2023-01-29T02:28:54,973 Created temporary directory: /tmp/pip-ephem-wheel-cache-7tkzd25s
2023-01-29T02:28:54,975 Created temporary directory: /tmp/pip-build-tracker-nzy4y_0n
2023-01-29T02:28:54,975 Initialized build tracking at /tmp/pip-build-tracker-nzy4y_0n
2023-01-29T02:28:54,975 Created build tracker: /tmp/pip-build-tracker-nzy4y_0n
2023-01-29T02:28:54,976 Entered build tracker: /tmp/pip-build-tracker-nzy4y_0n
2023-01-29T02:28:54,976 Created temporary directory: /tmp/pip-wheel-_8cimluq
2023-01-29T02:28:54,979 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2023-01-29T02:28:54,982 Created temporary directory: /tmp/pip-ephem-wheel-cache-aguninuj
2023-01-29T02:28:55,004 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-01-29T02:28:55,008 2 location(s) to search for versions of pgenlib:
2023-01-29T02:28:55,008 * https://pypi.org/simple/pgenlib/
2023-01-29T02:28:55,008 * https://www.piwheels.org/simple/pgenlib/
2023-01-29T02:28:55,008 Fetching project page and analyzing links: https://pypi.org/simple/pgenlib/
2023-01-29T02:28:55,009 Getting page https://pypi.org/simple/pgenlib/
2023-01-29T02:28:55,010 Found index url https://pypi.org/simple
2023-01-29T02:28:55,062 Fetched page https://pypi.org/simple/pgenlib/ as application/vnd.pypi.simple.v1+json
2023-01-29T02:28:55,064   Found link https://files.pythonhosted.org/packages/d9/cc/f3bbaa8da897e9a04e1a885183a0c533ba563bb3a1dbfba6680704473336/Pgenlib-0.81.1.tar.gz (from https://pypi.org/simple/pgenlib/) (requires-python:>=3.5), version: 0.81.1
2023-01-29T02:28:55,064   Skipping link: No binaries permitted for pgenlib: https://files.pythonhosted.org/packages/22/06/d83bcf26ea2212baccc88b3771c78dce0eff643a1293aa3f8993c242fe02/Pgenlib-0.81.2-cp37-cp37m-macosx_10_13_x86_64.whl (from https://pypi.org/simple/pgenlib/) (requires-python:>=3.5)
2023-01-29T02:28:55,065   Found link https://files.pythonhosted.org/packages/6d/f7/c286a64ec213ea42bfa67b20ce1271b0b8699ac3880854657f8ed1620759/Pgenlib-0.81.2.tar.gz (from https://pypi.org/simple/pgenlib/) (requires-python:>=3.5), version: 0.81.2
2023-01-29T02:28:55,065   Found link https://files.pythonhosted.org/packages/38/09/74ec09b0c9ddde6a3562898507b99b47adde5350248f2899b59edcc082b0/Pgenlib-0.81.3.tar.gz (from https://pypi.org/simple/pgenlib/) (requires-python:>=3.5), version: 0.81.3
2023-01-29T02:28:55,066 Fetching project page and analyzing links: https://www.piwheels.org/simple/pgenlib/
2023-01-29T02:28:55,066 Getting page https://www.piwheels.org/simple/pgenlib/
2023-01-29T02:28:55,067 Found index url https://www.piwheels.org/simple
2023-01-29T02:28:55,255 Fetched page https://www.piwheels.org/simple/pgenlib/ as text/html
2023-01-29T02:28:55,257   Skipping link: No binaries permitted for pgenlib: https://www.piwheels.org/simple/pgenlib/Pgenlib-0.81.2-cp39-cp39-linux_armv7l.whl#sha256=2e0ad339664cbc60a4ae0b3a935afcf56d3e1a344387d8327ae50b03dce0d852 (from https://www.piwheels.org/simple/pgenlib/) (requires-python:>=3.5)
2023-01-29T02:28:55,257   Skipping link: No binaries permitted for pgenlib: https://www.piwheels.org/simple/pgenlib/Pgenlib-0.81.2-cp39-cp39-linux_armv6l.whl#sha256=2e0ad339664cbc60a4ae0b3a935afcf56d3e1a344387d8327ae50b03dce0d852 (from https://www.piwheels.org/simple/pgenlib/) (requires-python:>=3.5)
2023-01-29T02:28:55,257   Skipping link: No binaries permitted for pgenlib: https://www.piwheels.org/simple/pgenlib/Pgenlib-0.81.1-cp39-cp39-linux_armv7l.whl#sha256=7fe4ecefc0464d30dc029a926937523d919f28fa0320e6522fa229764a168909 (from https://www.piwheels.org/simple/pgenlib/) (requires-python:>=3.5)
2023-01-29T02:28:55,258   Skipping link: No binaries permitted for pgenlib: https://www.piwheels.org/simple/pgenlib/Pgenlib-0.81.1-cp39-cp39-linux_armv6l.whl#sha256=7fe4ecefc0464d30dc029a926937523d919f28fa0320e6522fa229764a168909 (from https://www.piwheels.org/simple/pgenlib/) (requires-python:>=3.5)
2023-01-29T02:28:55,258 Skipping link: not a file: https://www.piwheels.org/simple/pgenlib/
2023-01-29T02:28:55,258 Skipping link: not a file: https://pypi.org/simple/pgenlib/
2023-01-29T02:28:55,276 Given no hashes to check 1 links for project 'pgenlib': discarding no candidates
2023-01-29T02:28:55,293 Collecting pgenlib==0.81.3
2023-01-29T02:28:55,295   Created temporary directory: /tmp/pip-unpack-qubyj_q2
2023-01-29T02:28:55,338   Downloading Pgenlib-0.81.3.tar.gz (386 kB)
2023-01-29T02:28:55,559   Added pgenlib==0.81.3 from https://files.pythonhosted.org/packages/38/09/74ec09b0c9ddde6a3562898507b99b47adde5350248f2899b59edcc082b0/Pgenlib-0.81.3.tar.gz to build tracker '/tmp/pip-build-tracker-nzy4y_0n'
2023-01-29T02:28:55,565   Created temporary directory: /tmp/pip-build-env-3al5al07
2023-01-29T02:28:55,572   Installing build dependencies: started
2023-01-29T02:28:55,573   Running command pip subprocess to install build dependencies
2023-01-29T02:28:56,776   Using pip 22.3 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9)
2023-01-29T02:28:57,164   DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2023-01-29T02:28:57,189   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-01-29T02:28:58,845   Collecting setuptools
2023-01-29T02:28:58,947     Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.0.0-py3-none-any.whl (1.1 MB)
2023-01-29T02:28:59,212   Collecting wheel
2023-01-29T02:28:59,230     Using cached https://www.piwheels.org/simple/wheel/wheel-0.38.4-py3-none-any.whl (36 kB)
2023-01-29T02:28:59,363   Collecting oldest-supported-numpy>=2022.8.16
2023-01-29T02:28:59,380     Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2022.11.19-py3-none-any.whl (4.9 kB)
2023-01-29T02:29:00,726   Collecting Cython>=0.29.21
2023-01-29T02:29:02,033     Using cached https://www.piwheels.org/simple/cython/Cython-0.29.33-cp39-cp39-linux_armv7l.whl (5.0 MB)
2023-01-29T02:29:03,799   Collecting numpy==1.19.3
2023-01-29T02:29:04,747     Using cached https://www.piwheels.org/simple/numpy/numpy-1.19.3-cp39-cp39-linux_armv7l.whl (10.5 MB)
2023-01-29T02:29:07,127   Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy
2023-01-29T02:29:07,272     Creating /tmp/pip-build-env-3al5al07/overlay/bin
2023-01-29T02:29:07,274     changing mode of /tmp/pip-build-env-3al5al07/overlay/bin/wheel to 755
2023-01-29T02:29:16,498     changing mode of /tmp/pip-build-env-3al5al07/overlay/bin/f2py to 755
2023-01-29T02:29:16,501     changing mode of /tmp/pip-build-env-3al5al07/overlay/bin/f2py3 to 755
2023-01-29T02:29:16,503     changing mode of /tmp/pip-build-env-3al5al07/overlay/bin/f2py3.9 to 755
2023-01-29T02:29:19,356     changing mode of /tmp/pip-build-env-3al5al07/overlay/bin/cygdb to 755
2023-01-29T02:29:19,359     changing mode of /tmp/pip-build-env-3al5al07/overlay/bin/cython to 755
2023-01-29T02:29:19,362     changing mode of /tmp/pip-build-env-3al5al07/overlay/bin/cythonize to 755
2023-01-29T02:29:19,410   Successfully installed Cython-0.29.33 numpy-1.19.3 oldest-supported-numpy-2022.11.19 setuptools-67.0.0 wheel-0.38.4

2023-01-29T02:29:19,425   [notice] A new release of pip available: 22.3 -> 22.3.1
2023-01-29T02:29:19,426   [notice] To update, run: python3 -m pip install --upgrade pip
2023-01-29T02:29:19,798   Installing build dependencies: finished with status 'done'
2023-01-29T02:29:19,804   Getting requirements to build wheel: started
2023-01-29T02:29:19,805   Running command Getting requirements to build wheel
2023-01-29T02:29:24,917   Compiling src/pgenlib/pgenlib.pyx because it depends on /tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd.
2023-01-29T02:29:24,918   [1/1] Cythonizing src/pgenlib/pgenlib.pyx
2023-01-29T02:29:24,993   running egg_info
2023-01-29T02:29:25,000   writing src/Pgenlib.egg-info/PKG-INFO
2023-01-29T02:29:25,002   writing dependency_links to src/Pgenlib.egg-info/dependency_links.txt
2023-01-29T02:29:25,005   writing top-level names to src/Pgenlib.egg-info/top_level.txt
2023-01-29T02:29:25,025   reading manifest file 'src/Pgenlib.egg-info/SOURCES.txt'
2023-01-29T02:29:25,029   reading manifest template 'MANIFEST.in'
2023-01-29T02:29:25,031   adding license file 'LICENSE'
2023-01-29T02:29:25,034   writing manifest file 'src/Pgenlib.egg-info/SOURCES.txt'
2023-01-29T02:29:25,351   Getting requirements to build wheel: finished with status 'done'
2023-01-29T02:29:25,363   Created temporary directory: /tmp/pip-modern-metadata-ty4m94jo
2023-01-29T02:29:25,365   Preparing metadata (pyproject.toml): started
2023-01-29T02:29:25,366   Running command Preparing metadata (pyproject.toml)
2023-01-29T02:29:27,000   running dist_info
2023-01-29T02:29:27,023   creating /tmp/pip-modern-metadata-ty4m94jo/Pgenlib.egg-info
2023-01-29T02:29:27,029   writing /tmp/pip-modern-metadata-ty4m94jo/Pgenlib.egg-info/PKG-INFO
2023-01-29T02:29:27,031   writing dependency_links to /tmp/pip-modern-metadata-ty4m94jo/Pgenlib.egg-info/dependency_links.txt
2023-01-29T02:29:27,034   writing top-level names to /tmp/pip-modern-metadata-ty4m94jo/Pgenlib.egg-info/top_level.txt
2023-01-29T02:29:27,036   writing manifest file '/tmp/pip-modern-metadata-ty4m94jo/Pgenlib.egg-info/SOURCES.txt'
2023-01-29T02:29:27,052   reading manifest file '/tmp/pip-modern-metadata-ty4m94jo/Pgenlib.egg-info/SOURCES.txt'
2023-01-29T02:29:27,054   reading manifest template 'MANIFEST.in'
2023-01-29T02:29:27,056   adding license file 'LICENSE'
2023-01-29T02:29:27,059   writing manifest file '/tmp/pip-modern-metadata-ty4m94jo/Pgenlib.egg-info/SOURCES.txt'
2023-01-29T02:29:27,060   creating '/tmp/pip-modern-metadata-ty4m94jo/Pgenlib-0.81.3.dist-info'
2023-01-29T02:29:27,302   Preparing metadata (pyproject.toml): finished with status 'done'
2023-01-29T02:29:27,309   Source in /tmp/pip-wheel-_8cimluq/pgenlib_751260df5d1f499eb08a88aff1d0941e has version 0.81.3, which satisfies requirement pgenlib==0.81.3 from https://files.pythonhosted.org/packages/38/09/74ec09b0c9ddde6a3562898507b99b47adde5350248f2899b59edcc082b0/Pgenlib-0.81.3.tar.gz
2023-01-29T02:29:27,310   Removed pgenlib==0.81.3 from https://files.pythonhosted.org/packages/38/09/74ec09b0c9ddde6a3562898507b99b47adde5350248f2899b59edcc082b0/Pgenlib-0.81.3.tar.gz from build tracker '/tmp/pip-build-tracker-nzy4y_0n'
2023-01-29T02:29:27,316 Created temporary directory: /tmp/pip-unpack-yw_vj0k7
2023-01-29T02:29:27,317 Building wheels for collected packages: pgenlib
2023-01-29T02:29:27,322   Created temporary directory: /tmp/pip-wheel-m36nwhrk
2023-01-29T02:29:27,322   Destination directory: /tmp/pip-wheel-m36nwhrk
2023-01-29T02:29:27,325   Building wheel for pgenlib (pyproject.toml): started
2023-01-29T02:29:27,326   Running command Building wheel for pgenlib (pyproject.toml)
2023-01-29T02:29:28,951   running bdist_wheel
2023-01-29T02:29:28,977   running build
2023-01-29T02:29:28,977   running build_ext
2023-01-29T02:29:28,982   building 'pgenlib' extension
2023-01-29T02:29:28,983   creating build
2023-01-29T02:29:28,983   creating build/temp.linux-armv7l-cpython-39
2023-01-29T02:29:28,984   creating build/temp.linux-armv7l-cpython-39/src
2023-01-29T02:29:28,985   creating build/temp.linux-armv7l-cpython-39/src/pgenlib
2023-01-29T02:29:28,986   creating build/temp.linux-armv7l-cpython-39/src/plink2
2023-01-29T02:29:28,987   creating build/temp.linux-armv7l-cpython-39/src/plink2/include
2023-01-29T02:29:28,988   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pgenlib -I/tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c src/pgenlib/pgenlib.cpp -o build/temp.linux-armv7l-cpython-39/src/pgenlib/pgenlib.o -std=c++98 -Wno-unused-function -Wno-macro-redefined
2023-01-29T02:29:30,738   In file included from /tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
2023-01-29T02:29:30,739                    from /tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2023-01-29T02:29:30,739                    from /tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2023-01-29T02:29:30,739                    from src/pgenlib/pgenlib.cpp:799:
2023-01-29T02:29:30,739   /tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2023-01-29T02:29:30,739      17 | #warning "Using deprecated NumPy API, disable it with " \
2023-01-29T02:29:30,739         |  ^~~~~~~
2023-01-29T02:29:30,800   src/pgenlib/pgenlib.cpp:994: warning: "likely" redefined
2023-01-29T02:29:30,800     994 |   #define likely(x)   __builtin_expect(!!(x), 1)
2023-01-29T02:29:30,800         |
2023-01-29T02:29:30,801   In file included from src/pgenlib/../plink2/include/plink2_bits.h:23,
2023-01-29T02:29:30,801                    from src/pgenlib/../plink2/include/pgenlib_misc.h:77,
2023-01-29T02:29:30,801                    from src/pgenlib/../plink2/pgenlib_ffi_support.h:20,
2023-01-29T02:29:30,801                    from src/pgenlib/pgenlib.cpp:804:
2023-01-29T02:29:30,802   src/pgenlib/../plink2/include/plink2_base.h:252: note: this is the location of the previous definition
2023-01-29T02:29:30,802     252 | #  define likely(expr) __builtin_expect(!!(expr), 1)
2023-01-29T02:29:30,802         |
2023-01-29T02:29:30,802   src/pgenlib/pgenlib.cpp:995: warning: "unlikely" redefined
2023-01-29T02:29:30,802     995 |   #define unlikely(x) __builtin_expect(!!(x), 0)
2023-01-29T02:29:30,802         |
2023-01-29T02:29:30,803   In file included from src/pgenlib/../plink2/include/plink2_bits.h:23,
2023-01-29T02:29:30,803                    from src/pgenlib/../plink2/include/pgenlib_misc.h:77,
2023-01-29T02:29:30,803                    from src/pgenlib/../plink2/pgenlib_ffi_support.h:20,
2023-01-29T02:29:30,803                    from src/pgenlib/pgenlib.cpp:804:
2023-01-29T02:29:30,803   src/pgenlib/../plink2/include/plink2_base.h:253: note: this is the location of the previous definition
2023-01-29T02:29:30,803     253 | #  define unlikely(expr) __builtin_expect(!!(expr), 0)
2023-01-29T02:29:30,803         |
2023-01-29T02:29:31,744   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read(__pyx_obj_7pgenlib_PgenReader*, uint32_t, PyArrayObject*, int, __pyx_opt_args_7pgenlib_10PgenReader_read*)’:
2023-01-29T02:29:31,744   src/pgenlib/pgenlib.cpp:5306:55: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,744    5306 |   __pyx_t_9 = (((__pyx_v_geno_int_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,744         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,773   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_dosages(__pyx_obj_7pgenlib_PgenReader*, uint32_t, PyArrayObject*, int, __pyx_opt_args_7pgenlib_10PgenReader_read_dosages*)’:
2023-01-29T02:29:31,773   src/pgenlib/pgenlib.cpp:5960:55: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,773    5960 |   __pyx_t_9 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,773         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,800   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles(__pyx_obj_7pgenlib_PgenReader*, uint32_t, PyArrayObject*, int)’:
2023-01-29T02:29:31,800   src/pgenlib/pgenlib.cpp:6520:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,800    6520 |   __pyx_t_8 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,800         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,824   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles_and_phasepresent(__pyx_obj_7pgenlib_PgenReader*, uint32_t, PyArrayObject*, PyArrayObject*, int)’:
2023-01-29T02:29:31,824   src/pgenlib/pgenlib.cpp:7016:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,824    7016 |   __pyx_t_8 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2023-01-29T02:29:31,824         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,828   src/pgenlib/pgenlib.cpp:7072:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,828    7072 |   __pyx_t_8 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,828         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,851   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_range_internal8(__pyx_obj_7pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, __pyx_opt_args_7pgenlib_10PgenReader_read_range_internal8*)’:
2023-01-29T02:29:31,851   src/pgenlib/pgenlib.cpp:7562:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,851    7562 |     __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:31,851         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,855   src/pgenlib/pgenlib.cpp:7618:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,855    7618 |     __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,855         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,863   src/pgenlib/pgenlib.cpp:7843:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,863    7843 |   __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,864         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,867   src/pgenlib/pgenlib.cpp:7899:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,867    7899 |   __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:31,867         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,881   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_range_internal32(__pyx_obj_7pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, __pyx_opt_args_7pgenlib_10PgenReader_read_range_internal32*)’:
2023-01-29T02:29:31,881   src/pgenlib/pgenlib.cpp:8498:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,881    8498 |     __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:31,881         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,885   src/pgenlib/pgenlib.cpp:8554:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,885    8554 |     __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,885         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,893   src/pgenlib/pgenlib.cpp:8779:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,894    8779 |   __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,894         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,897   src/pgenlib/pgenlib.cpp:8835:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,897    8835 |   __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:31,897         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,911   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_range_internal64(__pyx_obj_7pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, __pyx_opt_args_7pgenlib_10PgenReader_read_range_internal64*)’:
2023-01-29T02:29:31,911   src/pgenlib/pgenlib.cpp:9434:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,911    9434 |     __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:31,912         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,915   src/pgenlib/pgenlib.cpp:9490:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,915    9490 |     __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,915         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,924   src/pgenlib/pgenlib.cpp:9715:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,924    9715 |   __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,924         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,927   src/pgenlib/pgenlib.cpp:9771:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,928    9771 |   __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:31,928         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,968   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_list_internal8(__pyx_obj_7pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_7pgenlib_10PgenReader_read_list_internal8*)’:
2023-01-29T02:29:31,968   src/pgenlib/pgenlib.cpp:10923:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,969   10923 |     __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:31,969         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,972   src/pgenlib/pgenlib.cpp:10979:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,972   10979 |     __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,972         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,981   src/pgenlib/pgenlib.cpp:11220:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,982   11220 |   __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:31,982         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:31,985   src/pgenlib/pgenlib.cpp:11276:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:31,985   11276 |   __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:31,985         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,004   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_list_internal32(__pyx_obj_7pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_7pgenlib_10PgenReader_read_list_internal32*)’:
2023-01-29T02:29:32,004   src/pgenlib/pgenlib.cpp:11971:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,004   11971 |     __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,004         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,007   src/pgenlib/pgenlib.cpp:12027:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,008   12027 |     __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:32,008         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,017   src/pgenlib/pgenlib.cpp:12268:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,017   12268 |   __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:32,017         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,020   src/pgenlib/pgenlib.cpp:12324:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,021   12324 |   __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,021         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,039   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_list_internal64(__pyx_obj_7pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_7pgenlib_10PgenReader_read_list_internal64*)’:
2023-01-29T02:29:32,039   src/pgenlib/pgenlib.cpp:13019:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,040   13019 |     __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,040         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,043   src/pgenlib/pgenlib.cpp:13075:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,043   13075 |     __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:32,043         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,052   src/pgenlib/pgenlib.cpp:13316:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,053   13316 |   __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:32,053         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,056   src/pgenlib/pgenlib.cpp:13372:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,056   13372 |   __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,056         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,107   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles_range(__pyx_obj_7pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, int, __pyx_opt_args_7pgenlib_10PgenReader_read_alleles_range*)’:
2023-01-29T02:29:32,107   src/pgenlib/pgenlib.cpp:14716:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,107   14716 |     __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,107         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,111   src/pgenlib/pgenlib.cpp:14772:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,111   14772 |     __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2023-01-29T02:29:32,111         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,121   src/pgenlib/pgenlib.cpp:15009:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,121   15009 |   __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2023-01-29T02:29:32,121         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,124   src/pgenlib/pgenlib.cpp:15065:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,125   15065 |   __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,125         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,164   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles_list(__pyx_obj_7pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, int, __pyx_opt_args_7pgenlib_10PgenReader_read_alleles_list*)’:
2023-01-29T02:29:32,164   src/pgenlib/pgenlib.cpp:16124:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,164   16124 |     __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,164         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,168   src/pgenlib/pgenlib.cpp:16180:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,168   16180 |     __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2023-01-29T02:29:32,168         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,177   src/pgenlib/pgenlib.cpp:16421:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,177   16421 |   __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2023-01-29T02:29:32,177         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,181   src/pgenlib/pgenlib.cpp:16477:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,181   16477 |   __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,181         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,219   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles_and_phasepresent_range(__pyx_obj_7pgenlib_PgenReader*, uint32_t, uint32_t, PyArrayObject*, PyArrayObject*, int, __pyx_opt_args_7pgenlib_10PgenReader_read_alleles_and_phasepresent_range*)’:
2023-01-29T02:29:32,220   src/pgenlib/pgenlib.cpp:17614:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,220   17614 |     __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,220         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,223   src/pgenlib/pgenlib.cpp:17670:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,223   17670 |     __pyx_t_10 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,223         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,227   src/pgenlib/pgenlib.cpp:17726:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,227   17726 |     __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2023-01-29T02:29:32,227         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,230   src/pgenlib/pgenlib.cpp:17782:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,230   17782 |     __pyx_t_10 = (((__pyx_v_phasepresent_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:32,231         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,263   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles_and_phasepresent_list(__pyx_obj_7pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, PyArrayObject*, int, __pyx_opt_args_7pgenlib_10PgenReader_read_alleles_and_phasepresent_list*)’:
2023-01-29T02:29:32,264   src/pgenlib/pgenlib.cpp:18478:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,264   18478 |     __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,264         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,267   src/pgenlib/pgenlib.cpp:18534:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,268   18534 |     __pyx_t_12 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,268         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,271   src/pgenlib/pgenlib.cpp:18590:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,271   18590 |     __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2023-01-29T02:29:32,271         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,275   src/pgenlib/pgenlib.cpp:18646:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,275   18646 |     __pyx_t_12 = (((__pyx_v_phasepresent_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:32,275         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,341   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_dosages_list_internal32(__pyx_obj_7pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_7pgenlib_10PgenReader_read_dosages_list_internal32*)’:
2023-01-29T02:29:32,341   src/pgenlib/pgenlib.cpp:20405:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,341   20405 |     __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,341         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,344   src/pgenlib/pgenlib.cpp:20461:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,345   20461 |     __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:32,345         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,360   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_dosages_list_internal64(__pyx_obj_7pgenlib_PgenReader*, PyArrayObject*, PyArrayObject*, __pyx_opt_args_7pgenlib_10PgenReader_read_dosages_list_internal64*)’:
2023-01-29T02:29:32,360   src/pgenlib/pgenlib.cpp:20922:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,360   20922 |     __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2023-01-29T02:29:32,360         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:32,364   src/pgenlib/pgenlib.cpp:20978:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-01-29T02:29:32,364   20978 |     __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2023-01-29T02:29:32,364         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2023-01-29T02:29:58,859   At global scope:
2023-01-29T02:29:58,859   cc1plus: note: unrecognized command-line option ‘-Wno-macro-redefined’ may have been intended to silence earlier diagnostics
2023-01-29T02:30:01,438   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pgenlib -I/tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c src/plink2/include/pgenlib_misc.cc -o build/temp.linux-armv7l-cpython-39/src/plink2/include/pgenlib_misc.o -std=c++98 -Wno-unused-function -Wno-macro-redefined
2023-01-29T02:30:04,610   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pgenlib -I/tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c src/plink2/include/pgenlib_read.cc -o build/temp.linux-armv7l-cpython-39/src/plink2/include/pgenlib_read.o -std=c++98 -Wno-unused-function -Wno-macro-redefined
2023-01-29T02:30:17,997   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pgenlib -I/tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c src/plink2/include/pgenlib_write.cc -o build/temp.linux-armv7l-cpython-39/src/plink2/include/pgenlib_write.o -std=c++98 -Wno-unused-function -Wno-macro-redefined
2023-01-29T02:30:21,221   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pgenlib -I/tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c src/plink2/include/plink2_base.cc -o build/temp.linux-armv7l-cpython-39/src/plink2/include/plink2_base.o -std=c++98 -Wno-unused-function -Wno-macro-redefined
2023-01-29T02:30:21,607   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pgenlib -I/tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c src/plink2/include/plink2_bits.cc -o build/temp.linux-armv7l-cpython-39/src/plink2/include/plink2_bits.o -std=c++98 -Wno-unused-function -Wno-macro-redefined
2023-01-29T02:30:23,377   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/pgenlib -I/tmp/pip-build-env-3al5al07/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c src/plink2/pgenlib_ffi_support.cc -o build/temp.linux-armv7l-cpython-39/src/plink2/pgenlib_ffi_support.o -std=c++98 -Wno-unused-function -Wno-macro-redefined
2023-01-29T02:30:24,407   creating build/lib.linux-armv7l-cpython-39
2023-01-29T02:30:24,408   arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/src/pgenlib/pgenlib.o build/temp.linux-armv7l-cpython-39/src/plink2/include/pgenlib_misc.o build/temp.linux-armv7l-cpython-39/src/plink2/include/pgenlib_read.o build/temp.linux-armv7l-cpython-39/src/plink2/include/pgenlib_write.o build/temp.linux-armv7l-cpython-39/src/plink2/include/plink2_base.o build/temp.linux-armv7l-cpython-39/src/plink2/include/plink2_bits.o build/temp.linux-armv7l-cpython-39/src/plink2/pgenlib_ffi_support.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/pgenlib.cpython-39-arm-linux-gnueabihf.so -std=c++98
2023-01-29T02:30:24,846   installing to build/bdist.linux-armv7l/wheel
2023-01-29T02:30:24,847   running install
2023-01-29T02:30:24,872   running install_lib
2023-01-29T02:30:24,882   creating build/bdist.linux-armv7l
2023-01-29T02:30:24,882   creating build/bdist.linux-armv7l/wheel
2023-01-29T02:30:24,884   copying build/lib.linux-armv7l-cpython-39/pgenlib.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel
2023-01-29T02:30:24,954   running install_egg_info
2023-01-29T02:30:24,984   running egg_info
2023-01-29T02:30:24,989   writing src/Pgenlib.egg-info/PKG-INFO
2023-01-29T02:30:24,990   writing dependency_links to src/Pgenlib.egg-info/dependency_links.txt
2023-01-29T02:30:24,992   writing top-level names to src/Pgenlib.egg-info/top_level.txt
2023-01-29T02:30:25,001   reading manifest file 'src/Pgenlib.egg-info/SOURCES.txt'
2023-01-29T02:30:25,003   reading manifest template 'MANIFEST.in'
2023-01-29T02:30:25,005   adding license file 'LICENSE'
2023-01-29T02:30:25,008   writing manifest file 'src/Pgenlib.egg-info/SOURCES.txt'
2023-01-29T02:30:25,010   Copying src/Pgenlib.egg-info to build/bdist.linux-armv7l/wheel/Pgenlib-0.81.3-py3.9.egg-info
2023-01-29T02:30:25,019   running install_scripts
2023-01-29T02:30:25,082   creating build/bdist.linux-armv7l/wheel/Pgenlib-0.81.3.dist-info/WHEEL
2023-01-29T02:30:25,086   creating '/tmp/pip-wheel-m36nwhrk/.tmp-otm5o5m5/Pgenlib-0.81.3-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-01-29T02:30:25,752   adding 'pgenlib.cpython-39-arm-linux-gnueabihf.so'
2023-01-29T02:30:25,777   adding 'Pgenlib-0.81.3.dist-info/LICENSE'
2023-01-29T02:30:25,778   adding 'Pgenlib-0.81.3.dist-info/METADATA'
2023-01-29T02:30:25,779   adding 'Pgenlib-0.81.3.dist-info/WHEEL'
2023-01-29T02:30:25,780   adding 'Pgenlib-0.81.3.dist-info/top_level.txt'
2023-01-29T02:30:25,781   adding 'Pgenlib-0.81.3.dist-info/RECORD'
2023-01-29T02:30:25,802   removing build/bdist.linux-armv7l/wheel
2023-01-29T02:30:25,976   Building wheel for pgenlib (pyproject.toml): finished with status 'done'
2023-01-29T02:30:26,018   Created wheel for pgenlib: filename=Pgenlib-0.81.3-cp39-cp39-linux_armv7l.whl size=1243337 sha256=5a7e6ce67f2000041a2e5d373924f58245f07fb04f09b9c5740c8554ff44d333
2023-01-29T02:30:26,019   Stored in directory: /tmp/pip-ephem-wheel-cache-aguninuj/wheels/97/3f/d9/48ad0634bbcc46c7be96045a62bf7ffdc61179b631872f8bce
2023-01-29T02:30:26,041 Successfully built pgenlib
2023-01-29T02:30:26,092 Removed build tracker: '/tmp/pip-build-tracker-nzy4y_0n'