2023-09-15T04:33:53,684 Created temporary directory: /tmp/pip-build-tracker-oyrgt4cw 2023-09-15T04:33:53,688 Initialized build tracking at /tmp/pip-build-tracker-oyrgt4cw 2023-09-15T04:33:53,689 Created build tracker: /tmp/pip-build-tracker-oyrgt4cw 2023-09-15T04:33:53,689 Entered build tracker: /tmp/pip-build-tracker-oyrgt4cw 2023-09-15T04:33:53,690 Created temporary directory: /tmp/pip-wheel-7bwek8ud 2023-09-15T04:33:53,694 Created temporary directory: /tmp/pip-ephem-wheel-cache-xklf2_br 2023-09-15T04:33:53,728 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-15T04:33:53,732 2 location(s) to search for versions of denovonear: 2023-09-15T04:33:53,732 * https://pypi.org/simple/denovonear/ 2023-09-15T04:33:53,732 * https://www.piwheels.org/simple/denovonear/ 2023-09-15T04:33:53,733 Fetching project page and analyzing links: https://pypi.org/simple/denovonear/ 2023-09-15T04:33:53,733 Getting page https://pypi.org/simple/denovonear/ 2023-09-15T04:33:53,735 Found index url https://pypi.org/simple/ 2023-09-15T04:33:53,874 Fetched page https://pypi.org/simple/denovonear/ as application/vnd.pypi.simple.v1+json 2023-09-15T04:33:53,887 Found link https://files.pythonhosted.org/packages/5f/25/aa72bf3769052c8002b830283a8bbacb2cd6e1a2a22c12ee9859022fece0/denovonear-0.5.0.tar.gz (from https://pypi.org/simple/denovonear/), version: 0.5.0 2023-09-15T04:33:53,887 Found link https://files.pythonhosted.org/packages/0a/62/5608d43d65589a21a7f6b725ec78fcce289da0e725280b7d874f8ddbe3ad/denovonear-0.5.1.tar.gz (from https://pypi.org/simple/denovonear/), version: 0.5.1 2023-09-15T04:33:53,888 Found link https://files.pythonhosted.org/packages/75/b3/535a16bff66cb3cb259afae1d4e1003258b4cb4af7bc81c7b2c76adc6ff2/denovonear-0.5.2.tar.gz (from https://pypi.org/simple/denovonear/), version: 0.5.2 2023-09-15T04:33:53,889 Found link 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https://files.pythonhosted.org/packages/c4/17/06377d6ebd931ec0d1bcd7b2c0df67da483d90cc59503a4fe5c163cd6c14/denovonear-0.8.1.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.8.1 2023-09-15T04:33:53,895 Found link https://files.pythonhosted.org/packages/ef/b4/e860d4a4ead9864f588d6a02e1d5f5f4faa83f7c90991c5665d0161cbd55/denovonear-0.8.2.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.8.2 2023-09-15T04:33:53,896 Found link https://files.pythonhosted.org/packages/a8/fb/8601613cae1e1165ca87dd3f39442ae6f72768d1854cf05fc91fe54c74e3/denovonear-0.8.4.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.8.4 2023-09-15T04:33:53,897 Found link https://files.pythonhosted.org/packages/5e/40/6235d5a69a1954d94ffd5fe8db17ae0825866255cc69b8caf3057df33ec3/denovonear-0.8.5.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.8.5 2023-09-15T04:33:53,898 Found link https://files.pythonhosted.org/packages/51/a0/1e7699fe5b5a6ab27d2916c14ff76000d8026f85a668b1b50c7b51cdf187/denovonear-0.8.6.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.8.6 2023-09-15T04:33:53,899 Found link https://files.pythonhosted.org/packages/05/b7/51b6fa99afd7e2f06e37c1fb17f4e718dfe6fd88f99923aa504ba91c0d21/denovonear-0.9.0.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.0 2023-09-15T04:33:53,900 Found link https://files.pythonhosted.org/packages/ae/32/7045cbf27fe7e43ae39cba1d19346228c7b0a1024a66a8dcab60945c751e/denovonear-0.9.1.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.1 2023-09-15T04:33:53,901 Found link https://files.pythonhosted.org/packages/d1/cc/a5808715b8059599540330936ecfabfccc30e7ecdb8e8b887f457dd986d2/denovonear-0.9.2.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.2 2023-09-15T04:33:53,902 Found link https://files.pythonhosted.org/packages/93/ff/4342795158be053b54c5d74cb0fcd52feeb33e61155ccb76d437cd06b139/denovonear-0.9.3.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.3 2023-09-15T04:33:53,902 Found link https://files.pythonhosted.org/packages/02/48/8f2b2f11c127e1bf317ae078a555b85bb2665f70cf6672bd0414fbbd7fd0/denovonear-0.9.4.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.4 2023-09-15T04:33:53,903 Found link https://files.pythonhosted.org/packages/62/a1/6b40eaef00037c3c56e82f095d753df6d599f8f874febc3ee03156ca64a1/denovonear-0.9.5.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.5 2023-09-15T04:33:53,904 Found link https://files.pythonhosted.org/packages/01/46/239a02cf2658b4d90cfd6cd992f4bdfd005470dab0f80059bb1d8f2b0cbd/denovonear-0.9.6.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.6 2023-09-15T04:33:53,905 Found link https://files.pythonhosted.org/packages/69/66/64b9e8478912776a898522ec981e17ea828f0d2404a202822a1bf8f17924/denovonear-0.9.7.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.7 2023-09-15T04:33:53,906 Found link https://files.pythonhosted.org/packages/1d/ab/fde01a1b55c35ed26ac2efab95c534885523e1deb326b73a26c85729ff3d/denovonear-0.9.8.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.8 2023-09-15T04:33:53,907 Found link https://files.pythonhosted.org/packages/68/27/a9d9b5774581f96b261e6e3ad29d507b758b00f439ba79395bfb2308c899/denovonear-0.9.9.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.9 2023-09-15T04:33:53,908 Found link https://files.pythonhosted.org/packages/96/33/ac5e75b03040450f4641a95439641072b601fad0907cd741c195ffbe8e3e/denovonear-0.9.10.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.10 2023-09-15T04:33:53,909 Found link https://files.pythonhosted.org/packages/12/9f/45dedde087739cf468a82e996894170ca0d714f6fea3f5d51b271f901dce/denovonear-0.9.11.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.11 2023-09-15T04:33:53,910 Found link https://files.pythonhosted.org/packages/be/7c/9ea6d2254514972a9fdc7ae5c63f9fd9fadc806ca1ecd2a9736dc562a7bf/denovonear-0.9.12.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.12 2023-09-15T04:33:53,911 Found link https://files.pythonhosted.org/packages/a8/81/98b198863831fedfca0a2258b11f5bf3547c26b77161b5e4c4fce756bb7d/denovonear-0.9.13.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.13 2023-09-15T04:33:53,912 Found link https://files.pythonhosted.org/packages/65/82/fe860fc52789f6a1fa32fa956b7da6b9ab5fa86a5daedc3a3ff9c75c1dbb/denovonear-0.9.14.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.14 2023-09-15T04:33:53,913 Found link https://files.pythonhosted.org/packages/e9/2e/233efc6d4174fabf974ddfe3f374756e2f2215fb0f04fc87e27699ba4034/denovonear-0.9.15.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.6), version: 0.9.15 2023-09-15T04:33:53,913 Skipping link: No binaries permitted for denovonear: https://files.pythonhosted.org/packages/63/83/1ec946a2d408725339ef473840a42494aaa99277a3e2241c80dbbab6a4ef/denovonear-0.9.16-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,914 Skipping link: No binaries permitted for denovonear: https://files.pythonhosted.org/packages/fb/ad/77cae8401c9c2ff178c5aa03349df040a05d24571bbb777a852b1b62a225/denovonear-0.9.16-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,914 Skipping link: No binaries permitted for denovonear: https://files.pythonhosted.org/packages/16/04/503acaa318f3c9a4e58bcb1d1c026c4f7bdc839c6117de46c991e699f629/denovonear-0.9.16-cp310-cp310-win_amd64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,915 Skipping link: No binaries permitted for denovonear: https://files.pythonhosted.org/packages/1e/b7/6963ea9d2cb7ed6b5b6d56e8448326a372119ea56de39ecbb0927d1bb088/denovonear-0.9.16-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,915 Skipping link: No binaries permitted for denovonear: https://files.pythonhosted.org/packages/0a/15/fdbe384253c46962dc9b9a83ed761d64b14b793addd421019698555d7deb/denovonear-0.9.16-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,916 Skipping link: No binaries permitted for denovonear: 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https://files.pythonhosted.org/packages/d6/5e/ff94336bbde5276639186d9a16d19e2aaeee72944f6478a293021bb2a269/denovonear-0.9.16-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,920 Found link https://files.pythonhosted.org/packages/1c/75/d9936d228b26ca2fa0a00fbd5d14c2b9b7af9f54f4f1afe5b563fea7f156/denovonear-0.9.16.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8), version: 0.9.16 2023-09-15T04:33:53,921 Skipping link: No binaries permitted for denovonear: https://files.pythonhosted.org/packages/26/52/36cc61443eab7e14895ff3cecc1ff21764c519723704b8d5e598e035579e/denovonear-0.10.0-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,921 Skipping link: No binaries permitted for denovonear: 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https://files.pythonhosted.org/packages/1f/fc/9d8d58b517a47544a7c1f85c73fbd2e7f9513bcfa8f092b9587aa4900802/denovonear-0.10.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,925 Skipping link: No binaries permitted for denovonear: https://files.pythonhosted.org/packages/64/96/174090fb6d252d7257e2c72e6fba8488cb5c98edb8804491aac7410b8f4a/denovonear-0.10.0-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,925 Skipping link: No binaries permitted for denovonear: https://files.pythonhosted.org/packages/cc/8c/c1a5c81607701adc2271510014ad2019456c05e2875b88bd43e96f3c01c9/denovonear-0.10.0-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,926 Skipping link: No binaries permitted for denovonear: 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https://files.pythonhosted.org/packages/17/4d/a6d42f793b4f33a7a662f0eb10f2d8dd1b0f4d021d6ee91ac317272ad07b/denovonear-0.10.1-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,933 Skipping link: No binaries permitted for denovonear: https://files.pythonhosted.org/packages/d5/a5/70a4c7f8ea55a6c28c1af39596a130bdcc810c4662f9a8f2728a09cb9dac/denovonear-0.10.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,933 Skipping link: No binaries permitted for denovonear: https://files.pythonhosted.org/packages/c0/89/988085dcb87761d53e23a722036428803bf44b4657109b5184f3e42f28ce/denovonear-0.10.1-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:53,934 Found link https://files.pythonhosted.org/packages/31/22/96469c9f34d20dd92581f79d349824e50613d8e8f93213d8f9006d2fc68e/denovonear-0.10.1.tar.gz (from https://pypi.org/simple/denovonear/) (requires-python:>=3.8), version: 0.10.1 2023-09-15T04:33:53,935 Fetching project page and analyzing links: https://www.piwheels.org/simple/denovonear/ 2023-09-15T04:33:53,935 Getting page https://www.piwheels.org/simple/denovonear/ 2023-09-15T04:33:53,937 Found index url https://www.piwheels.org/simple/ 2023-09-15T04:33:54,202 Fetched page https://www.piwheels.org/simple/denovonear/ as text/html 2023-09-15T04:33:54,251 Skipping link: No binaries permitted for denovonear: https://www.piwheels.org/simple/denovonear/denovonear-0.10.1-cp39-cp39-linux_armv7l.whl#sha256=74213d76f9c959594d135e0638d35ccfb4383603c233f3ab7dbcf15fdf9ba755 (from https://www.piwheels.org/simple/denovonear/) (requires-python:>=3.8) 2023-09-15T04:33:54,251 Skipping link: No binaries permitted for denovonear: 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https://www.piwheels.org/simple/denovonear/denovonear-0.5.1-cp39-cp39-linux_armv6l.whl#sha256=598cd12d23cbf8b85f25def9743994bdeb2538dc91244253bcaa93ac5f3f7bf3 (from https://www.piwheels.org/simple/denovonear/) 2023-09-15T04:33:54,353 Skipping link: No binaries permitted for denovonear: https://www.piwheels.org/simple/denovonear/denovonear-0.5.1-cp37-cp37m-linux_armv6l.whl#sha256=681cc5b7d29e939b82caa7090b39cd4cc7f8e8d9b1185cad2a3cdcd6efb4b187 (from https://www.piwheels.org/simple/denovonear/) 2023-09-15T04:33:54,354 Skipping link: No binaries permitted for denovonear: https://www.piwheels.org/simple/denovonear/denovonear-0.5.1-cp37-cp37m-linux_armv7l.whl#sha256=681cc5b7d29e939b82caa7090b39cd4cc7f8e8d9b1185cad2a3cdcd6efb4b187 (from https://www.piwheels.org/simple/denovonear/) 2023-09-15T04:33:54,354 Skipping link: No binaries permitted for denovonear: https://www.piwheels.org/simple/denovonear/denovonear-0.5.1-cp34-cp34m-linux_armv7l.whl#sha256=4a835657600bbe4fbd1610bb49d3db23fb8bb50f08bf25d9b19c511d9ce23e1f (from https://www.piwheels.org/simple/denovonear/) 2023-09-15T04:33:54,355 Skipping link: No binaries permitted for denovonear: https://www.piwheels.org/simple/denovonear/denovonear-0.5.1-cp34-cp34m-linux_armv6l.whl#sha256=4a835657600bbe4fbd1610bb49d3db23fb8bb50f08bf25d9b19c511d9ce23e1f (from https://www.piwheels.org/simple/denovonear/) 2023-09-15T04:33:54,355 Skipping link: No binaries permitted for denovonear: https://www.piwheels.org/simple/denovonear/denovonear-0.5.1-cp35-cp35m-linux_armv6l.whl#sha256=0ee6166f9c1ac9fff8a335ae0af7d21db6457276ec38258e3e7aa8e8a6fd6fb7 (from https://www.piwheels.org/simple/denovonear/) 2023-09-15T04:33:54,356 Skipping link: No binaries permitted for denovonear: https://www.piwheels.org/simple/denovonear/denovonear-0.5.1-cp35-cp35m-linux_armv7l.whl#sha256=0ee6166f9c1ac9fff8a335ae0af7d21db6457276ec38258e3e7aa8e8a6fd6fb7 (from https://www.piwheels.org/simple/denovonear/) 2023-09-15T04:33:54,356 Skipping link: No binaries permitted for denovonear: https://www.piwheels.org/simple/denovonear/denovonear-0.5.0-py3-none-any.whl#sha256=2c89b66f43fab8b25680fd49e32aebb2a208618abce5f0474c0fcc92fda022e6 (from https://www.piwheels.org/simple/denovonear/) 2023-09-15T04:33:54,357 Skipping link: not a file: https://www.piwheels.org/simple/denovonear/ 2023-09-15T04:33:54,357 Skipping link: not a file: https://pypi.org/simple/denovonear/ 2023-09-15T04:33:54,380 Given no hashes to check 1 links for project 'denovonear': discarding no candidates 2023-09-15T04:33:54,398 Collecting denovonear==0.9.7 2023-09-15T04:33:54,400 Created temporary directory: /tmp/pip-unpack-ek511bs8 2023-09-15T04:33:54,616 Downloading denovonear-0.9.7.tar.gz (320 kB) 2023-09-15T04:33:54,908 Added denovonear==0.9.7 from https://files.pythonhosted.org/packages/69/66/64b9e8478912776a898522ec981e17ea828f0d2404a202822a1bf8f17924/denovonear-0.9.7.tar.gz to build tracker '/tmp/pip-build-tracker-oyrgt4cw' 2023-09-15T04:33:54,913 Created temporary directory: /tmp/pip-build-env-mbmg0slr 2023-09-15T04:33:54,917 Installing build dependencies: started 2023-09-15T04:33:54,919 Running command pip subprocess to install build dependencies 2023-09-15T04:33:56,078 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-15T04:33:56,573 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-15T04:33:58,336 Collecting cython 2023-09-15T04:33:58,337 Obtaining dependency information for cython from https://files.pythonhosted.org/packages/03/e9/9cc0c4f0d8a566089d096254cd25168a0db02dd047863a7f995d8d3eefa7/Cython-3.0.2-py2.py3-none-any.whl.metadata 2023-09-15T04:33:58,343 Using cached Cython-3.0.2-py2.py3-none-any.whl.metadata (3.1 kB) 2023-09-15T04:33:59,613 Collecting setuptools>=40.6.0 2023-09-15T04:33:59,614 Obtaining dependency information for setuptools>=40.6.0 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata 2023-09-15T04:33:59,620 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-15T04:33:59,825 Collecting wheel 2023-09-15T04:33:59,840 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-15T04:34:00,030 Using cached Cython-3.0.2-py2.py3-none-any.whl (1.2 MB) 2023-09-15T04:34:00,072 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-15T04:34:02,547 Installing collected packages: wheel, setuptools, cython 2023-09-15T04:34:02,779 Creating /tmp/pip-build-env-mbmg0slr/overlay/local/bin 2023-09-15T04:34:02,781 changing mode of /tmp/pip-build-env-mbmg0slr/overlay/local/bin/wheel to 755 2023-09-15T04:34:09,900 changing mode of /tmp/pip-build-env-mbmg0slr/overlay/local/bin/cygdb to 755 2023-09-15T04:34:09,902 changing mode of /tmp/pip-build-env-mbmg0slr/overlay/local/bin/cython to 755 2023-09-15T04:34:09,904 changing mode of /tmp/pip-build-env-mbmg0slr/overlay/local/bin/cythonize to 755 2023-09-15T04:34:09,930 Successfully installed cython-3.0.2 setuptools-68.2.2 wheel-0.41.2 2023-09-15T04:34:10,544 Installing build dependencies: finished with status 'done' 2023-09-15T04:34:10,557 Getting requirements to build wheel: started 2023-09-15T04:34:10,559 Running command Getting requirements to build wheel 2023-09-15T04:34:13,892 warning: denovonear/gencode.pyx:70:0: Global name __genome_ matched from within class scope in contradiction to to Python 'class private name' rules. This may change in a future release. 2023-09-15T04:34:13,892 warning: denovonear/gencode.pyx:70:0: Global name __genome_ matched from within class scope in contradiction to to Python 'class private name' rules. This may change in a future release. 2023-09-15T04:34:13,996 warning: denovonear/gencode.pyx:70:0: Global name __genome_ matched from within class scope in contradiction to to Python 'class private name' rules. This may change in a future release. 2023-09-15T04:34:14,000 warning: denovonear/gencode.pyx:70:0: Global name __genome_ matched from within class scope in contradiction to to Python 'class private name' rules. This may change in a future release. 2023-09-15T04:34:17,763 Compiling denovonear/weights.pyx because it changed. 2023-09-15T04:34:17,763 Compiling denovonear/transcript.pyx because it changed. 2023-09-15T04:34:17,764 Compiling denovonear/gencode.pyx because it changed. 2023-09-15T04:34:17,764 Compiling denovonear/site_specific_rates.pyx because it changed. 2023-09-15T04:34:17,765 [1/4] Cythonizing denovonear/gencode.pyx 2023-09-15T04:34:17,765 [2/4] Cythonizing denovonear/site_specific_rates.pyx 2023-09-15T04:34:17,766 [3/4] Cythonizing denovonear/transcript.pyx 2023-09-15T04:34:17,767 [4/4] Cythonizing denovonear/weights.pyx 2023-09-15T04:34:17,836 running egg_info 2023-09-15T04:34:17,842 writing denovonear.egg-info/PKG-INFO 2023-09-15T04:34:17,845 writing dependency_links to denovonear.egg-info/dependency_links.txt 2023-09-15T04:34:17,847 writing entry points to denovonear.egg-info/entry_points.txt 2023-09-15T04:34:17,848 writing requirements to denovonear.egg-info/requires.txt 2023-09-15T04:34:17,850 writing top-level names to denovonear.egg-info/top_level.txt 2023-09-15T04:34:17,888 reading manifest file 'denovonear.egg-info/SOURCES.txt' 2023-09-15T04:34:17,891 reading manifest template 'MANIFEST.in' 2023-09-15T04:34:17,899 adding license file 'LICENSE.txt' 2023-09-15T04:34:17,904 writing manifest file 'denovonear.egg-info/SOURCES.txt' 2023-09-15T04:34:18,259 Getting requirements to build wheel: finished with status 'done' 2023-09-15T04:34:18,269 Created temporary directory: /tmp/pip-modern-metadata-rxeg2ksj 2023-09-15T04:34:18,272 Preparing metadata (pyproject.toml): started 2023-09-15T04:34:18,273 Running command Preparing metadata (pyproject.toml) 2023-09-15T04:34:19,823 running dist_info 2023-09-15T04:34:19,842 creating /tmp/pip-modern-metadata-rxeg2ksj/denovonear.egg-info 2023-09-15T04:34:19,847 writing /tmp/pip-modern-metadata-rxeg2ksj/denovonear.egg-info/PKG-INFO 2023-09-15T04:34:19,850 writing dependency_links to /tmp/pip-modern-metadata-rxeg2ksj/denovonear.egg-info/dependency_links.txt 2023-09-15T04:34:19,852 writing entry points to /tmp/pip-modern-metadata-rxeg2ksj/denovonear.egg-info/entry_points.txt 2023-09-15T04:34:19,853 writing requirements to /tmp/pip-modern-metadata-rxeg2ksj/denovonear.egg-info/requires.txt 2023-09-15T04:34:19,854 writing top-level names to /tmp/pip-modern-metadata-rxeg2ksj/denovonear.egg-info/top_level.txt 2023-09-15T04:34:19,855 writing manifest file '/tmp/pip-modern-metadata-rxeg2ksj/denovonear.egg-info/SOURCES.txt' 2023-09-15T04:34:19,887 reading manifest file '/tmp/pip-modern-metadata-rxeg2ksj/denovonear.egg-info/SOURCES.txt' 2023-09-15T04:34:19,889 reading manifest template 'MANIFEST.in' 2023-09-15T04:34:19,896 adding license file 'LICENSE.txt' 2023-09-15T04:34:19,900 writing manifest file '/tmp/pip-modern-metadata-rxeg2ksj/denovonear.egg-info/SOURCES.txt' 2023-09-15T04:34:19,901 creating '/tmp/pip-modern-metadata-rxeg2ksj/denovonear-0.9.7.dist-info' 2023-09-15T04:34:20,112 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-15T04:34:20,117 Source in /tmp/pip-wheel-7bwek8ud/denovonear_c24ddeff72ce4dda93c76b620c3cfa66 has version 0.9.7, which satisfies requirement denovonear==0.9.7 from https://files.pythonhosted.org/packages/69/66/64b9e8478912776a898522ec981e17ea828f0d2404a202822a1bf8f17924/denovonear-0.9.7.tar.gz 2023-09-15T04:34:20,118 Removed denovonear==0.9.7 from https://files.pythonhosted.org/packages/69/66/64b9e8478912776a898522ec981e17ea828f0d2404a202822a1bf8f17924/denovonear-0.9.7.tar.gz from build tracker '/tmp/pip-build-tracker-oyrgt4cw' 2023-09-15T04:34:20,124 Created temporary directory: /tmp/pip-unpack-3p85qge9 2023-09-15T04:34:20,124 Created temporary directory: /tmp/pip-unpack-agt_naen 2023-09-15T04:34:20,135 Building wheels for collected packages: denovonear 2023-09-15T04:34:20,139 Created temporary directory: /tmp/pip-wheel-m04ygnw1 2023-09-15T04:34:20,139 Destination directory: /tmp/pip-wheel-m04ygnw1 2023-09-15T04:34:20,141 Building wheel for denovonear (pyproject.toml): started 2023-09-15T04:34:20,143 Running command Building wheel for denovonear (pyproject.toml) 2023-09-15T04:34:21,459 running bdist_wheel 2023-09-15T04:34:21,504 running build 2023-09-15T04:34:21,505 running build_py 2023-09-15T04:34:21,512 creating build 2023-09-15T04:34:21,513 creating build/lib.linux-armv7l-cpython-311 2023-09-15T04:34:21,514 creating build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,515 copying denovonear/ensembl_cache.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,519 copying denovonear/load_mutation_rates.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,522 copying denovonear/log_transform_rates.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,526 copying denovonear/__init__.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,529 copying denovonear/ensembl_requester.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,532 copying denovonear/cluster_test.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,534 copying denovonear/rate_limiter.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,535 copying denovonear/rate_limiter_retries.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,537 copying denovonear/frameshift_rate.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,538 copying denovonear/simulate.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,540 copying denovonear/__main__.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,542 copying denovonear/load_gene.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,544 copying denovonear/load_de_novos.py -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,546 creating build/lib.linux-armv7l-cpython-311/denovonear/data 2023-09-15T04:34:21,547 copying denovonear/data/rates.txt -> build/lib.linux-armv7l-cpython-311/denovonear/data 2023-09-15T04:34:21,550 copying denovonear/weights.pxd -> build/lib.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,552 running build_ext 2023-09-15T04:34:21,558 building 'denovonear.weights' extension 2023-09-15T04:34:21,559 creating build/temp.linux-armv7l-cpython-311 2023-09-15T04:34:21,559 creating build/temp.linux-armv7l-cpython-311/denovonear 2023-09-15T04:34:21,560 creating build/temp.linux-armv7l-cpython-311/src 2023-09-15T04:34:21,561 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -I/usr/include/python3.11 -c denovonear/weights.cpp -o build/temp.linux-armv7l-cpython-311/denovonear/weights.o -std=c++11 2023-09-15T04:34:30,940 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -I/usr/include/python3.11 -c src/simulate.cpp -o build/temp.linux-armv7l-cpython-311/src/simulate.o -std=c++11 2023-09-15T04:34:32,671 In file included from /usr/include/c++/12/bits/stl_algo.h:60, 2023-09-15T04:34:32,672 from /usr/include/c++/12/algorithm:61, 2023-09-15T04:34:32,673 from src/simulate.cpp:2: 2023-09-15T04:34:32,673 /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2023-09-15T04:34:32,674 /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:32,674 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2023-09-15T04:34:32,675 | ^~~~~~~~~~~~~ 2023-09-15T04:34:32,712 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2023-09-15T04:34:32,712 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:32,713 1802 | __insertion_sort(_RandomAccessIterator __first, 2023-09-15T04:34:32,714 | ^~~~~~~~~~~~~~~~ 2023-09-15T04:34:32,714 /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:32,763 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: 2023-09-15T04:34:32,763 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:32,764 1908 | __introsort_loop(_RandomAccessIterator __first, 2023-09-15T04:34:32,765 | ^~~~~~~~~~~~~~~~ 2023-09-15T04:34:32,765 /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:32,766 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:32,767 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2023-09-15T04:34:32,767 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:34:32,953 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, 2023-09-15T04:34:32,954 inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, 2023-09-15T04:34:32,955 inlined from ‘std::vector _simulate_distribution(Chooser&, int, int)’ at src/simulate.cpp:117:14: 2023-09-15T04:34:32,955 /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:32,956 1937 | std::__introsort_loop(__first, __last, 2023-09-15T04:34:32,956 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-15T04:34:32,957 1938 | std::__lg(__last - __first) * 2, 2023-09-15T04:34:32,957 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:34:32,958 1939 | __comp); 2023-09-15T04:34:32,958 | ~~~~~~~ 2023-09-15T04:34:32,959 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, 2023-09-15T04:34:32,960 inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, 2023-09-15T04:34:32,960 inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, 2023-09-15T04:34:32,961 inlined from ‘std::vector _simulate_distribution(Chooser&, int, int)’ at src/simulate.cpp:117:14: 2023-09-15T04:34:32,961 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:32,962 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2023-09-15T04:34:32,962 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:34:32,963 /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:32,964 1854 | std::__insertion_sort(__first, __last, __comp); 2023-09-15T04:34:32,964 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:34:33,488 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -I/usr/include/python3.11 -c src/weighted_choice.cpp -o build/temp.linux-armv7l-cpython-311/src/weighted_choice.o -std=c++11 2023-09-15T04:34:35,347 In file included from /usr/include/c++/12/vector:70, 2023-09-15T04:34:35,347 from /usr/include/c++/12/bits/random.h:34, 2023-09-15T04:34:35,348 from /usr/include/c++/12/random:49, 2023-09-15T04:34:35,349 from src/weighted_choice.cpp:1: 2023-09-15T04:34:35,349 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-15T04:34:35,350 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-15T04:34:35,350 439 | vector<_Tp, _Alloc>:: 2023-09-15T04:34:35,351 | ^~~~~~~~~~~~~~~~~~~ 2023-09-15T04:34:35,395 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AlleleChoice&}; _Tp = AlleleChoice; _Alloc = std::allocator]’: 2023-09-15T04:34:35,396 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-15T04:34:35,447 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {AlleleChoice}; _Tp = AlleleChoice; _Alloc = std::allocator]’: 2023-09-15T04:34:35,448 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-15T04:34:35,488 In file included from /usr/include/c++/12/vector:64: 2023-09-15T04:34:35,489 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-15T04:34:35,489 inlined from ‘void Chooser::add_choice(int, double, char, char, int)’ at src/weighted_choice.cpp:33:25: 2023-09-15T04:34:35,490 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:35,491 1287 | _M_realloc_insert(end(), __x); 2023-09-15T04:34:35,491 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-15T04:34:35,492 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlleleChoice}; _Tp = AlleleChoice; _Alloc = std::allocator]’, 2023-09-15T04:34:35,492 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = AlleleChoice; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-15T04:34:35,493 inlined from ‘void Chooser::add_choice(int, double, char, char, int)’ at src/weighted_choice.cpp:35:20: 2023-09-15T04:34:35,493 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:35,494 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-15T04:34:35,495 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:34:35,526 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-15T04:34:35,527 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-15T04:34:35,527 439 | vector<_Tp, _Alloc>:: 2023-09-15T04:34:35,528 | ^~~~~~~~~~~~~~~~~~~ 2023-09-15T04:34:35,568 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-15T04:34:35,569 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-15T04:34:35,570 inlined from ‘void Chooser::append(Chooser)’ at src/weighted_choice.cpp:84:29: 2023-09-15T04:34:35,570 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:35,571 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-15T04:34:35,572 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:34:35,572 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AlleleChoice; _Alloc = std::allocator]’, 2023-09-15T04:34:35,573 inlined from ‘void Chooser::append(Chooser)’ at src/weighted_choice.cpp:85:24: 2023-09-15T04:34:35,573 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:34:35,574 1287 | _M_realloc_insert(end(), __x); 2023-09-15T04:34:35,574 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-15T04:34:35,834 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/denovonear/weights.o build/temp.linux-armv7l-cpython-311/src/simulate.o build/temp.linux-armv7l-cpython-311/src/weighted_choice.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/denovonear/weights.cpython-311-arm-linux-gnueabihf.so 2023-09-15T04:34:36,107 building 'denovonear.transcript' extension 2023-09-15T04:34:36,108 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -I/usr/include/python3.11 -c denovonear/transcript.cpp -o build/temp.linux-armv7l-cpython-311/denovonear/transcript.o -std=c++11 2023-09-15T04:35:06,683 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -I/usr/include/python3.11 -c src/tx.cpp -o build/temp.linux-armv7l-cpython-311/src/tx.o -std=c++11 2023-09-15T04:35:14,879 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/denovonear/transcript.o build/temp.linux-armv7l-cpython-311/src/tx.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/denovonear/transcript.cpython-311-arm-linux-gnueabihf.so 2023-09-15T04:35:15,209 building 'denovonear.gencode' extension 2023-09-15T04:35:15,210 creating build/temp.linux-armv7l-cpython-311/src/gzstream 2023-09-15T04:35:15,211 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -Isrc/gzstream -I/usr/include/python3.11 -c denovonear/gencode.cpp -o build/temp.linux-armv7l-cpython-311/denovonear/gencode.o -std=c++11 2023-09-15T04:35:43,693 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -Isrc/gzstream -I/usr/include/python3.11 -c src/gencode.cpp -o build/temp.linux-armv7l-cpython-311/src/gencode.o -std=c++11 2023-09-15T04:35:53,868 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -Isrc/gzstream -I/usr/include/python3.11 -c src/gtf.cpp -o build/temp.linux-armv7l-cpython-311/src/gtf.o -std=c++11 2023-09-15T04:35:55,298 src/gtf.cpp: In function ‘void gencode::get_attributes_fields(GTFLine&, std::string&, int)’: 2023-09-15T04:35:55,299 src/gtf.cpp:24:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2023-09-15T04:35:55,299 24 | if (tx_start - 15 == std::string::npos) { 2023-09-15T04:35:55,300 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:35:55,301 src/gtf.cpp:33:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2023-09-15T04:35:55,302 33 | if (gene_start - 11 == std::string::npos) { 2023-09-15T04:35:55,302 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:35:55,303 src/gtf.cpp:42:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2023-09-15T04:35:55,304 42 | if (type_start - 17 == std::string::npos) { 2023-09-15T04:35:55,304 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:35:56,537 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -Isrc/gzstream -I/usr/include/python3.11 -c src/gzstream/gzstream.C -o build/temp.linux-armv7l-cpython-311/src/gzstream/gzstream.o -std=c++11 2023-09-15T04:35:58,111 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -Isrc/gzstream -I/usr/include/python3.11 -c src/tx.cpp -o build/temp.linux-armv7l-cpython-311/src/tx.o -std=c++11 2023-09-15T04:36:06,960 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/denovonear/gencode.o build/temp.linux-armv7l-cpython-311/src/gencode.o build/temp.linux-armv7l-cpython-311/src/gtf.o build/temp.linux-armv7l-cpython-311/src/gzstream/gzstream.o build/temp.linux-armv7l-cpython-311/src/tx.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/denovonear/gencode.cpython-311-arm-linux-gnueabihf.so 2023-09-15T04:36:07,445 building 'denovonear.site_specific_rates' extension 2023-09-15T04:36:07,446 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -I/usr/include/python3.11 -c denovonear/site_specific_rates.cpp -o build/temp.linux-armv7l-cpython-311/denovonear/site_specific_rates.o -std=c++11 2023-09-15T04:36:23,059 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -I/usr/include/python3.11 -c src/site_rates.cpp -o build/temp.linux-armv7l-cpython-311/src/site_rates.o -std=c++11 2023-09-15T04:36:28,312 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -I/usr/include/python3.11 -c src/tx.cpp -o build/temp.linux-armv7l-cpython-311/src/tx.o -std=c++11 2023-09-15T04:36:36,530 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Isrc/ -I/usr/include/python3.11 -c src/weighted_choice.cpp -o build/temp.linux-armv7l-cpython-311/src/weighted_choice.o -std=c++11 2023-09-15T04:36:38,399 In file included from /usr/include/c++/12/vector:70, 2023-09-15T04:36:38,400 from /usr/include/c++/12/bits/random.h:34, 2023-09-15T04:36:38,401 from /usr/include/c++/12/random:49, 2023-09-15T04:36:38,401 from src/weighted_choice.cpp:1: 2023-09-15T04:36:38,402 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-09-15T04:36:38,402 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-15T04:36:38,403 439 | vector<_Tp, _Alloc>:: 2023-09-15T04:36:38,403 | ^~~~~~~~~~~~~~~~~~~ 2023-09-15T04:36:38,448 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AlleleChoice&}; _Tp = AlleleChoice; _Alloc = std::allocator]’: 2023-09-15T04:36:38,449 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-15T04:36:38,500 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {AlleleChoice}; _Tp = AlleleChoice; _Alloc = std::allocator]’: 2023-09-15T04:36:38,501 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-15T04:36:38,541 In file included from /usr/include/c++/12/vector:64: 2023-09-15T04:36:38,542 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2023-09-15T04:36:38,543 inlined from ‘void Chooser::add_choice(int, double, char, char, int)’ at src/weighted_choice.cpp:33:25: 2023-09-15T04:36:38,543 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:36:38,544 1287 | _M_realloc_insert(end(), __x); 2023-09-15T04:36:38,544 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-15T04:36:38,544 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlleleChoice}; _Tp = AlleleChoice; _Alloc = std::allocator]’, 2023-09-15T04:36:38,545 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = AlleleChoice; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-15T04:36:38,546 inlined from ‘void Chooser::add_choice(int, double, char, char, int)’ at src/weighted_choice.cpp:35:20: 2023-09-15T04:36:38,546 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:36:38,547 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-15T04:36:38,547 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:36:38,580 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-09-15T04:36:38,581 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-15T04:36:38,582 439 | vector<_Tp, _Alloc>:: 2023-09-15T04:36:38,582 | ^~~~~~~~~~~~~~~~~~~ 2023-09-15T04:36:38,624 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, 2023-09-15T04:36:38,624 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-15T04:36:38,625 inlined from ‘void Chooser::append(Chooser)’ at src/weighted_choice.cpp:84:29: 2023-09-15T04:36:38,625 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:36:38,626 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-15T04:36:38,627 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-15T04:36:38,627 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AlleleChoice; _Alloc = std::allocator]’, 2023-09-15T04:36:38,628 inlined from ‘void Chooser::append(Chooser)’ at src/weighted_choice.cpp:85:24: 2023-09-15T04:36:38,629 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-15T04:36:38,630 1287 | _M_realloc_insert(end(), __x); 2023-09-15T04:36:38,630 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-09-15T04:36:38,890 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/denovonear/site_specific_rates.o build/temp.linux-armv7l-cpython-311/src/site_rates.o build/temp.linux-armv7l-cpython-311/src/tx.o build/temp.linux-armv7l-cpython-311/src/weighted_choice.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/denovonear/site_specific_rates.cpython-311-arm-linux-gnueabihf.so 2023-09-15T04:36:39,276 installing to build/bdist.linux-armv7l/wheel 2023-09-15T04:36:39,276 running install 2023-09-15T04:36:39,301 running install_lib 2023-09-15T04:36:39,308 creating build/bdist.linux-armv7l 2023-09-15T04:36:39,309 creating build/bdist.linux-armv7l/wheel 2023-09-15T04:36:39,311 creating build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,312 copying build/lib.linux-armv7l-cpython-311/denovonear/ensembl_cache.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,315 copying build/lib.linux-armv7l-cpython-311/denovonear/load_mutation_rates.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,317 creating build/bdist.linux-armv7l/wheel/denovonear/data 2023-09-15T04:36:39,318 copying build/lib.linux-armv7l-cpython-311/denovonear/data/rates.txt -> build/bdist.linux-armv7l/wheel/denovonear/data 2023-09-15T04:36:39,321 copying build/lib.linux-armv7l-cpython-311/denovonear/site_specific_rates.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,366 copying build/lib.linux-armv7l-cpython-311/denovonear/log_transform_rates.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,368 copying build/lib.linux-armv7l-cpython-311/denovonear/weights.pxd -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,371 copying build/lib.linux-armv7l-cpython-311/denovonear/__init__.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,373 copying build/lib.linux-armv7l-cpython-311/denovonear/ensembl_requester.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,375 copying build/lib.linux-armv7l-cpython-311/denovonear/cluster_test.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,378 copying build/lib.linux-armv7l-cpython-311/denovonear/rate_limiter.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,380 copying build/lib.linux-armv7l-cpython-311/denovonear/rate_limiter_retries.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,382 copying build/lib.linux-armv7l-cpython-311/denovonear/gencode.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,457 copying build/lib.linux-armv7l-cpython-311/denovonear/frameshift_rate.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,459 copying build/lib.linux-armv7l-cpython-311/denovonear/simulate.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,461 copying build/lib.linux-armv7l-cpython-311/denovonear/__main__.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,464 copying build/lib.linux-armv7l-cpython-311/denovonear/weights.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,478 copying build/lib.linux-armv7l-cpython-311/denovonear/transcript.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,513 copying build/lib.linux-armv7l-cpython-311/denovonear/load_gene.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,515 copying build/lib.linux-armv7l-cpython-311/denovonear/load_de_novos.py -> build/bdist.linux-armv7l/wheel/denovonear 2023-09-15T04:36:39,517 running install_egg_info 2023-09-15T04:36:39,529 running egg_info 2023-09-15T04:36:39,534 writing denovonear.egg-info/PKG-INFO 2023-09-15T04:36:39,537 writing dependency_links to denovonear.egg-info/dependency_links.txt 2023-09-15T04:36:39,539 writing entry points to denovonear.egg-info/entry_points.txt 2023-09-15T04:36:39,540 writing requirements to denovonear.egg-info/requires.txt 2023-09-15T04:36:39,542 writing top-level names to denovonear.egg-info/top_level.txt 2023-09-15T04:36:39,558 reading manifest file 'denovonear.egg-info/SOURCES.txt' 2023-09-15T04:36:39,562 reading manifest template 'MANIFEST.in' 2023-09-15T04:36:39,569 adding license file 'LICENSE.txt' 2023-09-15T04:36:39,574 writing manifest file 'denovonear.egg-info/SOURCES.txt' 2023-09-15T04:36:39,576 Copying denovonear.egg-info to build/bdist.linux-armv7l/wheel/denovonear-0.9.7-py3.11.egg-info 2023-09-15T04:36:39,587 running install_scripts 2023-09-15T04:36:39,641 creating build/bdist.linux-armv7l/wheel/denovonear-0.9.7.dist-info/WHEEL 2023-09-15T04:36:39,644 creating '/tmp/pip-wheel-m04ygnw1/.tmp-1cxc59e0/denovonear-0.9.7-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-15T04:36:39,647 adding 'denovonear/__init__.py' 2023-09-15T04:36:39,650 adding 'denovonear/__main__.py' 2023-09-15T04:36:39,652 adding 'denovonear/cluster_test.py' 2023-09-15T04:36:39,654 adding 'denovonear/ensembl_cache.py' 2023-09-15T04:36:39,656 adding 'denovonear/ensembl_requester.py' 2023-09-15T04:36:39,657 adding 'denovonear/frameshift_rate.py' 2023-09-15T04:36:40,344 adding 'denovonear/gencode.cpython-311-arm-linux-gnueabihf.so' 2023-09-15T04:36:40,374 adding 'denovonear/load_de_novos.py' 2023-09-15T04:36:40,376 adding 'denovonear/load_gene.py' 2023-09-15T04:36:40,378 adding 'denovonear/load_mutation_rates.py' 2023-09-15T04:36:40,380 adding 'denovonear/log_transform_rates.py' 2023-09-15T04:36:40,381 adding 'denovonear/rate_limiter.py' 2023-09-15T04:36:40,383 adding 'denovonear/rate_limiter_retries.py' 2023-09-15T04:36:40,385 adding 'denovonear/simulate.py' 2023-09-15T04:36:40,840 adding 'denovonear/site_specific_rates.cpython-311-arm-linux-gnueabihf.so' 2023-09-15T04:36:41,296 adding 'denovonear/transcript.cpython-311-arm-linux-gnueabihf.so' 2023-09-15T04:36:41,474 adding 'denovonear/weights.cpython-311-arm-linux-gnueabihf.so' 2023-09-15T04:36:41,481 adding 'denovonear/weights.pxd' 2023-09-15T04:36:41,484 adding 'denovonear/data/rates.txt' 2023-09-15T04:36:41,487 adding 'denovonear-0.9.7.dist-info/LICENSE.txt' 2023-09-15T04:36:41,488 adding 'denovonear-0.9.7.dist-info/METADATA' 2023-09-15T04:36:41,490 adding 'denovonear-0.9.7.dist-info/WHEEL' 2023-09-15T04:36:41,491 adding 'denovonear-0.9.7.dist-info/entry_points.txt' 2023-09-15T04:36:41,493 adding 'denovonear-0.9.7.dist-info/top_level.txt' 2023-09-15T04:36:41,494 adding 'denovonear-0.9.7.dist-info/RECORD' 2023-09-15T04:36:41,529 removing build/bdist.linux-armv7l/wheel 2023-09-15T04:36:41,672 Building wheel for denovonear (pyproject.toml): finished with status 'done' 2023-09-15T04:36:41,751 Created wheel for denovonear: filename=denovonear-0.9.7-cp311-cp311-linux_armv7l.whl size=3408061 sha256=f5ddd175f519e72712f053cf1fe7ae6abeb2fb009ed0d4b226d0d4ce969cbf1f 2023-09-15T04:36:41,752 Stored in directory: /tmp/pip-ephem-wheel-cache-xklf2_br/wheels/d9/c2/3b/e2d65485dfd04b586a5c04dcd417536d70b5519e3c3674612f 2023-09-15T04:36:41,765 Successfully built denovonear 2023-09-15T04:36:41,842 Removed build tracker: '/tmp/pip-build-tracker-oyrgt4cw'