2022-07-21T17:16:52,706 Created temporary directory: /tmp/pip-ephem-wheel-cache-wnpj7th8
2022-07-21T17:16:52,712 Created temporary directory: /tmp/pip-build-tracker-kndaeju_
2022-07-21T17:16:52,713 Initialized build tracking at /tmp/pip-build-tracker-kndaeju_
2022-07-21T17:16:52,713 Created build tracker: /tmp/pip-build-tracker-kndaeju_
2022-07-21T17:16:52,713 Entered build tracker: /tmp/pip-build-tracker-kndaeju_
2022-07-21T17:16:52,715 Created temporary directory: /tmp/pip-wheel-hrkz7pvz
2022-07-21T17:16:52,786 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2022-07-21T17:16:52,794 2 location(s) to search for versions of pgenlib:
2022-07-21T17:16:52,794 * https://pypi.org/simple/pgenlib/
2022-07-21T17:16:52,794 * https://www.piwheels.org/simple/pgenlib/
2022-07-21T17:16:52,795 Fetching project page and analyzing links: https://pypi.org/simple/pgenlib/
2022-07-21T17:16:52,796 Getting page https://pypi.org/simple/pgenlib/
2022-07-21T17:16:52,800 Found index url https://pypi.org/simple
2022-07-21T17:16:52,917   Found link https://files.pythonhosted.org/packages/d9/cc/f3bbaa8da897e9a04e1a885183a0c533ba563bb3a1dbfba6680704473336/Pgenlib-0.81.1.tar.gz#sha256=6fcde4c14d8a28033f1401fceb30e7d38140ff0cf24295114ef00b7ebfe904a8 (from https://pypi.org/simple/pgenlib/) (requires-python:>=3.5), version: 0.81.1
2022-07-21T17:16:52,919   Found link https://files.pythonhosted.org/packages/6d/f7/c286a64ec213ea42bfa67b20ce1271b0b8699ac3880854657f8ed1620759/Pgenlib-0.81.2.tar.gz#sha256=c8dac92add708197b3ffe41f9fa7612bc48765483295d360b9820a2636094467 (from https://pypi.org/simple/pgenlib/) (requires-python:>=3.5), version: 0.81.2
2022-07-21T17:16:52,920 Fetching project page and analyzing links: https://www.piwheels.org/simple/pgenlib/
2022-07-21T17:16:52,920 Getting page https://www.piwheels.org/simple/pgenlib/
2022-07-21T17:16:52,922 Found index url https://www.piwheels.org/simple
2022-07-21T17:16:53,140   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)
2022-07-21T17:16:53,141   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)
2022-07-21T17:16:53,141 Skipping link: not a file: https://www.piwheels.org/simple/pgenlib/
2022-07-21T17:16:53,142 Skipping link: not a file: https://pypi.org/simple/pgenlib/
2022-07-21T17:16:53,187 Given no hashes to check 1 links for project 'pgenlib': discarding no candidates
2022-07-21T17:16:53,228 Collecting pgenlib==0.81.2
2022-07-21T17:16:53,233   Created temporary directory: /tmp/pip-unpack-u5thkdcx
2022-07-21T17:16:53,343   Downloading Pgenlib-0.81.2.tar.gz (385 kB)
2022-07-21T17:16:53,851   Added pgenlib==0.81.2 from https://files.pythonhosted.org/packages/6d/f7/c286a64ec213ea42bfa67b20ce1271b0b8699ac3880854657f8ed1620759/Pgenlib-0.81.2.tar.gz#sha256=c8dac92add708197b3ffe41f9fa7612bc48765483295d360b9820a2636094467 to build tracker '/tmp/pip-build-tracker-kndaeju_'
2022-07-21T17:16:53,865   Created temporary directory: /tmp/pip-build-env-sjqw0xyg
2022-07-21T17:16:53,885   Created temporary directory: /tmp/pip-standalone-pip-7bp8k3sy
2022-07-21T17:16:56,279   Installing build dependencies: started
2022-07-21T17:16:56,281   Running command pip subprocess to install build dependencies
2022-07-21T17:17:07,525   Using pip 22.1.2 from /tmp/pip-standalone-pip-7bp8k3sy/__env_pip__.zip/pip (python 3.9)
2022-07-21T17:17:09,462   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2022-07-21T17:17:13,676   Collecting setuptools
2022-07-21T17:17:13,964     Using cached https://www.piwheels.org/simple/setuptools/setuptools-63.2.0-py3-none-any.whl (1.2 MB)
2022-07-21T17:17:14,618   Collecting wheel
2022-07-21T17:17:14,651     Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB)
2022-07-21T17:17:18,324   Collecting numpy>=1.19.0
2022-07-21T17:17:20,869     Using cached https://www.piwheels.org/simple/numpy/numpy-1.23.1-cp39-cp39-linux_armv7l.whl (12.3 MB)
2022-07-21T17:17:25,506   Collecting Cython>=0.29.21
2022-07-21T17:17:26,540     Using cached https://www.piwheels.org/simple/cython/Cython-0.29.30-cp39-cp39-linux_armv7l.whl (5.0 MB)
2022-07-21T17:17:37,431   Installing collected packages: wheel, setuptools, numpy, Cython
2022-07-21T17:17:37,722     Creating /tmp/pip-build-env-sjqw0xyg/overlay/bin
2022-07-21T17:17:37,726     changing mode of /tmp/pip-build-env-sjqw0xyg/overlay/bin/wheel to 755
2022-07-21T17:18:01,541     changing mode of /tmp/pip-build-env-sjqw0xyg/overlay/bin/f2py to 755
2022-07-21T17:18:01,546     changing mode of /tmp/pip-build-env-sjqw0xyg/overlay/bin/f2py3 to 755
2022-07-21T17:18:01,551     changing mode of /tmp/pip-build-env-sjqw0xyg/overlay/bin/f2py3.9 to 755
2022-07-21T17:18:07,839     changing mode of /tmp/pip-build-env-sjqw0xyg/overlay/bin/cygdb to 755
2022-07-21T17:18:07,843     changing mode of /tmp/pip-build-env-sjqw0xyg/overlay/bin/cython to 755
2022-07-21T17:18:07,847     changing mode of /tmp/pip-build-env-sjqw0xyg/overlay/bin/cythonize to 755
2022-07-21T17:18:07,900   Successfully installed Cython-0.29.30 numpy-1.23.1 setuptools-63.2.0 wheel-0.37.1
2022-07-21T17:18:08,822   Installing build dependencies: finished with status 'done'
2022-07-21T17:18:08,852   Getting requirements to build wheel: started
2022-07-21T17:18:08,854   Running command Getting requirements to build wheel
2022-07-21T17:18:16,729   running egg_info
2022-07-21T17:18:17,387   writing src/Pgenlib.egg-info/PKG-INFO
2022-07-21T17:18:17,947   writing dependency_links to src/Pgenlib.egg-info/dependency_links.txt
2022-07-21T17:18:21,325   writing top-level names to src/Pgenlib.egg-info/top_level.txt
2022-07-21T17:18:21,991   reading manifest file 'src/Pgenlib.egg-info/SOURCES.txt'
2022-07-21T17:18:22,000   reading manifest template 'MANIFEST.in'
2022-07-21T17:18:22,004   adding license file 'LICENSE'
2022-07-21T17:18:22,010   writing manifest file 'src/Pgenlib.egg-info/SOURCES.txt'
2022-07-21T17:18:22,346   Getting requirements to build wheel: finished with status 'done'
2022-07-21T17:18:22,370   Created temporary directory: /tmp/pip-modern-metadata-se9kgz0l
2022-07-21T17:18:22,375   Preparing metadata (pyproject.toml): started
2022-07-21T17:18:22,377   Running command Preparing metadata (pyproject.toml)
2022-07-21T17:18:29,760   running dist_info
2022-07-21T17:18:30,369   creating /tmp/pip-modern-metadata-se9kgz0l/Pgenlib.egg-info
2022-07-21T17:18:31,006   writing /tmp/pip-modern-metadata-se9kgz0l/Pgenlib.egg-info/PKG-INFO
2022-07-21T17:18:31,558   writing dependency_links to /tmp/pip-modern-metadata-se9kgz0l/Pgenlib.egg-info/dependency_links.txt
2022-07-21T17:18:34,857   writing top-level names to /tmp/pip-modern-metadata-se9kgz0l/Pgenlib.egg-info/top_level.txt
2022-07-21T17:18:34,860   writing manifest file '/tmp/pip-modern-metadata-se9kgz0l/Pgenlib.egg-info/SOURCES.txt'
2022-07-21T17:18:35,514   reading manifest file '/tmp/pip-modern-metadata-se9kgz0l/Pgenlib.egg-info/SOURCES.txt'
2022-07-21T17:18:35,517   reading manifest template 'MANIFEST.in'
2022-07-21T17:18:35,524   adding license file 'LICENSE'
2022-07-21T17:18:35,531   writing manifest file '/tmp/pip-modern-metadata-se9kgz0l/Pgenlib.egg-info/SOURCES.txt'
2022-07-21T17:18:35,534   creating '/tmp/pip-modern-metadata-se9kgz0l/Pgenlib-0.81.2.dist-info'
2022-07-21T17:18:35,706   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2022-07-21T17:18:36,048   Preparing metadata (pyproject.toml): finished with status 'done'
2022-07-21T17:18:36,062   Source in /tmp/pip-wheel-hrkz7pvz/pgenlib_10dcdb87e72b4c1e8009ca422bf8d52a has version 0.81.2, which satisfies requirement pgenlib==0.81.2 from https://files.pythonhosted.org/packages/6d/f7/c286a64ec213ea42bfa67b20ce1271b0b8699ac3880854657f8ed1620759/Pgenlib-0.81.2.tar.gz#sha256=c8dac92add708197b3ffe41f9fa7612bc48765483295d360b9820a2636094467
2022-07-21T17:18:36,064   Removed pgenlib==0.81.2 from https://files.pythonhosted.org/packages/6d/f7/c286a64ec213ea42bfa67b20ce1271b0b8699ac3880854657f8ed1620759/Pgenlib-0.81.2.tar.gz#sha256=c8dac92add708197b3ffe41f9fa7612bc48765483295d360b9820a2636094467 from build tracker '/tmp/pip-build-tracker-kndaeju_'
2022-07-21T17:18:36,077 Created temporary directory: /tmp/pip-unpack-m815koft
2022-07-21T17:18:36,078 Building wheels for collected packages: pgenlib
2022-07-21T17:18:36,088   Created temporary directory: /tmp/pip-wheel-_t37qm65
2022-07-21T17:18:36,088   Destination directory: /tmp/pip-wheel-_t37qm65
2022-07-21T17:18:36,093   Building wheel for pgenlib (pyproject.toml): started
2022-07-21T17:18:36,095   Running command Building wheel for pgenlib (pyproject.toml)
2022-07-21T17:18:43,043   running bdist_wheel
2022-07-21T17:18:43,784   running build
2022-07-21T17:18:43,785   running build_ext
2022-07-21T17:18:43,797   building 'pgenlib' extension
2022-07-21T17:18:43,798   creating build
2022-07-21T17:18:43,799   creating build/temp.linux-armv7l-cpython-39
2022-07-21T17:18:43,800   creating build/temp.linux-armv7l-cpython-39/src
2022-07-21T17:18:43,802   creating build/temp.linux-armv7l-cpython-39/src/pgenlib
2022-07-21T17:18:43,803   creating build/temp.linux-armv7l-cpython-39/src/plink2
2022-07-21T17:18:43,804   creating build/temp.linux-armv7l-cpython-39/src/plink2/include
2022-07-21T17:18:43,806   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/usr/local/lib/python3.9/dist-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
2022-07-21T17:18:44,481   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
2022-07-21T17:18:44,482                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2022-07-21T17:18:44,482                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
2022-07-21T17:18:44,483                    from src/pgenlib/pgenlib.cpp:754:
2022-07-21T17:18:44,483   /usr/local/lib/python3.9/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]
2022-07-21T17:18:44,483      17 | #warning "Using deprecated NumPy API, disable it with " \
2022-07-21T17:18:44,484         |  ^~~~~~~
2022-07-21T17:18:44,622   src/pgenlib/pgenlib.cpp:952: warning: "likely" redefined
2022-07-21T17:18:44,623     952 |   #define likely(x)   __builtin_expect(!!(x), 1)
2022-07-21T17:18:44,623         |
2022-07-21T17:18:44,624   In file included from src/pgenlib/../plink2/include/plink2_bits.h:23,
2022-07-21T17:18:44,624                    from src/pgenlib/../plink2/include/pgenlib_misc.h:77,
2022-07-21T17:18:44,624                    from src/pgenlib/../plink2/pgenlib_ffi_support.h:20,
2022-07-21T17:18:44,625                    from src/pgenlib/pgenlib.cpp:762:
2022-07-21T17:18:44,625   src/pgenlib/../plink2/include/plink2_base.h:252: note: this is the location of the previous definition
2022-07-21T17:18:44,625     252 | #  define likely(expr) __builtin_expect(!!(expr), 1)
2022-07-21T17:18:44,626         |
2022-07-21T17:18:44,626   src/pgenlib/pgenlib.cpp:953: warning: "unlikely" redefined
2022-07-21T17:18:44,626     953 |   #define unlikely(x) __builtin_expect(!!(x), 0)
2022-07-21T17:18:44,627         |
2022-07-21T17:18:44,627   In file included from src/pgenlib/../plink2/include/plink2_bits.h:23,
2022-07-21T17:18:44,627                    from src/pgenlib/../plink2/include/pgenlib_misc.h:77,
2022-07-21T17:18:44,628                    from src/pgenlib/../plink2/pgenlib_ffi_support.h:20,
2022-07-21T17:18:44,628                    from src/pgenlib/pgenlib.cpp:762:
2022-07-21T17:18:44,628   src/pgenlib/../plink2/include/plink2_base.h:253: note: this is the location of the previous definition
2022-07-21T17:18:44,628     253 | #  define unlikely(expr) __builtin_expect(!!(expr), 0)
2022-07-21T17:18:44,629         |
2022-07-21T17:18:46,850   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*)’:
2022-07-21T17:18:46,850   src/pgenlib/pgenlib.cpp:5274:55: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:46,850    5274 |   __pyx_t_9 = (((__pyx_v_geno_int_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:46,851         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:46,917   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*)’:
2022-07-21T17:18:46,918   src/pgenlib/pgenlib.cpp:5928:55: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:46,918    5928 |   __pyx_t_9 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:46,918         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:46,980   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles(__pyx_obj_7pgenlib_PgenReader*, uint32_t, PyArrayObject*, int)’:
2022-07-21T17:18:46,980   src/pgenlib/pgenlib.cpp:6488:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:46,980    6488 |   __pyx_t_8 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:46,981         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,036   src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles_and_phasepresent(__pyx_obj_7pgenlib_PgenReader*, uint32_t, PyArrayObject*, PyArrayObject*, int)’:
2022-07-21T17:18:47,036   src/pgenlib/pgenlib.cpp:6984:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,037    6984 |   __pyx_t_8 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2022-07-21T17:18:47,037         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,043   src/pgenlib/pgenlib.cpp:7040:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,044    7040 |   __pyx_t_8 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,044         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,096   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*)’:
2022-07-21T17:18:47,097   src/pgenlib/pgenlib.cpp:7530:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,097    7530 |     __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,098         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,103   src/pgenlib/pgenlib.cpp:7586:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,104    7586 |     __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,104         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,123   src/pgenlib/pgenlib.cpp:7811:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,123    7811 |   __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,124         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,130   src/pgenlib/pgenlib.cpp:7867:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,130    7867 |   __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,131         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,162   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*)’:
2022-07-21T17:18:47,163   src/pgenlib/pgenlib.cpp:8466:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,163    8466 |     __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,163         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,169   src/pgenlib/pgenlib.cpp:8522:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,169    8522 |     __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,170         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,188   src/pgenlib/pgenlib.cpp:8747:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,189    8747 |   __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,189         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,196   src/pgenlib/pgenlib.cpp:8803:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,196    8803 |   __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,197         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,228   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*)’:
2022-07-21T17:18:47,229   src/pgenlib/pgenlib.cpp:9402:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,229    9402 |     __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,230         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,236   src/pgenlib/pgenlib.cpp:9458:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,236    9458 |     __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,237         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,255   src/pgenlib/pgenlib.cpp:9683:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,256    9683 |   __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,256         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,263   src/pgenlib/pgenlib.cpp:9739:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,263    9739 |   __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,264         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,360   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*)’:
2022-07-21T17:18:47,361   src/pgenlib/pgenlib.cpp:10891:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,361   10891 |     __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,361         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,367   src/pgenlib/pgenlib.cpp:10947:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,368   10947 |     __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,368         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,388   src/pgenlib/pgenlib.cpp:11188:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,389   11188 |   __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,389         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,396   src/pgenlib/pgenlib.cpp:11244:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,396   11244 |   __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,396         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,439   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*)’:
2022-07-21T17:18:47,439   src/pgenlib/pgenlib.cpp:11939:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,440   11939 |     __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,440         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,447   src/pgenlib/pgenlib.cpp:11995:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,447   11995 |     __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,447         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,467   src/pgenlib/pgenlib.cpp:12236:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,468   12236 |   __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,468         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,474   src/pgenlib/pgenlib.cpp:12292:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,475   12292 |   __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,475         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,518   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*)’:
2022-07-21T17:18:47,519   src/pgenlib/pgenlib.cpp:12987:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,519   12987 |     __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,519         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,526   src/pgenlib/pgenlib.cpp:13043:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,526   13043 |     __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,526         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,547   src/pgenlib/pgenlib.cpp:13284:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,547   13284 |   __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,547         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,554   src/pgenlib/pgenlib.cpp:13340:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,554   13340 |   __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,554         |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,674   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*)’:
2022-07-21T17:18:47,675   src/pgenlib/pgenlib.cpp:14684:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,675   14684 |     __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,676         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,682   src/pgenlib/pgenlib.cpp:14740:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,682   14740 |     __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2022-07-21T17:18:47,682         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,704   src/pgenlib/pgenlib.cpp:14977:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,704   14977 |   __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2022-07-21T17:18:47,705         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,711   src/pgenlib/pgenlib.cpp:15033:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,712   15033 |   __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,712         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,802   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*)’:
2022-07-21T17:18:47,803   src/pgenlib/pgenlib.cpp:16092:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,803   16092 |     __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,804         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,810   src/pgenlib/pgenlib.cpp:16148:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,810   16148 |     __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2022-07-21T17:18:47,810         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,830   src/pgenlib/pgenlib.cpp:16389:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,831   16389 |   __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0);
2022-07-21T17:18:47,831         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,837   src/pgenlib/pgenlib.cpp:16445:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,838   16445 |   __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,838         |                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,929   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*)’:
2022-07-21T17:18:47,929   src/pgenlib/pgenlib.cpp:17582:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,930   17582 |     __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,930         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,936   src/pgenlib/pgenlib.cpp:17638:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,936   17638 |     __pyx_t_10 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:47,937         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,943   src/pgenlib/pgenlib.cpp:17694:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,944   17694 |     __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2022-07-21T17:18:47,944         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:47,950   src/pgenlib/pgenlib.cpp:17750:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:47,951   17750 |     __pyx_t_10 = (((__pyx_v_phasepresent_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:47,951         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:48,027   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*)’:
2022-07-21T17:18:48,028   src/pgenlib/pgenlib.cpp:18446:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:48,028   18446 |     __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:48,029         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:48,034   src/pgenlib/pgenlib.cpp:18502:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:48,035   18502 |     __pyx_t_12 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:48,035         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:48,041   src/pgenlib/pgenlib.cpp:18558:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:48,042   18558 |     __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0);
2022-07-21T17:18:48,042         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:48,049   src/pgenlib/pgenlib.cpp:18614:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:48,049   18614 |     __pyx_t_12 = (((__pyx_v_phasepresent_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:48,050         |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:48,205   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*)’:
2022-07-21T17:18:48,206   src/pgenlib/pgenlib.cpp:20373:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:48,206   20373 |     __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:48,206         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:48,212   src/pgenlib/pgenlib.cpp:20429:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:48,213   20429 |     __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:48,213         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:48,249   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*)’:
2022-07-21T17:18:48,250   src/pgenlib/pgenlib.cpp:20890:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:48,250   20890 |     __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0);
2022-07-21T17:18:48,250         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:18:48,256   src/pgenlib/pgenlib.cpp:20946:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2022-07-21T17:18:48,256   20946 |     __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[1]) < __pyx_v_subset_size) != 0);
2022-07-21T17:18:48,257         |                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
2022-07-21T17:19:50,386   At global scope:
2022-07-21T17:19:50,386   cc1plus: note: unrecognized command-line option ‘-Wno-macro-redefined’ may have been intended to silence earlier diagnostics
2022-07-21T17:19:56,003   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/usr/local/lib/python3.9/dist-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
2022-07-21T17:20:03,631   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/usr/local/lib/python3.9/dist-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
2022-07-21T17:20:35,458   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/usr/local/lib/python3.9/dist-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
2022-07-21T17:20:43,258   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/usr/local/lib/python3.9/dist-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
2022-07-21T17:20:44,158   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/usr/local/lib/python3.9/dist-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
2022-07-21T17:20:48,398   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/usr/local/lib/python3.9/dist-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
2022-07-21T17:20:50,846   creating build/lib.linux-armv7l-cpython-39
2022-07-21T17:20:50,849   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
2022-07-21T17:20:52,945   installing to build/bdist.linux-armv7l/wheel
2022-07-21T17:20:52,946   running install
2022-07-21T17:20:53,009   running install_lib
2022-07-21T17:20:53,608   creating build/bdist.linux-armv7l
2022-07-21T17:20:53,609   creating build/bdist.linux-armv7l/wheel
2022-07-21T17:20:53,611   copying build/lib.linux-armv7l-cpython-39/pgenlib.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel
2022-07-21T17:20:53,786   running install_egg_info
2022-07-21T17:20:54,999   running egg_info
2022-07-21T17:20:55,583   writing src/Pgenlib.egg-info/PKG-INFO
2022-07-21T17:20:56,135   writing dependency_links to src/Pgenlib.egg-info/dependency_links.txt
2022-07-21T17:20:59,444   writing top-level names to src/Pgenlib.egg-info/top_level.txt
2022-07-21T17:20:59,483   reading manifest file 'src/Pgenlib.egg-info/SOURCES.txt'
2022-07-21T17:20:59,488   reading manifest template 'MANIFEST.in'
2022-07-21T17:20:59,493   adding license file 'LICENSE'
2022-07-21T17:20:59,500   writing manifest file 'src/Pgenlib.egg-info/SOURCES.txt'
2022-07-21T17:20:59,503   Copying src/Pgenlib.egg-info to build/bdist.linux-armv7l/wheel/Pgenlib-0.81.2-py3.9.egg-info
2022-07-21T17:20:59,520   running install_scripts
2022-07-21T17:20:59,628   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2022-07-21T17:20:59,679   creating build/bdist.linux-armv7l/wheel/Pgenlib-0.81.2.dist-info/WHEEL
2022-07-21T17:20:59,685   creating '/tmp/pip-wheel-_t37qm65/tmp7o2y_klz/Pgenlib-0.81.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2022-07-21T17:21:01,357   adding 'pgenlib.cpython-39-arm-linux-gnueabihf.so'
2022-07-21T17:21:01,435   adding 'Pgenlib-0.81.2.dist-info/LICENSE'
2022-07-21T17:21:01,438   adding 'Pgenlib-0.81.2.dist-info/METADATA'
2022-07-21T17:21:01,440   adding 'Pgenlib-0.81.2.dist-info/WHEEL'
2022-07-21T17:21:01,442   adding 'Pgenlib-0.81.2.dist-info/top_level.txt'
2022-07-21T17:21:01,444   adding 'Pgenlib-0.81.2.dist-info/RECORD'
2022-07-21T17:21:01,484   removing build/bdist.linux-armv7l/wheel
2022-07-21T17:21:01,883   Building wheel for pgenlib (pyproject.toml): finished with status 'done'
2022-07-21T17:21:01,958   Created wheel for pgenlib: filename=Pgenlib-0.81.2-cp39-cp39-linux_armv7l.whl size=1243839 sha256=2e0ad339664cbc60a4ae0b3a935afcf56d3e1a344387d8327ae50b03dce0d852
2022-07-21T17:21:01,960   Stored in directory: /tmp/pip-ephem-wheel-cache-wnpj7th8/wheels/c8/21/33/6b72ff1dbbd96728b29ba523fe54759631da9cfc26d1fe1b05
2022-07-21T17:21:01,983 Successfully built pgenlib
2022-07-21T17:21:02,079 Removed build tracker: '/tmp/pip-build-tracker-kndaeju_'