2023-03-11T18:09:59,980 Created temporary directory: /tmp/pip-ephem-wheel-cache-s44r81zi 2023-03-11T18:09:59,983 Created temporary directory: /tmp/pip-build-tracker-5c3w63s2 2023-03-11T18:09:59,983 Initialized build tracking at /tmp/pip-build-tracker-5c3w63s2 2023-03-11T18:09:59,983 Created build tracker: /tmp/pip-build-tracker-5c3w63s2 2023-03-11T18:09:59,984 Entered build tracker: /tmp/pip-build-tracker-5c3w63s2 2023-03-11T18:09:59,984 Created temporary directory: /tmp/pip-wheel-4tp_4zpx 2023-03-11T18:09:59,989 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 2023-03-11T18:09:59,992 Created temporary directory: /tmp/pip-ephem-wheel-cache-jkz4c85d 2023-03-11T18:10:00,021 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-03-11T18:10:00,024 2 location(s) to search for versions of pgenlib: 2023-03-11T18:10:00,024 * https://pypi.org/simple/pgenlib/ 2023-03-11T18:10:00,024 * https://www.piwheels.org/simple/pgenlib/ 2023-03-11T18:10:00,025 Fetching project page and analyzing links: https://pypi.org/simple/pgenlib/ 2023-03-11T18:10:00,025 Getting page https://pypi.org/simple/pgenlib/ 2023-03-11T18:10:00,027 Found index url https://pypi.org/simple 2023-03-11T18:10:00,078 Fetched page https://pypi.org/simple/pgenlib/ as application/vnd.pypi.simple.v1+json 2023-03-11T18:10:00,081 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 2023-03-11T18:10:00,081 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) 2023-03-11T18:10:00,081 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 2023-03-11T18:10:00,082 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 2023-03-11T18:10:00,083 Found link https://files.pythonhosted.org/packages/29/d3/311512e956d1bc898cd6020e15691e2778e1bf3a1c2e01eadbb6031d8bd5/Pgenlib-0.82.0.tar.gz (from https://pypi.org/simple/pgenlib/) (requires-python:>=3.5), version: 0.82.0 2023-03-11T18:10:00,083 Found link https://files.pythonhosted.org/packages/9b/d1/73c8eb879691b5ef443cf3c26e801590a7eac657264f80538c7541266fa8/Pgenlib-0.82.1.tar.gz (from https://pypi.org/simple/pgenlib/) (requires-python:>=3.5), version: 0.82.1 2023-03-11T18:10:00,083 Fetching project page and analyzing links: https://www.piwheels.org/simple/pgenlib/ 2023-03-11T18:10:00,084 Getting page https://www.piwheels.org/simple/pgenlib/ 2023-03-11T18:10:00,085 Found index url https://www.piwheels.org/simple 2023-03-11T18:10:00,260 Fetched page https://www.piwheels.org/simple/pgenlib/ as text/html 2023-03-11T18:10:00,263 Skipping link: No binaries permitted for pgenlib: https://www.piwheels.org/simple/pgenlib/Pgenlib-0.82.0-cp39-cp39-linux_armv7l.whl#sha256=b38d7233c5515f730969499da3b95e95f64109573755cdda562026109c999c33 (from https://www.piwheels.org/simple/pgenlib/) (requires-python:>=3.5) 2023-03-11T18:10:00,263 Skipping link: No binaries permitted for pgenlib: https://www.piwheels.org/simple/pgenlib/Pgenlib-0.82.0-cp39-cp39-linux_armv6l.whl#sha256=b38d7233c5515f730969499da3b95e95f64109573755cdda562026109c999c33 (from https://www.piwheels.org/simple/pgenlib/) (requires-python:>=3.5) 2023-03-11T18:10:00,263 Skipping link: No binaries permitted for pgenlib: https://www.piwheels.org/simple/pgenlib/Pgenlib-0.81.3-cp39-cp39-linux_armv7l.whl#sha256=5a7e6ce67f2000041a2e5d373924f58245f07fb04f09b9c5740c8554ff44d333 (from https://www.piwheels.org/simple/pgenlib/) (requires-python:>=3.5) 2023-03-11T18:10:00,264 Skipping link: No binaries permitted for pgenlib: https://www.piwheels.org/simple/pgenlib/Pgenlib-0.81.3-cp39-cp39-linux_armv6l.whl#sha256=5a7e6ce67f2000041a2e5d373924f58245f07fb04f09b9c5740c8554ff44d333 (from https://www.piwheels.org/simple/pgenlib/) (requires-python:>=3.5) 2023-03-11T18:10:00,264 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) 2023-03-11T18:10:00,264 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) 2023-03-11T18:10:00,264 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) 2023-03-11T18:10:00,264 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) 2023-03-11T18:10:00,265 Skipping link: not a file: https://www.piwheels.org/simple/pgenlib/ 2023-03-11T18:10:00,265 Skipping link: not a file: https://pypi.org/simple/pgenlib/ 2023-03-11T18:10:00,284 Given no hashes to check 1 links for project 'pgenlib': discarding no candidates 2023-03-11T18:10:00,300 Collecting pgenlib==0.82.1 2023-03-11T18:10:00,303 Created temporary directory: /tmp/pip-unpack-mjav9ez8 2023-03-11T18:10:00,401 Downloading Pgenlib-0.82.1.tar.gz (489 kB) 2023-03-11T18:10:00,704 Added pgenlib==0.82.1 from https://files.pythonhosted.org/packages/9b/d1/73c8eb879691b5ef443cf3c26e801590a7eac657264f80538c7541266fa8/Pgenlib-0.82.1.tar.gz to build tracker '/tmp/pip-build-tracker-5c3w63s2' 2023-03-11T18:10:00,710 Created temporary directory: /tmp/pip-build-env-scrz2k8m 2023-03-11T18:10:00,721 Installing build dependencies: started 2023-03-11T18:10:00,722 Running command pip subprocess to install build dependencies 2023-03-11T18:10:02,100 Using pip 23.0.1 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2023-03-11T18:10:02,676 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 2023-03-11T18:10:02,702 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-03-11T18:10:04,440 Collecting setuptools 2023-03-11T18:10:04,607 Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.6.0-py3-none-any.whl (1.1 MB) 2023-03-11T18:10:04,902 Collecting wheel 2023-03-11T18:10:04,920 Using cached https://www.piwheels.org/simple/wheel/wheel-0.38.4-py3-none-any.whl (36 kB) 2023-03-11T18:10:05,108 Collecting oldest-supported-numpy>=2022.8.16 2023-03-11T18:10:05,183 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2022.11.19-py3-none-any.whl (4.9 kB) 2023-03-11T18:10:06,616 Collecting Cython>=0.29.21 2023-03-11T18:10:07,097 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.33-cp39-cp39-linux_armv7l.whl (5.0 MB) 2023-03-11T18:10:08,598 Collecting numpy==1.19.3 2023-03-11T18:10:09,993 Using cached https://www.piwheels.org/simple/numpy/numpy-1.19.3-cp39-cp39-linux_armv7l.whl (10.5 MB) 2023-03-11T18:10:12,333 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2023-03-11T18:10:12,482 Creating /tmp/pip-build-env-scrz2k8m/overlay/bin 2023-03-11T18:10:12,484 changing mode of /tmp/pip-build-env-scrz2k8m/overlay/bin/wheel to 755 2023-03-11T18:10:21,443 changing mode of /tmp/pip-build-env-scrz2k8m/overlay/bin/f2py to 755 2023-03-11T18:10:21,445 changing mode of /tmp/pip-build-env-scrz2k8m/overlay/bin/f2py3 to 755 2023-03-11T18:10:21,447 changing mode of /tmp/pip-build-env-scrz2k8m/overlay/bin/f2py3.9 to 755 2023-03-11T18:10:24,338 changing mode of /tmp/pip-build-env-scrz2k8m/overlay/bin/cygdb to 755 2023-03-11T18:10:24,341 changing mode of /tmp/pip-build-env-scrz2k8m/overlay/bin/cython to 755 2023-03-11T18:10:24,343 changing mode of /tmp/pip-build-env-scrz2k8m/overlay/bin/cythonize to 755 2023-03-11T18:10:24,389 Successfully installed Cython-0.29.33 numpy-1.19.3 oldest-supported-numpy-2022.11.19 setuptools-67.6.0 wheel-0.38.4 2023-03-11T18:10:24,995 Installing build dependencies: finished with status 'done' 2023-03-11T18:10:25,000 Getting requirements to build wheel: started 2023-03-11T18:10:25,001 Running command Getting requirements to build wheel 2023-03-11T18:10:29,891 Compiling src/pgenlib/pgenlib.pyx because it depends on /tmp/pip-build-env-scrz2k8m/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-11T18:10:29,892 [1/1] Cythonizing src/pgenlib/pgenlib.pyx 2023-03-11T18:10:29,972 running egg_info 2023-03-11T18:10:29,981 writing src/Pgenlib.egg-info/PKG-INFO 2023-03-11T18:10:29,983 writing dependency_links to src/Pgenlib.egg-info/dependency_links.txt 2023-03-11T18:10:29,986 writing top-level names to src/Pgenlib.egg-info/top_level.txt 2023-03-11T18:10:30,007 reading manifest file 'src/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:10:30,013 reading manifest template 'MANIFEST.in' 2023-03-11T18:10:30,016 adding license file 'LICENSE' 2023-03-11T18:10:30,020 writing manifest file 'src/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:10:30,318 Getting requirements to build wheel: finished with status 'done' 2023-03-11T18:10:30,330 Created temporary directory: /tmp/pip-modern-metadata-5i3_jdha 2023-03-11T18:10:30,333 Preparing metadata (pyproject.toml): started 2023-03-11T18:10:30,334 Running command Preparing metadata (pyproject.toml) 2023-03-11T18:10:31,906 running dist_info 2023-03-11T18:10:31,930 creating /tmp/pip-modern-metadata-5i3_jdha/Pgenlib.egg-info 2023-03-11T18:10:31,936 writing /tmp/pip-modern-metadata-5i3_jdha/Pgenlib.egg-info/PKG-INFO 2023-03-11T18:10:31,938 writing dependency_links to /tmp/pip-modern-metadata-5i3_jdha/Pgenlib.egg-info/dependency_links.txt 2023-03-11T18:10:31,941 writing top-level names to /tmp/pip-modern-metadata-5i3_jdha/Pgenlib.egg-info/top_level.txt 2023-03-11T18:10:31,942 writing manifest file '/tmp/pip-modern-metadata-5i3_jdha/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:10:31,959 reading manifest file '/tmp/pip-modern-metadata-5i3_jdha/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:10:31,961 reading manifest template 'MANIFEST.in' 2023-03-11T18:10:31,965 adding license file 'LICENSE' 2023-03-11T18:10:31,968 writing manifest file '/tmp/pip-modern-metadata-5i3_jdha/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:10:31,969 creating '/tmp/pip-modern-metadata-5i3_jdha/Pgenlib-0.82.1.dist-info' 2023-03-11T18:10:32,296 Preparing metadata (pyproject.toml): finished with status 'done' 2023-03-11T18:10:32,303 Source in /tmp/pip-wheel-4tp_4zpx/pgenlib_e3b788f34f204545b75d7e0243101dd0 has version 0.82.1, which satisfies requirement pgenlib==0.82.1 from https://files.pythonhosted.org/packages/9b/d1/73c8eb879691b5ef443cf3c26e801590a7eac657264f80538c7541266fa8/Pgenlib-0.82.1.tar.gz 2023-03-11T18:10:32,304 Removed pgenlib==0.82.1 from https://files.pythonhosted.org/packages/9b/d1/73c8eb879691b5ef443cf3c26e801590a7eac657264f80538c7541266fa8/Pgenlib-0.82.1.tar.gz from build tracker '/tmp/pip-build-tracker-5c3w63s2' 2023-03-11T18:10:32,310 Created temporary directory: /tmp/pip-unpack-55l6d6fk 2023-03-11T18:10:32,310 Building wheels for collected packages: pgenlib 2023-03-11T18:10:32,316 Created temporary directory: /tmp/pip-wheel-eq5r10yd 2023-03-11T18:10:32,316 Destination directory: /tmp/pip-wheel-eq5r10yd 2023-03-11T18:10:32,319 Building wheel for pgenlib (pyproject.toml): started 2023-03-11T18:10:32,319 Running command Building wheel for pgenlib (pyproject.toml) 2023-03-11T18:10:33,933 running bdist_wheel 2023-03-11T18:10:33,958 running build 2023-03-11T18:10:33,958 running build_ext 2023-03-11T18:10:33,966 building 'pgenlib' extension 2023-03-11T18:10:33,967 creating build 2023-03-11T18:10:33,967 creating build/temp.linux-armv7l-cpython-39 2023-03-11T18:10:33,968 creating build/temp.linux-armv7l-cpython-39/src 2023-03-11T18:10:33,969 creating build/temp.linux-armv7l-cpython-39/src/pgenlib 2023-03-11T18:10:33,970 creating build/temp.linux-armv7l-cpython-39/src/plink2 2023-03-11T18:10:33,971 creating build/temp.linux-armv7l-cpython-39/src/plink2/include 2023-03-11T18:10:33,972 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-scrz2k8m/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 2023-03-11T18:10:34,277 In file included from /tmp/pip-build-env-scrz2k8m/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-03-11T18:10:34,277 from /tmp/pip-build-env-scrz2k8m/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-11T18:10:34,278 from /tmp/pip-build-env-scrz2k8m/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-11T18:10:34,278 from src/pgenlib/pgenlib.cpp:799: 2023-03-11T18:10:34,278 /tmp/pip-build-env-scrz2k8m/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] 2023-03-11T18:10:34,278 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-11T18:10:34,278 | ^~~~~~~ 2023-03-11T18:10:34,363 src/pgenlib/pgenlib.cpp:994: warning: "likely" redefined 2023-03-11T18:10:34,363 994 | #define likely(x) __builtin_expect(!!(x), 1) 2023-03-11T18:10:34,364 | 2023-03-11T18:10:34,364 In file included from src/pgenlib/../plink2/include/plink2_bits.h:23, 2023-03-11T18:10:34,364 from src/pgenlib/../plink2/include/pgenlib_misc.h:77, 2023-03-11T18:10:34,364 from src/pgenlib/../plink2/pgenlib_ffi_support.h:20, 2023-03-11T18:10:34,365 from src/pgenlib/pgenlib.cpp:804: 2023-03-11T18:10:34,365 src/pgenlib/../plink2/include/plink2_base.h:252: note: this is the location of the previous definition 2023-03-11T18:10:34,365 252 | # define likely(expr) __builtin_expect(!!(expr), 1) 2023-03-11T18:10:34,365 | 2023-03-11T18:10:34,365 src/pgenlib/pgenlib.cpp:995: warning: "unlikely" redefined 2023-03-11T18:10:34,366 995 | #define unlikely(x) __builtin_expect(!!(x), 0) 2023-03-11T18:10:34,366 | 2023-03-11T18:10:34,366 In file included from src/pgenlib/../plink2/include/plink2_bits.h:23, 2023-03-11T18:10:34,366 from src/pgenlib/../plink2/include/pgenlib_misc.h:77, 2023-03-11T18:10:34,366 from src/pgenlib/../plink2/pgenlib_ffi_support.h:20, 2023-03-11T18:10:34,367 from src/pgenlib/pgenlib.cpp:804: 2023-03-11T18:10:34,367 src/pgenlib/../plink2/include/plink2_base.h:253: note: this is the location of the previous definition 2023-03-11T18:10:34,367 253 | # define unlikely(expr) __builtin_expect(!!(expr), 0) 2023-03-11T18:10:34,367 | 2023-03-11T18:10:35,325 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*)’: 2023-03-11T18:10:35,325 src/pgenlib/pgenlib.cpp:5347:55: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,325 5347 | __pyx_t_9 = (((__pyx_v_geno_int_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,326 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,353 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*)’: 2023-03-11T18:10:35,353 src/pgenlib/pgenlib.cpp:6001:55: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,353 6001 | __pyx_t_9 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,353 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,379 src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles(__pyx_obj_7pgenlib_PgenReader*, uint32_t, PyArrayObject*, int)’: 2023-03-11T18:10:35,379 src/pgenlib/pgenlib.cpp:6561:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,379 6561 | __pyx_t_8 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,379 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,402 src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles_and_phasepresent(__pyx_obj_7pgenlib_PgenReader*, uint32_t, PyArrayObject*, PyArrayObject*, int)’: 2023-03-11T18:10:35,402 src/pgenlib/pgenlib.cpp:7057:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,403 7057 | __pyx_t_8 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:10:35,403 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,405 src/pgenlib/pgenlib.cpp:7113:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,405 7113 | __pyx_t_8 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,405 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,427 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*)’: 2023-03-11T18:10:35,428 src/pgenlib/pgenlib.cpp:7603:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,428 7603 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,428 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,430 src/pgenlib/pgenlib.cpp:7659:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,431 7659 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,431 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,438 src/pgenlib/pgenlib.cpp:7884:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,438 7884 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,439 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,441 src/pgenlib/pgenlib.cpp:7940:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,441 7940 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,441 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,454 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*)’: 2023-03-11T18:10:35,455 src/pgenlib/pgenlib.cpp:8539:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,455 8539 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,455 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,457 src/pgenlib/pgenlib.cpp:8595:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,458 8595 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,458 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,465 src/pgenlib/pgenlib.cpp:8820:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,466 8820 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,466 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,468 src/pgenlib/pgenlib.cpp:8876:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,469 8876 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,469 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,482 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*)’: 2023-03-11T18:10:35,482 src/pgenlib/pgenlib.cpp:9475:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,482 9475 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,482 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,485 src/pgenlib/pgenlib.cpp:9531:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,485 9531 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,485 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,493 src/pgenlib/pgenlib.cpp:9756:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,493 9756 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,493 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,496 src/pgenlib/pgenlib.cpp:9812:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,496 9812 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,496 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,536 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*)’: 2023-03-11T18:10:35,536 src/pgenlib/pgenlib.cpp:10964:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,536 10964 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,536 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,539 src/pgenlib/pgenlib.cpp:11020:58: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,539 11020 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,539 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,547 src/pgenlib/pgenlib.cpp:11261:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,548 11261 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,548 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,550 src/pgenlib/pgenlib.cpp:11317:56: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,550 11317 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,551 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,568 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*)’: 2023-03-11T18:10:35,568 src/pgenlib/pgenlib.cpp:12012:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,569 12012 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,569 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,571 src/pgenlib/pgenlib.cpp:12068:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,571 12068 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,571 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,580 src/pgenlib/pgenlib.cpp:12309:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,580 12309 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,580 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,583 src/pgenlib/pgenlib.cpp:12365:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,583 12365 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,583 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,601 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*)’: 2023-03-11T18:10:35,601 src/pgenlib/pgenlib.cpp:13060:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,601 13060 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,601 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,604 src/pgenlib/pgenlib.cpp:13116:59: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,604 13116 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,604 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,612 src/pgenlib/pgenlib.cpp:13357:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,613 13357 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,613 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,615 src/pgenlib/pgenlib.cpp:13413:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,615 13413 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,616 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,665 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*)’: 2023-03-11T18:10:35,665 src/pgenlib/pgenlib.cpp:14757:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,666 14757 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,666 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,668 src/pgenlib/pgenlib.cpp:14813:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,669 14813 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:10:35,669 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,678 src/pgenlib/pgenlib.cpp:15050:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,678 15050 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:10:35,678 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,681 src/pgenlib/pgenlib.cpp:15106:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,681 15106 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,681 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,719 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*)’: 2023-03-11T18:10:35,719 src/pgenlib/pgenlib.cpp:16165:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,720 16165 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,720 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,722 src/pgenlib/pgenlib.cpp:16221:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,723 16221 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:10:35,723 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,731 src/pgenlib/pgenlib.cpp:16462:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,731 16462 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:10:35,731 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,734 src/pgenlib/pgenlib.cpp:16518:60: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,734 16518 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,734 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,772 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*)’: 2023-03-11T18:10:35,772 src/pgenlib/pgenlib.cpp:17655:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,772 17655 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,772 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,775 src/pgenlib/pgenlib.cpp:17711:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,775 17711 | __pyx_t_10 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,775 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,778 src/pgenlib/pgenlib.cpp:17767:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,778 17767 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:10:35,778 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,781 src/pgenlib/pgenlib.cpp:17823:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,781 17823 | __pyx_t_10 = (((__pyx_v_phasepresent_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,781 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,813 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*)’: 2023-03-11T18:10:35,813 src/pgenlib/pgenlib.cpp:18519:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,813 18519 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,813 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,816 src/pgenlib/pgenlib.cpp:18575:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,816 18575 | __pyx_t_12 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,816 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,819 src/pgenlib/pgenlib.cpp:18631:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,819 18631 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:10:35,819 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,822 src/pgenlib/pgenlib.cpp:18687:62: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,822 18687 | __pyx_t_12 = (((__pyx_v_phasepresent_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,822 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,887 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*)’: 2023-03-11T18:10:35,887 src/pgenlib/pgenlib.cpp:20446:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,887 20446 | __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,887 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,890 src/pgenlib/pgenlib.cpp:20502:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,890 20502 | __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,890 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,904 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*)’: 2023-03-11T18:10:35,905 src/pgenlib/pgenlib.cpp:20963:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,905 20963 | __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:10:35,905 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:10:35,907 src/pgenlib/pgenlib.cpp:21019:57: warning: comparison of integer expressions of different signedness: ‘npy_intp’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-03-11T18:10:35,908 21019 | __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:10:35,908 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:11:02,532 At global scope: 2023-03-11T18:11:02,532 cc1plus: note: unrecognized command-line option ‘-Wno-macro-redefined’ may have been intended to silence earlier diagnostics 2023-03-11T18:11:05,113 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-scrz2k8m/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 2023-03-11T18:11:08,284 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-scrz2k8m/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 2023-03-11T18:11:21,592 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-scrz2k8m/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 2023-03-11T18:11:24,823 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-scrz2k8m/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 2023-03-11T18:11:25,243 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-scrz2k8m/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 2023-03-11T18:11:27,017 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-scrz2k8m/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 2023-03-11T18:11:28,078 creating build/lib.linux-armv7l-cpython-39 2023-03-11T18:11:28,079 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 2023-03-11T18:11:28,524 installing to build/bdist.linux-armv7l/wheel 2023-03-11T18:11:28,524 running install 2023-03-11T18:11:28,550 running install_lib 2023-03-11T18:11:28,558 creating build/bdist.linux-armv7l 2023-03-11T18:11:28,559 creating build/bdist.linux-armv7l/wheel 2023-03-11T18:11:28,560 copying build/lib.linux-armv7l-cpython-39/pgenlib.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-03-11T18:11:28,633 running install_egg_info 2023-03-11T18:11:28,662 running egg_info 2023-03-11T18:11:28,668 writing src/Pgenlib.egg-info/PKG-INFO 2023-03-11T18:11:28,669 writing dependency_links to src/Pgenlib.egg-info/dependency_links.txt 2023-03-11T18:11:28,671 writing top-level names to src/Pgenlib.egg-info/top_level.txt 2023-03-11T18:11:28,679 reading manifest file 'src/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:11:28,684 reading manifest template 'MANIFEST.in' 2023-03-11T18:11:28,687 adding license file 'LICENSE' 2023-03-11T18:11:28,691 writing manifest file 'src/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:11:28,693 Copying src/Pgenlib.egg-info to build/bdist.linux-armv7l/wheel/Pgenlib-0.82.1-py3.9.egg-info 2023-03-11T18:11:28,701 running install_scripts 2023-03-11T18:11:28,745 creating build/bdist.linux-armv7l/wheel/Pgenlib-0.82.1.dist-info/WHEEL 2023-03-11T18:11:28,748 creating '/tmp/pip-wheel-eq5r10yd/.tmp-4jr84bp3/Pgenlib-0.82.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-03-11T18:11:29,414 adding 'pgenlib.cpython-39-arm-linux-gnueabihf.so' 2023-03-11T18:11:29,438 adding 'Pgenlib-0.82.1.dist-info/LICENSE' 2023-03-11T18:11:29,439 adding 'Pgenlib-0.82.1.dist-info/METADATA' 2023-03-11T18:11:29,441 adding 'Pgenlib-0.82.1.dist-info/WHEEL' 2023-03-11T18:11:29,441 adding 'Pgenlib-0.82.1.dist-info/top_level.txt' 2023-03-11T18:11:29,442 adding 'Pgenlib-0.82.1.dist-info/RECORD' 2023-03-11T18:11:29,467 removing build/bdist.linux-armv7l/wheel 2023-03-11T18:11:29,636 Building wheel for pgenlib (pyproject.toml): finished with status 'done' 2023-03-11T18:11:29,673 Created wheel for pgenlib: filename=Pgenlib-0.82.1-cp39-cp39-linux_armv7l.whl size=1244492 sha256=7f2cd443fbc7956edef6af632c8b31dc2b48cd9cca92bacece82495cdff52291 2023-03-11T18:11:29,674 Stored in directory: /tmp/pip-ephem-wheel-cache-jkz4c85d/wheels/1c/ce/44/6bae8d8465792382135441074a63a0a5bce6cff02e0705f792 2023-03-11T18:11:29,686 Successfully built pgenlib 2023-03-11T18:11:29,728 Removed build tracker: '/tmp/pip-build-tracker-5c3w63s2'