2023-02-25T04:06:39,791 Created temporary directory: /tmp/pip-ephem-wheel-cache-evxq9bs8 2023-02-25T04:06:39,793 Created temporary directory: /tmp/pip-build-tracker-zqz12m74 2023-02-25T04:06:39,794 Initialized build tracking at /tmp/pip-build-tracker-zqz12m74 2023-02-25T04:06:39,794 Created build tracker: /tmp/pip-build-tracker-zqz12m74 2023-02-25T04:06:39,794 Entered build tracker: /tmp/pip-build-tracker-zqz12m74 2023-02-25T04:06:39,795 Created temporary directory: /tmp/pip-wheel-snfoxozv 2023-02-25T04:06:39,799 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 2023-02-25T04:06:39,802 Created temporary directory: /tmp/pip-ephem-wheel-cache-3theom9m 2023-02-25T04:06:39,832 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-02-25T04:06:39,835 2 location(s) to search for versions of diploshic: 2023-02-25T04:06:39,835 * https://pypi.org/simple/diploshic/ 2023-02-25T04:06:39,835 * https://www.piwheels.org/simple/diploshic/ 2023-02-25T04:06:39,836 Fetching project page and analyzing links: https://pypi.org/simple/diploshic/ 2023-02-25T04:06:39,836 Getting page https://pypi.org/simple/diploshic/ 2023-02-25T04:06:39,838 Found index url https://pypi.org/simple 2023-02-25T04:06:39,890 Fetched page https://pypi.org/simple/diploshic/ as application/vnd.pypi.simple.v1+json 2023-02-25T04:06:39,896 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/) 2023-02-25T04:06:39,897 Found link https://files.pythonhosted.org/packages/a6/c2/86153839edc17cf57860b6fb6a15595a430050a4a13be6bd00fb6c5295b7/diploSHIC-0.4.tar.gz (from https://pypi.org/simple/diploshic/), version: 0.4 2023-02-25T04:06:39,897 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/) 2023-02-25T04:06:39,897 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/) 2023-02-25T04:06:39,897 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/) 2023-02-25T04:06:39,898 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/) 2023-02-25T04:06:39,898 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/) 2023-02-25T04:06:39,898 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/) 2023-02-25T04:06:39,898 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/) 2023-02-25T04:06:39,898 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/) 2023-02-25T04:06:39,899 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/) 2023-02-25T04:06:39,899 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/) 2023-02-25T04:06:39,899 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/) 2023-02-25T04:06:39,899 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/) 2023-02-25T04:06:39,899 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/) 2023-02-25T04:06:39,900 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/) 2023-02-25T04:06:39,900 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/) 2023-02-25T04:06:39,900 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/) 2023-02-25T04:06:39,900 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/) 2023-02-25T04:06:39,900 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/) 2023-02-25T04:06:39,901 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/) 2023-02-25T04:06:39,901 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/) 2023-02-25T04:06:39,901 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/) 2023-02-25T04:06:39,901 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/) 2023-02-25T04:06:39,901 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/) 2023-02-25T04:06:39,902 Found link https://files.pythonhosted.org/packages/8e/79/bc66897efa74f1283c4830fe5531de3c5cd3cf92457ee7b67ce3bf1325f5/diploSHIC-0.333333.tar.gz (from https://pypi.org/simple/diploshic/), version: 0.333333 2023-02-25T04:06:39,902 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/42/cb/35722847899fdb73cbbf899d1037bdf59a2e2199fb64654fe24cb1e65744/diploSHIC-1.0.4-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-02-25T04:06:39,902 Found link https://files.pythonhosted.org/packages/c7/c8/b90a016e57751797e821176810a08eb1f667e3e25d4ae6723676361186b9/diploSHIC-1.0.4.tar.gz (from https://pypi.org/simple/diploshic/), version: 1.0.4 2023-02-25T04:06:39,903 Fetching project page and analyzing links: https://www.piwheels.org/simple/diploshic/ 2023-02-25T04:06:39,903 Getting page https://www.piwheels.org/simple/diploshic/ 2023-02-25T04:06:39,904 Found index url https://www.piwheels.org/simple 2023-02-25T04:06:40,150 Fetched page https://www.piwheels.org/simple/diploshic/ as text/html 2023-02-25T04:06:40,154 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-1.0.4-cp37-cp37m-linux_armv7l.whl#sha256=04abfe638d4d7cb48a9b74e46209f62672ba5835d5d6537634ae3d769b25fa57 (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T04:06:40,154 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-1.0.4-cp37-cp37m-linux_armv6l.whl#sha256=04abfe638d4d7cb48a9b74e46209f62672ba5835d5d6537634ae3d769b25fa57 (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T04:06:40,155 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/) 2023-02-25T04:06:40,155 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/) 2023-02-25T04:06:40,155 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/) 2023-02-25T04:06:40,155 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/) 2023-02-25T04:06:40,155 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/) 2023-02-25T04:06:40,156 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/) 2023-02-25T04:06:40,156 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-0.4-cp39-cp39-linux_armv7l.whl#sha256=6e6ed02a4d79d462ccfed7a9472f6ef3db6c4bd148ffdc32a183a5d951bf5d03 (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T04:06:40,156 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-0.4-cp39-cp39-linux_armv6l.whl#sha256=6e6ed02a4d79d462ccfed7a9472f6ef3db6c4bd148ffdc32a183a5d951bf5d03 (from https://www.piwheels.org/simple/diploshic/) 2023-02-25T04:06:40,156 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/) 2023-02-25T04:06:40,156 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/) 2023-02-25T04:06:40,157 Skipping link: not a file: https://www.piwheels.org/simple/diploshic/ 2023-02-25T04:06:40,157 Skipping link: not a file: https://pypi.org/simple/diploshic/ 2023-02-25T04:06:40,173 Given no hashes to check 1 links for project 'diploshic': discarding no candidates 2023-02-25T04:06:40,189 Collecting diploshic==1.0.4 2023-02-25T04:06:40,191 Created temporary directory: /tmp/pip-unpack-c5akalg2 2023-02-25T04:06:40,235 Downloading diploSHIC-1.0.4.tar.gz (13.9 MB) 2023-02-25T04:06:43,115 Added diploshic==1.0.4 from https://files.pythonhosted.org/packages/c7/c8/b90a016e57751797e821176810a08eb1f667e3e25d4ae6723676361186b9/diploSHIC-1.0.4.tar.gz to build tracker '/tmp/pip-build-tracker-zqz12m74' 2023-02-25T04:06:43,119 Created temporary directory: /tmp/pip-build-env-t41fmk4g 2023-02-25T04:06:43,130 Installing build dependencies: started 2023-02-25T04:06:43,131 Running command pip subprocess to install build dependencies 2023-02-25T04:06:44,358 Using pip 23.0.1 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2023-02-25T04:06:44,919 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 2023-02-25T04:06:44,944 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-02-25T04:06:46,597 Collecting setuptools 2023-02-25T04:06:47,327 Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.4.0-py3-none-any.whl (1.1 MB) 2023-02-25T04:06:48,646 Collecting numpy 2023-02-25T04:06:50,305 Using cached https://www.piwheels.org/simple/numpy/numpy-1.24.2-cp39-cp39-linux_armv7l.whl (12.3 MB) 2023-02-25T04:06:52,463 Installing collected packages: setuptools, numpy 2023-02-25T04:07:03,604 Creating /tmp/pip-build-env-t41fmk4g/overlay/bin 2023-02-25T04:07:03,606 changing mode of /tmp/pip-build-env-t41fmk4g/overlay/bin/f2py to 755 2023-02-25T04:07:03,608 changing mode of /tmp/pip-build-env-t41fmk4g/overlay/bin/f2py3 to 755 2023-02-25T04:07:03,610 changing mode of /tmp/pip-build-env-t41fmk4g/overlay/bin/f2py3.9 to 755 2023-02-25T04:07:03,647 Successfully installed numpy-1.24.2 setuptools-67.4.0 2023-02-25T04:07:04,176 Installing build dependencies: finished with status 'done' 2023-02-25T04:07:04,182 Getting requirements to build wheel: started 2023-02-25T04:07:04,183 Running command Getting requirements to build wheel 2023-02-25T04:07:04,994 :2: DeprecationWarning: 2023-02-25T04:07:04,995 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-02-25T04:07:04,995 of the deprecation of `distutils` itself. It will be removed for 2023-02-25T04:07:04,996 Python >= 3.12. For older Python versions it will remain present. 2023-02-25T04:07:04,996 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-02-25T04:07:04,996 For more details, see: 2023-02-25T04:07:04,996 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-02-25T04:07:05,664 running egg_info 2023-02-25T04:07:05,665 running build_src 2023-02-25T04:07:05,666 INFO: build_src 2023-02-25T04:07:05,666 INFO: building extension "diploshic.shicstats" sources 2023-02-25T04:07:05,668 creating build 2023-02-25T04:07:05,668 creating build/src.linux-armv7l-3.9 2023-02-25T04:07:05,669 creating build/src.linux-armv7l-3.9/diploshic 2023-02-25T04:07:05,669 INFO: f2py options: [] 2023-02-25T04:07:05,670 INFO: f2py: diploshic/shicstats.pyf 2023-02-25T04:07:06,038 Reading fortran codes... 2023-02-25T04:07:06,038 Reading file 'diploshic/shicstats.pyf' (format:free) 2023-02-25T04:07:06,038 Line #6 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T04:07:06,038 All arguments will have attribute intent(c) 2023-02-25T04:07:06,038 Line #14 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T04:07:06,038 All arguments will have attribute intent(c) 2023-02-25T04:07:06,039 Line #21 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T04:07:06,039 All arguments will have attribute intent(c) 2023-02-25T04:07:06,039 Line #28 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T04:07:06,039 All arguments will have attribute intent(c) 2023-02-25T04:07:06,039 Line #36 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T04:07:06,039 All arguments will have attribute intent(c) 2023-02-25T04:07:06,040 Line #44 in diploshic/shicstats.pyf:" intent(c) " 2023-02-25T04:07:06,040 All arguments will have attribute intent(c) 2023-02-25T04:07:06,040 crackline: groupcounter=1 groupname={0: '', 1: 'python module', 2: 'interface', 3: 'subroutine'} 2023-02-25T04:07:06,040 crackline: Mismatch of blocks encountered. Trying to fix it by assuming "end" statement. 2023-02-25T04:07:06,040 Post-processing... 2023-02-25T04:07:06,040 Block: shicstats 2023-02-25T04:07:06,041 Block: computeR2Matrix 2023-02-25T04:07:06,041 Block: omega 2023-02-25T04:07:06,041 Block: ZnS 2023-02-25T04:07:06,041 Block: pairwiseDiffs 2023-02-25T04:07:06,041 Block: pairwiseDiffsDiplo 2023-02-25T04:07:06,042 Block: getHaplotypeFreqSpec 2023-02-25T04:07:06,042 Applying post-processing hooks... 2023-02-25T04:07:06,042 character_backward_compatibility_hook 2023-02-25T04:07:06,043 Post-processing (stage 2)... 2023-02-25T04:07:06,043 Building modules... 2023-02-25T04:07:06,043 Building module "shicstats"... 2023-02-25T04:07:06,044 Generating possibly empty wrappers" 2023-02-25T04:07:06,044 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T04:07:06,044 Constructing wrapper function "computeR2Matrix"... 2023-02-25T04:07:06,044 r2Matrix = computeR2Matrix(haps) 2023-02-25T04:07:06,044 Generating possibly empty wrappers" 2023-02-25T04:07:06,044 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T04:07:06,045 Constructing wrapper function "omega"... 2023-02-25T04:07:06,045 omegaMax = omega(r2Matrix) 2023-02-25T04:07:06,045 Generating possibly empty wrappers" 2023-02-25T04:07:06,045 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T04:07:06,046 Constructing wrapper function "ZnS"... 2023-02-25T04:07:06,046 zns = ZnS(r2Matrix) 2023-02-25T04:07:06,046 Generating possibly empty wrappers" 2023-02-25T04:07:06,046 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T04:07:06,046 Constructing wrapper function "pairwiseDiffs"... 2023-02-25T04:07:06,046 diffLs = pairwiseDiffs(haps) 2023-02-25T04:07:06,047 Generating possibly empty wrappers" 2023-02-25T04:07:06,047 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T04:07:06,047 Constructing wrapper function "pairwiseDiffsDiplo"... 2023-02-25T04:07:06,047 diffLs = pairwiseDiffsDiplo(haps) 2023-02-25T04:07:06,047 Generating possibly empty wrappers" 2023-02-25T04:07:06,047 Maybe empty "shicstats-f2pywrappers.f" 2023-02-25T04:07:06,047 Constructing wrapper function "getHaplotypeFreqSpec"... 2023-02-25T04:07:06,048 hapCounts = getHaplotypeFreqSpec(haps) 2023-02-25T04:07:06,048 Wrote C/API module "shicstats" to file "build/src.linux-armv7l-3.9/diploshic/shicstatsmodule.c" 2023-02-25T04:07:06,048 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c' to sources. 2023-02-25T04:07:06,048 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic' to include_dirs. 2023-02-25T04:07:06,048 creating build/src.linux-armv7l-3.9/build 2023-02-25T04:07:06,048 creating build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9 2023-02-25T04:07:06,048 creating build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-02-25T04:07:06,049 copying /tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-02-25T04:07:06,049 copying /tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-02-25T04:07:06,049 INFO: adding 'build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f' to sources. 2023-02-25T04:07:06,049 INFO: build_src: building npy-pkg config files 2023-02-25T04:07:06,049 /tmp/pip-build-env-t41fmk4g/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. 2023-02-25T04:07:06,049 warnings.warn( 2023-02-25T04:07:06,075 writing diploSHIC.egg-info/PKG-INFO 2023-02-25T04:07:06,077 writing dependency_links to diploSHIC.egg-info/dependency_links.txt 2023-02-25T04:07:06,080 writing requirements to diploSHIC.egg-info/requires.txt 2023-02-25T04:07:06,081 writing top-level names to diploSHIC.egg-info/top_level.txt 2023-02-25T04:07:06,089 /tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py:661: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-02-25T04:07:06,090 Please extend command classes from setuptools instead of distutils. 2023-02-25T04:07:06,090 warnings.warn( 2023-02-25T04:07:06,092 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-02-25T04:07:06,093 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-02-25T04:07:06,096 reading manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-02-25T04:07:06,101 reading manifest template 'MANIFEST.in' 2023-02-25T04:07:06,102 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-02-25T04:07:06,104 adding license file 'LICENSE' 2023-02-25T04:07:06,107 writing manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-02-25T04:07:06,247 Getting requirements to build wheel: finished with status 'done' 2023-02-25T04:07:06,260 Installing backend dependencies: started 2023-02-25T04:07:06,261 Running command pip subprocess to install backend dependencies 2023-02-25T04:07:07,474 Using pip 23.0.1 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2023-02-25T04:07:08,059 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 2023-02-25T04:07:08,086 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-02-25T04:07:08,519 Collecting wheel 2023-02-25T04:07:08,537 Using cached https://www.piwheels.org/simple/wheel/wheel-0.38.4-py3-none-any.whl (36 kB) 2023-02-25T04:07:09,952 Installing collected packages: wheel 2023-02-25T04:07:10,140 Creating /tmp/pip-build-env-t41fmk4g/normal/bin 2023-02-25T04:07:10,142 changing mode of /tmp/pip-build-env-t41fmk4g/normal/bin/wheel to 755 2023-02-25T04:07:10,156 Successfully installed wheel-0.38.4 2023-02-25T04:07:10,583 Installing backend dependencies: finished with status 'done' 2023-02-25T04:07:10,585 Created temporary directory: /tmp/pip-modern-metadata-e_6bqbfb 2023-02-25T04:07:10,589 Preparing metadata (pyproject.toml): started 2023-02-25T04:07:10,590 Running command Preparing metadata (pyproject.toml) 2023-02-25T04:07:11,385 :2: DeprecationWarning: 2023-02-25T04:07:11,386 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-02-25T04:07:11,386 of the deprecation of `distutils` itself. It will be removed for 2023-02-25T04:07:11,386 Python >= 3.12. For older Python versions it will remain present. 2023-02-25T04:07:11,386 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-02-25T04:07:11,387 For more details, see: 2023-02-25T04:07:11,387 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-02-25T04:07:11,741 running dist_info 2023-02-25T04:07:11,742 running build_src 2023-02-25T04:07:11,743 INFO: build_src 2023-02-25T04:07:11,743 INFO: building extension "diploshic.shicstats" sources 2023-02-25T04:07:11,744 INFO: f2py options: [] 2023-02-25T04:07:11,744 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c' to sources. 2023-02-25T04:07:11,745 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic' to include_dirs. 2023-02-25T04:07:11,852 INFO: adding 'build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f' to sources. 2023-02-25T04:07:11,852 INFO: build_src: building npy-pkg config files 2023-02-25T04:07:11,853 /tmp/pip-build-env-t41fmk4g/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. 2023-02-25T04:07:11,853 warnings.warn( 2023-02-25T04:07:11,875 creating /tmp/pip-modern-metadata-e_6bqbfb/diploSHIC.egg-info 2023-02-25T04:07:11,881 writing /tmp/pip-modern-metadata-e_6bqbfb/diploSHIC.egg-info/PKG-INFO 2023-02-25T04:07:11,884 writing dependency_links to /tmp/pip-modern-metadata-e_6bqbfb/diploSHIC.egg-info/dependency_links.txt 2023-02-25T04:07:11,887 writing requirements to /tmp/pip-modern-metadata-e_6bqbfb/diploSHIC.egg-info/requires.txt 2023-02-25T04:07:11,888 writing top-level names to /tmp/pip-modern-metadata-e_6bqbfb/diploSHIC.egg-info/top_level.txt 2023-02-25T04:07:11,889 writing manifest file '/tmp/pip-modern-metadata-e_6bqbfb/diploSHIC.egg-info/SOURCES.txt' 2023-02-25T04:07:11,894 /tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py:661: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-02-25T04:07:11,894 Please extend command classes from setuptools instead of distutils. 2023-02-25T04:07:11,894 warnings.warn( 2023-02-25T04:07:11,896 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-02-25T04:07:11,896 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-02-25T04:07:11,901 reading manifest file '/tmp/pip-modern-metadata-e_6bqbfb/diploSHIC.egg-info/SOURCES.txt' 2023-02-25T04:07:11,903 reading manifest template 'MANIFEST.in' 2023-02-25T04:07:11,904 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-02-25T04:07:11,905 adding license file 'LICENSE' 2023-02-25T04:07:11,908 writing manifest file '/tmp/pip-modern-metadata-e_6bqbfb/diploSHIC.egg-info/SOURCES.txt' 2023-02-25T04:07:11,909 creating '/tmp/pip-modern-metadata-e_6bqbfb/diploSHIC-1.0.4.dist-info' 2023-02-25T04:07:12,121 Preparing metadata (pyproject.toml): finished with status 'done' 2023-02-25T04:07:12,130 Source in /tmp/pip-wheel-snfoxozv/diploshic_39f11554e6d4426aa625911ff2ab49c1 has version 1.0.4, which satisfies requirement diploshic==1.0.4 from https://files.pythonhosted.org/packages/c7/c8/b90a016e57751797e821176810a08eb1f667e3e25d4ae6723676361186b9/diploSHIC-1.0.4.tar.gz 2023-02-25T04:07:12,131 Removed diploshic==1.0.4 from https://files.pythonhosted.org/packages/c7/c8/b90a016e57751797e821176810a08eb1f667e3e25d4ae6723676361186b9/diploSHIC-1.0.4.tar.gz from build tracker '/tmp/pip-build-tracker-zqz12m74' 2023-02-25T04:07:12,137 Created temporary directory: /tmp/pip-unpack-12m71thk 2023-02-25T04:07:12,138 Building wheels for collected packages: diploshic 2023-02-25T04:07:12,143 Created temporary directory: /tmp/pip-wheel-z0scozv5 2023-02-25T04:07:12,144 Destination directory: /tmp/pip-wheel-z0scozv5 2023-02-25T04:07:12,147 Building wheel for diploshic (pyproject.toml): started 2023-02-25T04:07:12,148 Running command Building wheel for diploshic (pyproject.toml) 2023-02-25T04:07:12,861 :2: DeprecationWarning: 2023-02-25T04:07:12,862 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-02-25T04:07:12,862 of the deprecation of `distutils` itself. It will be removed for 2023-02-25T04:07:12,862 Python >= 3.12. For older Python versions it will remain present. 2023-02-25T04:07:12,862 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-02-25T04:07:12,862 For more details, see: 2023-02-25T04:07:12,862 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-02-25T04:07:13,207 running bdist_wheel 2023-02-25T04:07:13,212 running build 2023-02-25T04:07:13,213 running config_cc 2023-02-25T04:07:13,213 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-02-25T04:07:13,213 running config_fc 2023-02-25T04:07:13,213 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-02-25T04:07:13,213 running build_src 2023-02-25T04:07:13,213 INFO: build_src 2023-02-25T04:07:13,214 INFO: building extension "diploshic.shicstats" sources 2023-02-25T04:07:13,214 INFO: f2py options: [] 2023-02-25T04:07:13,214 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c' to sources. 2023-02-25T04:07:13,215 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic' to include_dirs. 2023-02-25T04:07:13,318 INFO: adding 'build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f' to sources. 2023-02-25T04:07:13,318 INFO: build_src: building npy-pkg config files 2023-02-25T04:07:13,341 running build_py 2023-02-25T04:07:13,343 creating build/lib.linux-armv7l-cpython-39 2023-02-25T04:07:13,343 creating build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,345 copying diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,348 copying diploshic/makeTrainingSets.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,350 copying diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,352 copying diploshic/__init__.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,354 copying diploshic/setup.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,356 copying diploshic/generateSimLaunchScript.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,358 copying diploshic/misc.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,361 copying diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,364 copying diploshic/msTools.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,366 copying diploshic/fvTools.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,370 copying diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:13,373 running build_ext 2023-02-25T04:07:13,380 INFO: customize UnixCCompiler 2023-02-25T04:07:13,381 INFO: customize UnixCCompiler using build_ext 2023-02-25T04:07:13,525 INFO: CCompilerOpt.cc_test_cexpr[1089] : testing compiler expression defined(__ARM_ARCH_7__) || defined(__ARM_ARCH_7A__) 2023-02-25T04:07:13,528 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 2023-02-25T04:07:13,529 creating /tmp/tmpp61s1j37/tmp 2023-02-25T04:07:13,529 creating /tmp/tmpp61s1j37/tmp/tmpp61s1j37 2023-02-25T04:07:13,530 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-02-25T04:07:13,610 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/tmpp61s1j37/npy_dist_test_cexpr.c -o /tmp/tmpp61s1j37/tmp/tmpp61s1j37/npy_dist_test_cexpr.o -MMD -MF /tmp/tmpp61s1j37/tmp/tmpp61s1j37/npy_dist_test_cexpr.o.d) failed with exit status 1 output -> 2023-02-25T04:07:13,610 /tmp/tmpp61s1j37/npy_dist_test_cexpr.c:2:6: error: #error "unsupported expression" 2023-02-25T04:07:13,610 2 | #error "unsupported expression" 2023-02-25T04:07:13,610 | ^~~~~ 2023-02-25T04:07:13,617 WARN: CCompilerOpt.cc_test_cexpr[1100] : testing failed 2023-02-25T04:07:13,627 WARN: CCompilerOpt.__init__[1016] : unable to detect CPU architecture which lead to disable the optimization. check dist_info:<< 2023-02-25T04:07:13,627 ('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') 2023-02-25T04:07:13,627 >> 2023-02-25T04:07:13,635 INFO: CCompilerOpt.cc_test_flags[1077] : testing flags (-march=native) 2023-02-25T04:07:13,635 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 2023-02-25T04:07:13,636 creating /tmp/tmpp61s1j37/tmp/pip-build-env-t41fmk4g 2023-02-25T04:07:13,636 creating /tmp/tmpp61s1j37/tmp/pip-build-env-t41fmk4g/overlay 2023-02-25T04:07:13,637 creating /tmp/tmpp61s1j37/tmp/pip-build-env-t41fmk4g/overlay/lib 2023-02-25T04:07:13,638 creating /tmp/tmpp61s1j37/tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9 2023-02-25T04:07:13,638 creating /tmp/tmpp61s1j37/tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages 2023-02-25T04:07:13,639 creating /tmp/tmpp61s1j37/tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages/numpy 2023-02-25T04:07:13,640 creating /tmp/tmpp61s1j37/tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages/numpy/distutils 2023-02-25T04:07:13,640 creating /tmp/tmpp61s1j37/tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages/numpy/distutils/checks 2023-02-25T04:07:13,641 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-02-25T04:07:13,641 extra options: '-march=native' 2023-02-25T04:07:13,731 INFO: CCompilerOpt.cc_test_flags[1077] : testing flags (-O3) 2023-02-25T04:07:13,731 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 2023-02-25T04:07:13,732 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-02-25T04:07:13,732 extra options: '-O3' 2023-02-25T04:07:13,819 INFO: CCompilerOpt.cc_test_flags[1077] : testing flags (-Werror) 2023-02-25T04:07:13,819 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 2023-02-25T04:07:13,819 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-02-25T04:07:13,819 extra options: '-Werror' 2023-02-25T04:07:13,907 INFO: CCompilerOpt.__init__[1786] : check requested baseline 2023-02-25T04:07:13,914 INFO: CCompilerOpt.__init__[1795] : check requested dispatch-able features 2023-02-25T04:07:13,921 INFO: CCompilerOpt.__init__[1811] : initialize targets groups 2023-02-25T04:07:13,928 INFO: CCompilerOpt.__init__[1813] : parse target group simd_test 2023-02-25T04:07:13,935 INFO: CCompilerOpt._parse_target_tokens[2024] : skip targets (XOP VSX3 ASIMD VSX VSX2 AVX512_SKX VXE2 VXE FMA4 (AVX2 FMA3) SSE42 VX AVX512F VSX4 SSE2 NEON) not part of baseline or dispatch-able features 2023-02-25T04:07:13,943 INFO: CCompilerOpt.generate_dispatch_header[2357] : generate CPU dispatch header: (build/src.linux-armv7l-3.9/numpy/distutils/include/npy_cpu_dispatch_config.h) 2023-02-25T04:07:13,950 WARN: CCompilerOpt.generate_dispatch_header[2366] : dispatch header dir build/src.linux-armv7l-3.9/numpy/distutils/include does not exist, creating it 2023-02-25T04:07:14,002 INFO: get_default_fcompiler: matching types: '['arm', 'gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor', 'fujitsu']' 2023-02-25T04:07:14,002 INFO: customize ArmFlangCompiler 2023-02-25T04:07:14,005 WARN: Could not locate executable armflang 2023-02-25T04:07:14,006 INFO: customize Gnu95FCompiler 2023-02-25T04:07:14,008 INFO: Found executable /usr/bin/gfortran 2023-02-25T04:07:14,073 INFO: customize Gnu95FCompiler 2023-02-25T04:07:14,123 INFO: customize Gnu95FCompiler using build_ext 2023-02-25T04:07:14,123 INFO: building 'diploshic.shicstats' extension 2023-02-25T04:07:14,124 INFO: compiling C sources 2023-02-25T04:07:14,125 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 2023-02-25T04:07:14,125 creating build/temp.linux-armv7l-cpython-39/build 2023-02-25T04:07:14,126 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9 2023-02-25T04:07:14,126 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/diploshic 2023-02-25T04:07:14,127 creating build/temp.linux-armv7l-cpython-39/diploshic 2023-02-25T04:07:14,128 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/build 2023-02-25T04:07:14,128 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9 2023-02-25T04:07:14,129 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-02-25T04:07:14,129 INFO: compile options: '-Ibuild/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic -I/tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages/numpy/core/include -Ibuild/src.linux-armv7l-3.9/numpy/distutils/include -I/usr/include/python3.9 -c' 2023-02-25T04:07:14,138 INFO: arm-linux-gnueabihf-gcc: build/src.linux-armv7l-3.9/diploshic/shicstatsmodule.c 2023-02-25T04:07:14,139 INFO: arm-linux-gnueabihf-gcc: diploshic/utils.c 2023-02-25T04:07:14,153 INFO: arm-linux-gnueabihf-gcc: build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c 2023-02-25T04:07:15,986 INFO: compiling Fortran sources 2023-02-25T04:07:15,987 INFO: Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops 2023-02-25T04:07:15,987 Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops 2023-02-25T04:07:15,987 Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops 2023-02-25T04:07:15,988 INFO: compile options: '-Ibuild/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic -I/tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages/numpy/core/include -Ibuild/src.linux-armv7l-3.9/numpy/distutils/include -I/usr/include/python3.9 -c' 2023-02-25T04:07:15,990 INFO: gfortran:f77: build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f 2023-02-25T04:07:16,094 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 2023-02-25T04:07:16,246 running build_scripts 2023-02-25T04:07:16,247 creating build/scripts.linux-armv7l-3.9 2023-02-25T04:07:16,248 copying and adjusting diploshic/diploSHIC -> build/scripts.linux-armv7l-3.9 2023-02-25T04:07:16,252 copying diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/scripts.linux-armv7l-3.9 2023-02-25T04:07:16,255 copying diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/scripts.linux-armv7l-3.9 2023-02-25T04:07:16,258 copying diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/scripts.linux-armv7l-3.9 2023-02-25T04:07:16,260 copying diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/scripts.linux-armv7l-3.9 2023-02-25T04:07:16,263 copying diploshic/makeTrainingSets.py -> build/scripts.linux-armv7l-3.9 2023-02-25T04:07:16,264 changing mode of build/scripts.linux-armv7l-3.9/diploSHIC from 644 to 755 2023-02-25T04:07:16,265 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcfDiploid.py from 644 to 755 2023-02-25T04:07:16,265 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcf_ogSHIC.py from 644 to 755 2023-02-25T04:07:16,265 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMsDiploid.py from 644 to 755 2023-02-25T04:07:16,266 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMs_ogSHIC.py from 644 to 755 2023-02-25T04:07:16,266 changing mode of build/scripts.linux-armv7l-3.9/makeTrainingSets.py from 644 to 755 2023-02-25T04:07:16,275 installing to build/bdist.linux-armv7l/wheel 2023-02-25T04:07:16,275 running install 2023-02-25T04:07:16,299 running install_lib 2023-02-25T04:07:16,307 creating build/bdist.linux-armv7l 2023-02-25T04:07:16,307 creating build/bdist.linux-armv7l/wheel 2023-02-25T04:07:16,309 creating build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,310 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,313 copying build/lib.linux-armv7l-cpython-39/diploshic/makeTrainingSets.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,315 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,317 copying build/lib.linux-armv7l-cpython-39/diploshic/__init__.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,319 copying build/lib.linux-armv7l-cpython-39/diploshic/setup.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,321 copying build/lib.linux-armv7l-cpython-39/diploshic/generateSimLaunchScript.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,323 copying build/lib.linux-armv7l-cpython-39/diploshic/shicstats.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,328 copying build/lib.linux-armv7l-cpython-39/diploshic/misc.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,331 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,333 copying build/lib.linux-armv7l-cpython-39/diploshic/msTools.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,336 copying build/lib.linux-armv7l-cpython-39/diploshic/fvTools.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,340 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-02-25T04:07:16,342 running install_egg_info 2023-02-25T04:07:16,349 running egg_info 2023-02-25T04:07:16,354 writing diploSHIC.egg-info/PKG-INFO 2023-02-25T04:07:16,356 writing dependency_links to diploSHIC.egg-info/dependency_links.txt 2023-02-25T04:07:16,358 writing requirements to diploSHIC.egg-info/requires.txt 2023-02-25T04:07:16,359 writing top-level names to diploSHIC.egg-info/top_level.txt 2023-02-25T04:07:16,364 /tmp/pip-build-env-t41fmk4g/overlay/lib/python3.9/site-packages/setuptools/command/egg_info.py:661: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-02-25T04:07:16,365 Please extend command classes from setuptools instead of distutils. 2023-02-25T04:07:16,365 warnings.warn( 2023-02-25T04:07:16,371 reading manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-02-25T04:07:16,374 reading manifest template 'MANIFEST.in' 2023-02-25T04:07:16,375 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-02-25T04:07:16,377 adding license file 'LICENSE' 2023-02-25T04:07:16,380 writing manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-02-25T04:07:16,382 Copying diploSHIC.egg-info to build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4-py3.9.egg-info 2023-02-25T04:07:16,396 running install_scripts 2023-02-25T04:07:16,397 creating build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data 2023-02-25T04:07:16,397 creating build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts 2023-02-25T04:07:16,398 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMsDiploid.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts 2023-02-25T04:07:16,401 copying build/scripts.linux-armv7l-3.9/makeTrainingSets.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts 2023-02-25T04:07:16,403 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts 2023-02-25T04:07:16,406 copying build/scripts.linux-armv7l-3.9/diploSHIC -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts 2023-02-25T04:07:16,409 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts 2023-02-25T04:07:16,411 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMs_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts 2023-02-25T04:07:16,413 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts/makeFeatureVecsForSingleMsDiploid.py to 755 2023-02-25T04:07:16,414 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts/makeTrainingSets.py to 755 2023-02-25T04:07:16,414 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts/makeFeatureVecsForChrArmFromVcfDiploid.py to 755 2023-02-25T04:07:16,414 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts/diploSHIC to 755 2023-02-25T04:07:16,414 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts/makeFeatureVecsForChrArmFromVcf_ogSHIC.py to 755 2023-02-25T04:07:16,415 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.data/scripts/makeFeatureVecsForSingleMs_ogSHIC.py to 755 2023-02-25T04:07:16,415 running install_clib 2023-02-25T04:07:16,415 INFO: customize UnixCCompiler 2023-02-25T04:07:16,469 creating build/bdist.linux-armv7l/wheel/diploSHIC-1.0.4.dist-info/WHEEL 2023-02-25T04:07:16,472 creating '/tmp/pip-wheel-z0scozv5/.tmp-iw6d70pt/diploSHIC-1.0.4-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-02-25T04:07:16,477 adding 'diploSHIC-1.0.4.data/scripts/diploSHIC' 2023-02-25T04:07:16,479 adding 'diploSHIC-1.0.4.data/scripts/makeFeatureVecsForChrArmFromVcfDiploid.py' 2023-02-25T04:07:16,481 adding 'diploSHIC-1.0.4.data/scripts/makeFeatureVecsForChrArmFromVcf_ogSHIC.py' 2023-02-25T04:07:16,483 adding 'diploSHIC-1.0.4.data/scripts/makeFeatureVecsForSingleMsDiploid.py' 2023-02-25T04:07:16,485 adding 'diploSHIC-1.0.4.data/scripts/makeFeatureVecsForSingleMs_ogSHIC.py' 2023-02-25T04:07:16,487 adding 'diploSHIC-1.0.4.data/scripts/makeTrainingSets.py' 2023-02-25T04:07:16,490 adding 'diploshic/__init__.py' 2023-02-25T04:07:16,494 adding 'diploshic/fvTools.py' 2023-02-25T04:07:16,496 adding 'diploshic/generateSimLaunchScript.py' 2023-02-25T04:07:16,498 adding 'diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py' 2023-02-25T04:07:16,500 adding 'diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py' 2023-02-25T04:07:16,503 adding 'diploshic/makeFeatureVecsForSingleMsDiploid.py' 2023-02-25T04:07:16,505 adding 'diploshic/makeFeatureVecsForSingleMs_ogSHIC.py' 2023-02-25T04:07:16,506 adding 'diploshic/makeTrainingSets.py' 2023-02-25T04:07:16,508 adding 'diploshic/misc.py' 2023-02-25T04:07:16,510 adding 'diploshic/msTools.py' 2023-02-25T04:07:16,512 adding 'diploshic/setup.py' 2023-02-25T04:07:16,539 adding 'diploshic/shicstats.cpython-39-arm-linux-gnueabihf.so' 2023-02-25T04:07:16,541 adding 'diploSHIC-1.0.4.dist-info/LICENSE' 2023-02-25T04:07:16,544 adding 'diploSHIC-1.0.4.dist-info/METADATA' 2023-02-25T04:07:16,545 adding 'diploSHIC-1.0.4.dist-info/WHEEL' 2023-02-25T04:07:16,546 adding 'diploSHIC-1.0.4.dist-info/top_level.txt' 2023-02-25T04:07:16,547 adding 'diploSHIC-1.0.4.dist-info/RECORD' 2023-02-25T04:07:16,550 removing build/bdist.linux-armv7l/wheel 2023-02-25T04:07:16,562 INFO: 2023-02-25T04:07:16,562 ########### EXT COMPILER OPTIMIZATION ########### 2023-02-25T04:07:16,563 INFO: Platform : 2023-02-25T04:07:16,563 Architecture: unsupported 2023-02-25T04:07:16,563 Compiler : gcc 2023-02-25T04:07:16,563 CPU baseline : 2023-02-25T04:07:16,563 Requested : optimization disabled 2023-02-25T04:07:16,563 Enabled : none 2023-02-25T04:07:16,563 Flags : none 2023-02-25T04:07:16,564 Extra checks: none 2023-02-25T04:07:16,564 Requested : optimization disabled 2023-02-25T04:07:16,564 CPU dispatch : 2023-02-25T04:07:16,564 Enabled : none 2023-02-25T04:07:16,564 Generated : none 2023-02-25T04:07:16,564 INFO: CCompilerOpt.cache_flush[857] : write cache to path -> /tmp/pip-wheel-snfoxozv/diploshic_39f11554e6d4426aa625911ff2ab49c1/build/temp.linux-armv7l-cpython-39/ccompiler_opt_cache_ext.py 2023-02-25T04:07:16,726 Building wheel for diploshic (pyproject.toml): finished with status 'done' 2023-02-25T04:07:16,735 Created wheel for diploshic: filename=diploSHIC-1.0.4-cp39-cp39-linux_armv7l.whl size=114437 sha256=1fc428ac7a43bf2b02a855215762a74a10f385de3702c9704a082518bda620ca 2023-02-25T04:07:16,736 Stored in directory: /tmp/pip-ephem-wheel-cache-3theom9m/wheels/d0/39/94/e6bacb72bea7c7c776be30692c2b40aee5571cf706ae7147b8 2023-02-25T04:07:16,749 Successfully built diploshic 2023-02-25T04:07:16,756 Removed build tracker: '/tmp/pip-build-tracker-zqz12m74'