2023-02-25T00:50:48,857 Created temporary directory: /tmp/pip-ephem-wheel-cache-1f29jve0 2023-02-25T00:50:48,859 Created temporary directory: /tmp/pip-build-tracker-qdntjo3p 2023-02-25T00:50:48,860 Initialized build tracking at /tmp/pip-build-tracker-qdntjo3p 2023-02-25T00:50:48,860 Created build tracker: /tmp/pip-build-tracker-qdntjo3p 2023-02-25T00:50:48,860 Entered build tracker: /tmp/pip-build-tracker-qdntjo3p 2023-02-25T00:50:48,861 Created temporary directory: /tmp/pip-wheel-9pzewj87 2023-02-25T00:50:48,865 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 2023-02-25T00:50:48,868 Created temporary directory: /tmp/pip-ephem-wheel-cache-7br6_c8d 2023-02-25T00:50:48,898 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-02-25T00:50:48,901 2 location(s) to search for versions of diploshic: 2023-02-25T00:50:48,901 * https://pypi.org/simple/diploshic/ 2023-02-25T00:50:48,901 * https://www.piwheels.org/simple/diploshic/ 2023-02-25T00:50:48,901 Fetching project page and analyzing links: https://pypi.org/simple/diploshic/ 2023-02-25T00:50:48,902 Getting page https://pypi.org/simple/diploshic/ 2023-02-25T00:50:48,903 Found index url https://pypi.org/simple 2023-02-25T00:50:48,966 Fetched page https://pypi.org/simple/diploshic/ as application/vnd.pypi.simple.v1+json 2023-02-25T00:50:48,972 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/02/99/1ff0abc6647a2c9dd2e4a3f9053540f9732b6dcf4047263d91a0df96c5f1/diploSHIC-0.4-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,972 Found link https://files.pythonhosted.org/packages/a6/c2/86153839edc17cf57860b6fb6a15595a430050a4a13be6bd00fb6c5295b7/diploSHIC-0.4.tar.gz (from https://pypi.org/simple/diploshic/), version: 0.4 2023-02-25T00:50:48,973 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/00/9c/d2e25202b955aac1aaac20efed3e63b052610e6ec0a13996405a0e03c67b/diploSHIC-0.333333-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,973 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/4d/46/2fbbe2d5986a5a252f3ac3ab9514762c6bc72a5cc043ed9b55f3137efccb/diploSHIC-0.333333-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,973 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/3f/e6/bad94b60dee10f010ec5d2482cd0cebdc36ce0cbdf7c2bde16eb552c34a5/diploSHIC-0.333333-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,973 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/22/49/714f6bb8b2649a57e9c90671113ae16afd5053f11ba4fef1ec1774202a11/diploSHIC-0.333333-cp310-cp310-musllinux_1_1_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,974 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/4f/de/c257892410d2cf05830ab52a583c0881bffa00f9ec4a5d092adf177348e9/diploSHIC-0.333333-cp310-cp310-musllinux_1_1_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,974 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/ed/90/5a5f381e5b65d6a6225d67205b1692f1adc9c352ca863736288860193854/diploSHIC-0.333333-cp36-cp36m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,974 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/ad/4d/17b0e2b2816ea5dad9a9ecb9b8783659c83be49bbcc173abc9f8ead305f2/diploSHIC-0.333333-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,974 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/d0/3c/d5fbade30fcd59017060d0283eaf724110bea2509f1b82a417a3d05684fd/diploSHIC-0.333333-cp36-cp36m-musllinux_1_1_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,974 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/9b/b2/d709fcbc6de2496ed3adc2c9f4b89124f410320eddda051cec9fbc3d5fad/diploSHIC-0.333333-cp36-cp36m-musllinux_1_1_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,975 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/76/0c/fe78832d33a86ed083e4054d8324174faa1856abce56f2d17199546c14a2/diploSHIC-0.333333-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,975 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/b0/bc/5b5928c3ce52b1350ef4188ceb58ac8086b275b7757a2490cf56dda59574/diploSHIC-0.333333-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,975 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/e3/63/399c9dcabbeb1d2d3114514bb3f71ea02c80602dc873bbc0a577aff30307/diploSHIC-0.333333-cp37-cp37m-musllinux_1_1_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,975 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/b1/a3/5b06a0194db6925c5facd450b6ead8e72a7ede6741b486f1268fa58abcc6/diploSHIC-0.333333-cp37-cp37m-musllinux_1_1_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,975 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/8b/42/5827ed208dd4a5bb376b8d8c2e6df3d7da4acb543893aa69c6a5cc2375fa/diploSHIC-0.333333-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,976 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/73/42/4d3b4eb60f67061115b19bb3373d6112c0dade3db6de3787bacf94576671/diploSHIC-0.333333-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,976 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/a1/f4/91e24beb41be5627e12a176c1b287caeb5d9429db0628071b0a2ff3fb220/diploSHIC-0.333333-cp38-cp38-musllinux_1_1_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,976 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/1f/13/f67bfe37155e29847297863b33237c7fa89186f8a6bbc67ec9f10885518d/diploSHIC-0.333333-cp38-cp38-musllinux_1_1_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,976 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/89/64/9c469c81953743e785914f4605feb70686ba4bf75f1f36f3be3ffa8cd666/diploSHIC-0.333333-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,976 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/48/bd/6ed9e4cc32178654817ca4fcb19e0808907bc5d424e4f9c985174e5ddc42/diploSHIC-0.333333-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,977 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/50/2d/91f6211d84bbd43ffe389d29bd1d92233a57580b4d6aaa9a457a30393e7c/diploSHIC-0.333333-cp39-cp39-musllinux_1_1_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,977 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/1f/e6/a7ce12139a20b5add882aa95b53a37713f7ef7a2a9b6bd2139a11f4c57eb/diploSHIC-0.333333-cp39-cp39-musllinux_1_1_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,977 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/0c/e9/f3c6ee5bc91624a7dff45477d9b3623cb8505d4d968cddcfb878f68c05e2/diploSHIC-0.333333-pp37-pypy37_pp73-manylinux_2_5_i686.manylinux1_i686.manylinux_2_12_i686.manylinux2010_i686.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,977 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/2c/00/fd70e2ae945f6bbdd3611e520cda448edbd7bcce6e7fb16344926a9bcd7c/diploSHIC-0.333333-pp37-pypy37_pp73-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T00:50:48,977 Found link https://files.pythonhosted.org/packages/8e/79/bc66897efa74f1283c4830fe5531de3c5cd3cf92457ee7b67ce3bf1325f5/diploSHIC-0.333333.tar.gz (from https://pypi.org/simple/diploshic/), version: 0.333333 2023-02-25T00:50:48,978 Fetching project page and analyzing links: https://www.piwheels.org/simple/diploshic/ 2023-02-25T00:50:48,978 Getting page https://www.piwheels.org/simple/diploshic/ 2023-02-25T00:50:48,979 Found index url https://www.piwheels.org/simple 2023-02-25T00:50:50,234 Fetched page https://www.piwheels.org/simple/diploshic/ as text/html 2023-02-25T00:50:50,242 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-0.333333-cp39-cp39-linux_armv7l.whl#sha256=7ca555d0e535d90dd61472ba10efbff673caf0eb8edaa0deb8a1a99ba67315b9 (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T00:50:50,242 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-0.333333-cp39-cp39-linux_armv6l.whl#sha256=7ca555d0e535d90dd61472ba10efbff673caf0eb8edaa0deb8a1a99ba67315b9 (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T00:50:50,243 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-0.333333-cp37-cp37m-linux_armv7l.whl#sha256=61a44d79f6f61847d45ce52e3b5dd47b3a9d2e9f0c8c8db908cca251fd409bbc (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T00:50:50,244 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-0.333333-cp37-cp37m-linux_armv6l.whl#sha256=61a44d79f6f61847d45ce52e3b5dd47b3a9d2e9f0c8c8db908cca251fd409bbc (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T00:50:50,244 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-0.333333-cp35-cp35m-linux_armv7l.whl#sha256=17d5686c935f1e6e5d1c9b3c5f658748662db2885d092c82bcbb80a6cc771733 (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T00:50:50,244 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-0.333333-cp35-cp35m-linux_armv6l.whl#sha256=17d5686c935f1e6e5d1c9b3c5f658748662db2885d092c82bcbb80a6cc771733 (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T00:50:50,245 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-0.4-cp37-cp37m-linux_armv7l.whl#sha256=c2eb642811ff1aeb2fe51be63c9916b27ca7b31041dd5719fe9720ffbd60a197 (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T00:50:50,245 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-0.4-cp37-cp37m-linux_armv6l.whl#sha256=c2eb642811ff1aeb2fe51be63c9916b27ca7b31041dd5719fe9720ffbd60a197 (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T00:50:50,246 Skipping link: not a file: https://www.piwheels.org/simple/diploshic/ 2023-02-25T00:50:50,246 Skipping link: not a file: https://pypi.org/simple/diploshic/ 2023-02-25T00:50:50,290 Given no hashes to check 1 links for project 'diploshic': discarding no candidates 2023-02-25T00:50:50,320 Collecting diploshic==0.4 2023-02-25T00:50:50,322 Created temporary directory: /tmp/pip-unpack-01sxn_9m 2023-02-25T00:50:50,383 Downloading diploSHIC-0.4.tar.gz (13.9 MB) 2023-02-25T00:50:53,278 Added diploshic==0.4 from https://files.pythonhosted.org/packages/a6/c2/86153839edc17cf57860b6fb6a15595a430050a4a13be6bd00fb6c5295b7/diploSHIC-0.4.tar.gz to build tracker '/tmp/pip-build-tracker-qdntjo3p' 2023-02-25T00:50:53,282 Created temporary directory: /tmp/pip-build-env-9wneljz9 2023-02-25T00:50:53,292 Installing build dependencies: started 2023-02-25T00:50:53,293 Running command pip subprocess to install build dependencies 2023-02-25T00:50:54,516 Using pip 23.0.1 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2023-02-25T00:50:55,090 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 2023-02-25T00:50:55,117 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-02-25T00:50:57,744 Collecting setuptools 2023-02-25T00:51:01,769 Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.4.0-py3-none-any.whl (1.1 MB) 2023-02-25T00:51:03,010 Collecting numpy 2023-02-25T00:51:04,172 Using cached https://www.piwheels.org/simple/numpy/numpy-1.24.2-cp39-cp39-linux_armv7l.whl (12.3 MB) 2023-02-25T00:51:06,363 Installing collected packages: setuptools, numpy 2023-02-25T00:51:17,294 Creating /tmp/pip-build-env-9wneljz9/overlay/bin 2023-02-25T00:51:17,296 changing mode of /tmp/pip-build-env-9wneljz9/overlay/bin/f2py to 755 2023-02-25T00:51:17,298 changing mode of /tmp/pip-build-env-9wneljz9/overlay/bin/f2py3 to 755 2023-02-25T00:51:17,300 changing mode of /tmp/pip-build-env-9wneljz9/overlay/bin/f2py3.9 to 755 2023-02-25T00:51:17,335 Successfully installed numpy-1.24.2 setuptools-67.4.0 2023-02-25T00:51:17,866 Installing build dependencies: finished with status 'done' 2023-02-25T00:51:17,872 Getting requirements to build wheel: started 2023-02-25T00:51:17,873 Running command Getting requirements to build wheel 2023-02-25T00:51:18,698 :2: DeprecationWarning: 2023-02-25T00:51:18,699 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-02-25T00:51:18,699 of the deprecation of `distutils` itself. It will be removed for 2023-02-25T00:51:18,699 Python >= 3.12. For older Python versions it will remain present. 2023-02-25T00:51:18,699 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-02-25T00:51:18,700 For more details, see: 2023-02-25T00:51:18,700 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-02-25T00:51:19,516 running egg_info 2023-02-25T00:51:19,517 running build_src 2023-02-25T00:51:19,552 INFO: build_src 2023-02-25T00:51:19,552 INFO: building extension "diploshic.shicstats" sources 2023-02-25T00:51:19,554 creating build 2023-02-25T00:51:19,555 creating build/src.linux-armv7l-3.9 2023-02-25T00:51:19,556 creating build/src.linux-armv7l-3.9/diploshic 2023-02-25T00:51:19,557 INFO: f2py options: [] 2023-02-25T00:51:19,557 INFO: f2py: diploshic/shicstats.pyf 2023-02-25T00:51:19,972 Reading fortran codes... 2023-02-25T00:51:19,972 Reading file 'diploshic/shicstats.pyf' (format:free) 2023-02-25T00:51:19,973 Line #6 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T00:51:19,973 All arguments will have attribute intent(c) 2023-02-25T00:51:19,973 Line #14 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T00:51:19,973 All arguments will have attribute intent(c) 2023-02-25T00:51:19,973 Line #21 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T00:51:19,973 All arguments will have attribute intent(c) 2023-02-25T00:51:19,973 Line #28 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T00:51:19,973 All arguments will have attribute intent(c) 2023-02-25T00:51:19,974 Line #36 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T00:51:19,974 All arguments will have attribute intent(c) 2023-02-25T00:51:19,974 Line #44 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T00:51:19,974 All arguments will have attribute intent(c) 2023-02-25T00:51:19,974 crackline: groupcounter=1 groupname={0: '', 1: 'python module', 2: 'interface', 3: 'subroutine'} 2023-02-25T00:51:19,974 crackline: Mismatch of blocks encountered. Trying to fix it by assuming "end" statement. 2023-02-25T00:51:19,974 Post-processing... 2023-02-25T00:51:19,975 Block: shicstats 2023-02-25T00:51:19,975 Block: computeR2Matrix 2023-02-25T00:51:19,975 Block: omega 2023-02-25T00:51:19,975 Block: ZnS 2023-02-25T00:51:19,975 Block: pairwiseDiffs 2023-02-25T00:51:19,975 Block: pairwiseDiffsDiplo 2023-02-25T00:51:19,975 Block: getHaplotypeFreqSpec 2023-02-25T00:51:19,975 Applying post-processing hooks... 2023-02-25T00:51:19,976 character_backward_compatibility_hook 2023-02-25T00:51:19,976 Post-processing (stage 2)... 2023-02-25T00:51:19,976 Building modules... 2023-02-25T00:51:19,976 Building module "shicstats"... 2023-02-25T00:51:19,976 Generating possibly empty wrappers" 2023-02-25T00:51:19,976 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T00:51:19,977 Constructing wrapper function "computeR2Matrix"... 2023-02-25T00:51:19,978 r2Matrix = computeR2Matrix(haps) 2023-02-25T00:51:19,978 Generating possibly empty wrappers" 2023-02-25T00:51:19,978 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T00:51:19,978 Constructing wrapper function "omega"... 2023-02-25T00:51:19,978 omegaMax = omega(r2Matrix) 2023-02-25T00:51:19,978 Generating possibly empty wrappers" 2023-02-25T00:51:19,979 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T00:51:19,979 Constructing wrapper function "ZnS"... 2023-02-25T00:51:19,979 zns = ZnS(r2Matrix) 2023-02-25T00:51:19,979 Generating possibly empty wrappers" 2023-02-25T00:51:19,979 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T00:51:19,979 Constructing wrapper function "pairwiseDiffs"... 2023-02-25T00:51:19,979 diffLs = pairwiseDiffs(haps) 2023-02-25T00:51:19,979 Generating possibly empty wrappers" 2023-02-25T00:51:19,980 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T00:51:19,980 Constructing wrapper function "pairwiseDiffsDiplo"... 2023-02-25T00:51:19,980 diffLs = pairwiseDiffsDiplo(haps) 2023-02-25T00:51:19,980 Generating possibly empty wrappers" 2023-02-25T00:51:19,981 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T00:51:19,981 Constructing wrapper function "getHaplotypeFreqSpec"... 2023-02-25T00:51:19,981 hapCounts = getHaplotypeFreqSpec(haps) 2023-02-25T00:51:19,981 Wrote C/API module "shicstats" to file "build/src.linux-armv7l-3.9/diploshic/shicstatsmodule.c" 2023-02-25T00:51:19,981 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c' to sources. 2023-02-25T00:51:19,981 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic' to include_dirs. 2023-02-25T00:51:19,981 creating build/src.linux-armv7l-3.9/build 2023-02-25T00:51:19,981 creating build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9 2023-02-25T00:51:19,982 creating build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-02-25T00:51:19,982 copying /tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-02-25T00:51:19,982 copying /tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-02-25T00:51:19,982 INFO: adding 'build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f' to sources. 2023-02-25T00:51:19,982 INFO: build_src: building npy-pkg config files 2023-02-25T00:51:19,982 /tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. 2023-02-25T00:51:19,983 warnings.warn( 2023-02-25T00:51:20,009 writing diploSHIC.egg-info/PKG-INFO 2023-02-25T00:51:20,012 writing dependency_links to diploSHIC.egg-info/dependency_links.txt 2023-02-25T00:51:20,015 writing requirements to diploSHIC.egg-info/requires.txt 2023-02-25T00:51:20,016 writing top-level names to diploSHIC.egg-info/top_level.txt 2023-02-25T00:51:20,024 /tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py:661: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-02-25T00:51:20,025 Please extend command classes from setuptools instead of distutils. 2023-02-25T00:51:20,025 warnings.warn( 2023-02-25T00:51:20,027 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-02-25T00:51:20,027 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-02-25T00:51:20,031 reading manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-02-25T00:51:20,035 reading manifest template 'MANIFEST.in' 2023-02-25T00:51:20,037 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-02-25T00:51:20,039 adding license file 'LICENSE' 2023-02-25T00:51:20,042 writing manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-02-25T00:51:20,182 Getting requirements to build wheel: finished with status 'done' 2023-02-25T00:51:20,195 Installing backend dependencies: started 2023-02-25T00:51:20,196 Running command pip subprocess to install backend dependencies 2023-02-25T00:51:21,416 Using pip 23.0.1 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2023-02-25T00:51:21,992 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 2023-02-25T00:51:22,019 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-02-25T00:51:22,527 Collecting wheel 2023-02-25T00:51:22,553 Using cached https://www.piwheels.org/simple/wheel/wheel-0.38.4-py3-none-any.whl (36 kB) 2023-02-25T00:51:24,019 Installing collected packages: wheel 2023-02-25T00:51:24,169 Creating /tmp/pip-build-env-9wneljz9/normal/bin 2023-02-25T00:51:24,172 changing mode of /tmp/pip-build-env-9wneljz9/normal/bin/wheel to 755 2023-02-25T00:51:24,185 Successfully installed wheel-0.38.4 2023-02-25T00:51:24,611 Installing backend dependencies: finished with status 'done' 2023-02-25T00:51:24,613 Created temporary directory: /tmp/pip-modern-metadata-07b_si3z 2023-02-25T00:51:24,616 Preparing metadata (pyproject.toml): started 2023-02-25T00:51:24,618 Running command Preparing metadata (pyproject.toml) 2023-02-25T00:51:25,387 :2: DeprecationWarning: 2023-02-25T00:51:25,388 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-02-25T00:51:25,388 of the deprecation of `distutils` itself. It will be removed for 2023-02-25T00:51:25,389 Python >= 3.12. For older Python versions it will remain present. 2023-02-25T00:51:25,389 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-02-25T00:51:25,389 For more details, see: 2023-02-25T00:51:25,389 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-02-25T00:51:25,744 running dist_info 2023-02-25T00:51:25,746 running build_src 2023-02-25T00:51:25,747 INFO: build_src 2023-02-25T00:51:25,747 INFO: building extension "diploshic.shicstats" sources 2023-02-25T00:51:25,748 INFO: f2py options: [] 2023-02-25T00:51:25,748 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c' to sources. 2023-02-25T00:51:25,748 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic' to include_dirs. 2023-02-25T00:51:25,856 INFO: adding 'build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f' to sources. 2023-02-25T00:51:25,857 INFO: build_src: building npy-pkg config files 2023-02-25T00:51:25,857 /tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. 2023-02-25T00:51:25,858 warnings.warn( 2023-02-25T00:51:25,880 creating /tmp/pip-modern-metadata-07b_si3z/diploSHIC.egg-info 2023-02-25T00:51:25,886 writing /tmp/pip-modern-metadata-07b_si3z/diploSHIC.egg-info/PKG-INFO 2023-02-25T00:51:25,889 writing dependency_links to /tmp/pip-modern-metadata-07b_si3z/diploSHIC.egg-info/dependency_links.txt 2023-02-25T00:51:25,892 writing requirements to /tmp/pip-modern-metadata-07b_si3z/diploSHIC.egg-info/requires.txt 2023-02-25T00:51:25,893 writing top-level names to /tmp/pip-modern-metadata-07b_si3z/diploSHIC.egg-info/top_level.txt 2023-02-25T00:51:25,894 writing manifest file '/tmp/pip-modern-metadata-07b_si3z/diploSHIC.egg-info/SOURCES.txt' 2023-02-25T00:51:25,899 /tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py:661: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-02-25T00:51:25,899 Please extend command classes from setuptools instead of distutils. 2023-02-25T00:51:25,900 warnings.warn( 2023-02-25T00:51:25,901 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-02-25T00:51:25,902 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-02-25T00:51:25,906 reading manifest file '/tmp/pip-modern-metadata-07b_si3z/diploSHIC.egg-info/SOURCES.txt' 2023-02-25T00:51:25,908 reading manifest template 'MANIFEST.in' 2023-02-25T00:51:25,909 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-02-25T00:51:25,911 adding license file 'LICENSE' 2023-02-25T00:51:25,914 writing manifest file '/tmp/pip-modern-metadata-07b_si3z/diploSHIC.egg-info/SOURCES.txt' 2023-02-25T00:51:25,914 creating '/tmp/pip-modern-metadata-07b_si3z/diploSHIC-0.4.dist-info' 2023-02-25T00:51:26,128 Preparing metadata (pyproject.toml): finished with status 'done' 2023-02-25T00:51:26,136 Source in /tmp/pip-wheel-9pzewj87/diploshic_91a50803a5d646ceb1be38d9f6eb6c5a has version 0.4, which satisfies requirement diploshic==0.4 from https://files.pythonhosted.org/packages/a6/c2/86153839edc17cf57860b6fb6a15595a430050a4a13be6bd00fb6c5295b7/diploSHIC-0.4.tar.gz 2023-02-25T00:51:26,137 Removed diploshic==0.4 from https://files.pythonhosted.org/packages/a6/c2/86153839edc17cf57860b6fb6a15595a430050a4a13be6bd00fb6c5295b7/diploSHIC-0.4.tar.gz from build tracker '/tmp/pip-build-tracker-qdntjo3p' 2023-02-25T00:51:26,142 Created temporary directory: /tmp/pip-unpack-lpk7jidl 2023-02-25T00:51:26,143 Building wheels for collected packages: diploshic 2023-02-25T00:51:26,147 Created temporary directory: /tmp/pip-wheel-be3q29h1 2023-02-25T00:51:26,147 Destination directory: /tmp/pip-wheel-be3q29h1 2023-02-25T00:51:26,150 Building wheel for diploshic (pyproject.toml): started 2023-02-25T00:51:26,151 Running command Building wheel for diploshic (pyproject.toml) 2023-02-25T00:51:26,863 :2: DeprecationWarning: 2023-02-25T00:51:26,863 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-02-25T00:51:26,864 of the deprecation of `distutils` itself. It will be removed for 2023-02-25T00:51:26,864 Python >= 3.12. For older Python versions it will remain present. 2023-02-25T00:51:26,864 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-02-25T00:51:26,864 For more details, see: 2023-02-25T00:51:26,864 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-02-25T00:51:27,209 running bdist_wheel 2023-02-25T00:51:27,214 running build 2023-02-25T00:51:27,214 running config_cc 2023-02-25T00:51:27,215 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-02-25T00:51:27,215 running config_fc 2023-02-25T00:51:27,215 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-02-25T00:51:27,215 running build_src 2023-02-25T00:51:27,215 INFO: build_src 2023-02-25T00:51:27,215 INFO: building extension "diploshic.shicstats" sources 2023-02-25T00:51:27,216 INFO: f2py options: [] 2023-02-25T00:51:27,216 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c' to sources. 2023-02-25T00:51:27,216 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic' to include_dirs. 2023-02-25T00:51:27,318 INFO: adding 'build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f' to sources. 2023-02-25T00:51:27,319 INFO: build_src: building npy-pkg config files 2023-02-25T00:51:27,342 running build_py 2023-02-25T00:51:27,344 creating build/lib.linux-armv7l-cpython-39 2023-02-25T00:51:27,344 creating build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,345 copying diploshic/misc.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,348 copying diploshic/setup.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,350 copying diploshic/generateSimLaunchScript.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,352 copying diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,355 copying diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,357 copying diploshic/msTools.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,360 copying diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,363 copying diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,365 copying diploshic/makeTrainingSets.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,367 copying diploshic/fvTools.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,370 copying diploshic/__init__.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:27,373 running build_ext 2023-02-25T00:51:27,379 INFO: customize UnixCCompiler 2023-02-25T00:51:27,380 INFO: customize UnixCCompiler using build_ext 2023-02-25T00:51:27,522 INFO: CCompilerOpt.cc_test_cexpr[1089] : testing compiler expression defined(__ARM_ARCH_7__) || defined(__ARM_ARCH_7A__) 2023-02-25T00:51:27,524 INFO: C compiler: 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 2023-02-25T00:51:27,524 creating /tmp/tmp5um4fv5t/tmp 2023-02-25T00:51:27,524 creating /tmp/tmp5um4fv5t/tmp/tmp5um4fv5t 2023-02-25T00:51:27,525 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-02-25T00:51:27,617 WARN: CCompilerOpt.dist_test[630] : CCompilerOpt._dist_test_spawn[764] : Command (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 -I/usr/include/python3.9 -c /tmp/tmp5um4fv5t/npy_dist_test_cexpr.c -o /tmp/tmp5um4fv5t/tmp/tmp5um4fv5t/npy_dist_test_cexpr.o -MMD -MF /tmp/tmp5um4fv5t/tmp/tmp5um4fv5t/npy_dist_test_cexpr.o.d) failed with exit status 1 output -> 2023-02-25T00:51:27,618 /tmp/tmp5um4fv5t/npy_dist_test_cexpr.c:2:6: error: #error "unsupported expression" 2023-02-25T00:51:27,618 2 | #error "unsupported expression" 2023-02-25T00:51:27,618 | ^~~~~ 2023-02-25T00:51:27,625 WARN: CCompilerOpt.cc_test_cexpr[1100] : testing failed 2023-02-25T00:51:27,634 WARN: CCompilerOpt.__init__[1016] : unable to detect CPU architecture which lead to disable the optimization. check dist_info:<< 2023-02-25T00:51:27,635 ('linux-armv7l', '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') 2023-02-25T00:51:27,635 >> 2023-02-25T00:51:27,642 INFO: CCompilerOpt.cc_test_flags[1077] : testing flags (-march=native) 2023-02-25T00:51:27,642 INFO: C compiler: 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 2023-02-25T00:51:27,643 creating /tmp/tmp5um4fv5t/tmp/pip-build-env-9wneljz9 2023-02-25T00:51:27,643 creating /tmp/tmp5um4fv5t/tmp/pip-build-env-9wneljz9/overlay 2023-02-25T00:51:27,644 creating /tmp/tmp5um4fv5t/tmp/pip-build-env-9wneljz9/overlay/lib 2023-02-25T00:51:27,645 creating /tmp/tmp5um4fv5t/tmp/pip-build-env-9wneljz9/overlay/lib/python3.9 2023-02-25T00:51:27,645 creating /tmp/tmp5um4fv5t/tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages 2023-02-25T00:51:27,646 creating /tmp/tmp5um4fv5t/tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/numpy 2023-02-25T00:51:27,647 creating /tmp/tmp5um4fv5t/tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/numpy/distutils 2023-02-25T00:51:27,647 creating /tmp/tmp5um4fv5t/tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/numpy/distutils/checks 2023-02-25T00:51:27,648 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-02-25T00:51:27,648 extra options: '-march=native' 2023-02-25T00:51:27,735 INFO: CCompilerOpt.cc_test_flags[1077] : testing flags (-O3) 2023-02-25T00:51:27,735 INFO: C compiler: 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 2023-02-25T00:51:27,736 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-02-25T00:51:27,736 extra options: '-O3' 2023-02-25T00:51:27,822 INFO: CCompilerOpt.cc_test_flags[1077] : testing flags (-Werror) 2023-02-25T00:51:27,822 INFO: C compiler: 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 2023-02-25T00:51:27,823 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-02-25T00:51:27,823 extra options: '-Werror' 2023-02-25T00:51:27,911 INFO: CCompilerOpt.__init__[1786] : check requested baseline 2023-02-25T00:51:27,918 INFO: CCompilerOpt.__init__[1795] : check requested dispatch-able features 2023-02-25T00:51:27,925 INFO: CCompilerOpt.__init__[1811] : initialize targets groups 2023-02-25T00:51:27,932 INFO: CCompilerOpt.__init__[1813] : parse target group simd_test 2023-02-25T00:51:27,940 INFO: CCompilerOpt._parse_target_tokens[2024] : skip targets (ASIMD VSX2 XOP VSX4 AVX512F NEON VXE AVX512_SKX SSE42 (FMA3 AVX2) VX VSX FMA4 SSE2 VSX3 VXE2) not part of baseline or dispatch-able features 2023-02-25T00:51:27,947 INFO: CCompilerOpt.generate_dispatch_header[2357] : generate CPU dispatch header: (build/src.linux-armv7l-3.9/numpy/distutils/include/npy_cpu_dispatch_config.h) 2023-02-25T00:51:27,955 WARN: CCompilerOpt.generate_dispatch_header[2366] : dispatch header dir build/src.linux-armv7l-3.9/numpy/distutils/include does not exist, creating it 2023-02-25T00:51:28,007 INFO: get_default_fcompiler: matching types: '['arm', 'gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor', 'fujitsu']' 2023-02-25T00:51:28,007 INFO: customize ArmFlangCompiler 2023-02-25T00:51:28,010 WARN: Could not locate executable armflang 2023-02-25T00:51:28,010 INFO: customize Gnu95FCompiler 2023-02-25T00:51:28,012 INFO: Found executable /usr/bin/gfortran 2023-02-25T00:51:28,063 INFO: customize Gnu95FCompiler 2023-02-25T00:51:28,114 INFO: customize Gnu95FCompiler using build_ext 2023-02-25T00:51:28,115 INFO: building 'diploshic.shicstats' extension 2023-02-25T00:51:28,115 INFO: compiling C sources 2023-02-25T00:51:28,116 INFO: C compiler: 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 2023-02-25T00:51:28,117 creating build/temp.linux-armv7l-cpython-39/build 2023-02-25T00:51:28,117 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9 2023-02-25T00:51:28,118 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/diploshic 2023-02-25T00:51:28,119 creating build/temp.linux-armv7l-cpython-39/diploshic 2023-02-25T00:51:28,119 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/build 2023-02-25T00:51:28,120 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9 2023-02-25T00:51:28,120 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-02-25T00:51:28,121 INFO: compile options: '-Ibuild/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic -I/tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/numpy/core/include -Ibuild/src.linux-armv7l-3.9/numpy/distutils/include -I/usr/include/python3.9 -c' 2023-02-25T00:51:28,129 INFO: arm-linux-gnueabihf-gcc: build/src.linux-armv7l-3.9/diploshic/shicstatsmodule.c 2023-02-25T00:51:28,138 INFO: arm-linux-gnueabihf-gcc: diploshic/utils.c 2023-02-25T00:51:28,148 INFO: arm-linux-gnueabihf-gcc: build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c 2023-02-25T00:51:30,071 INFO: compiling Fortran sources 2023-02-25T00:51:30,071 INFO: Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops 2023-02-25T00:51:30,071 Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops 2023-02-25T00:51:30,071 Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops 2023-02-25T00:51:30,072 INFO: compile options: '-Ibuild/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic -I/tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/numpy/core/include -Ibuild/src.linux-armv7l-3.9/numpy/distutils/include -I/usr/include/python3.9 -c' 2023-02-25T00:51:30,074 INFO: gfortran:f77: build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f 2023-02-25T00:51:30,146 INFO: /usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/diploshic/shicstatsmodule.o build/temp.linux-armv7l-cpython-39/diploshic/utils.o build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.o build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.o -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib -lgfortran -o build/lib.linux-armv7l-cpython-39/diploshic/shicstats.cpython-39-arm-linux-gnueabihf.so 2023-02-25T00:51:30,305 running build_scripts 2023-02-25T00:51:30,306 creating build/scripts.linux-armv7l-3.9 2023-02-25T00:51:30,307 copying and adjusting diploshic/diploSHIC -> build/scripts.linux-armv7l-3.9 2023-02-25T00:51:30,311 copying diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/scripts.linux-armv7l-3.9 2023-02-25T00:51:30,314 copying diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/scripts.linux-armv7l-3.9 2023-02-25T00:51:30,317 copying diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/scripts.linux-armv7l-3.9 2023-02-25T00:51:30,320 copying diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/scripts.linux-armv7l-3.9 2023-02-25T00:51:30,323 copying diploshic/makeTrainingSets.py -> build/scripts.linux-armv7l-3.9 2023-02-25T00:51:30,324 changing mode of build/scripts.linux-armv7l-3.9/diploSHIC from 644 to 755 2023-02-25T00:51:30,324 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcfDiploid.py from 644 to 755 2023-02-25T00:51:30,325 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcf_ogSHIC.py from 644 to 755 2023-02-25T00:51:30,325 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMsDiploid.py from 644 to 755 2023-02-25T00:51:30,325 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMs_ogSHIC.py from 644 to 755 2023-02-25T00:51:30,326 changing mode of build/scripts.linux-armv7l-3.9/makeTrainingSets.py from 644 to 755 2023-02-25T00:51:30,334 installing to build/bdist.linux-armv7l/wheel 2023-02-25T00:51:30,335 running install 2023-02-25T00:51:30,359 running install_lib 2023-02-25T00:51:30,367 creating build/bdist.linux-armv7l 2023-02-25T00:51:30,368 creating build/bdist.linux-armv7l/wheel 2023-02-25T00:51:30,370 creating build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,371 copying build/lib.linux-armv7l-cpython-39/diploshic/misc.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,374 copying build/lib.linux-armv7l-cpython-39/diploshic/setup.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,376 copying build/lib.linux-armv7l-cpython-39/diploshic/generateSimLaunchScript.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,378 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,381 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,383 copying build/lib.linux-armv7l-cpython-39/diploshic/msTools.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,385 copying build/lib.linux-armv7l-cpython-39/diploshic/shicstats.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,391 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,393 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,396 copying build/lib.linux-armv7l-cpython-39/diploshic/makeTrainingSets.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,398 copying build/lib.linux-armv7l-cpython-39/diploshic/fvTools.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,401 copying build/lib.linux-armv7l-cpython-39/diploshic/__init__.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T00:51:30,402 running install_egg_info 2023-02-25T00:51:30,409 running egg_info 2023-02-25T00:51:30,414 writing diploSHIC.egg-info/PKG-INFO 2023-02-25T00:51:30,416 writing dependency_links to diploSHIC.egg-info/dependency_links.txt 2023-02-25T00:51:30,418 writing requirements to diploSHIC.egg-info/requires.txt 2023-02-25T00:51:30,419 writing top-level names to diploSHIC.egg-info/top_level.txt 2023-02-25T00:51:30,425 /tmp/pip-build-env-9wneljz9/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py:661: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-02-25T00:51:30,425 Please extend command classes from setuptools instead of distutils. 2023-02-25T00:51:30,425 warnings.warn( 2023-02-25T00:51:30,431 reading manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-02-25T00:51:30,435 reading manifest template 'MANIFEST.in' 2023-02-25T00:51:30,436 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-02-25T00:51:30,437 adding license file 'LICENSE' 2023-02-25T00:51:30,440 writing manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-02-25T00:51:30,442 Copying diploSHIC.egg-info to build/bdist.linux-armv7l/wheel/diploSHIC-0.4-py3.9.egg-info 2023-02-25T00:51:30,456 running install_scripts 2023-02-25T00:51:30,458 creating build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data 2023-02-25T00:51:30,458 creating build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts 2023-02-25T00:51:30,459 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts 2023-02-25T00:51:30,462 copying build/scripts.linux-armv7l-3.9/diploSHIC -> build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts 2023-02-25T00:51:30,465 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMs_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts 2023-02-25T00:51:30,469 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMsDiploid.py -> build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts 2023-02-25T00:51:30,472 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts 2023-02-25T00:51:30,476 copying build/scripts.linux-armv7l-3.9/makeTrainingSets.py -> build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts 2023-02-25T00:51:30,478 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts/makeFeatureVecsForChrArmFromVcfDiploid.py to 755 2023-02-25T00:51:30,478 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts/diploSHIC to 755 2023-02-25T00:51:30,479 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts/makeFeatureVecsForSingleMs_ogSHIC.py to 755 2023-02-25T00:51:30,479 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts/makeFeatureVecsForSingleMsDiploid.py to 755 2023-02-25T00:51:30,480 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts/makeFeatureVecsForChrArmFromVcf_ogSHIC.py to 755 2023-02-25T00:51:30,480 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-0.4.data/scripts/makeTrainingSets.py to 755 2023-02-25T00:51:30,480 running install_clib 2023-02-25T00:51:30,481 INFO: customize UnixCCompiler 2023-02-25T00:51:30,566 creating build/bdist.linux-armv7l/wheel/diploSHIC-0.4.dist-info/WHEEL 2023-02-25T00:51:30,569 creating '/tmp/pip-wheel-be3q29h1/.tmp-_jxx9xwf/diploSHIC-0.4-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-02-25T00:51:30,575 adding 'diploSHIC-0.4.data/scripts/diploSHIC' 2023-02-25T00:51:30,577 adding 'diploSHIC-0.4.data/scripts/makeFeatureVecsForChrArmFromVcfDiploid.py' 2023-02-25T00:51:30,579 adding 'diploSHIC-0.4.data/scripts/makeFeatureVecsForChrArmFromVcf_ogSHIC.py' 2023-02-25T00:51:30,581 adding 'diploSHIC-0.4.data/scripts/makeFeatureVecsForSingleMsDiploid.py' 2023-02-25T00:51:30,583 adding 'diploSHIC-0.4.data/scripts/makeFeatureVecsForSingleMs_ogSHIC.py' 2023-02-25T00:51:30,584 adding 'diploSHIC-0.4.data/scripts/makeTrainingSets.py' 2023-02-25T00:51:30,587 adding 'diploshic/__init__.py' 2023-02-25T00:51:30,592 adding 'diploshic/fvTools.py' 2023-02-25T00:51:30,594 adding 'diploshic/generateSimLaunchScript.py' 2023-02-25T00:51:30,596 adding 'diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py' 2023-02-25T00:51:30,598 adding 'diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py' 2023-02-25T00:51:30,600 adding 'diploshic/makeFeatureVecsForSingleMsDiploid.py' 2023-02-25T00:51:30,602 adding 'diploshic/makeFeatureVecsForSingleMs_ogSHIC.py' 2023-02-25T00:51:30,604 adding 'diploshic/makeTrainingSets.py' 2023-02-25T00:51:30,606 adding 'diploshic/misc.py' 2023-02-25T00:51:30,608 adding 'diploshic/msTools.py' 2023-02-25T00:51:30,609 adding 'diploshic/setup.py' 2023-02-25T00:51:30,637 adding 'diploshic/shicstats.cpython-39-arm-linux-gnueabihf.so' 2023-02-25T00:51:30,639 adding 'diploSHIC-0.4.dist-info/LICENSE' 2023-02-25T00:51:30,642 adding 'diploSHIC-0.4.dist-info/METADATA' 2023-02-25T00:51:30,643 adding 'diploSHIC-0.4.dist-info/WHEEL' 2023-02-25T00:51:30,644 adding 'diploSHIC-0.4.dist-info/top_level.txt' 2023-02-25T00:51:30,645 adding 'diploSHIC-0.4.dist-info/RECORD' 2023-02-25T00:51:30,648 removing build/bdist.linux-armv7l/wheel 2023-02-25T00:51:30,660 INFO: 2023-02-25T00:51:30,660 ########### EXT COMPILER OPTIMIZATION ########### 2023-02-25T00:51:30,660 INFO: Platform : 2023-02-25T00:51:30,660 Architecture: unsupported 2023-02-25T00:51:30,661 Compiler : gcc 2023-02-25T00:51:30,661 CPU baseline : 2023-02-25T00:51:30,661 Requested : optimization disabled 2023-02-25T00:51:30,661 Enabled : none 2023-02-25T00:51:30,661 Flags : none 2023-02-25T00:51:30,661 Extra checks: none 2023-02-25T00:51:30,661 Requested : optimization disabled 2023-02-25T00:51:30,662 CPU dispatch : 2023-02-25T00:51:30,662 Enabled : none 2023-02-25T00:51:30,662 Generated : none 2023-02-25T00:51:30,662 INFO: CCompilerOpt.cache_flush[857] : write cache to path -> /tmp/pip-wheel-9pzewj87/diploshic_91a50803a5d646ceb1be38d9f6eb6c5a/build/temp.linux-armv7l-cpython-39/ccompiler_opt_cache_ext.py 2023-02-25T00:51:30,823 Building wheel for diploshic (pyproject.toml): finished with status 'done' 2023-02-25T00:51:30,831 Created wheel for diploshic: filename=diploSHIC-0.4-cp39-cp39-linux_armv7l.whl size=114388 sha256=6e6ed02a4d79d462ccfed7a9472f6ef3db6c4bd148ffdc32a183a5d951bf5d03 2023-02-25T00:51:30,832 Stored in directory: /tmp/pip-ephem-wheel-cache-7br6_c8d/wheels/2b/0b/10/2e7ef03e0c60d2f3000d37eda1f35a4bc55c28bdb954981eda 2023-02-25T00:51:30,846 Successfully built diploshic 2023-02-25T00:51:30,854 Removed build tracker: '/tmp/pip-build-tracker-qdntjo3p'