:13:48,163   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:454: UserWarning: Normalizing '2.0-dev1' to '2.0.dev1'
2020-07-07T15:13:48,164     warnings.warn(tmpl.format(**locals()))
2020-07-07T15:13:48,183   running clean
2020-07-07T15:13:48,188   removing 'build/temp.linux-armv7l-3.7' (and everything under it)
2020-07-07T15:13:48,199   removing 'build/lib.linux-armv7l-3.7' (and everything under it)
2020-07-07T15:13:48,209   'build/bdist.linux-armv7l' does not exist -- can't clean it
2020-07-07T15:13:48,210   'build/scripts-3.7' does not exist -- can't clean it
2020-07-07T15:13:48,210   removing 'build'
2020-07-07T15:13:48,433 Failed to build hapflk
2020-07-07T15:13:48,434 ERROR: Failed to build one or more wheels
2020-07-07T15:13:48,435 Exception information:
2020-07-07T15:13:48,435 Traceback (most recent call last):
2020-07-07T15:13:48,435   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 188, in _main
2020-07-07T15:13:48,435     status = self.run(options, args)
2020-07-07T15:13:48,435   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/req_command.py", line 185, in wrapper
2020-07-07T15:13:48,435     return func(self, options, args)
2020-07-07T15:13:48,435   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 189, in run
2020-07-07T15:13:48,435     "Failed to build one or more wheels"
2020-07-07T15:13:48,435 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2020-07-07T15:13:48,443 Removed build tracker: '/tmp/pip-req-tracker-opjfmqu8'