2023-03-11T18:03:55,572 Created temporary directory: /tmp/pip-ephem-wheel-cache-o1790og7 2023-03-11T18:03:55,575 Created temporary directory: /tmp/pip-build-tracker-gyo9l7ay 2023-03-11T18:03:55,576 Initialized build tracking at /tmp/pip-build-tracker-gyo9l7ay 2023-03-11T18:03:55,576 Created build tracker: /tmp/pip-build-tracker-gyo9l7ay 2023-03-11T18:03:55,576 Entered build tracker: /tmp/pip-build-tracker-gyo9l7ay 2023-03-11T18:03:55,576 Created temporary directory: /tmp/pip-wheel-0zsf2z_3 2023-03-11T18:03:55,581 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 2023-03-11T18:03:55,584 Created temporary directory: /tmp/pip-ephem-wheel-cache-8co5ocon 2023-03-11T18:03:55,612 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-03-11T18:03:55,615 2 location(s) to search for versions of pgenlib: 2023-03-11T18:03:55,615 * https://pypi.org/simple/pgenlib/ 2023-03-11T18:03:55,615 * https://www.piwheels.org/simple/pgenlib/ 2023-03-11T18:03:55,616 Fetching project page and analyzing links: https://pypi.org/simple/pgenlib/ 2023-03-11T18:03:55,616 Getting page https://pypi.org/simple/pgenlib/ 2023-03-11T18:03:55,618 Found index url https://pypi.org/simple 2023-03-11T18:03:55,670 Fetched page https://pypi.org/simple/pgenlib/ as application/vnd.pypi.simple.v1+json 2023-03-11T18:03:55,672 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 2023-03-11T18:03:55,672 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) 2023-03-11T18:03:55,673 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 2023-03-11T18:03:55,673 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 2023-03-11T18:03:55,674 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 2023-03-11T18:03:55,675 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 2023-03-11T18:03:55,675 Fetching project page and analyzing links: https://www.piwheels.org/simple/pgenlib/ 2023-03-11T18:03:55,675 Getting page https://www.piwheels.org/simple/pgenlib/ 2023-03-11T18:03:55,676 Found index url https://www.piwheels.org/simple 2023-03-11T18:03:55,834 Fetched page https://www.piwheels.org/simple/pgenlib/ as text/html 2023-03-11T18:03:55,837 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) 2023-03-11T18:03:55,837 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) 2023-03-11T18:03:55,838 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) 2023-03-11T18:03:55,838 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) 2023-03-11T18:03:55,838 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) 2023-03-11T18:03:55,838 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) 2023-03-11T18:03:55,838 Skipping link: not a file: https://www.piwheels.org/simple/pgenlib/ 2023-03-11T18:03:55,839 Skipping link: not a file: https://pypi.org/simple/pgenlib/ 2023-03-11T18:03:55,856 Given no hashes to check 1 links for project 'pgenlib': discarding no candidates 2023-03-11T18:03:55,871 Collecting pgenlib==0.82.0 2023-03-11T18:03:55,873 Created temporary directory: /tmp/pip-unpack-u3ztvy0r 2023-03-11T18:03:55,918 Downloading Pgenlib-0.82.0.tar.gz (387 kB) 2023-03-11T18:03:56,138 Added pgenlib==0.82.0 from https://files.pythonhosted.org/packages/29/d3/311512e956d1bc898cd6020e15691e2778e1bf3a1c2e01eadbb6031d8bd5/Pgenlib-0.82.0.tar.gz to build tracker '/tmp/pip-build-tracker-gyo9l7ay' 2023-03-11T18:03:56,145 Created temporary directory: /tmp/pip-build-env-gofyxwru 2023-03-11T18:03:56,156 Installing build dependencies: started 2023-03-11T18:03:56,157 Running command pip subprocess to install build dependencies 2023-03-11T18:03:57,355 Using pip 23.0.1 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2023-03-11T18:03:57,919 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 2023-03-11T18:03:57,946 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-03-11T18:03:59,642 Collecting setuptools 2023-03-11T18:03:59,784 Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.6.0-py3-none-any.whl (1.1 MB) 2023-03-11T18:04:00,046 Collecting wheel 2023-03-11T18:04:00,064 Using cached https://www.piwheels.org/simple/wheel/wheel-0.38.4-py3-none-any.whl (36 kB) 2023-03-11T18:04:00,608 Collecting oldest-supported-numpy>=2022.8.16 2023-03-11T18:04:00,654 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2022.11.19-py3-none-any.whl (4.9 kB) 2023-03-11T18:04:01,982 Collecting Cython>=0.29.21 2023-03-11T18:04:02,462 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.33-cp39-cp39-linux_armv7l.whl (5.0 MB) 2023-03-11T18:04:04,087 Collecting numpy==1.19.3 2023-03-11T18:04:05,130 Using cached https://www.piwheels.org/simple/numpy/numpy-1.19.3-cp39-cp39-linux_armv7l.whl (10.5 MB) 2023-03-11T18:04:07,395 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2023-03-11T18:04:07,544 Creating /tmp/pip-build-env-gofyxwru/overlay/bin 2023-03-11T18:04:07,546 changing mode of /tmp/pip-build-env-gofyxwru/overlay/bin/wheel to 755 2023-03-11T18:04:16,540 changing mode of /tmp/pip-build-env-gofyxwru/overlay/bin/f2py to 755 2023-03-11T18:04:16,542 changing mode of /tmp/pip-build-env-gofyxwru/overlay/bin/f2py3 to 755 2023-03-11T18:04:16,545 changing mode of /tmp/pip-build-env-gofyxwru/overlay/bin/f2py3.9 to 755 2023-03-11T18:04:19,385 changing mode of /tmp/pip-build-env-gofyxwru/overlay/bin/cygdb to 755 2023-03-11T18:04:19,387 changing mode of /tmp/pip-build-env-gofyxwru/overlay/bin/cython to 755 2023-03-11T18:04:19,390 changing mode of /tmp/pip-build-env-gofyxwru/overlay/bin/cythonize to 755 2023-03-11T18:04:19,448 Successfully installed Cython-0.29.33 numpy-1.19.3 oldest-supported-numpy-2022.11.19 setuptools-67.6.0 wheel-0.38.4 2023-03-11T18:04:20,059 Installing build dependencies: finished with status 'done' 2023-03-11T18:04:20,064 Getting requirements to build wheel: started 2023-03-11T18:04:20,065 Running command Getting requirements to build wheel 2023-03-11T18:04:25,584 Compiling src/pgenlib/pgenlib.pyx because it depends on /tmp/pip-build-env-gofyxwru/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-11T18:04:25,585 [1/1] Cythonizing src/pgenlib/pgenlib.pyx 2023-03-11T18:04:25,664 running egg_info 2023-03-11T18:04:25,673 writing src/Pgenlib.egg-info/PKG-INFO 2023-03-11T18:04:25,675 writing dependency_links to src/Pgenlib.egg-info/dependency_links.txt 2023-03-11T18:04:25,677 writing top-level names to src/Pgenlib.egg-info/top_level.txt 2023-03-11T18:04:25,698 reading manifest file 'src/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:04:25,701 reading manifest template 'MANIFEST.in' 2023-03-11T18:04:25,703 adding license file 'LICENSE' 2023-03-11T18:04:25,706 writing manifest file 'src/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:04:26,011 Getting requirements to build wheel: finished with status 'done' 2023-03-11T18:04:26,022 Created temporary directory: /tmp/pip-modern-metadata-mnay3qqd 2023-03-11T18:04:26,025 Preparing metadata (pyproject.toml): started 2023-03-11T18:04:26,026 Running command Preparing metadata (pyproject.toml) 2023-03-11T18:04:27,563 running dist_info 2023-03-11T18:04:27,587 creating /tmp/pip-modern-metadata-mnay3qqd/Pgenlib.egg-info 2023-03-11T18:04:27,593 writing /tmp/pip-modern-metadata-mnay3qqd/Pgenlib.egg-info/PKG-INFO 2023-03-11T18:04:27,595 writing dependency_links to /tmp/pip-modern-metadata-mnay3qqd/Pgenlib.egg-info/dependency_links.txt 2023-03-11T18:04:27,598 writing top-level names to /tmp/pip-modern-metadata-mnay3qqd/Pgenlib.egg-info/top_level.txt 2023-03-11T18:04:27,599 writing manifest file '/tmp/pip-modern-metadata-mnay3qqd/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:04:27,616 reading manifest file '/tmp/pip-modern-metadata-mnay3qqd/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:04:27,618 reading manifest template 'MANIFEST.in' 2023-03-11T18:04:27,621 adding license file 'LICENSE' 2023-03-11T18:04:27,623 writing manifest file '/tmp/pip-modern-metadata-mnay3qqd/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:04:27,624 creating '/tmp/pip-modern-metadata-mnay3qqd/Pgenlib-0.82.0.dist-info' 2023-03-11T18:04:27,949 Preparing metadata (pyproject.toml): finished with status 'done' 2023-03-11T18:04:27,956 Source in /tmp/pip-wheel-0zsf2z_3/pgenlib_90b7f3fa619c4dacaeacd49eb69ba7c2 has version 0.82.0, which satisfies requirement pgenlib==0.82.0 from https://files.pythonhosted.org/packages/29/d3/311512e956d1bc898cd6020e15691e2778e1bf3a1c2e01eadbb6031d8bd5/Pgenlib-0.82.0.tar.gz 2023-03-11T18:04:27,957 Removed pgenlib==0.82.0 from https://files.pythonhosted.org/packages/29/d3/311512e956d1bc898cd6020e15691e2778e1bf3a1c2e01eadbb6031d8bd5/Pgenlib-0.82.0.tar.gz from build tracker '/tmp/pip-build-tracker-gyo9l7ay' 2023-03-11T18:04:27,963 Created temporary directory: /tmp/pip-unpack-at2eok44 2023-03-11T18:04:27,964 Building wheels for collected packages: pgenlib 2023-03-11T18:04:27,969 Created temporary directory: /tmp/pip-wheel-agyuzk8_ 2023-03-11T18:04:27,969 Destination directory: /tmp/pip-wheel-agyuzk8_ 2023-03-11T18:04:27,973 Building wheel for pgenlib (pyproject.toml): started 2023-03-11T18:04:27,974 Running command Building wheel for pgenlib (pyproject.toml) 2023-03-11T18:04:29,545 running bdist_wheel 2023-03-11T18:04:29,569 running build 2023-03-11T18:04:29,569 running build_ext 2023-03-11T18:04:29,576 building 'pgenlib' extension 2023-03-11T18:04:29,577 creating build 2023-03-11T18:04:29,577 creating build/temp.linux-armv7l-cpython-39 2023-03-11T18:04:29,578 creating build/temp.linux-armv7l-cpython-39/src 2023-03-11T18:04:29,579 creating build/temp.linux-armv7l-cpython-39/src/pgenlib 2023-03-11T18:04:29,580 creating build/temp.linux-armv7l-cpython-39/src/plink2 2023-03-11T18:04:29,581 creating build/temp.linux-armv7l-cpython-39/src/plink2/include 2023-03-11T18:04:29,582 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-gofyxwru/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 2023-03-11T18:04:30,193 In file included from /tmp/pip-build-env-gofyxwru/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2023-03-11T18:04:30,193 from /tmp/pip-build-env-gofyxwru/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-11T18:04:30,193 from /tmp/pip-build-env-gofyxwru/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-11T18:04:30,193 from src/pgenlib/pgenlib.cpp:799: 2023-03-11T18:04:30,194 /tmp/pip-build-env-gofyxwru/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] 2023-03-11T18:04:30,194 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-11T18:04:30,194 | ^~~~~~~ 2023-03-11T18:04:30,266 src/pgenlib/pgenlib.cpp:994: warning: "likely" redefined 2023-03-11T18:04:30,266 994 | #define likely(x) __builtin_expect(!!(x), 1) 2023-03-11T18:04:30,266 | 2023-03-11T18:04:30,267 In file included from src/pgenlib/../plink2/include/plink2_bits.h:23, 2023-03-11T18:04:30,267 from src/pgenlib/../plink2/include/pgenlib_misc.h:77, 2023-03-11T18:04:30,267 from src/pgenlib/../plink2/pgenlib_ffi_support.h:20, 2023-03-11T18:04:30,268 from src/pgenlib/pgenlib.cpp:804: 2023-03-11T18:04:30,268 src/pgenlib/../plink2/include/plink2_base.h:252: note: this is the location of the previous definition 2023-03-11T18:04:30,268 252 | # define likely(expr) __builtin_expect(!!(expr), 1) 2023-03-11T18:04:30,268 | 2023-03-11T18:04:30,268 src/pgenlib/pgenlib.cpp:995: warning: "unlikely" redefined 2023-03-11T18:04:30,268 995 | #define unlikely(x) __builtin_expect(!!(x), 0) 2023-03-11T18:04:30,269 | 2023-03-11T18:04:30,269 In file included from src/pgenlib/../plink2/include/plink2_bits.h:23, 2023-03-11T18:04:30,269 from src/pgenlib/../plink2/include/pgenlib_misc.h:77, 2023-03-11T18:04:30,269 from src/pgenlib/../plink2/pgenlib_ffi_support.h:20, 2023-03-11T18:04:30,269 from src/pgenlib/pgenlib.cpp:804: 2023-03-11T18:04:30,269 src/pgenlib/../plink2/include/plink2_base.h:253: note: this is the location of the previous definition 2023-03-11T18:04:30,269 253 | # define unlikely(expr) __builtin_expect(!!(expr), 0) 2023-03-11T18:04:30,270 | 2023-03-11T18:04:31,807 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*)’: 2023-03-11T18:04:31,807 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] 2023-03-11T18:04:31,807 5347 | __pyx_t_9 = (((__pyx_v_geno_int_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:31,807 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,834 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*)’: 2023-03-11T18:04:31,835 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] 2023-03-11T18:04:31,835 6001 | __pyx_t_9 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:31,835 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,860 src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles(__pyx_obj_7pgenlib_PgenReader*, uint32_t, PyArrayObject*, int)’: 2023-03-11T18:04:31,861 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] 2023-03-11T18:04:31,861 6561 | __pyx_t_8 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:31,861 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,884 src/pgenlib/pgenlib.cpp: In function ‘PyObject* __pyx_f_7pgenlib_10PgenReader_read_alleles_and_phasepresent(__pyx_obj_7pgenlib_PgenReader*, uint32_t, PyArrayObject*, PyArrayObject*, int)’: 2023-03-11T18:04:31,884 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] 2023-03-11T18:04:31,884 7057 | __pyx_t_8 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:04:31,885 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,887 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] 2023-03-11T18:04:31,887 7113 | __pyx_t_8 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:31,887 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,909 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*)’: 2023-03-11T18:04:31,909 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] 2023-03-11T18:04:31,910 7603 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:31,910 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,912 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] 2023-03-11T18:04:31,913 7659 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:31,913 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,920 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] 2023-03-11T18:04:31,920 7884 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:31,921 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,923 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] 2023-03-11T18:04:31,923 7940 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:31,924 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,937 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*)’: 2023-03-11T18:04:31,937 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] 2023-03-11T18:04:31,937 8539 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:31,937 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,940 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] 2023-03-11T18:04:31,940 8595 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:31,940 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,948 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] 2023-03-11T18:04:31,948 8820 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:31,948 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,951 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] 2023-03-11T18:04:31,951 8876 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:31,951 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,964 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*)’: 2023-03-11T18:04:31,964 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] 2023-03-11T18:04:31,965 9475 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:31,965 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,967 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] 2023-03-11T18:04:31,967 9531 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:31,967 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,975 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] 2023-03-11T18:04:31,975 9756 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:31,976 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:31,978 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] 2023-03-11T18:04:31,978 9812 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:31,979 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,018 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*)’: 2023-03-11T18:04:32,019 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] 2023-03-11T18:04:32,019 10964 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,019 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,021 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] 2023-03-11T18:04:32,022 11020 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:32,022 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,030 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] 2023-03-11T18:04:32,031 11261 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:32,031 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,033 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] 2023-03-11T18:04:32,033 11317 | __pyx_t_5 = (((__pyx_v_geno_int8_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,034 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,051 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*)’: 2023-03-11T18:04:32,052 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] 2023-03-11T18:04:32,052 12012 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,052 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,054 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] 2023-03-11T18:04:32,055 12068 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:32,055 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,063 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] 2023-03-11T18:04:32,063 12309 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:32,064 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,066 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] 2023-03-11T18:04:32,066 12365 | __pyx_t_5 = (((__pyx_v_geno_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,066 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,084 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*)’: 2023-03-11T18:04:32,084 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] 2023-03-11T18:04:32,085 13060 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,085 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,087 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] 2023-03-11T18:04:32,087 13116 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:32,087 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,096 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] 2023-03-11T18:04:32,096 13357 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[0]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:32,096 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,099 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] 2023-03-11T18:04:32,099 13413 | __pyx_t_5 = (((__pyx_v_geno_int64_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,099 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,149 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*)’: 2023-03-11T18:04:32,149 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] 2023-03-11T18:04:32,150 14757 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,150 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,152 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] 2023-03-11T18:04:32,152 14813 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:04:32,153 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,162 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] 2023-03-11T18:04:32,162 15050 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:04:32,162 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,165 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] 2023-03-11T18:04:32,165 15106 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,165 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,204 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*)’: 2023-03-11T18:04:32,204 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] 2023-03-11T18:04:32,204 16165 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,204 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,207 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] 2023-03-11T18:04:32,207 16221 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:04:32,207 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,215 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] 2023-03-11T18:04:32,216 16462 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:04:32,216 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,219 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] 2023-03-11T18:04:32,219 16518 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,219 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,257 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*)’: 2023-03-11T18:04:32,257 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] 2023-03-11T18:04:32,257 17655 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,257 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,260 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] 2023-03-11T18:04:32,260 17711 | __pyx_t_10 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,260 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,263 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] 2023-03-11T18:04:32,263 17767 | __pyx_t_10 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:04:32,263 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,266 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] 2023-03-11T18:04:32,266 17823 | __pyx_t_10 = (((__pyx_v_phasepresent_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:32,266 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,298 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*)’: 2023-03-11T18:04:32,298 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] 2023-03-11T18:04:32,299 18519 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,299 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,301 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] 2023-03-11T18:04:32,301 18575 | __pyx_t_12 = (((__pyx_v_phasepresent_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,302 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,304 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] 2023-03-11T18:04:32,304 18631 | __pyx_t_12 = (((__pyx_v_allele_int32_out->dimensions[1]) < (2 * __pyx_v_subset_size)) != 0); 2023-03-11T18:04:32,305 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,307 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] 2023-03-11T18:04:32,307 18687 | __pyx_t_12 = (((__pyx_v_phasepresent_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:32,308 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,373 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*)’: 2023-03-11T18:04:32,373 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] 2023-03-11T18:04:32,373 20446 | __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,373 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,376 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] 2023-03-11T18:04:32,376 20502 | __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:32,376 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,390 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*)’: 2023-03-11T18:04:32,391 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] 2023-03-11T18:04:32,391 20963 | __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[0]) < __pyx_v_variant_idx_ct) != 0); 2023-03-11T18:04:32,391 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:32,393 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] 2023-03-11T18:04:32,394 21019 | __pyx_t_6 = (((__pyx_v_floatarr_out->dimensions[1]) < __pyx_v_subset_size) != 0); 2023-03-11T18:04:32,394 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-03-11T18:04:59,050 At global scope: 2023-03-11T18:04:59,051 cc1plus: note: unrecognized command-line option ‘-Wno-macro-redefined’ may have been intended to silence earlier diagnostics 2023-03-11T18:05:01,600 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-gofyxwru/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 2023-03-11T18:05:04,759 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-gofyxwru/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 2023-03-11T18:05:18,083 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-gofyxwru/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 2023-03-11T18:05:21,312 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-gofyxwru/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 2023-03-11T18:05:21,698 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-gofyxwru/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 2023-03-11T18:05:23,467 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-gofyxwru/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 2023-03-11T18:05:24,501 creating build/lib.linux-armv7l-cpython-39 2023-03-11T18:05:24,503 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 2023-03-11T18:05:24,956 installing to build/bdist.linux-armv7l/wheel 2023-03-11T18:05:24,956 running install 2023-03-11T18:05:24,982 running install_lib 2023-03-11T18:05:25,007 creating build/bdist.linux-armv7l 2023-03-11T18:05:25,007 creating build/bdist.linux-armv7l/wheel 2023-03-11T18:05:25,009 copying build/lib.linux-armv7l-cpython-39/pgenlib.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-03-11T18:05:25,095 running install_egg_info 2023-03-11T18:05:25,125 running egg_info 2023-03-11T18:05:25,130 writing src/Pgenlib.egg-info/PKG-INFO 2023-03-11T18:05:25,132 writing dependency_links to src/Pgenlib.egg-info/dependency_links.txt 2023-03-11T18:05:25,141 writing top-level names to src/Pgenlib.egg-info/top_level.txt 2023-03-11T18:05:25,150 reading manifest file 'src/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:05:25,153 reading manifest template 'MANIFEST.in' 2023-03-11T18:05:25,155 adding license file 'LICENSE' 2023-03-11T18:05:25,158 writing manifest file 'src/Pgenlib.egg-info/SOURCES.txt' 2023-03-11T18:05:25,159 Copying src/Pgenlib.egg-info to build/bdist.linux-armv7l/wheel/Pgenlib-0.82.0-py3.9.egg-info 2023-03-11T18:05:25,169 running install_scripts 2023-03-11T18:05:25,213 creating build/bdist.linux-armv7l/wheel/Pgenlib-0.82.0.dist-info/WHEEL 2023-03-11T18:05:25,216 creating '/tmp/pip-wheel-agyuzk8_/.tmp-ta0cdy2p/Pgenlib-0.82.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-03-11T18:05:25,885 adding 'pgenlib.cpython-39-arm-linux-gnueabihf.so' 2023-03-11T18:05:25,910 adding 'Pgenlib-0.82.0.dist-info/LICENSE' 2023-03-11T18:05:25,912 adding 'Pgenlib-0.82.0.dist-info/METADATA' 2023-03-11T18:05:25,914 adding 'Pgenlib-0.82.0.dist-info/WHEEL' 2023-03-11T18:05:25,915 adding 'Pgenlib-0.82.0.dist-info/top_level.txt' 2023-03-11T18:05:25,915 adding 'Pgenlib-0.82.0.dist-info/RECORD' 2023-03-11T18:05:25,934 removing build/bdist.linux-armv7l/wheel 2023-03-11T18:05:26,105 Building wheel for pgenlib (pyproject.toml): finished with status 'done' 2023-03-11T18:05:26,139 Created wheel for pgenlib: filename=Pgenlib-0.82.0-cp39-cp39-linux_armv7l.whl size=1244517 sha256=b38d7233c5515f730969499da3b95e95f64109573755cdda562026109c999c33 2023-03-11T18:05:26,140 Stored in directory: /tmp/pip-ephem-wheel-cache-8co5ocon/wheels/6b/0f/12/acd930df1edac449679d909311cca520eced482b402fcdb56e 2023-03-11T18:05:26,153 Successfully built pgenlib 2023-03-11T18:05:26,212 Removed build tracker: '/tmp/pip-build-tracker-gyo9l7ay'