2023-11-24T05:18:27,866 Created temporary directory: /tmp/pip-build-tracker-9_owfr_z 2023-11-24T05:18:27,867 Initialized build tracking at /tmp/pip-build-tracker-9_owfr_z 2023-11-24T05:18:27,867 Created build tracker: /tmp/pip-build-tracker-9_owfr_z 2023-11-24T05:18:27,867 Entered build tracker: /tmp/pip-build-tracker-9_owfr_z 2023-11-24T05:18:27,868 Created temporary directory: /tmp/pip-wheel-33w5z873 2023-11-24T05:18:27,872 Created temporary directory: /tmp/pip-ephem-wheel-cache-mm6p_9p4 2023-11-24T05:18:27,898 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T05:18:27,901 2 location(s) to search for versions of diploshic: 2023-11-24T05:18:27,901 * https://pypi.org/simple/diploshic/ 2023-11-24T05:18:27,901 * https://www.piwheels.org/simple/diploshic/ 2023-11-24T05:18:27,902 Fetching project page and analyzing links: https://pypi.org/simple/diploshic/ 2023-11-24T05:18:27,902 Getting page https://pypi.org/simple/diploshic/ 2023-11-24T05:18:27,904 Found index url https://pypi.org/simple/ 2023-11-24T05:18:27,955 Fetched page https://pypi.org/simple/diploshic/ as application/vnd.pypi.simple.v1+json 2023-11-24T05:18:27,962 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/) 2023-11-24T05:18:27,962 Found link https://files.pythonhosted.org/packages/a6/c2/86153839edc17cf57860b6fb6a15595a430050a4a13be6bd00fb6c5295b7/diploSHIC-0.4.tar.gz (from https://pypi.org/simple/diploshic/), version: 0.4 2023-11-24T05:18:27,962 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/) 2023-11-24T05:18:27,963 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/) 2023-11-24T05:18:27,963 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/) 2023-11-24T05:18:27,963 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/) 2023-11-24T05:18:27,963 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/) 2023-11-24T05:18:27,963 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/) 2023-11-24T05:18:27,964 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/) 2023-11-24T05:18:27,964 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/) 2023-11-24T05:18:27,964 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/) 2023-11-24T05:18:27,964 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/) 2023-11-24T05:18:27,964 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/) 2023-11-24T05:18:27,965 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/) 2023-11-24T05:18:27,965 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/) 2023-11-24T05:18:27,965 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/) 2023-11-24T05:18:27,965 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/) 2023-11-24T05:18:27,965 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/) 2023-11-24T05:18:27,966 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/) 2023-11-24T05:18:27,966 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/) 2023-11-24T05:18:27,966 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/) 2023-11-24T05:18:27,966 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/) 2023-11-24T05:18:27,966 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/) 2023-11-24T05:18:27,967 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/) 2023-11-24T05:18:27,967 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/) 2023-11-24T05:18:27,967 Found link https://files.pythonhosted.org/packages/8e/79/bc66897efa74f1283c4830fe5531de3c5cd3cf92457ee7b67ce3bf1325f5/diploSHIC-0.333333.tar.gz (from https://pypi.org/simple/diploshic/), version: 0.333333 2023-11-24T05:18:27,967 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/) 2023-11-24T05:18:27,967 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/5e/18/89000e37569524d590e3b3c40e7bd29a41690acfb40d7487c0f1ddc66059/diploSHIC-1.0.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-11-24T05:18:27,968 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 2023-11-24T05:18:27,968 Skipping link: No binaries permitted for diploshic: https://files.pythonhosted.org/packages/67/06/3c5bdf6afc99738c4aadfa894959e2354fae491a66047bae5ed5f3a2c323/diploSHIC-1.0.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/diploshic/) 2023-11-24T05:18:27,968 Found link https://files.pythonhosted.org/packages/12/bd/e811845aaf4d50d3e3197cf46dde64cdef271d370a0658f015db8aa52ca3/diploSHIC-1.0.5.tar.gz (from https://pypi.org/simple/diploshic/), version: 1.0.5 2023-11-24T05:18:27,969 Fetching project page and analyzing links: https://www.piwheels.org/simple/diploshic/ 2023-11-24T05:18:27,969 Getting page https://www.piwheels.org/simple/diploshic/ 2023-11-24T05:18:27,970 Found index url https://www.piwheels.org/simple/ 2023-11-24T05:18:28,042 Fetched page https://www.piwheels.org/simple/diploshic/ as text/html 2023-11-24T05:18:28,048 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-1.0.5-cp37-cp37m-linux_armv7l.whl#sha256=41b8f2eb27aa014147ec307357fb070db640293ecf50397553fe67f90f679dc9 (from https://www.piwheels.org/simple/diploshic/) 2023-11-24T05:18:28,048 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-1.0.5-cp37-cp37m-linux_armv6l.whl#sha256=41b8f2eb27aa014147ec307357fb070db640293ecf50397553fe67f90f679dc9 (from https://www.piwheels.org/simple/diploshic/) 2023-11-24T05:18:28,048 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-1.0.5-cp311-cp311-linux_armv7l.whl#sha256=d678d3f25afea80ef9c8ea0ac31533b388392df5cda0905cc3595b87bf8bf786 (from https://www.piwheels.org/simple/diploshic/) 2023-11-24T05:18:28,049 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-1.0.5-cp311-cp311-linux_armv6l.whl#sha256=d678d3f25afea80ef9c8ea0ac31533b388392df5cda0905cc3595b87bf8bf786 (from https://www.piwheels.org/simple/diploshic/) 2023-11-24T05:18:28,049 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-1.0.4-cp39-cp39-linux_armv7l.whl#sha256=1fc428ac7a43bf2b02a855215762a74a10f385de3702c9704a082518bda620ca (from https://www.piwheels.org/simple/diploshic/) 2023-11-24T05:18:28,049 Skipping link: No binaries permitted for diploshic: https://www.piwheels.org/simple/diploshic/diploSHIC-1.0.4-cp39-cp39-linux_armv6l.whl#sha256=1fc428ac7a43bf2b02a855215762a74a10f385de3702c9704a082518bda620ca (from https://www.piwheels.org/simple/diploshic/) 2023-11-24T05:18:28,049 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/) 2023-11-24T05:18:28,049 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/) 2023-11-24T05:18:28,050 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/) 2023-11-24T05:18:28,050 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/) 2023-11-24T05:18:28,050 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/) 2023-11-24T05:18:28,050 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/) 2023-11-24T05:18:28,050 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/) 2023-11-24T05:18:28,051 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/) 2023-11-24T05:18:28,051 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/) 2023-11-24T05:18:28,051 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/) 2023-11-24T05:18:28,051 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/) 2023-11-24T05:18:28,051 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/) 2023-11-24T05:18:28,052 Skipping link: not a file: https://www.piwheels.org/simple/diploshic/ 2023-11-24T05:18:28,052 Skipping link: not a file: https://pypi.org/simple/diploshic/ 2023-11-24T05:18:28,069 Given no hashes to check 1 links for project 'diploshic': discarding no candidates 2023-11-24T05:18:28,086 Collecting diploshic==1.0.5 2023-11-24T05:18:28,088 Created temporary directory: /tmp/pip-unpack-a9wy7dx8 2023-11-24T05:18:28,131 Downloading diploSHIC-1.0.5.tar.gz (13.9 MB) 2023-11-24T05:18:30,806 Added diploshic==1.0.5 from https://files.pythonhosted.org/packages/12/bd/e811845aaf4d50d3e3197cf46dde64cdef271d370a0658f015db8aa52ca3/diploSHIC-1.0.5.tar.gz to build tracker '/tmp/pip-build-tracker-9_owfr_z' 2023-11-24T05:18:30,810 Created temporary directory: /tmp/pip-build-env-1ucdooao 2023-11-24T05:18:30,820 Installing build dependencies: started 2023-11-24T05:18:30,821 Running command pip subprocess to install build dependencies 2023-11-24T05:18:32,241 Using pip 23.3.1 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9) 2023-11-24T05:18:32,774 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T05:18:34,187 Collecting setuptools 2023-11-24T05:18:34,188 Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/bb/e1/ed2dd0850446b8697ad28d118df885ad04140c64ace06c4bd559f7c8a94f/setuptools-69.0.2-py3-none-any.whl.metadata 2023-11-24T05:18:34,196 Using cached setuptools-69.0.2-py3-none-any.whl.metadata (6.3 kB) 2023-11-24T05:18:35,104 Collecting numpy 2023-11-24T05:18:35,121 Using cached https://www.piwheels.org/simple/numpy/numpy-1.26.2-cp39-cp39-linux_armv7l.whl (19.4 MB) 2023-11-24T05:18:35,854 Using cached setuptools-69.0.2-py3-none-any.whl (819 kB) 2023-11-24T05:18:37,720 Installing collected packages: setuptools, numpy 2023-11-24T05:18:47,150 Creating /tmp/pip-build-env-1ucdooao/overlay/bin 2023-11-24T05:18:47,152 changing mode of /tmp/pip-build-env-1ucdooao/overlay/bin/f2py to 755 2023-11-24T05:18:47,186 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. 2023-11-24T05:18:47,187 scipy 1.8.1 requires numpy<1.25.0,>=1.17.3, but you have numpy 1.26.2 which is incompatible. 2023-11-24T05:18:47,187 Successfully installed numpy-1.26.2 setuptools-69.0.2 2023-11-24T05:18:47,706 Installing build dependencies: finished with status 'done' 2023-11-24T05:18:47,711 Getting requirements to build wheel: started 2023-11-24T05:18:47,712 Running command Getting requirements to build wheel 2023-11-24T05:18:48,460 :2: DeprecationWarning: 2023-11-24T05:18:48,461 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-11-24T05:18:48,461 of the deprecation of `distutils` itself. It will be removed for 2023-11-24T05:18:48,461 Python >= 3.12. For older Python versions it will remain present. 2023-11-24T05:18:48,461 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-11-24T05:18:48,461 For more details, see: 2023-11-24T05:18:48,462 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-11-24T05:18:48,830 running egg_info 2023-11-24T05:18:48,831 running build_src 2023-11-24T05:18:48,832 INFO: build_src 2023-11-24T05:18:48,832 INFO: building extension "diploshic.shicstats" sources 2023-11-24T05:18:48,834 creating build 2023-11-24T05:18:48,834 creating build/src.linux-armv7l-3.9 2023-11-24T05:18:48,834 creating build/src.linux-armv7l-3.9/diploshic 2023-11-24T05:18:48,835 INFO: f2py options: [] 2023-11-24T05:18:48,835 INFO: f2py: diploshic/shicstats.pyf 2023-11-24T05:18:49,213 Reading fortran codes... 2023-11-24T05:18:49,213 Reading file 'diploshic/shicstats.pyf' (format:free) 2023-11-24T05:18:49,213 Line #6 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T05:18:49,213 All arguments will have attribute intent(c) 2023-11-24T05:18:49,213 Line #14 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T05:18:49,214 All arguments will have attribute intent(c) 2023-11-24T05:18:49,214 Line #21 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T05:18:49,214 All arguments will have attribute intent(c) 2023-11-24T05:18:49,214 Line #28 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T05:18:49,214 All arguments will have attribute intent(c) 2023-11-24T05:18:49,214 Line #36 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T05:18:49,214 All arguments will have attribute intent(c) 2023-11-24T05:18:49,215 Line #44 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T05:18:49,215 All arguments will have attribute intent(c) 2023-11-24T05:18:49,215 crackline: groupcounter=1 groupname={0: '', 1: 'python module', 2: 'interface', 3: 'subroutine'} 2023-11-24T05:18:49,215 crackline: Mismatch of blocks encountered. Trying to fix it by assuming "end" statement. 2023-11-24T05:18:49,215 Post-processing... 2023-11-24T05:18:49,215 Block: shicstats 2023-11-24T05:18:49,215 Block: computeR2Matrix 2023-11-24T05:18:49,215 Block: omega 2023-11-24T05:18:49,216 Block: ZnS 2023-11-24T05:18:49,216 Block: pairwiseDiffs 2023-11-24T05:18:49,216 Block: pairwiseDiffsDiplo 2023-11-24T05:18:49,216 Block: getHaplotypeFreqSpec 2023-11-24T05:18:49,216 Applying post-processing hooks... 2023-11-24T05:18:49,216 character_backward_compatibility_hook 2023-11-24T05:18:49,216 Post-processing (stage 2)... 2023-11-24T05:18:49,217 Building modules... 2023-11-24T05:18:49,217 Building module "shicstats"... 2023-11-24T05:18:49,217 Generating possibly empty wrappers" 2023-11-24T05:18:49,217 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T05:18:49,217 Constructing wrapper function "computeR2Matrix"... 2023-11-24T05:18:49,217 r2Matrix = computeR2Matrix(haps) 2023-11-24T05:18:49,217 Generating possibly empty wrappers" 2023-11-24T05:18:49,218 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T05:18:49,218 Constructing wrapper function "omega"... 2023-11-24T05:18:49,218 omegaMax = omega(r2Matrix) 2023-11-24T05:18:49,218 Generating possibly empty wrappers" 2023-11-24T05:18:49,218 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T05:18:49,218 Constructing wrapper function "ZnS"... 2023-11-24T05:18:49,218 zns = ZnS(r2Matrix) 2023-11-24T05:18:49,218 Generating possibly empty wrappers" 2023-11-24T05:18:49,219 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T05:18:49,219 Constructing wrapper function "pairwiseDiffs"... 2023-11-24T05:18:49,219 diffLs = pairwiseDiffs(haps) 2023-11-24T05:18:49,219 Generating possibly empty wrappers" 2023-11-24T05:18:49,219 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T05:18:49,219 Constructing wrapper function "pairwiseDiffsDiplo"... 2023-11-24T05:18:49,219 diffLs = pairwiseDiffsDiplo(haps) 2023-11-24T05:18:49,220 Generating possibly empty wrappers" 2023-11-24T05:18:49,220 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T05:18:49,220 Constructing wrapper function "getHaplotypeFreqSpec"... 2023-11-24T05:18:49,220 hapCounts = getHaplotypeFreqSpec(haps) 2023-11-24T05:18:49,220 Wrote C/API module "shicstats" to file "build/src.linux-armv7l-3.9/diploshic/shicstatsmodule.c" 2023-11-24T05:18:49,220 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c' to sources. 2023-11-24T05:18:49,220 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic' to include_dirs. 2023-11-24T05:18:49,220 creating build/src.linux-armv7l-3.9/build 2023-11-24T05:18:49,221 creating build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9 2023-11-24T05:18:49,221 creating build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-11-24T05:18:49,221 copying /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-11-24T05:18:49,221 copying /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-11-24T05:18:49,221 INFO: adding 'build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f' to sources. 2023-11-24T05:18:49,221 INFO: build_src: building npy-pkg config files 2023-11-24T05:18:49,222 /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-11-24T05:18:49,222 !! 2023-11-24T05:18:49,222 ******************************************************************************** 2023-11-24T05:18:49,222 Please avoid running ``setup.py`` directly. 2023-11-24T05:18:49,222 Instead, use pypa/build, pypa/installer or other 2023-11-24T05:18:49,222 standards-based tools. 2023-11-24T05:18:49,223 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-11-24T05:18:49,223 ******************************************************************************** 2023-11-24T05:18:49,223 !! 2023-11-24T05:18:49,223 self.initialize_options() 2023-11-24T05:18:49,248 writing diploSHIC.egg-info/PKG-INFO 2023-11-24T05:18:49,251 writing dependency_links to diploSHIC.egg-info/dependency_links.txt 2023-11-24T05:18:49,253 writing requirements to diploSHIC.egg-info/requires.txt 2023-11-24T05:18:49,254 writing top-level names to diploSHIC.egg-info/top_level.txt 2023-11-24T05:18:49,261 /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py:125: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`. 2023-11-24T05:18:49,261 !! 2023-11-24T05:18:49,262 ******************************************************************************** 2023-11-24T05:18:49,262 Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-11-24T05:18:49,262 Please extend command classes from setuptools instead of distutils. 2023-11-24T05:18:49,262 See https://peps.python.org/pep-0632/ for details. 2023-11-24T05:18:49,262 ******************************************************************************** 2023-11-24T05:18:49,263 !! 2023-11-24T05:18:49,263 self._add_data_files(self._safe_data_files(build_py)) 2023-11-24T05:18:49,264 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-11-24T05:18:49,264 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-11-24T05:18:49,267 reading manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-11-24T05:18:49,271 reading manifest template 'MANIFEST.in' 2023-11-24T05:18:49,272 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-11-24T05:18:49,274 adding license file 'LICENSE' 2023-11-24T05:18:49,277 writing manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-11-24T05:18:49,411 Getting requirements to build wheel: finished with status 'done' 2023-11-24T05:18:49,422 Installing backend dependencies: started 2023-11-24T05:18:49,423 Running command pip subprocess to install backend dependencies 2023-11-24T05:18:50,617 Using pip 23.3.1 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9) 2023-11-24T05:18:51,151 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T05:18:51,490 Collecting wheel 2023-11-24T05:18:51,506 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.3-py3-none-any.whl (65 kB) 2023-11-24T05:18:53,125 Installing collected packages: wheel 2023-11-24T05:18:53,345 Creating /tmp/pip-build-env-1ucdooao/normal/bin 2023-11-24T05:18:53,347 changing mode of /tmp/pip-build-env-1ucdooao/normal/bin/wheel to 755 2023-11-24T05:18:53,359 Successfully installed wheel-0.41.3 2023-11-24T05:18:53,767 Installing backend dependencies: finished with status 'done' 2023-11-24T05:18:53,770 Created temporary directory: /tmp/pip-modern-metadata-llrncekh 2023-11-24T05:18:53,772 Preparing metadata (pyproject.toml): started 2023-11-24T05:18:53,773 Running command Preparing metadata (pyproject.toml) 2023-11-24T05:18:54,552 :2: DeprecationWarning: 2023-11-24T05:18:54,553 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-11-24T05:18:54,553 of the deprecation of `distutils` itself. It will be removed for 2023-11-24T05:18:54,553 Python >= 3.12. For older Python versions it will remain present. 2023-11-24T05:18:54,553 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-11-24T05:18:54,553 For more details, see: 2023-11-24T05:18:54,553 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-11-24T05:18:55,092 running dist_info 2023-11-24T05:18:55,094 running build_src 2023-11-24T05:18:55,095 INFO: build_src 2023-11-24T05:18:55,095 INFO: building extension "diploshic.shicstats" sources 2023-11-24T05:18:55,096 INFO: f2py options: [] 2023-11-24T05:18:55,096 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c' to sources. 2023-11-24T05:18:55,096 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic' to include_dirs. 2023-11-24T05:18:55,208 copying /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-11-24T05:18:55,211 copying /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-11-24T05:18:55,213 INFO: adding 'build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f' to sources. 2023-11-24T05:18:55,213 INFO: build_src: building npy-pkg config files 2023-11-24T05:18:55,214 /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-11-24T05:18:55,215 !! 2023-11-24T05:18:55,215 ******************************************************************************** 2023-11-24T05:18:55,215 Please avoid running ``setup.py`` directly. 2023-11-24T05:18:55,215 Instead, use pypa/build, pypa/installer or other 2023-11-24T05:18:55,215 standards-based tools. 2023-11-24T05:18:55,215 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-11-24T05:18:55,215 ******************************************************************************** 2023-11-24T05:18:55,216 !! 2023-11-24T05:18:55,216 self.initialize_options() 2023-11-24T05:18:55,238 creating /tmp/pip-modern-metadata-llrncekh/diploSHIC.egg-info 2023-11-24T05:18:55,243 writing /tmp/pip-modern-metadata-llrncekh/diploSHIC.egg-info/PKG-INFO 2023-11-24T05:18:55,249 writing dependency_links to /tmp/pip-modern-metadata-llrncekh/diploSHIC.egg-info/dependency_links.txt 2023-11-24T05:18:55,252 writing requirements to /tmp/pip-modern-metadata-llrncekh/diploSHIC.egg-info/requires.txt 2023-11-24T05:18:55,254 writing top-level names to /tmp/pip-modern-metadata-llrncekh/diploSHIC.egg-info/top_level.txt 2023-11-24T05:18:55,256 writing manifest file '/tmp/pip-modern-metadata-llrncekh/diploSHIC.egg-info/SOURCES.txt' 2023-11-24T05:18:55,266 /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py:125: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`. 2023-11-24T05:18:55,266 !! 2023-11-24T05:18:55,266 ******************************************************************************** 2023-11-24T05:18:55,266 Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-11-24T05:18:55,266 Please extend command classes from setuptools instead of distutils. 2023-11-24T05:18:55,267 See https://peps.python.org/pep-0632/ for details. 2023-11-24T05:18:55,267 ******************************************************************************** 2023-11-24T05:18:55,267 !! 2023-11-24T05:18:55,267 self._add_data_files(self._safe_data_files(build_py)) 2023-11-24T05:18:55,270 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-11-24T05:18:55,270 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-11-24T05:18:55,493 reading manifest file '/tmp/pip-modern-metadata-llrncekh/diploSHIC.egg-info/SOURCES.txt' 2023-11-24T05:18:55,495 reading manifest template 'MANIFEST.in' 2023-11-24T05:18:55,496 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-11-24T05:18:55,498 adding license file 'LICENSE' 2023-11-24T05:18:55,501 writing manifest file '/tmp/pip-modern-metadata-llrncekh/diploSHIC.egg-info/SOURCES.txt' 2023-11-24T05:18:55,502 creating '/tmp/pip-modern-metadata-llrncekh/diploSHIC-1.0.5.dist-info' 2023-11-24T05:18:55,761 Preparing metadata (pyproject.toml): finished with status 'done' 2023-11-24T05:18:55,768 Source in /tmp/pip-wheel-33w5z873/diploshic_04c3df10726f48e8a4d9745ce7576282 has version 1.0.5, which satisfies requirement diploshic==1.0.5 from https://files.pythonhosted.org/packages/12/bd/e811845aaf4d50d3e3197cf46dde64cdef271d370a0658f015db8aa52ca3/diploSHIC-1.0.5.tar.gz 2023-11-24T05:18:55,769 Removed diploshic==1.0.5 from https://files.pythonhosted.org/packages/12/bd/e811845aaf4d50d3e3197cf46dde64cdef271d370a0658f015db8aa52ca3/diploSHIC-1.0.5.tar.gz from build tracker '/tmp/pip-build-tracker-9_owfr_z' 2023-11-24T05:18:55,773 Created temporary directory: /tmp/pip-unpack-alvhzufs 2023-11-24T05:18:55,774 Created temporary directory: /tmp/pip-unpack-zz1is7nr 2023-11-24T05:18:55,788 Building wheels for collected packages: diploshic 2023-11-24T05:18:55,792 Created temporary directory: /tmp/pip-wheel-ezp9lvbi 2023-11-24T05:18:55,792 Destination directory: /tmp/pip-wheel-ezp9lvbi 2023-11-24T05:18:55,794 Building wheel for diploshic (pyproject.toml): started 2023-11-24T05:18:55,795 Running command Building wheel for diploshic (pyproject.toml) 2023-11-24T05:18:56,494 :2: DeprecationWarning: 2023-11-24T05:18:56,495 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-11-24T05:18:56,495 of the deprecation of `distutils` itself. It will be removed for 2023-11-24T05:18:56,495 Python >= 3.12. For older Python versions it will remain present. 2023-11-24T05:18:56,495 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-11-24T05:18:56,495 For more details, see: 2023-11-24T05:18:56,495 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-11-24T05:18:56,837 running bdist_wheel 2023-11-24T05:18:56,842 running build 2023-11-24T05:18:56,842 running config_cc 2023-11-24T05:18:56,843 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-11-24T05:18:56,843 running config_fc 2023-11-24T05:18:56,843 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-11-24T05:18:56,843 running build_src 2023-11-24T05:18:56,843 INFO: build_src 2023-11-24T05:18:56,843 INFO: building extension "diploshic.shicstats" sources 2023-11-24T05:18:56,844 INFO: f2py options: [] 2023-11-24T05:18:56,844 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c' to sources. 2023-11-24T05:18:56,844 INFO: adding 'build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic' to include_dirs. 2023-11-24T05:18:56,949 copying /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-11-24T05:18:56,952 copying /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-11-24T05:18:56,954 INFO: adding 'build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f' to sources. 2023-11-24T05:18:56,954 INFO: build_src: building npy-pkg config files 2023-11-24T05:18:56,977 running build_py 2023-11-24T05:18:56,979 creating build/lib.linux-armv7l-cpython-39 2023-11-24T05:18:56,979 creating build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,980 copying diploshic/generateSimLaunchScript.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,982 copying diploshic/__init__.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,984 copying diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,986 copying diploshic/fvTools.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,988 copying diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,990 copying diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,992 copying diploshic/misc.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,994 copying diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,996 copying diploshic/makeTrainingSets.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,998 copying diploshic/msTools.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:56,999 copying diploshic/setup.py -> build/lib.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:57,002 running build_ext 2023-11-24T05:18:57,008 INFO: customize UnixCCompiler 2023-11-24T05:18:57,009 INFO: customize UnixCCompiler using build_ext 2023-11-24T05:18:57,145 INFO: CCompilerOpt.cc_test_cexpr[1098] : testing compiler expression defined(__ARM_ARCH_7__) || defined(__ARM_ARCH_7A__) 2023-11-24T05:18:57,147 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 2023-11-24T05:18:57,147 creating /tmp/tmp2zag33t1/tmp 2023-11-24T05:18:57,147 creating /tmp/tmp2zag33t1/tmp/tmp2zag33t1 2023-11-24T05:18:57,148 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-11-24T05:18:57,219 WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : 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/tmp2zag33t1/npy_dist_test_cexpr.c -o /tmp/tmp2zag33t1/tmp/tmp2zag33t1/npy_dist_test_cexpr.o -MMD -MF /tmp/tmp2zag33t1/tmp/tmp2zag33t1/npy_dist_test_cexpr.o.d) failed with exit status 1 output -> 2023-11-24T05:18:57,219 /tmp/tmp2zag33t1/npy_dist_test_cexpr.c:2:6: error: #error "unsupported expression" 2023-11-24T05:18:57,219 2 | #error "unsupported expression" 2023-11-24T05:18:57,219 | ^~~~~ 2023-11-24T05:18:57,226 WARN: CCompilerOpt.cc_test_cexpr[1109] : testing failed 2023-11-24T05:18:57,236 WARN: CCompilerOpt.__init__[1025] : unable to detect CPU architecture which lead to disable the optimization. check dist_info:<< 2023-11-24T05:18:57,236 ('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') 2023-11-24T05:18:57,236 >> 2023-11-24T05:18:57,245 INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-march=native) 2023-11-24T05:18:57,246 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 2023-11-24T05:18:57,246 creating /tmp/tmp2zag33t1/tmp/pip-build-env-1ucdooao 2023-11-24T05:18:57,247 creating /tmp/tmp2zag33t1/tmp/pip-build-env-1ucdooao/overlay 2023-11-24T05:18:57,247 creating /tmp/tmp2zag33t1/tmp/pip-build-env-1ucdooao/overlay/lib 2023-11-24T05:18:57,248 creating /tmp/tmp2zag33t1/tmp/pip-build-env-1ucdooao/overlay/lib/python3.9 2023-11-24T05:18:57,249 creating /tmp/tmp2zag33t1/tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages 2023-11-24T05:18:57,250 creating /tmp/tmp2zag33t1/tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy 2023-11-24T05:18:57,250 creating /tmp/tmp2zag33t1/tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy/distutils 2023-11-24T05:18:57,251 creating /tmp/tmp2zag33t1/tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy/distutils/checks 2023-11-24T05:18:57,251 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-11-24T05:18:57,251 extra options: '-march=native' 2023-11-24T05:18:57,327 INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-O3) 2023-11-24T05:18:57,327 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 2023-11-24T05:18:57,328 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-11-24T05:18:57,328 extra options: '-O3' 2023-11-24T05:18:57,404 INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-Werror) 2023-11-24T05:18:57,404 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 2023-11-24T05:18:57,404 INFO: compile options: '-I/usr/include/python3.9 -c' 2023-11-24T05:18:57,404 extra options: '-Werror' 2023-11-24T05:18:57,480 INFO: CCompilerOpt.__init__[1795] : check requested baseline 2023-11-24T05:18:57,487 INFO: CCompilerOpt.__init__[1804] : check requested dispatch-able features 2023-11-24T05:18:57,494 INFO: CCompilerOpt.__init__[1820] : initialize targets groups 2023-11-24T05:18:57,501 INFO: CCompilerOpt.__init__[1822] : parse target group simd_test 2023-11-24T05:18:57,508 INFO: CCompilerOpt._parse_target_tokens[2033] : skip targets (AVX512_SKX VSX3 VX ASIMD VSX2 NEON SSE2 VXE AVX512F VSX VSX4 XOP SSE42 VXE2 (AVX2 FMA3) FMA4) not part of baseline or dispatch-able features 2023-11-24T05:18:57,516 INFO: CCompilerOpt.generate_dispatch_header[2366] : generate CPU dispatch header: (build/src.linux-armv7l-3.9/numpy/distutils/include/npy_cpu_dispatch_config.h) 2023-11-24T05:18:57,523 WARN: CCompilerOpt.generate_dispatch_header[2375] : dispatch header dir build/src.linux-armv7l-3.9/numpy/distutils/include does not exist, creating it 2023-11-24T05:18:57,569 INFO: get_default_fcompiler: matching types: '['arm', 'gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor', 'fujitsu']' 2023-11-24T05:18:57,569 INFO: customize ArmFlangCompiler 2023-11-24T05:18:57,571 WARN: Could not locate executable armflang 2023-11-24T05:18:57,571 INFO: customize Gnu95FCompiler 2023-11-24T05:18:57,573 INFO: Found executable /usr/bin/gfortran 2023-11-24T05:18:57,619 INFO: customize Gnu95FCompiler 2023-11-24T05:18:57,663 INFO: customize Gnu95FCompiler using build_ext 2023-11-24T05:18:57,663 INFO: building 'diploshic.shicstats' extension 2023-11-24T05:18:57,664 INFO: compiling C sources 2023-11-24T05:18:57,664 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 2023-11-24T05:18:57,665 creating build/temp.linux-armv7l-cpython-39/build 2023-11-24T05:18:57,665 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9 2023-11-24T05:18:57,666 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/diploshic 2023-11-24T05:18:57,666 creating build/temp.linux-armv7l-cpython-39/diploshic 2023-11-24T05:18:57,667 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/build 2023-11-24T05:18:57,667 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9 2023-11-24T05:18:57,668 creating build/temp.linux-armv7l-cpython-39/build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic 2023-11-24T05:18:57,668 INFO: compile options: '-Ibuild/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic -I/tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy/core/include -Ibuild/src.linux-armv7l-3.9/numpy/distutils/include -I/usr/include/python3.9 -c' 2023-11-24T05:18:57,676 INFO: arm-linux-gnueabihf-gcc: build/src.linux-armv7l-3.9/diploshic/shicstatsmodule.c 2023-11-24T05:18:57,677 INFO: arm-linux-gnueabihf-gcc: diploshic/utils.c 2023-11-24T05:18:57,684 INFO: arm-linux-gnueabihf-gcc: build/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic/fortranobject.c 2023-11-24T05:18:59,494 INFO: compiling Fortran sources 2023-11-24T05:18:59,494 INFO: Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops 2023-11-24T05:18:59,495 Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops 2023-11-24T05:18:59,495 Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops 2023-11-24T05:18:59,495 INFO: compile options: '-Ibuild/src.linux-armv7l-3.9/build/src.linux-armv7l-3.9/diploshic -I/tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/numpy/core/include -Ibuild/src.linux-armv7l-3.9/numpy/distutils/include -I/usr/include/python3.9 -c' 2023-11-24T05:18:59,501 INFO: gfortran:f77: build/src.linux-armv7l-3.9/diploshic/shicstats-f2pywrappers.f 2023-11-24T05:18:59,563 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 2023-11-24T05:18:59,701 running build_scripts 2023-11-24T05:18:59,702 creating build/scripts.linux-armv7l-3.9 2023-11-24T05:18:59,703 copying and adjusting diploshic/diploSHIC -> build/scripts.linux-armv7l-3.9 2023-11-24T05:18:59,706 copying diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/scripts.linux-armv7l-3.9 2023-11-24T05:18:59,708 copying diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/scripts.linux-armv7l-3.9 2023-11-24T05:18:59,710 copying diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/scripts.linux-armv7l-3.9 2023-11-24T05:18:59,712 copying diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/scripts.linux-armv7l-3.9 2023-11-24T05:18:59,714 copying diploshic/makeTrainingSets.py -> build/scripts.linux-armv7l-3.9 2023-11-24T05:18:59,716 changing mode of build/scripts.linux-armv7l-3.9/diploSHIC from 644 to 755 2023-11-24T05:18:59,716 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcfDiploid.py from 644 to 755 2023-11-24T05:18:59,716 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcf_ogSHIC.py from 644 to 755 2023-11-24T05:18:59,716 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMsDiploid.py from 644 to 755 2023-11-24T05:18:59,717 changing mode of build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMs_ogSHIC.py from 644 to 755 2023-11-24T05:18:59,717 changing mode of build/scripts.linux-armv7l-3.9/makeTrainingSets.py from 644 to 755 2023-11-24T05:18:59,724 installing to build/bdist.linux-armv7l/wheel 2023-11-24T05:18:59,724 running install 2023-11-24T05:18:59,749 running install_lib 2023-11-24T05:18:59,756 creating build/bdist.linux-armv7l 2023-11-24T05:18:59,756 creating build/bdist.linux-armv7l/wheel 2023-11-24T05:18:59,757 creating build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,758 copying build/lib.linux-armv7l-cpython-39/diploshic/generateSimLaunchScript.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,760 copying build/lib.linux-armv7l-cpython-39/diploshic/__init__.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,762 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,764 copying build/lib.linux-armv7l-cpython-39/diploshic/fvTools.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,766 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,768 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,770 copying build/lib.linux-armv7l-cpython-39/diploshic/shicstats.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,774 copying build/lib.linux-armv7l-cpython-39/diploshic/misc.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,776 copying build/lib.linux-armv7l-cpython-39/diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,778 copying build/lib.linux-armv7l-cpython-39/diploshic/makeTrainingSets.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,780 copying build/lib.linux-armv7l-cpython-39/diploshic/msTools.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,782 copying build/lib.linux-armv7l-cpython-39/diploshic/setup.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T05:18:59,783 running install_egg_info 2023-11-24T05:18:59,788 running egg_info 2023-11-24T05:18:59,792 writing diploSHIC.egg-info/PKG-INFO 2023-11-24T05:18:59,796 writing dependency_links to diploSHIC.egg-info/dependency_links.txt 2023-11-24T05:18:59,798 writing requirements to diploSHIC.egg-info/requires.txt 2023-11-24T05:18:59,799 writing top-level names to diploSHIC.egg-info/top_level.txt 2023-11-24T05:18:59,803 /tmp/pip-build-env-1ucdooao/overlay/lib/python3.9/site-packages/setuptools/command/sdist.py:125: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`. 2023-11-24T05:18:59,803 !! 2023-11-24T05:18:59,804 ******************************************************************************** 2023-11-24T05:18:59,804 Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-11-24T05:18:59,804 Please extend command classes from setuptools instead of distutils. 2023-11-24T05:18:59,804 See https://peps.python.org/pep-0632/ for details. 2023-11-24T05:18:59,804 ******************************************************************************** 2023-11-24T05:18:59,804 !! 2023-11-24T05:18:59,805 self._add_data_files(self._safe_data_files(build_py)) 2023-11-24T05:18:59,809 reading manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-11-24T05:18:59,811 reading manifest template 'MANIFEST.in' 2023-11-24T05:18:59,812 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-11-24T05:18:59,813 adding license file 'LICENSE' 2023-11-24T05:18:59,817 writing manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-11-24T05:18:59,818 Copying diploSHIC.egg-info to build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5-py3.9.egg-info 2023-11-24T05:18:59,829 running install_scripts 2023-11-24T05:18:59,830 creating build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data 2023-11-24T05:18:59,830 creating build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T05:18:59,831 copying build/scripts.linux-armv7l-3.9/diploSHIC -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T05:18:59,834 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T05:18:59,836 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T05:18:59,838 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMs_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T05:18:59,840 copying build/scripts.linux-armv7l-3.9/makeFeatureVecsForSingleMsDiploid.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T05:18:59,842 copying build/scripts.linux-armv7l-3.9/makeTrainingSets.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T05:18:59,843 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/diploSHIC to 755 2023-11-24T05:18:59,843 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/makeFeatureVecsForChrArmFromVcf_ogSHIC.py to 755 2023-11-24T05:18:59,843 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/makeFeatureVecsForChrArmFromVcfDiploid.py to 755 2023-11-24T05:18:59,844 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/makeFeatureVecsForSingleMs_ogSHIC.py to 755 2023-11-24T05:18:59,844 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/makeFeatureVecsForSingleMsDiploid.py to 755 2023-11-24T05:18:59,844 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/makeTrainingSets.py to 755 2023-11-24T05:18:59,844 running install_clib 2023-11-24T05:18:59,845 INFO: customize UnixCCompiler 2023-11-24T05:18:59,893 creating build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.dist-info/WHEEL 2023-11-24T05:18:59,896 creating '/tmp/pip-wheel-ezp9lvbi/.tmp-pajuuwk_/diploSHIC-1.0.5-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-11-24T05:18:59,901 adding 'diploSHIC-1.0.5.data/scripts/diploSHIC' 2023-11-24T05:18:59,903 adding 'diploSHIC-1.0.5.data/scripts/makeFeatureVecsForChrArmFromVcfDiploid.py' 2023-11-24T05:18:59,905 adding 'diploSHIC-1.0.5.data/scripts/makeFeatureVecsForChrArmFromVcf_ogSHIC.py' 2023-11-24T05:18:59,907 adding 'diploSHIC-1.0.5.data/scripts/makeFeatureVecsForSingleMsDiploid.py' 2023-11-24T05:18:59,909 adding 'diploSHIC-1.0.5.data/scripts/makeFeatureVecsForSingleMs_ogSHIC.py' 2023-11-24T05:18:59,910 adding 'diploSHIC-1.0.5.data/scripts/makeTrainingSets.py' 2023-11-24T05:18:59,913 adding 'diploshic/__init__.py' 2023-11-24T05:18:59,917 adding 'diploshic/fvTools.py' 2023-11-24T05:18:59,919 adding 'diploshic/generateSimLaunchScript.py' 2023-11-24T05:18:59,921 adding 'diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py' 2023-11-24T05:18:59,923 adding 'diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py' 2023-11-24T05:18:59,925 adding 'diploshic/makeFeatureVecsForSingleMsDiploid.py' 2023-11-24T05:18:59,926 adding 'diploshic/makeFeatureVecsForSingleMs_ogSHIC.py' 2023-11-24T05:18:59,928 adding 'diploshic/makeTrainingSets.py' 2023-11-24T05:18:59,930 adding 'diploshic/misc.py' 2023-11-24T05:18:59,932 adding 'diploshic/msTools.py' 2023-11-24T05:18:59,933 adding 'diploshic/setup.py' 2023-11-24T05:18:59,961 adding 'diploshic/shicstats.cpython-39-arm-linux-gnueabihf.so' 2023-11-24T05:18:59,963 adding 'diploSHIC-1.0.5.dist-info/LICENSE' 2023-11-24T05:18:59,966 adding 'diploSHIC-1.0.5.dist-info/METADATA' 2023-11-24T05:18:59,967 adding 'diploSHIC-1.0.5.dist-info/WHEEL' 2023-11-24T05:18:59,968 adding 'diploSHIC-1.0.5.dist-info/top_level.txt' 2023-11-24T05:18:59,969 adding 'diploSHIC-1.0.5.dist-info/RECORD' 2023-11-24T05:18:59,971 removing build/bdist.linux-armv7l/wheel 2023-11-24T05:18:59,980 INFO: 2023-11-24T05:18:59,981 ########### EXT COMPILER OPTIMIZATION ########### 2023-11-24T05:18:59,981 INFO: Platform : 2023-11-24T05:18:59,981 Architecture: unsupported 2023-11-24T05:18:59,981 Compiler : gcc 2023-11-24T05:18:59,981 CPU baseline : 2023-11-24T05:18:59,981 Requested : optimization disabled 2023-11-24T05:18:59,982 Enabled : none 2023-11-24T05:18:59,982 Flags : none 2023-11-24T05:18:59,982 Extra checks: none 2023-11-24T05:18:59,982 Requested : optimization disabled 2023-11-24T05:18:59,982 CPU dispatch : 2023-11-24T05:18:59,982 Enabled : none 2023-11-24T05:18:59,982 Generated : none 2023-11-24T05:18:59,983 INFO: CCompilerOpt.cache_flush[864] : write cache to path -> /tmp/pip-wheel-33w5z873/diploshic_04c3df10726f48e8a4d9745ce7576282/build/temp.linux-armv7l-cpython-39/ccompiler_opt_cache_ext.py 2023-11-24T05:19:00,139 Building wheel for diploshic (pyproject.toml): finished with status 'done' 2023-11-24T05:19:00,147 Created wheel for diploshic: filename=diploSHIC-1.0.5-cp39-cp39-linux_armv7l.whl size=114406 sha256=9721921ddde6954e2407918dd25cd4fcaa8d89ac153a12ed226c256f808c4d8b 2023-11-24T05:19:00,148 Stored in directory: /tmp/pip-ephem-wheel-cache-mm6p_9p4/wheels/49/9e/4a/aff795a5db474fcdfe9e7fde6c95bbd90c60a5303dbf59795f 2023-11-24T05:19:00,160 Successfully built diploshic 2023-11-24T05:19:00,166 Removed build tracker: '/tmp/pip-build-tracker-9_owfr_z'