2023-11-24T03:05:18,499 Created temporary directory: /tmp/pip-build-tracker-lvh9j3gr 2023-11-24T03:05:18,500 Initialized build tracking at /tmp/pip-build-tracker-lvh9j3gr 2023-11-24T03:05:18,501 Created build tracker: /tmp/pip-build-tracker-lvh9j3gr 2023-11-24T03:05:18,501 Entered build tracker: /tmp/pip-build-tracker-lvh9j3gr 2023-11-24T03:05:18,502 Created temporary directory: /tmp/pip-wheel-ic8730qt 2023-11-24T03:05:18,505 Created temporary directory: /tmp/pip-ephem-wheel-cache-leuaweqj 2023-11-24T03:05:18,527 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T03:05:18,530 2 location(s) to search for versions of diploshic: 2023-11-24T03:05:18,530 * https://pypi.org/simple/diploshic/ 2023-11-24T03:05:18,530 * https://www.piwheels.org/simple/diploshic/ 2023-11-24T03:05:18,531 Fetching project page and analyzing links: https://pypi.org/simple/diploshic/ 2023-11-24T03:05:18,532 Getting page https://pypi.org/simple/diploshic/ 2023-11-24T03:05:18,533 Found index url https://pypi.org/simple/ 2023-11-24T03:05:18,787 Fetched page https://pypi.org/simple/diploshic/ as application/vnd.pypi.simple.v1+json 2023-11-24T03:05:18,794 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/) 2023-11-24T03:05:18,795 Found link https://files.pythonhosted.org/packages/a6/c2/86153839edc17cf57860b6fb6a15595a430050a4a13be6bd00fb6c5295b7/diploSHIC-0.4.tar.gz (from https://pypi.org/simple/diploshic/), version: 0.4 2023-11-24T03:05:18,795 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/) 2023-11-24T03:05:18,796 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/) 2023-11-24T03:05:18,796 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/) 2023-11-24T03:05:18,797 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/) 2023-11-24T03:05:18,798 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/) 2023-11-24T03:05:18,798 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/) 2023-11-24T03:05:18,799 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/) 2023-11-24T03:05:18,800 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/) 2023-11-24T03:05:18,800 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/) 2023-11-24T03:05:18,801 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/) 2023-11-24T03:05:18,801 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/) 2023-11-24T03:05:18,802 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/) 2023-11-24T03:05:18,803 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/) 2023-11-24T03:05:18,803 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/) 2023-11-24T03:05:18,803 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/) 2023-11-24T03:05:18,804 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/) 2023-11-24T03:05:18,805 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/) 2023-11-24T03:05:18,805 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/) 2023-11-24T03:05:18,806 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/) 2023-11-24T03:05:18,806 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/) 2023-11-24T03:05:18,807 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/) 2023-11-24T03:05:18,807 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/) 2023-11-24T03:05:18,808 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/) 2023-11-24T03:05:18,809 Found link https://files.pythonhosted.org/packages/8e/79/bc66897efa74f1283c4830fe5531de3c5cd3cf92457ee7b67ce3bf1325f5/diploSHIC-0.333333.tar.gz (from https://pypi.org/simple/diploshic/), version: 0.333333 2023-11-24T03:05:18,810 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/) 2023-11-24T03:05:18,810 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/) 2023-11-24T03:05:18,811 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 2023-11-24T03:05:18,811 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/) 2023-11-24T03:05:18,812 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 2023-11-24T03:05:18,813 Fetching project page and analyzing links: https://www.piwheels.org/simple/diploshic/ 2023-11-24T03:05:18,813 Getting page https://www.piwheels.org/simple/diploshic/ 2023-11-24T03:05:18,815 Found index url https://www.piwheels.org/simple/ 2023-11-24T03:05:18,977 Fetched page https://www.piwheels.org/simple/diploshic/ as text/html 2023-11-24T03:05:18,982 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/) 2023-11-24T03:05:18,983 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/) 2023-11-24T03:05:18,983 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/) 2023-11-24T03:05:18,984 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/) 2023-11-24T03:05:18,984 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/) 2023-11-24T03:05:18,985 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/) 2023-11-24T03:05:18,985 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/) 2023-11-24T03:05:18,986 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/) 2023-11-24T03:05:18,987 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/) 2023-11-24T03:05:18,987 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/) 2023-11-24T03:05:18,987 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/) 2023-11-24T03:05:18,988 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/) 2023-11-24T03:05:18,988 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/) 2023-11-24T03:05:18,989 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/) 2023-11-24T03:05:18,989 Skipping link: not a file: https://www.piwheels.org/simple/diploshic/ 2023-11-24T03:05:18,990 Skipping link: not a file: https://pypi.org/simple/diploshic/ 2023-11-24T03:05:19,010 Given no hashes to check 1 links for project 'diploshic': discarding no candidates 2023-11-24T03:05:19,029 Collecting diploshic==1.0.5 2023-11-24T03:05:19,032 Created temporary directory: /tmp/pip-unpack-oz3ha2x_ 2023-11-24T03:05:19,592 Downloading diploSHIC-1.0.5.tar.gz (13.9 MB) 2023-11-24T03:05:28,780 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-lvh9j3gr' 2023-11-24T03:05:28,784 Created temporary directory: /tmp/pip-build-env-bnfn1d_b 2023-11-24T03:05:28,789 Installing build dependencies: started 2023-11-24T03:05:28,791 Running command pip subprocess to install build dependencies 2023-11-24T03:05:29,942 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-11-24T03:05:30,430 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T03:05:31,996 Collecting setuptools 2023-11-24T03:05:31,998 Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/bb/e1/ed2dd0850446b8697ad28d118df885ad04140c64ace06c4bd559f7c8a94f/setuptools-69.0.2-py3-none-any.whl.metadata 2023-11-24T03:05:32,004 Using cached setuptools-69.0.2-py3-none-any.whl.metadata (6.3 kB) 2023-11-24T03:05:32,741 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2023-11-24T03:05:32,750 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2023-11-24T03:05:32,757 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2023-11-24T03:05:32,765 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2023-11-24T03:05:32,772 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2023-11-24T03:05:33,180 Collecting numpy 2023-11-24T03:05:34,544 Using cached https://www.piwheels.org/simple/numpy/numpy-1.26.2-cp311-cp311-linux_armv7l.whl (19.5 MB) 2023-11-24T03:05:35,243 Using cached setuptools-69.0.2-py3-none-any.whl (819 kB) 2023-11-24T03:05:37,723 Installing collected packages: setuptools, numpy 2023-11-24T03:05:47,776 Creating /tmp/pip-build-env-bnfn1d_b/overlay/local/bin 2023-11-24T03:05:47,779 changing mode of /tmp/pip-build-env-bnfn1d_b/overlay/local/bin/f2py to 755 2023-11-24T03:05:47,811 Successfully installed numpy-1.26.2 setuptools-69.0.2 2023-11-24T03:05:48,091 [notice] A new release of pip is available: 23.2.1 -> 23.3.1 2023-11-24T03:05:48,092 [notice] To update, run: python3 -m pip install --upgrade pip 2023-11-24T03:05:48,425 Installing build dependencies: finished with status 'done' 2023-11-24T03:05:48,428 Getting requirements to build wheel: started 2023-11-24T03:05:48,429 Running command Getting requirements to build wheel 2023-11-24T03:05:49,168 :2: DeprecationWarning: 2023-11-24T03:05:49,169 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-11-24T03:05:49,170 of the deprecation of `distutils` itself. It will be removed for 2023-11-24T03:05:49,170 Python >= 3.12. For older Python versions it will remain present. 2023-11-24T03:05:49,171 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-11-24T03:05:49,171 For more details, see: 2023-11-24T03:05:49,172 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-11-24T03:05:49,510 running egg_info 2023-11-24T03:05:49,511 running build_src 2023-11-24T03:05:49,512 INFO: build_src 2023-11-24T03:05:49,513 INFO: building extension "diploshic.shicstats" sources 2023-11-24T03:05:49,514 creating build 2023-11-24T03:05:49,515 creating build/src.linux-armv7l-3.11 2023-11-24T03:05:49,516 creating build/src.linux-armv7l-3.11/diploshic 2023-11-24T03:05:49,516 INFO: f2py options: [] 2023-11-24T03:05:49,517 INFO: f2py: diploshic/shicstats.pyf 2023-11-24T03:05:49,839 Reading fortran codes... 2023-11-24T03:05:49,840 Reading file 'diploshic/shicstats.pyf' (format:free) 2023-11-24T03:05:49,840 Line #6 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T03:05:49,841 All arguments will have attribute intent(c) 2023-11-24T03:05:49,841 Line #14 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T03:05:49,842 All arguments will have attribute intent(c) 2023-11-24T03:05:49,843 Line #21 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T03:05:49,843 All arguments will have attribute intent(c) 2023-11-24T03:05:49,844 Line #28 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T03:05:49,845 All arguments will have attribute intent(c) 2023-11-24T03:05:49,845 Line #36 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T03:05:49,846 All arguments will have attribute intent(c) 2023-11-24T03:05:49,846 Line #44 in diploshic/shicstats.pyf:" intent(c) " 2023-11-24T03:05:49,847 All arguments will have attribute intent(c) 2023-11-24T03:05:49,847 crackline: groupcounter=1 groupname={0: '', 1: 'python module', 2: 'interface', 3: 'subroutine'} 2023-11-24T03:05:49,848 crackline: Mismatch of blocks encountered. Trying to fix it by assuming "end" statement. 2023-11-24T03:05:49,848 Post-processing... 2023-11-24T03:05:49,848 Block: shicstats 2023-11-24T03:05:49,849 Block: computeR2Matrix 2023-11-24T03:05:49,849 Block: omega 2023-11-24T03:05:49,850 Block: ZnS 2023-11-24T03:05:49,850 Block: pairwiseDiffs 2023-11-24T03:05:49,851 Block: pairwiseDiffsDiplo 2023-11-24T03:05:49,851 Block: getHaplotypeFreqSpec 2023-11-24T03:05:49,851 Applying post-processing hooks... 2023-11-24T03:05:49,852 character_backward_compatibility_hook 2023-11-24T03:05:49,852 Post-processing (stage 2)... 2023-11-24T03:05:49,852 Building modules... 2023-11-24T03:05:49,853 Building module "shicstats"... 2023-11-24T03:05:49,853 Generating possibly empty wrappers" 2023-11-24T03:05:49,854 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T03:05:49,854 Constructing wrapper function "computeR2Matrix"... 2023-11-24T03:05:49,854 r2Matrix = computeR2Matrix(haps) 2023-11-24T03:05:49,855 Generating possibly empty wrappers" 2023-11-24T03:05:49,855 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T03:05:49,856 Constructing wrapper function "omega"... 2023-11-24T03:05:49,857 omegaMax = omega(r2Matrix) 2023-11-24T03:05:49,857 Generating possibly empty wrappers" 2023-11-24T03:05:49,858 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T03:05:49,858 Constructing wrapper function "ZnS"... 2023-11-24T03:05:49,859 zns = ZnS(r2Matrix) 2023-11-24T03:05:49,859 Generating possibly empty wrappers" 2023-11-24T03:05:49,860 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T03:05:49,860 Constructing wrapper function "pairwiseDiffs"... 2023-11-24T03:05:49,861 diffLs = pairwiseDiffs(haps) 2023-11-24T03:05:49,862 Generating possibly empty wrappers" 2023-11-24T03:05:49,862 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T03:05:49,863 Constructing wrapper function "pairwiseDiffsDiplo"... 2023-11-24T03:05:49,863 diffLs = pairwiseDiffsDiplo(haps) 2023-11-24T03:05:49,864 Generating possibly empty wrappers" 2023-11-24T03:05:49,864 Maybe empty "shicstats-f2pywrappers.f" 2023-11-24T03:05:49,865 Constructing wrapper function "getHaplotypeFreqSpec"... 2023-11-24T03:05:49,865 hapCounts = getHaplotypeFreqSpec(haps) 2023-11-24T03:05:49,866 Wrote C/API module "shicstats" to file "build/src.linux-armv7l-3.11/diploshic/shicstatsmodule.c" 2023-11-24T03:05:49,866 INFO: adding 'build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic/fortranobject.c' to sources. 2023-11-24T03:05:49,867 INFO: adding 'build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic' to include_dirs. 2023-11-24T03:05:49,867 creating build/src.linux-armv7l-3.11/build 2023-11-24T03:05:49,868 creating build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11 2023-11-24T03:05:49,868 creating build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic 2023-11-24T03:05:49,869 copying /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic 2023-11-24T03:05:49,870 copying /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic 2023-11-24T03:05:49,870 INFO: adding 'build/src.linux-armv7l-3.11/diploshic/shicstats-f2pywrappers.f' to sources. 2023-11-24T03:05:49,871 INFO: build_src: building npy-pkg config files 2023-11-24T03:05:49,871 /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-11-24T03:05:49,872 !! 2023-11-24T03:05:49,873 ******************************************************************************** 2023-11-24T03:05:49,873 Please avoid running ``setup.py`` directly. 2023-11-24T03:05:49,874 Instead, use pypa/build, pypa/installer or other 2023-11-24T03:05:49,874 standards-based tools. 2023-11-24T03:05:49,875 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-11-24T03:05:49,875 ******************************************************************************** 2023-11-24T03:05:49,876 !! 2023-11-24T03:05:49,877 self.initialize_options() 2023-11-24T03:05:49,877 writing diploSHIC.egg-info/PKG-INFO 2023-11-24T03:05:49,879 writing dependency_links to diploSHIC.egg-info/dependency_links.txt 2023-11-24T03:05:49,881 writing requirements to diploSHIC.egg-info/requires.txt 2023-11-24T03:05:49,882 writing top-level names to diploSHIC.egg-info/top_level.txt 2023-11-24T03:05:49,888 /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/setuptools/command/sdist.py:125: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`. 2023-11-24T03:05:49,889 !! 2023-11-24T03:05:49,890 ******************************************************************************** 2023-11-24T03:05:49,890 Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-11-24T03:05:49,891 Please extend command classes from setuptools instead of distutils. 2023-11-24T03:05:49,892 See https://peps.python.org/pep-0632/ for details. 2023-11-24T03:05:49,893 ******************************************************************************** 2023-11-24T03:05:49,894 !! 2023-11-24T03:05:49,894 self._add_data_files(self._safe_data_files(build_py)) 2023-11-24T03:05:49,895 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-11-24T03:05:49,895 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-11-24T03:05:49,896 reading manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-11-24T03:05:49,898 reading manifest template 'MANIFEST.in' 2023-11-24T03:05:49,899 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-11-24T03:05:49,901 adding license file 'LICENSE' 2023-11-24T03:05:49,904 writing manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-11-24T03:05:50,058 Getting requirements to build wheel: finished with status 'done' 2023-11-24T03:05:50,067 Installing backend dependencies: started 2023-11-24T03:05:50,069 Running command pip subprocess to install backend dependencies 2023-11-24T03:05:51,198 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-11-24T03:05:51,685 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-11-24T03:05:52,197 Collecting wheel 2023-11-24T03:05:52,213 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.3-py3-none-any.whl (65 kB) 2023-11-24T03:05:54,418 Installing collected packages: wheel 2023-11-24T03:05:54,639 Creating /tmp/pip-build-env-bnfn1d_b/normal/local/bin 2023-11-24T03:05:54,641 changing mode of /tmp/pip-build-env-bnfn1d_b/normal/local/bin/wheel to 755 2023-11-24T03:05:54,652 Successfully installed wheel-0.41.3 2023-11-24T03:05:54,930 [notice] A new release of pip is available: 23.2.1 -> 23.3.1 2023-11-24T03:05:54,930 [notice] To update, run: python3 -m pip install --upgrade pip 2023-11-24T03:05:55,157 Installing backend dependencies: finished with status 'done' 2023-11-24T03:05:55,159 Created temporary directory: /tmp/pip-modern-metadata-u5elcolw 2023-11-24T03:05:55,162 Preparing metadata (pyproject.toml): started 2023-11-24T03:05:55,163 Running command Preparing metadata (pyproject.toml) 2023-11-24T03:05:55,914 :2: DeprecationWarning: 2023-11-24T03:05:55,915 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-11-24T03:05:55,915 of the deprecation of `distutils` itself. It will be removed for 2023-11-24T03:05:55,916 Python >= 3.12. For older Python versions it will remain present. 2023-11-24T03:05:55,916 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-11-24T03:05:55,917 For more details, see: 2023-11-24T03:05:55,917 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-11-24T03:05:56,225 running dist_info 2023-11-24T03:05:56,227 running build_src 2023-11-24T03:05:56,229 INFO: build_src 2023-11-24T03:05:56,229 INFO: building extension "diploshic.shicstats" sources 2023-11-24T03:05:56,230 INFO: f2py options: [] 2023-11-24T03:05:56,231 INFO: adding 'build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic/fortranobject.c' to sources. 2023-11-24T03:05:56,231 INFO: adding 'build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic' to include_dirs. 2023-11-24T03:05:56,329 copying /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic 2023-11-24T03:05:56,332 copying /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic 2023-11-24T03:05:56,335 INFO: adding 'build/src.linux-armv7l-3.11/diploshic/shicstats-f2pywrappers.f' to sources. 2023-11-24T03:05:56,336 INFO: build_src: building npy-pkg config files 2023-11-24T03:05:56,337 /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-11-24T03:05:56,338 !! 2023-11-24T03:05:56,339 ******************************************************************************** 2023-11-24T03:05:56,340 Please avoid running ``setup.py`` directly. 2023-11-24T03:05:56,340 Instead, use pypa/build, pypa/installer or other 2023-11-24T03:05:56,341 standards-based tools. 2023-11-24T03:05:56,342 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-11-24T03:05:56,343 ******************************************************************************** 2023-11-24T03:05:56,344 !! 2023-11-24T03:05:56,344 self.initialize_options() 2023-11-24T03:05:56,364 creating /tmp/pip-modern-metadata-u5elcolw/diploSHIC.egg-info 2023-11-24T03:05:56,369 writing /tmp/pip-modern-metadata-u5elcolw/diploSHIC.egg-info/PKG-INFO 2023-11-24T03:05:56,373 writing dependency_links to /tmp/pip-modern-metadata-u5elcolw/diploSHIC.egg-info/dependency_links.txt 2023-11-24T03:05:56,375 writing requirements to /tmp/pip-modern-metadata-u5elcolw/diploSHIC.egg-info/requires.txt 2023-11-24T03:05:56,377 writing top-level names to /tmp/pip-modern-metadata-u5elcolw/diploSHIC.egg-info/top_level.txt 2023-11-24T03:05:56,379 writing manifest file '/tmp/pip-modern-metadata-u5elcolw/diploSHIC.egg-info/SOURCES.txt' 2023-11-24T03:05:56,384 /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/setuptools/command/sdist.py:125: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`. 2023-11-24T03:05:56,385 !! 2023-11-24T03:05:56,386 ******************************************************************************** 2023-11-24T03:05:56,386 Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-11-24T03:05:56,387 Please extend command classes from setuptools instead of distutils. 2023-11-24T03:05:56,388 See https://peps.python.org/pep-0632/ for details. 2023-11-24T03:05:56,389 ******************************************************************************** 2023-11-24T03:05:56,390 !! 2023-11-24T03:05:56,390 self._add_data_files(self._safe_data_files(build_py)) 2023-11-24T03:05:56,391 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-11-24T03:05:56,392 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-11-24T03:05:56,396 reading manifest file '/tmp/pip-modern-metadata-u5elcolw/diploSHIC.egg-info/SOURCES.txt' 2023-11-24T03:05:56,398 reading manifest template 'MANIFEST.in' 2023-11-24T03:05:56,399 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-11-24T03:05:56,402 adding license file 'LICENSE' 2023-11-24T03:05:56,405 writing manifest file '/tmp/pip-modern-metadata-u5elcolw/diploSHIC.egg-info/SOURCES.txt' 2023-11-24T03:05:56,406 creating '/tmp/pip-modern-metadata-u5elcolw/diploSHIC-1.0.5.dist-info' 2023-11-24T03:05:56,667 Preparing metadata (pyproject.toml): finished with status 'done' 2023-11-24T03:05:56,672 Source in /tmp/pip-wheel-ic8730qt/diploshic_635cc5aad7d046a3a6c87328df25abd8 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 2023-11-24T03:05:56,673 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-lvh9j3gr' 2023-11-24T03:05:56,678 Created temporary directory: /tmp/pip-unpack-xp6s_zt1 2023-11-24T03:05:56,679 Created temporary directory: /tmp/pip-unpack-ku80lf43 2023-11-24T03:05:56,692 Building wheels for collected packages: diploshic 2023-11-24T03:05:56,696 Created temporary directory: /tmp/pip-wheel-aq1zrgvu 2023-11-24T03:05:56,697 Destination directory: /tmp/pip-wheel-aq1zrgvu 2023-11-24T03:05:56,699 Building wheel for diploshic (pyproject.toml): started 2023-11-24T03:05:56,700 Running command Building wheel for diploshic (pyproject.toml) 2023-11-24T03:05:57,382 :2: DeprecationWarning: 2023-11-24T03:05:57,383 `numpy.distutils` is deprecated since NumPy 1.23.0, as a result 2023-11-24T03:05:57,384 of the deprecation of `distutils` itself. It will be removed for 2023-11-24T03:05:57,384 Python >= 3.12. For older Python versions it will remain present. 2023-11-24T03:05:57,385 It is recommended to use `setuptools < 60.0` for those Python versions. 2023-11-24T03:05:57,386 For more details, see: 2023-11-24T03:05:57,386 https://numpy.org/devdocs/reference/distutils_status_migration.html 2023-11-24T03:05:57,709 running bdist_wheel 2023-11-24T03:05:57,714 running build 2023-11-24T03:05:57,714 running config_cc 2023-11-24T03:05:57,715 INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options 2023-11-24T03:05:57,716 running config_fc 2023-11-24T03:05:57,716 INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options 2023-11-24T03:05:57,717 running build_src 2023-11-24T03:05:57,717 INFO: build_src 2023-11-24T03:05:57,718 INFO: building extension "diploshic.shicstats" sources 2023-11-24T03:05:57,719 INFO: f2py options: [] 2023-11-24T03:05:57,719 INFO: adding 'build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic/fortranobject.c' to sources. 2023-11-24T03:05:57,720 INFO: adding 'build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic' to include_dirs. 2023-11-24T03:05:57,806 copying /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic 2023-11-24T03:05:57,809 copying /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic 2023-11-24T03:05:57,811 INFO: adding 'build/src.linux-armv7l-3.11/diploshic/shicstats-f2pywrappers.f' to sources. 2023-11-24T03:05:57,811 INFO: build_src: building npy-pkg config files 2023-11-24T03:05:57,833 running build_py 2023-11-24T03:05:57,835 creating build/lib.linux-armv7l-cpython-311 2023-11-24T03:05:57,835 creating build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,836 copying diploshic/generateSimLaunchScript.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,838 copying diploshic/__init__.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,839 copying diploshic/misc.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,841 copying diploshic/fvTools.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,844 copying diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,846 copying diploshic/setup.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,847 copying diploshic/msTools.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,849 copying diploshic/makeTrainingSets.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,851 copying diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,852 copying diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,854 copying diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/lib.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:57,857 running build_ext 2023-11-24T03:05:57,867 INFO: customize UnixCCompiler 2023-11-24T03:05:57,868 INFO: customize UnixCCompiler using build_ext 2023-11-24T03:05:57,995 INFO: CCompilerOpt.cc_test_cexpr[1098] : testing compiler expression defined(__ARM_ARCH_7__) || defined(__ARM_ARCH_7A__) 2023-11-24T03:05:57,996 INFO: C compiler: arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-11-24T03:05:57,997 creating /tmp/tmp_9vs3h0h/tmp 2023-11-24T03:05:57,998 creating /tmp/tmp_9vs3h0h/tmp/tmp_9vs3h0h 2023-11-24T03:05:57,998 INFO: compile options: '-I/usr/include/python3.11 -c' 2023-11-24T03:05:58,065 WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.11 -c /tmp/tmp_9vs3h0h/npy_dist_test_cexpr.c -o /tmp/tmp_9vs3h0h/tmp/tmp_9vs3h0h/npy_dist_test_cexpr.o -MMD -MF /tmp/tmp_9vs3h0h/tmp/tmp_9vs3h0h/npy_dist_test_cexpr.o.d) failed with exit status 1 output -> 2023-11-24T03:05:58,065 /tmp/tmp_9vs3h0h/npy_dist_test_cexpr.c:2:6: error: #error "unsupported expression" 2023-11-24T03:05:58,066 2 | #error "unsupported expression" 2023-11-24T03:05:58,067 | ^~~~~ 2023-11-24T03:05:58,074 WARN: CCompilerOpt.cc_test_cexpr[1109] : testing failed 2023-11-24T03:05:58,084 WARN: CCompilerOpt.__init__[1025] : unable to detect CPU architecture which lead to disable the optimization. check dist_info:<< 2023-11-24T03:05:58,084 ('linux-armv7l', 'arm-linux-gnueabihf-gcc', '-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2') 2023-11-24T03:05:58,085 >> 2023-11-24T03:05:58,093 INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-march=native) 2023-11-24T03:05:58,093 INFO: C compiler: arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-11-24T03:05:58,094 creating /tmp/tmp_9vs3h0h/tmp/pip-build-env-bnfn1d_b 2023-11-24T03:05:58,095 creating /tmp/tmp_9vs3h0h/tmp/pip-build-env-bnfn1d_b/overlay 2023-11-24T03:05:58,096 creating /tmp/tmp_9vs3h0h/tmp/pip-build-env-bnfn1d_b/overlay/local 2023-11-24T03:05:58,096 creating /tmp/tmp_9vs3h0h/tmp/pip-build-env-bnfn1d_b/overlay/local/lib 2023-11-24T03:05:58,097 creating /tmp/tmp_9vs3h0h/tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11 2023-11-24T03:05:58,097 creating /tmp/tmp_9vs3h0h/tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages 2023-11-24T03:05:58,098 creating /tmp/tmp_9vs3h0h/tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy 2023-11-24T03:05:58,098 creating /tmp/tmp_9vs3h0h/tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy/distutils 2023-11-24T03:05:58,099 creating /tmp/tmp_9vs3h0h/tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy/distutils/checks 2023-11-24T03:05:58,100 INFO: compile options: '-I/usr/include/python3.11 -c' 2023-11-24T03:05:58,100 extra options: '-march=native' 2023-11-24T03:05:58,165 INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-O3) 2023-11-24T03:05:58,166 INFO: C compiler: arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-11-24T03:05:58,167 INFO: compile options: '-I/usr/include/python3.11 -c' 2023-11-24T03:05:58,168 extra options: '-O3' 2023-11-24T03:05:58,231 INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (-Werror) 2023-11-24T03:05:58,232 INFO: C compiler: arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-11-24T03:05:58,233 INFO: compile options: '-I/usr/include/python3.11 -c' 2023-11-24T03:05:58,233 extra options: '-Werror' 2023-11-24T03:05:58,296 INFO: CCompilerOpt.__init__[1795] : check requested baseline 2023-11-24T03:05:58,304 INFO: CCompilerOpt.__init__[1804] : check requested dispatch-able features 2023-11-24T03:05:58,311 INFO: CCompilerOpt.__init__[1820] : initialize targets groups 2023-11-24T03:05:58,319 INFO: CCompilerOpt.__init__[1822] : parse target group simd_test 2023-11-24T03:05:58,328 INFO: CCompilerOpt._parse_target_tokens[2033] : skip targets (VX SSE42 FMA4 AVX512F AVX512_SKX VSX3 VXE2 VXE (FMA3 AVX2) VSX2 VSX VSX4 SSE2 ASIMD XOP NEON) not part of baseline or dispatch-able features 2023-11-24T03:05:58,336 INFO: CCompilerOpt.generate_dispatch_header[2366] : generate CPU dispatch header: (build/src.linux-armv7l-3.11/numpy/distutils/include/npy_cpu_dispatch_config.h) 2023-11-24T03:05:58,343 WARN: CCompilerOpt.generate_dispatch_header[2375] : dispatch header dir build/src.linux-armv7l-3.11/numpy/distutils/include does not exist, creating it 2023-11-24T03:05:58,380 INFO: get_default_fcompiler: matching types: '['arm', 'gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor', 'fujitsu']' 2023-11-24T03:05:58,381 INFO: customize ArmFlangCompiler 2023-11-24T03:05:58,383 WARN: Could not locate executable armflang 2023-11-24T03:05:58,384 INFO: customize Gnu95FCompiler 2023-11-24T03:05:58,386 INFO: Found executable /usr/bin/gfortran 2023-11-24T03:05:58,406 INFO: customize Gnu95FCompiler 2023-11-24T03:05:58,426 INFO: customize Gnu95FCompiler using build_ext 2023-11-24T03:05:58,426 INFO: building 'diploshic.shicstats' extension 2023-11-24T03:05:58,427 INFO: compiling C sources 2023-11-24T03:05:58,427 INFO: C compiler: arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-11-24T03:05:58,428 creating build/temp.linux-armv7l-cpython-311/build 2023-11-24T03:05:58,429 creating build/temp.linux-armv7l-cpython-311/build/src.linux-armv7l-3.11 2023-11-24T03:05:58,430 creating build/temp.linux-armv7l-cpython-311/build/src.linux-armv7l-3.11/diploshic 2023-11-24T03:05:58,430 creating build/temp.linux-armv7l-cpython-311/diploshic 2023-11-24T03:05:58,431 creating build/temp.linux-armv7l-cpython-311/build/src.linux-armv7l-3.11/build 2023-11-24T03:05:58,431 creating build/temp.linux-armv7l-cpython-311/build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11 2023-11-24T03:05:58,432 creating build/temp.linux-armv7l-cpython-311/build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic 2023-11-24T03:05:58,432 INFO: compile options: '-Ibuild/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic -I/tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy/core/include -Ibuild/src.linux-armv7l-3.11/numpy/distutils/include -I/usr/include/python3.11 -c' 2023-11-24T03:05:58,439 INFO: arm-linux-gnueabihf-gcc: build/src.linux-armv7l-3.11/diploshic/shicstatsmodule.c 2023-11-24T03:05:58,440 INFO: arm-linux-gnueabihf-gcc: diploshic/utils.c 2023-11-24T03:05:58,442 INFO: arm-linux-gnueabihf-gcc: build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic/fortranobject.c 2023-11-24T03:06:00,585 INFO: compiling Fortran sources 2023-11-24T03:06:00,586 INFO: Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops 2023-11-24T03:06:00,586 Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops 2023-11-24T03:06:00,587 Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops 2023-11-24T03:06:00,587 INFO: compile options: '-Ibuild/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic -I/tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/numpy/core/include -Ibuild/src.linux-armv7l-3.11/numpy/distutils/include -I/usr/include/python3.11 -c' 2023-11-24T03:06:00,588 INFO: gfortran:f77: build/src.linux-armv7l-3.11/diploshic/shicstats-f2pywrappers.f 2023-11-24T03:06:00,639 INFO: /usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-armv7l-cpython-311/build/src.linux-armv7l-3.11/diploshic/shicstatsmodule.o build/temp.linux-armv7l-cpython-311/diploshic/utils.o build/temp.linux-armv7l-cpython-311/build/src.linux-armv7l-3.11/build/src.linux-armv7l-3.11/diploshic/fortranobject.o build/temp.linux-armv7l-cpython-311/build/src.linux-armv7l-3.11/diploshic/shicstats-f2pywrappers.o -L/usr/lib/gcc/arm-linux-gnueabihf/12 -L/usr/lib/gcc/arm-linux-gnueabihf/12 -L/usr/lib/arm-linux-gnueabihf -lgfortran -o build/lib.linux-armv7l-cpython-311/diploshic/shicstats.cpython-311-arm-linux-gnueabihf.so 2023-11-24T03:06:00,770 running build_scripts 2023-11-24T03:06:00,771 creating build/scripts.linux-armv7l-3.11 2023-11-24T03:06:00,772 copying and adjusting diploshic/diploSHIC -> build/scripts.linux-armv7l-3.11 2023-11-24T03:06:00,775 copying diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/scripts.linux-armv7l-3.11 2023-11-24T03:06:00,778 copying diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/scripts.linux-armv7l-3.11 2023-11-24T03:06:00,780 copying diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/scripts.linux-armv7l-3.11 2023-11-24T03:06:00,782 copying diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/scripts.linux-armv7l-3.11 2023-11-24T03:06:00,784 copying diploshic/makeTrainingSets.py -> build/scripts.linux-armv7l-3.11 2023-11-24T03:06:00,786 changing mode of build/scripts.linux-armv7l-3.11/diploSHIC from 644 to 755 2023-11-24T03:06:00,786 changing mode of build/scripts.linux-armv7l-3.11/makeFeatureVecsForChrArmFromVcfDiploid.py from 644 to 755 2023-11-24T03:06:00,787 changing mode of build/scripts.linux-armv7l-3.11/makeFeatureVecsForChrArmFromVcf_ogSHIC.py from 644 to 755 2023-11-24T03:06:00,787 changing mode of build/scripts.linux-armv7l-3.11/makeFeatureVecsForSingleMsDiploid.py from 644 to 755 2023-11-24T03:06:00,788 changing mode of build/scripts.linux-armv7l-3.11/makeFeatureVecsForSingleMs_ogSHIC.py from 644 to 755 2023-11-24T03:06:00,789 changing mode of build/scripts.linux-armv7l-3.11/makeTrainingSets.py from 644 to 755 2023-11-24T03:06:00,793 installing to build/bdist.linux-armv7l/wheel 2023-11-24T03:06:00,794 running install 2023-11-24T03:06:00,817 running install_lib 2023-11-24T03:06:00,824 creating build/bdist.linux-armv7l 2023-11-24T03:06:00,824 creating build/bdist.linux-armv7l/wheel 2023-11-24T03:06:00,826 creating build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,827 copying build/lib.linux-armv7l-cpython-311/diploshic/generateSimLaunchScript.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,829 copying build/lib.linux-armv7l-cpython-311/diploshic/__init__.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,830 copying build/lib.linux-armv7l-cpython-311/diploshic/misc.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,832 copying build/lib.linux-armv7l-cpython-311/diploshic/fvTools.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,835 copying build/lib.linux-armv7l-cpython-311/diploshic/makeFeatureVecsForSingleMs_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,837 copying build/lib.linux-armv7l-cpython-311/diploshic/setup.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,839 copying build/lib.linux-armv7l-cpython-311/diploshic/shicstats.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,843 copying build/lib.linux-armv7l-cpython-311/diploshic/msTools.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,845 copying build/lib.linux-armv7l-cpython-311/diploshic/makeTrainingSets.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,847 copying build/lib.linux-armv7l-cpython-311/diploshic/makeFeatureVecsForSingleMsDiploid.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,849 copying build/lib.linux-armv7l-cpython-311/diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,851 copying build/lib.linux-armv7l-cpython-311/diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/bdist.linux-armv7l/wheel/diploshic 2023-11-24T03:06:00,853 running install_egg_info 2023-11-24T03:06:00,858 running egg_info 2023-11-24T03:06:00,862 writing diploSHIC.egg-info/PKG-INFO 2023-11-24T03:06:00,865 writing dependency_links to diploSHIC.egg-info/dependency_links.txt 2023-11-24T03:06:00,866 writing requirements to diploSHIC.egg-info/requires.txt 2023-11-24T03:06:00,867 writing top-level names to diploSHIC.egg-info/top_level.txt 2023-11-24T03:06:00,871 /tmp/pip-build-env-bnfn1d_b/overlay/local/lib/python3.11/dist-packages/setuptools/command/sdist.py:125: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`. 2023-11-24T03:06:00,872 !! 2023-11-24T03:06:00,872 ******************************************************************************** 2023-11-24T03:06:00,873 Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2023-11-24T03:06:00,873 Please extend command classes from setuptools instead of distutils. 2023-11-24T03:06:00,875 See https://peps.python.org/pep-0632/ for details. 2023-11-24T03:06:00,875 ******************************************************************************** 2023-11-24T03:06:00,876 !! 2023-11-24T03:06:00,877 self._add_data_files(self._safe_data_files(build_py)) 2023-11-24T03:06:00,878 reading manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-11-24T03:06:00,880 reading manifest template 'MANIFEST.in' 2023-11-24T03:06:00,881 warning: no files found matching 'diploshic/testEmpirical.fvec' 2023-11-24T03:06:00,882 adding license file 'LICENSE' 2023-11-24T03:06:00,885 writing manifest file 'diploSHIC.egg-info/SOURCES.txt' 2023-11-24T03:06:00,887 Copying diploSHIC.egg-info to build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5-py3.11.egg-info 2023-11-24T03:06:00,898 running install_scripts 2023-11-24T03:06:00,899 creating build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data 2023-11-24T03:06:00,900 creating build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T03:06:00,901 copying build/scripts.linux-armv7l-3.11/makeFeatureVecsForSingleMs_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T03:06:00,903 copying build/scripts.linux-armv7l-3.11/diploSHIC -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T03:06:00,906 copying build/scripts.linux-armv7l-3.11/makeTrainingSets.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T03:06:00,908 copying build/scripts.linux-armv7l-3.11/makeFeatureVecsForSingleMsDiploid.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T03:06:00,910 copying build/scripts.linux-armv7l-3.11/makeFeatureVecsForChrArmFromVcf_ogSHIC.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T03:06:00,912 copying build/scripts.linux-armv7l-3.11/makeFeatureVecsForChrArmFromVcfDiploid.py -> build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts 2023-11-24T03:06:00,914 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/makeFeatureVecsForSingleMs_ogSHIC.py to 755 2023-11-24T03:06:00,914 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/diploSHIC to 755 2023-11-24T03:06:00,914 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/makeTrainingSets.py to 755 2023-11-24T03:06:00,915 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/makeFeatureVecsForSingleMsDiploid.py to 755 2023-11-24T03:06:00,915 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/makeFeatureVecsForChrArmFromVcf_ogSHIC.py to 755 2023-11-24T03:06:00,916 changing mode of build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.data/scripts/makeFeatureVecsForChrArmFromVcfDiploid.py to 755 2023-11-24T03:06:00,916 running install_clib 2023-11-24T03:06:00,917 INFO: customize UnixCCompiler 2023-11-24T03:06:00,967 creating build/bdist.linux-armv7l/wheel/diploSHIC-1.0.5.dist-info/WHEEL 2023-11-24T03:06:00,970 creating '/tmp/pip-wheel-aq1zrgvu/.tmp-k4iohw0b/diploSHIC-1.0.5-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-11-24T03:06:00,974 adding 'diploSHIC-1.0.5.data/scripts/diploSHIC' 2023-11-24T03:06:00,976 adding 'diploSHIC-1.0.5.data/scripts/makeFeatureVecsForChrArmFromVcfDiploid.py' 2023-11-24T03:06:00,978 adding 'diploSHIC-1.0.5.data/scripts/makeFeatureVecsForChrArmFromVcf_ogSHIC.py' 2023-11-24T03:06:00,980 adding 'diploSHIC-1.0.5.data/scripts/makeFeatureVecsForSingleMsDiploid.py' 2023-11-24T03:06:00,982 adding 'diploSHIC-1.0.5.data/scripts/makeFeatureVecsForSingleMs_ogSHIC.py' 2023-11-24T03:06:00,984 adding 'diploSHIC-1.0.5.data/scripts/makeTrainingSets.py' 2023-11-24T03:06:00,987 adding 'diploshic/__init__.py' 2023-11-24T03:06:00,991 adding 'diploshic/fvTools.py' 2023-11-24T03:06:00,993 adding 'diploshic/generateSimLaunchScript.py' 2023-11-24T03:06:00,995 adding 'diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py' 2023-11-24T03:06:00,997 adding 'diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py' 2023-11-24T03:06:00,999 adding 'diploshic/makeFeatureVecsForSingleMsDiploid.py' 2023-11-24T03:06:01,000 adding 'diploshic/makeFeatureVecsForSingleMs_ogSHIC.py' 2023-11-24T03:06:01,002 adding 'diploshic/makeTrainingSets.py' 2023-11-24T03:06:01,004 adding 'diploshic/misc.py' 2023-11-24T03:06:01,006 adding 'diploshic/msTools.py' 2023-11-24T03:06:01,007 adding 'diploshic/setup.py' 2023-11-24T03:06:01,033 adding 'diploshic/shicstats.cpython-311-arm-linux-gnueabihf.so' 2023-11-24T03:06:01,035 adding 'diploSHIC-1.0.5.dist-info/LICENSE' 2023-11-24T03:06:01,038 adding 'diploSHIC-1.0.5.dist-info/METADATA' 2023-11-24T03:06:01,039 adding 'diploSHIC-1.0.5.dist-info/WHEEL' 2023-11-24T03:06:01,040 adding 'diploSHIC-1.0.5.dist-info/top_level.txt' 2023-11-24T03:06:01,041 adding 'diploSHIC-1.0.5.dist-info/RECORD' 2023-11-24T03:06:01,043 removing build/bdist.linux-armv7l/wheel 2023-11-24T03:06:01,052 INFO: 2023-11-24T03:06:01,053 ########### EXT COMPILER OPTIMIZATION ########### 2023-11-24T03:06:01,053 INFO: Platform : 2023-11-24T03:06:01,054 Architecture: unsupported 2023-11-24T03:06:01,054 Compiler : gcc 2023-11-24T03:06:01,055 CPU baseline : 2023-11-24T03:06:01,056 Requested : optimization disabled 2023-11-24T03:06:01,056 Enabled : none 2023-11-24T03:06:01,057 Flags : none 2023-11-24T03:06:01,057 Extra checks: none 2023-11-24T03:06:01,057 Requested : optimization disabled 2023-11-24T03:06:01,058 CPU dispatch : 2023-11-24T03:06:01,059 Enabled : none 2023-11-24T03:06:01,059 Generated : none 2023-11-24T03:06:01,059 INFO: CCompilerOpt.cache_flush[864] : write cache to path -> /tmp/pip-wheel-ic8730qt/diploshic_635cc5aad7d046a3a6c87328df25abd8/build/temp.linux-armv7l-cpython-311/ccompiler_opt_cache_ext.py 2023-11-24T03:06:01,231 Building wheel for diploshic (pyproject.toml): finished with status 'done' 2023-11-24T03:06:01,237 Created wheel for diploshic: filename=diploSHIC-1.0.5-cp311-cp311-linux_armv7l.whl size=115515 sha256=d678d3f25afea80ef9c8ea0ac31533b388392df5cda0905cc3595b87bf8bf786 2023-11-24T03:06:01,239 Stored in directory: /tmp/pip-ephem-wheel-cache-leuaweqj/wheels/41/7b/45/506392239873dfa22d0e64f600481612b29cc3f57870149cf3 2023-11-24T03:06:01,251 Successfully built diploshic 2023-11-24T03:06:01,257 Removed build tracker: '/tmp/pip-build-tracker-lvh9j3gr'