2023-09-14T00:09:58,847 Created temporary directory: /tmp/pip-build-tracker-397bmtav 2023-09-14T00:09:58,849 Initialized build tracking at /tmp/pip-build-tracker-397bmtav 2023-09-14T00:09:58,849 Created build tracker: /tmp/pip-build-tracker-397bmtav 2023-09-14T00:09:58,850 Entered build tracker: /tmp/pip-build-tracker-397bmtav 2023-09-14T00:09:58,851 Created temporary directory: /tmp/pip-wheel-4f52la9s 2023-09-14T00:09:58,854 Created temporary directory: /tmp/pip-ephem-wheel-cache-dxyfgmqc 2023-09-14T00:09:58,878 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-14T00:09:58,882 2 location(s) to search for versions of indelpost: 2023-09-14T00:09:58,882 * https://pypi.org/simple/indelpost/ 2023-09-14T00:09:58,882 * https://www.piwheels.org/simple/indelpost/ 2023-09-14T00:09:58,883 Fetching project page and analyzing links: https://pypi.org/simple/indelpost/ 2023-09-14T00:09:58,884 Getting page https://pypi.org/simple/indelpost/ 2023-09-14T00:09:58,886 Found index url https://pypi.org/simple/ 2023-09-14T00:09:59,067 Fetched page https://pypi.org/simple/indelpost/ as application/vnd.pypi.simple.v1+json 2023-09-14T00:09:59,075 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/2c/1d/2aaf490785fed09605d1194a93f0d4c6693e0700fe2fcd9185b1aac27ef2/indelpost-0.0.1-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,076 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/54/c1/a67da73389badb8221981f0fb0fbbbfdb7342ab8f85f905d6698c6347f6b/indelpost-0.0.2-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,077 Found link https://files.pythonhosted.org/packages/de/7b/8b8e90a4883daa231b77b3b20d07430734622d3dabe47f8d341f6b9ebb49/indelpost-0.0.2.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.0.2 2023-09-14T00:09:59,078 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/dc/d5/5e20c3069e99a36caf23bbf9ac6e0f654a23178bb7346541676872fa9bbe/indelpost-0.0.3-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,079 Found link https://files.pythonhosted.org/packages/8d/6a/e12e7e15eeb48b35ae38b9382b0e3b8853fe62c2147f13c7152c1285efe0/indelpost-0.0.3.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.0.3 2023-09-14T00:09:59,081 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/bf/82/58a1ee8cb0385c502afceb21d718179cbe56dd2318656de1c11f1d16af8b/indelpost-0.0.4-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,082 Found link https://files.pythonhosted.org/packages/ef/04/6d459daa1e4c992bc65ee1bedd624a7c061e7026df01e2f835591a205a54/indelpost-0.0.4.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.0.4 2023-09-14T00:09:59,083 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/fc/60/d2dc04e1503d76a934265af72306fe6883bbeab466e30e4104e04565da6f/indelpost-0.0.5-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,120 Found link https://files.pythonhosted.org/packages/59/c4/b639f75fe326c6712d462f6154ea6047c4774a661f00c2551fff984db194/indelpost-0.0.5.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.0.5 2023-09-14T00:09:59,121 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/f1/6e/26ec6199f8df542adc339cf3caebfdcfd5cdf438591aa6e7b3881b2d9682/indelpost-0.0.6-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,122 Found link https://files.pythonhosted.org/packages/82/50/d5d04f27a9317f5c24850b2388713c240a6c07fdb5f9a3cbc5b3aef6032c/indelpost-0.0.6.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.0.6 2023-09-14T00:09:59,122 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/ea/da/03d68b7bb51d84b8c88303fc6c7554db09bb3ec1fc6e01db8445b936bd6c/indelpost-0.0.7-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,123 Found link https://files.pythonhosted.org/packages/97/55/92a64a3f1d8bbe3b3d326f32aeb87516e3c461ce8f44a4d09cc10de90077/indelpost-0.0.7.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.0.7 2023-09-14T00:09:59,124 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/33/67/ae5323d7d9c609a60fb4d425b0d8ba5299453b63b9125f35e3743636bf12/indelpost-0.1.0-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,125 Found link https://files.pythonhosted.org/packages/ad/13/3367cfe66b9dee3034ca7f4188d61a55e7cf1817558dd1322313ea693384/indelpost-0.1.0.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.1.0 2023-09-14T00:09:59,126 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/c7/09/70c352d9d6f3bcdc410810d35d44cf66493f66c07ac996c07da53d5a6375/indelpost-0.1.2-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,126 Found link https://files.pythonhosted.org/packages/28/7f/62eb40e0bdf79cc0b56bd12c4fa5598e13bbf140f44080c842d5284acc6f/indelpost-0.1.2.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.1.2 2023-09-14T00:09:59,127 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/7f/a2/1341f6e0b449d1fa03df8b323c79c236ec134ed4b98808fd0e9b64083394/indelpost-0.1.3-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,127 Found link https://files.pythonhosted.org/packages/bf/c0/fa6d273124ec3d739322db2f82410b21cfa06961e8ad74a75b4049780489/indelpost-0.1.3.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.1.3 2023-09-14T00:09:59,128 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/84/b8/2960198caddb27814e86ee54022a85834c9315e08250df8210108e608832/indelpost-0.1.4-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,129 Found link https://files.pythonhosted.org/packages/8b/94/e98ddc3e8f24f3a3ac5f5ef94d4f2db0346e0a14e5cdbbdd3e1dd4a01e98/indelpost-0.1.4.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.1.4 2023-09-14T00:09:59,130 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/5b/ad/d974f31584f0e4fede49aa915151215142af3c2a96be0169464b2d0b0948/indelpost-0.1.5-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,130 Found link https://files.pythonhosted.org/packages/1f/31/fa53ce469a6aea3029caa39b715d7eec5378b466038591b954e0f356e907/indelpost-0.1.5.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.1.5 2023-09-14T00:09:59,131 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/46/f9/706bf8cae759e72d9da70746ef37ea6b72b746786582fc16aafe0a140d68/indelpost-0.1.6-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,132 Found link https://files.pythonhosted.org/packages/81/75/62103326be8bd02fc0f7d11a3f20693fcb106f39e8c0c09204ec662d9c96/indelpost-0.1.6.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.1.6 2023-09-14T00:09:59,133 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/b1/2d/d0e5613b6228ecaadc8426369234d2f2f845ef4b0efc37eb6a9334154eb6/indelpost-0.1.7-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,134 Found link https://files.pythonhosted.org/packages/1d/49/ad1dceecb2fc74d484b251f5065c94e5206a53613d3c24384c61201d15b3/indelpost-0.1.7.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.1.7 2023-09-14T00:09:59,134 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/46/cb/e3d2658e49d38ec2d4e5c808890b859d40fea97cd421707db6efda498aa9/indelpost-0.1.8-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,136 Found link https://files.pythonhosted.org/packages/15/55/087b1218bd7993207557d92e81ffe95dacade518fa4ab67c5fe84bfa8797/indelpost-0.1.8.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.1.8 2023-09-14T00:09:59,137 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/06/8b/5520d53eb5db5ae352823c78ac6654ec5da871223b0fa68063be379c7578/indelpost-0.1.9-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,137 Found link https://files.pythonhosted.org/packages/cf/a2/c69a2fac134bdcb58260eba54f323af7085836fa1121f1435154259ed7ed/indelpost-0.1.9.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.1.9 2023-09-14T00:09:59,138 Skipping link: No binaries permitted for indelpost: https://files.pythonhosted.org/packages/42/b3/6a3c01ebd2e4c8dd58a77514107e169d1c2449e92bfb9241ac4a27c49c01/indelpost-0.2.0-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/indelpost/) 2023-09-14T00:09:59,139 Found link https://files.pythonhosted.org/packages/45/c6/32c785a6248aff255d9e10697a8822d175ae28303b8353fe27c4ee43b918/indelpost-0.2.0.tar.gz (from https://pypi.org/simple/indelpost/), version: 0.2.0 2023-09-14T00:09:59,140 Fetching project page and analyzing links: https://www.piwheels.org/simple/indelpost/ 2023-09-14T00:09:59,141 Getting page https://www.piwheels.org/simple/indelpost/ 2023-09-14T00:09:59,142 Found index url https://www.piwheels.org/simple/ 2023-09-14T00:09:59,445 Fetched page https://www.piwheels.org/simple/indelpost/ as text/html 2023-09-14T00:09:59,464 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.9-cp39-cp39-linux_armv7l.whl#sha256=4dc987d13c4f72a7a1d4bf6131048ff12c85ae931613d223aa2fc4d11fea4a14 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,465 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.9-cp39-cp39-linux_armv6l.whl#sha256=4dc987d13c4f72a7a1d4bf6131048ff12c85ae931613d223aa2fc4d11fea4a14 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,466 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.9-cp37-cp37m-linux_armv7l.whl#sha256=d8515637b1cd04c9689eac170771719fd2f1ea50f18aea3326616ae3f12b8183 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,466 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.9-cp37-cp37m-linux_armv6l.whl#sha256=d8515637b1cd04c9689eac170771719fd2f1ea50f18aea3326616ae3f12b8183 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,467 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.8-cp39-cp39-linux_armv7l.whl#sha256=99b4070611f04a313a631aa9d1abc38544818f03296cdd76021131318497ab11 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,467 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.8-cp39-cp39-linux_armv6l.whl#sha256=99b4070611f04a313a631aa9d1abc38544818f03296cdd76021131318497ab11 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,468 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.8-cp37-cp37m-linux_armv7l.whl#sha256=c40acb17510a588797f13ff0e101549ac2b9d2e61f82954a28f48edd6432e411 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,468 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.8-cp37-cp37m-linux_armv6l.whl#sha256=c40acb17510a588797f13ff0e101549ac2b9d2e61f82954a28f48edd6432e411 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,469 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.8-cp35-cp35m-linux_armv7l.whl#sha256=f7838c7a1da294affea271852d1e4dc31ae67d395ec0237bde5bce0fc8f3faf6 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,469 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.8-cp35-cp35m-linux_armv6l.whl#sha256=f7838c7a1da294affea271852d1e4dc31ae67d395ec0237bde5bce0fc8f3faf6 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,470 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.7-cp39-cp39-linux_armv7l.whl#sha256=0ce1dfc2ebbdf77714be1d25a5acb833a500dbf5f95a3539b6c4fa56d0938eed (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,470 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.7-cp39-cp39-linux_armv6l.whl#sha256=0ce1dfc2ebbdf77714be1d25a5acb833a500dbf5f95a3539b6c4fa56d0938eed (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,471 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.7-cp37-cp37m-linux_armv7l.whl#sha256=3ee6dc5d8f3af8abe85b3fbd0b57bfecf62440effa5e3dec2fb2d4af5582d6cb (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,471 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.7-cp37-cp37m-linux_armv6l.whl#sha256=3ee6dc5d8f3af8abe85b3fbd0b57bfecf62440effa5e3dec2fb2d4af5582d6cb (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,472 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.7-cp35-cp35m-linux_armv7l.whl#sha256=45d522081bd999e88622b3f6853ed39d08e9329a193c2802b370b31aeea4ac1f (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,472 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.7-cp35-cp35m-linux_armv6l.whl#sha256=45d522081bd999e88622b3f6853ed39d08e9329a193c2802b370b31aeea4ac1f (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,473 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.6-cp39-cp39-linux_armv7l.whl#sha256=40384927b582f8c1468e689af5467455482a2d8fe807f4fd39a85bce5aa3486e (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,473 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.6-cp39-cp39-linux_armv6l.whl#sha256=40384927b582f8c1468e689af5467455482a2d8fe807f4fd39a85bce5aa3486e (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,474 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.6-cp37-cp37m-linux_armv7l.whl#sha256=b87c71c0eef4a84e4273697527aced120c3f6618c1aca00df8a7e3c298f3b893 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,474 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.6-cp37-cp37m-linux_armv6l.whl#sha256=b87c71c0eef4a84e4273697527aced120c3f6618c1aca00df8a7e3c298f3b893 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,475 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.6-cp35-cp35m-linux_armv7l.whl#sha256=4f3c694ada7ad26f382ba87bcc9f19a66237df3db3c4a29020812c2006d1dcdb (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,476 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.6-cp35-cp35m-linux_armv6l.whl#sha256=4f3c694ada7ad26f382ba87bcc9f19a66237df3db3c4a29020812c2006d1dcdb (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,476 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.5-cp39-cp39-linux_armv7l.whl#sha256=8e716a1cb37b6a64ba5f610942d8762b4b3fe08d9ece4918bbdb930e2511acd9 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,477 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.5-cp39-cp39-linux_armv6l.whl#sha256=8e716a1cb37b6a64ba5f610942d8762b4b3fe08d9ece4918bbdb930e2511acd9 (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,478 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.5-cp37-cp37m-linux_armv7l.whl#sha256=6bf911db05b496bfe00bf54a79466323200b1d2cbf3d8013d835bd93a998604d (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,478 Skipping link: No binaries permitted for indelpost: https://www.piwheels.org/simple/indelpost/indelpost-0.1.5-cp37-cp37m-linux_armv6l.whl#sha256=6bf911db05b496bfe00bf54a79466323200b1d2cbf3d8013d835bd93a998604d (from https://www.piwheels.org/simple/indelpost/) 2023-09-14T00:09:59,478 Skipping link: No binaries permitted for indelpost: 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check 1 links for project 'indelpost': discarding no candidates 2023-09-14T00:09:59,541 Collecting indelpost==0.0.4 2023-09-14T00:09:59,543 Created temporary directory: /tmp/pip-unpack-ipy65_fo 2023-09-14T00:10:00,522 Downloading indelpost-0.0.4.tar.gz (875 kB) 2023-09-14T00:10:00,984 Added indelpost==0.0.4 from https://files.pythonhosted.org/packages/ef/04/6d459daa1e4c992bc65ee1bedd624a7c061e7026df01e2f835591a205a54/indelpost-0.0.4.tar.gz to build tracker '/tmp/pip-build-tracker-397bmtav' 2023-09-14T00:10:00,991 Created temporary directory: /tmp/pip-build-env-81o70t3g 2023-09-14T00:10:00,996 Installing build dependencies: started 2023-09-14T00:10:00,997 Running command pip subprocess to install build dependencies 2023-09-14T00:10:02,129 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-14T00:10:02,626 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-14T00:10:04,288 Collecting setuptools 2023-09-14T00:10:04,290 Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata 2023-09-14T00:10:04,295 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-14T00:10:04,499 Collecting wheel 2023-09-14T00:10:04,514 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-14T00:10:04,813 Collecting pysam>=0.15.0 2023-09-14T00:10:04,982 Downloading pysam-0.21.0.tar.gz (4.1 MB) 2023-09-14T00:10:05,407 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.1/4.1 MB 9.7 MB/s eta 0:00:00 2023-09-14T00:10:08,124 Installing build dependencies: started 2023-09-14T00:10:08,125 Running command pip subprocess to install build dependencies 2023-09-14T00:10:09,813 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-14T00:10:11,546 Collecting setuptools>=59.0 2023-09-14T00:10:11,547 Obtaining dependency information for setuptools>=59.0 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata 2023-09-14T00:10:11,553 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-14T00:10:11,776 Collecting wheel 2023-09-14T00:10:11,792 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-14T00:10:14,715 Collecting Cython<3.0,>=0.29.30 2023-09-14T00:10:14,717 Obtaining dependency information for Cython<3.0,>=0.29.30 from https://files.pythonhosted.org/packages/3f/d6/9eed523aeaca42acbaa3e6d3850edae780dc7f8da9df1bf6a2ceb851839c/Cython-0.29.36-py2.py3-none-any.whl.metadata 2023-09-14T00:10:14,722 Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB) 2023-09-14T00:10:14,905 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-14T00:10:14,949 Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB) 2023-09-14T00:10:17,477 Installing collected packages: wheel, setuptools, Cython 2023-09-14T00:10:23,103 Successfully installed Cython-0.29.36 setuptools-68.2.2 wheel-0.41.2 2023-09-14T00:10:23,725 Installing build dependencies: finished with status 'done' 2023-09-14T00:10:23,728 Getting requirements to build wheel: started 2023-09-14T00:10:23,729 Running command Getting requirements to build wheel 2023-09-14T00:10:24,416 # pysam: cython is available - using cythonize if necessary 2023-09-14T00:10:24,417 # pysam: htslib mode is shared 2023-09-14T00:10:24,418 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2023-09-14T00:10:24,419 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc 2023-09-14T00:10:24,420 # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-14T00:10:24,420 # pysam: (sysconfig) LDFLAGS= -g -fwrapv -O2 2023-09-14T00:10:24,718 checking for gcc... arm-linux-gnueabihf-gcc 2023-09-14T00:10:24,984 checking whether the C compiler works... yes 2023-09-14T00:10:24,985 checking for C compiler default output file name... a.out 2023-09-14T00:10:25,159 checking for suffix of executables... 2023-09-14T00:10:25,363 checking whether we are cross compiling... no 2023-09-14T00:10:25,467 checking for suffix of object files... o 2023-09-14T00:10:25,567 checking whether we are using the GNU C compiler... yes 2023-09-14T00:10:25,644 checking whether arm-linux-gnueabihf-gcc accepts -g... yes 2023-09-14T00:10:25,775 checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed 2023-09-14T00:10:25,778 checking for ranlib... ranlib 2023-09-14T00:10:25,786 checking for grep that handles long lines and -e... /usr/bin/grep 2023-09-14T00:10:25,862 checking for C compiler warning flags... -Wall 2023-09-14T00:10:25,873 configure: Default CFLAGS_ARM/X86: -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-14T00:10:25,935 checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no 2023-09-14T00:10:25,983 checking whether C compiler accepts -mavx2... no 2023-09-14T00:10:26,038 checking whether C compiler accepts -mavx512f... no 2023-09-14T00:10:26,528 checking whether C compiler supports ARM Neon... no 2023-09-14T00:10:26,532 checking for pkg-config... /usr/bin/pkg-config 2023-09-14T00:10:26,538 checking pkg-config is at least version 0.9.0... yes 2023-09-14T00:10:26,540 checking for special C compiler options needed for large files... no 2023-09-14T00:10:26,735 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-09-14T00:10:26,750 checking shared library type for unknown-Linux... plain .so 2023-09-14T00:10:26,863 checking whether the linker supports versioned symbols... no 2023-09-14T00:10:27,041 checking whether the compiler accepts -fvisibility=hidden... yes 2023-09-14T00:10:27,181 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E 2023-09-14T00:10:27,297 checking for egrep... /usr/bin/grep -E 2023-09-14T00:10:27,796 checking for ANSI C header files... yes 2023-09-14T00:10:27,965 checking for sys/types.h... yes 2023-09-14T00:10:28,101 checking for sys/stat.h... yes 2023-09-14T00:10:28,237 checking for stdlib.h... yes 2023-09-14T00:10:28,382 checking for string.h... yes 2023-09-14T00:10:28,525 checking for memory.h... yes 2023-09-14T00:10:28,674 checking for strings.h... yes 2023-09-14T00:10:28,843 checking for inttypes.h... yes 2023-09-14T00:10:28,989 checking for stdint.h... yes 2023-09-14T00:10:29,146 checking for unistd.h... yes 2023-09-14T00:10:29,170 checking for stdlib.h... (cached) yes 2023-09-14T00:10:29,193 checking for unistd.h... (cached) yes 2023-09-14T00:10:29,369 checking for sys/param.h... yes 2023-09-14T00:10:29,603 checking for getpagesize... yes 2023-09-14T00:10:29,952 checking for working mmap... yes 2023-09-14T00:10:30,154 checking for gmtime_r... yes 2023-09-14T00:10:30,392 checking for fsync... yes 2023-09-14T00:10:30,601 checking for drand48... yes 2023-09-14T00:10:30,827 checking for srand48_deterministic... no 2023-09-14T00:10:31,001 checking whether fdatasync is declared... yes 2023-09-14T00:10:31,223 checking for fdatasync... yes 2023-09-14T00:10:31,632 checking for library containing log... -lm 2023-09-14T00:10:31,742 checking for zlib.h... yes 2023-09-14T00:10:31,938 checking for inflate in -lz... yes 2023-09-14T00:10:32,196 checking for library containing recv... none required 2023-09-14T00:10:32,287 checking for bzlib.h... yes 2023-09-14T00:10:32,474 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-09-14T00:10:32,698 checking for lzma.h... yes 2023-09-14T00:10:32,891 checking for lzma_easy_buffer_encode in -llzma... yes 2023-09-14T00:10:32,896 checking whether htscodecs files are present... yes 2023-09-14T00:10:33,011 checking for libdeflate.h... yes 2023-09-14T00:10:33,200 checking for libdeflate_deflate_compress in -ldeflate... yes 2023-09-14T00:10:33,364 checking for curl/curl.h... yes 2023-09-14T00:10:33,733 checking for curl_easy_pause in -lcurl... yes 2023-09-14T00:10:33,947 checking for CCHmac... no 2023-09-14T00:10:34,584 checking for library containing HMAC... -lcrypto 2023-09-14T00:10:34,784 checking for library containing regcomp... none required 2023-09-14T00:10:34,909 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2023-09-14T00:10:34,976 configure: creating ./config.status 2023-09-14T00:10:35,301 config.status: creating config.mk 2023-09-14T00:10:35,364 config.status: creating htslib.pc.tmp 2023-09-14T00:10:35,431 config.status: creating config.h 2023-09-14T00:10:35,476 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-09-14T00:10:36,090 # pysam: htslib configure options: --enable-libcurl 2023-09-14T00:10:36,090 # pysam: htslib_config HTS_CFLAGS_AVX2= 2023-09-14T00:10:36,091 # pysam: htslib_config HTS_CFLAGS_AVX512= 2023-09-14T00:10:36,092 # pysam: htslib_config HTS_CFLAGS_SSE4= 2023-09-14T00:10:36,093 # pysam: htslib_config HTS_HAVE_NEON= 2023-09-14T00:10:36,093 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o 2023-09-14T00:10:36,094 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2023-09-14T00:10:36,094 # pysam: htslib_config PLATFORM=default 2023-09-14T00:10:36,095 # pysam: config_option: ENABLE_GCS=1 2023-09-14T00:10:36,095 # pysam: config_option: ENABLE_PLUGINS=0 2023-09-14T00:10:36,096 # pysam: config_option: ENABLE_S3=1 2023-09-14T00:10:36,097 # pysam: config_option: HAVE_COMMONCRYPTO=0 2023-09-14T00:10:36,098 # pysam: config_option: HAVE_HMAC=1 2023-09-14T00:10:36,099 # pysam: config_option: HAVE_LIBBZ2=1 2023-09-14T00:10:36,100 # pysam: config_option: HAVE_LIBCURL=1 2023-09-14T00:10:36,101 # pysam: config_option: HAVE_LIBDEFLATE=1 2023-09-14T00:10:36,102 # pysam: config_option: HAVE_LIBLZMA=1 2023-09-14T00:10:36,103 # pysam: config_option: HAVE_MMAP=1 2023-09-14T00:10:36,103 running egg_info 2023-09-14T00:10:36,104 writing pysam.egg-info/PKG-INFO 2023-09-14T00:10:36,105 writing dependency_links to pysam.egg-info/dependency_links.txt 2023-09-14T00:10:36,106 writing requirements to pysam.egg-info/requires.txt 2023-09-14T00:10:36,107 writing top-level names to pysam.egg-info/top_level.txt 2023-09-14T00:10:36,145 reading manifest file 'pysam.egg-info/SOURCES.txt' 2023-09-14T00:10:36,178 reading manifest template 'MANIFEST.in' 2023-09-14T00:10:36,179 warning: no files found matching 'KNOWN_BUGS' 2023-09-14T00:10:36,180 warning: no files found matching 'THANKS' 2023-09-14T00:10:36,188 no previously-included directories found matching 'tests/' 2023-09-14T00:10:36,302 adding license file 'COPYING' 2023-09-14T00:10:36,303 adding license file 'AUTHORS' 2023-09-14T00:10:36,325 writing manifest file 'pysam.egg-info/SOURCES.txt' 2023-09-14T00:10:36,447 Getting requirements to build wheel: finished with status 'done' 2023-09-14T00:10:36,458 Preparing metadata (pyproject.toml): started 2023-09-14T00:10:36,459 Running command Preparing metadata (pyproject.toml) 2023-09-14T00:10:37,143 # pysam: cython is available - using cythonize if necessary 2023-09-14T00:10:37,144 # pysam: htslib mode is shared 2023-09-14T00:10:37,145 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2023-09-14T00:10:37,146 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc 2023-09-14T00:10:37,147 # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-14T00:10:37,148 # pysam: (sysconfig) LDFLAGS= -g -fwrapv -O2 2023-09-14T00:10:37,441 checking for gcc... arm-linux-gnueabihf-gcc 2023-09-14T00:10:37,699 checking whether the C compiler works... yes 2023-09-14T00:10:37,700 checking for C compiler default output file name... a.out 2023-09-14T00:10:37,867 checking for suffix of executables... 2023-09-14T00:10:38,075 checking whether we are cross compiling... no 2023-09-14T00:10:38,192 checking for suffix of object files... o 2023-09-14T00:10:38,270 checking whether we are using the GNU C compiler... yes 2023-09-14T00:10:38,344 checking whether arm-linux-gnueabihf-gcc accepts -g... yes 2023-09-14T00:10:38,473 checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed 2023-09-14T00:10:38,476 checking for ranlib... ranlib 2023-09-14T00:10:38,483 checking for grep that handles long lines and -e... /usr/bin/grep 2023-09-14T00:10:38,558 checking for C compiler warning flags... -Wall 2023-09-14T00:10:38,569 configure: Default CFLAGS_ARM/X86: -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-14T00:10:38,627 checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no 2023-09-14T00:10:38,676 checking whether C compiler accepts -mavx2... no 2023-09-14T00:10:38,733 checking whether C compiler accepts -mavx512f... no 2023-09-14T00:10:39,221 checking whether C compiler supports ARM Neon... no 2023-09-14T00:10:39,223 checking for pkg-config... /usr/bin/pkg-config 2023-09-14T00:10:39,228 checking pkg-config is at least version 0.9.0... yes 2023-09-14T00:10:39,230 checking for special C compiler options needed for large files... no 2023-09-14T00:10:39,416 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-09-14T00:10:39,431 checking shared library type for unknown-Linux... plain .so 2023-09-14T00:10:39,542 checking whether the linker supports versioned symbols... no 2023-09-14T00:10:39,727 checking whether the compiler accepts -fvisibility=hidden... yes 2023-09-14T00:10:39,853 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E 2023-09-14T00:10:39,969 checking for egrep... /usr/bin/grep -E 2023-09-14T00:10:40,443 checking for ANSI C header files... yes 2023-09-14T00:10:40,598 checking for sys/types.h... yes 2023-09-14T00:10:40,749 checking for sys/stat.h... yes 2023-09-14T00:10:40,890 checking for stdlib.h... yes 2023-09-14T00:10:41,037 checking for string.h... yes 2023-09-14T00:10:41,180 checking for memory.h... yes 2023-09-14T00:10:41,322 checking for strings.h... yes 2023-09-14T00:10:41,476 checking for inttypes.h... yes 2023-09-14T00:10:41,622 checking for stdint.h... yes 2023-09-14T00:10:41,782 checking for unistd.h... yes 2023-09-14T00:10:41,805 checking for stdlib.h... (cached) yes 2023-09-14T00:10:41,828 checking for unistd.h... (cached) yes 2023-09-14T00:10:42,011 checking for sys/param.h... yes 2023-09-14T00:10:42,244 checking for getpagesize... yes 2023-09-14T00:10:42,589 checking for working mmap... yes 2023-09-14T00:10:42,788 checking for gmtime_r... yes 2023-09-14T00:10:43,031 checking for fsync... yes 2023-09-14T00:10:43,238 checking for drand48... yes 2023-09-14T00:10:43,464 checking for srand48_deterministic... no 2023-09-14T00:10:43,647 checking whether fdatasync is declared... yes 2023-09-14T00:10:43,853 checking for fdatasync... yes 2023-09-14T00:10:44,256 checking for library containing log... -lm 2023-09-14T00:10:44,364 checking for zlib.h... yes 2023-09-14T00:10:44,575 checking for inflate in -lz... yes 2023-09-14T00:10:44,765 checking for library containing recv... none required 2023-09-14T00:10:44,854 checking for bzlib.h... yes 2023-09-14T00:10:45,036 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-09-14T00:10:45,223 checking for lzma.h... yes 2023-09-14T00:10:45,442 checking for lzma_easy_buffer_encode in -llzma... yes 2023-09-14T00:10:45,449 checking whether htscodecs files are present... yes 2023-09-14T00:10:45,526 checking for libdeflate.h... yes 2023-09-14T00:10:45,710 checking for libdeflate_deflate_compress in -ldeflate... yes 2023-09-14T00:10:45,864 checking for curl/curl.h... yes 2023-09-14T00:10:46,254 checking for curl_easy_pause in -lcurl... yes 2023-09-14T00:10:46,469 checking for CCHmac... no 2023-09-14T00:10:47,101 checking for library containing HMAC... -lcrypto 2023-09-14T00:10:47,296 checking for library containing regcomp... none required 2023-09-14T00:10:47,421 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2023-09-14T00:10:47,486 configure: creating ./config.status 2023-09-14T00:10:47,828 config.status: creating config.mk 2023-09-14T00:10:47,888 config.status: creating htslib.pc.tmp 2023-09-14T00:10:47,948 config.status: creating config.h 2023-09-14T00:10:47,977 config.status: config.h is unchanged 2023-09-14T00:10:47,986 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-09-14T00:10:48,560 # pysam: htslib configure options: --enable-libcurl 2023-09-14T00:10:48,561 # pysam: htslib_config HTS_CFLAGS_AVX2= 2023-09-14T00:10:48,562 # pysam: htslib_config HTS_CFLAGS_AVX512= 2023-09-14T00:10:48,562 # pysam: htslib_config HTS_CFLAGS_SSE4= 2023-09-14T00:10:48,563 # pysam: htslib_config HTS_HAVE_NEON= 2023-09-14T00:10:48,564 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o 2023-09-14T00:10:48,565 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2023-09-14T00:10:48,566 # pysam: htslib_config PLATFORM=default 2023-09-14T00:10:48,567 # pysam: config_option: ENABLE_GCS=1 2023-09-14T00:10:48,568 # pysam: config_option: ENABLE_PLUGINS=0 2023-09-14T00:10:48,568 # pysam: config_option: ENABLE_S3=1 2023-09-14T00:10:48,569 # pysam: config_option: HAVE_COMMONCRYPTO=0 2023-09-14T00:10:48,570 # pysam: config_option: HAVE_HMAC=1 2023-09-14T00:10:48,571 # pysam: config_option: HAVE_LIBBZ2=1 2023-09-14T00:10:48,572 # pysam: config_option: HAVE_LIBCURL=1 2023-09-14T00:10:48,573 # pysam: config_option: HAVE_LIBDEFLATE=1 2023-09-14T00:10:48,574 # pysam: config_option: HAVE_LIBLZMA=1 2023-09-14T00:10:48,575 # pysam: config_option: HAVE_MMAP=1 2023-09-14T00:10:48,576 running dist_info 2023-09-14T00:10:48,577 creating /tmp/pip-modern-metadata-520an4rh/pysam.egg-info 2023-09-14T00:10:48,577 writing /tmp/pip-modern-metadata-520an4rh/pysam.egg-info/PKG-INFO 2023-09-14T00:10:48,578 writing dependency_links to /tmp/pip-modern-metadata-520an4rh/pysam.egg-info/dependency_links.txt 2023-09-14T00:10:48,580 writing requirements to /tmp/pip-modern-metadata-520an4rh/pysam.egg-info/requires.txt 2023-09-14T00:10:48,581 writing top-level names to /tmp/pip-modern-metadata-520an4rh/pysam.egg-info/top_level.txt 2023-09-14T00:10:48,582 writing manifest file '/tmp/pip-modern-metadata-520an4rh/pysam.egg-info/SOURCES.txt' 2023-09-14T00:10:48,649 reading manifest file '/tmp/pip-modern-metadata-520an4rh/pysam.egg-info/SOURCES.txt' 2023-09-14T00:10:48,651 reading manifest template 'MANIFEST.in' 2023-09-14T00:10:48,653 warning: no files found matching 'KNOWN_BUGS' 2023-09-14T00:10:48,654 warning: no files found matching 'THANKS' 2023-09-14T00:10:48,663 no previously-included directories found matching 'tests/' 2023-09-14T00:10:48,782 adding license file 'COPYING' 2023-09-14T00:10:48,783 adding license file 'AUTHORS' 2023-09-14T00:10:48,800 writing manifest file '/tmp/pip-modern-metadata-520an4rh/pysam.egg-info/SOURCES.txt' 2023-09-14T00:10:48,802 creating '/tmp/pip-modern-metadata-520an4rh/pysam-0.21.0.dist-info' 2023-09-14T00:10:48,955 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-14T00:10:49,700 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) 2023-09-14T00:10:49,708 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) 2023-09-14T00:10:49,715 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) 2023-09-14T00:10:49,722 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) 2023-09-14T00:10:49,729 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) 2023-09-14T00:10:50,573 Collecting numpy>=1.16.0 2023-09-14T00:10:51,528 Using cached https://www.piwheels.org/simple/numpy/numpy-1.25.2-cp311-cp311-linux_armv7l.whl (12.5 MB) 2023-09-14T00:10:53,268 Collecting cython>=0.29.12 2023-09-14T00:10:53,269 Obtaining dependency information for cython>=0.29.12 from https://files.pythonhosted.org/packages/03/e9/9cc0c4f0d8a566089d096254cd25168a0db02dd047863a7f995d8d3eefa7/Cython-3.0.2-py2.py3-none-any.whl.metadata 2023-09-14T00:10:53,274 Using cached Cython-3.0.2-py2.py3-none-any.whl.metadata (3.1 kB) 2023-09-14T00:10:53,528 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-14T00:10:53,575 Using cached Cython-3.0.2-py2.py3-none-any.whl (1.2 MB) 2023-09-14T00:10:53,660 Building wheels for collected packages: pysam 2023-09-14T00:10:53,665 Building wheel for pysam (pyproject.toml): started 2023-09-14T00:10:53,666 Running command Building wheel for pysam (pyproject.toml) 2023-09-14T00:10:54,301 # pysam: cython is available - using cythonize if necessary 2023-09-14T00:10:54,302 # pysam: htslib mode is shared 2023-09-14T00:10:54,303 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2023-09-14T00:10:54,305 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc 2023-09-14T00:10:54,306 # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-14T00:10:54,307 # pysam: (sysconfig) LDFLAGS= -g -fwrapv -O2 2023-09-14T00:10:54,604 checking for gcc... arm-linux-gnueabihf-gcc 2023-09-14T00:10:54,858 checking whether the C compiler works... yes 2023-09-14T00:10:54,859 checking for C compiler default output file name... a.out 2023-09-14T00:10:55,058 checking for suffix of executables... 2023-09-14T00:10:55,259 checking whether we are cross compiling... no 2023-09-14T00:10:55,346 checking for suffix of object files... o 2023-09-14T00:10:55,429 checking whether we are using the GNU C compiler... yes 2023-09-14T00:10:55,503 checking whether arm-linux-gnueabihf-gcc accepts -g... yes 2023-09-14T00:10:55,634 checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed 2023-09-14T00:10:55,637 checking for ranlib... ranlib 2023-09-14T00:10:55,645 checking for grep that handles long lines and -e... /usr/bin/grep 2023-09-14T00:10:55,720 checking for C compiler warning flags... -Wall 2023-09-14T00:10:55,731 configure: Default CFLAGS_ARM/X86: -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-14T00:10:55,804 checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no 2023-09-14T00:10:55,871 checking whether C compiler accepts -mavx2... no 2023-09-14T00:10:55,945 checking whether C compiler accepts -mavx512f... no 2023-09-14T00:10:56,433 checking whether C compiler supports ARM Neon... no 2023-09-14T00:10:56,436 checking for pkg-config... /usr/bin/pkg-config 2023-09-14T00:10:56,442 checking pkg-config is at least version 0.9.0... yes 2023-09-14T00:10:56,444 checking for special C compiler options needed for large files... no 2023-09-14T00:10:56,640 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-09-14T00:10:56,655 checking shared library type for unknown-Linux... plain .so 2023-09-14T00:10:56,769 checking whether the linker supports versioned symbols... no 2023-09-14T00:10:56,949 checking whether the compiler accepts -fvisibility=hidden... yes 2023-09-14T00:10:57,059 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E 2023-09-14T00:10:57,173 checking for egrep... /usr/bin/grep -E 2023-09-14T00:10:57,773 checking for ANSI C header files... yes 2023-09-14T00:10:58,122 checking for sys/types.h... yes 2023-09-14T00:10:58,257 checking for sys/stat.h... yes 2023-09-14T00:10:58,438 checking for stdlib.h... yes 2023-09-14T00:10:58,582 checking for string.h... yes 2023-09-14T00:10:58,726 checking for memory.h... yes 2023-09-14T00:10:58,870 checking for strings.h... yes 2023-09-14T00:10:59,017 checking for inttypes.h... yes 2023-09-14T00:10:59,207 checking for stdint.h... yes 2023-09-14T00:10:59,366 checking for unistd.h... yes 2023-09-14T00:10:59,390 checking for stdlib.h... (cached) yes 2023-09-14T00:10:59,413 checking for unistd.h... (cached) yes 2023-09-14T00:10:59,590 checking for sys/param.h... yes 2023-09-14T00:10:59,792 checking for getpagesize... yes 2023-09-14T00:11:00,168 checking for working mmap... yes 2023-09-14T00:11:00,371 checking for gmtime_r... yes 2023-09-14T00:11:00,584 checking for fsync... yes 2023-09-14T00:11:00,831 checking for drand48... yes 2023-09-14T00:11:01,067 checking for srand48_deterministic... no 2023-09-14T00:11:01,241 checking whether fdatasync is declared... yes 2023-09-14T00:11:01,442 checking for fdatasync... yes 2023-09-14T00:11:01,891 checking for library containing log... -lm 2023-09-14T00:11:02,002 checking for zlib.h... yes 2023-09-14T00:11:02,189 checking for inflate in -lz... yes 2023-09-14T00:11:02,407 checking for library containing recv... none required 2023-09-14T00:11:02,507 checking for bzlib.h... yes 2023-09-14T00:11:02,700 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-09-14T00:11:02,889 checking for lzma.h... yes 2023-09-14T00:11:03,082 checking for lzma_easy_buffer_encode in -llzma... yes 2023-09-14T00:11:03,088 checking whether htscodecs files are present... yes 2023-09-14T00:11:03,186 checking for libdeflate.h... yes 2023-09-14T00:11:03,423 checking for libdeflate_deflate_compress in -ldeflate... yes 2023-09-14T00:11:03,578 checking for curl/curl.h... yes 2023-09-14T00:11:03,951 checking for curl_easy_pause in -lcurl... yes 2023-09-14T00:11:04,167 checking for CCHmac... no 2023-09-14T00:11:04,769 checking for library containing HMAC... -lcrypto 2023-09-14T00:11:04,959 checking for library containing regcomp... none required 2023-09-14T00:11:05,089 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2023-09-14T00:11:05,155 configure: creating ./config.status 2023-09-14T00:11:05,446 config.status: creating config.mk 2023-09-14T00:11:05,503 config.status: creating htslib.pc.tmp 2023-09-14T00:11:05,569 config.status: creating config.h 2023-09-14T00:11:05,598 config.status: config.h is unchanged 2023-09-14T00:11:05,606 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-09-14T00:11:06,155 # pysam: htslib configure options: --enable-libcurl 2023-09-14T00:11:06,156 # pysam: htslib_config HTS_CFLAGS_AVX2= 2023-09-14T00:11:06,157 # pysam: htslib_config HTS_CFLAGS_AVX512= 2023-09-14T00:11:06,158 # pysam: htslib_config HTS_CFLAGS_SSE4= 2023-09-14T00:11:06,159 # pysam: htslib_config HTS_HAVE_NEON= 2023-09-14T00:11:06,160 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o 2023-09-14T00:11:06,161 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2023-09-14T00:11:06,162 # pysam: htslib_config PLATFORM=default 2023-09-14T00:11:06,163 # pysam: config_option: ENABLE_GCS=1 2023-09-14T00:11:06,164 # pysam: config_option: ENABLE_PLUGINS=0 2023-09-14T00:11:06,165 # pysam: config_option: ENABLE_S3=1 2023-09-14T00:11:06,166 # pysam: config_option: HAVE_COMMONCRYPTO=0 2023-09-14T00:11:06,167 # pysam: config_option: HAVE_HMAC=1 2023-09-14T00:11:06,168 # pysam: config_option: HAVE_LIBBZ2=1 2023-09-14T00:11:06,169 # pysam: config_option: HAVE_LIBCURL=1 2023-09-14T00:11:06,169 # pysam: config_option: HAVE_LIBDEFLATE=1 2023-09-14T00:11:06,170 # pysam: config_option: HAVE_LIBLZMA=1 2023-09-14T00:11:06,171 # pysam: config_option: HAVE_MMAP=1 2023-09-14T00:11:06,172 running bdist_wheel 2023-09-14T00:11:06,174 running build 2023-09-14T00:11:06,175 running build_py 2023-09-14T00:11:06,178 creating build 2023-09-14T00:11:06,178 creating build/lib.linux-armv7l-cpython-311 2023-09-14T00:11:06,179 creating build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,180 copying pysam/samtools.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,183 copying pysam/config.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,185 copying pysam/bcftools.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,187 copying pysam/__init__.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,189 copying pysam/version.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,191 copying pysam/utils.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,193 copying pysam/Pileup.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,195 creating build/lib.linux-armv7l-cpython-311/pysam/include 2023-09-14T00:11:06,197 copying pysam/include/__init__.py -> build/lib.linux-armv7l-cpython-311/pysam/include 2023-09-14T00:11:06,200 running egg_info 2023-09-14T00:11:06,205 writing pysam.egg-info/PKG-INFO 2023-09-14T00:11:06,208 writing dependency_links to pysam.egg-info/dependency_links.txt 2023-09-14T00:11:06,210 writing requirements to pysam.egg-info/requires.txt 2023-09-14T00:11:06,211 writing top-level names to pysam.egg-info/top_level.txt 2023-09-14T00:11:06,491 reading manifest file 'pysam.egg-info/SOURCES.txt' 2023-09-14T00:11:06,531 reading manifest template 'MANIFEST.in' 2023-09-14T00:11:06,533 warning: no files found matching 'KNOWN_BUGS' 2023-09-14T00:11:06,534 warning: no files found matching 'THANKS' 2023-09-14T00:11:06,541 no previously-included directories found matching 'tests/' 2023-09-14T00:11:06,656 adding license file 'COPYING' 2023-09-14T00:11:06,657 adding license file 'AUTHORS' 2023-09-14T00:11:06,678 writing manifest file 'pysam.egg-info/SOURCES.txt' 2023-09-14T00:11:06,686 /tmp/pip-build-env-2_kbmfrk/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pysam.include.htslib.cram' is absent from the `packages` configuration. 2023-09-14T00:11:06,687 !! 2023-09-14T00:11:06,689 ******************************************************************************** 2023-09-14T00:11:06,690 ############################ 2023-09-14T00:11:06,691 # Package would be ignored # 2023-09-14T00:11:06,692 ############################ 2023-09-14T00:11:06,693 Python recognizes 'pysam.include.htslib.cram' as an importable package[^1], 2023-09-14T00:11:06,694 but it is absent from setuptools' `packages` configuration. 2023-09-14T00:11:06,696 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T00:11:06,697 package, please make sure that 'pysam.include.htslib.cram' is explicitly added 2023-09-14T00:11:06,698 to the `packages` configuration field. 2023-09-14T00:11:06,701 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T00:11:06,702 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T00:11:06,703 instead of `find_packages(...)`/`find:`). 2023-09-14T00:11:06,705 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T00:11:06,707 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T00:11:06,709 If you don't want 'pysam.include.htslib.cram' to be distributed and are 2023-09-14T00:11:06,710 already explicitly excluding 'pysam.include.htslib.cram' via 2023-09-14T00:11:06,712 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T00:11:06,713 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T00:11:06,714 combination with a more fine grained `package-data` configuration. 2023-09-14T00:11:06,716 You can read more about "package data files" on setuptools documentation page: 2023-09-14T00:11:06,718 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T00:11:06,721 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T00:11:06,722 even if it does not contain any `.py` files. 2023-09-14T00:11:06,723 On the other hand, currently there is no concept of package data 2023-09-14T00:11:06,724 directory, all directories are treated like packages. 2023-09-14T00:11:06,725 ******************************************************************************** 2023-09-14T00:11:06,728 !! 2023-09-14T00:11:06,729 check.warn(importable) 2023-09-14T00:11:06,730 /tmp/pip-build-env-2_kbmfrk/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pysam.include.htslib.htscodecs.htscodecs' is absent from the `packages` configuration. 2023-09-14T00:11:06,731 !! 2023-09-14T00:11:06,733 ******************************************************************************** 2023-09-14T00:11:06,734 ############################ 2023-09-14T00:11:06,735 # Package would be ignored # 2023-09-14T00:11:06,736 ############################ 2023-09-14T00:11:06,737 Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package[^1], 2023-09-14T00:11:06,738 but it is absent from setuptools' `packages` configuration. 2023-09-14T00:11:06,741 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T00:11:06,742 package, please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is explicitly added 2023-09-14T00:11:06,743 to the `packages` configuration field. 2023-09-14T00:11:06,745 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T00:11:06,746 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T00:11:06,748 instead of `find_packages(...)`/`find:`). 2023-09-14T00:11:06,750 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T00:11:06,753 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T00:11:06,755 If you don't want 'pysam.include.htslib.htscodecs.htscodecs' to be distributed and are 2023-09-14T00:11:06,757 already explicitly excluding 'pysam.include.htslib.htscodecs.htscodecs' via 2023-09-14T00:11:06,758 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T00:11:06,759 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T00:11:06,760 combination with a more fine grained `package-data` configuration. 2023-09-14T00:11:06,763 You can read more about "package data files" on setuptools documentation page: 2023-09-14T00:11:06,765 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T00:11:06,768 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T00:11:06,769 even if it does not contain any `.py` files. 2023-09-14T00:11:06,770 On the other hand, currently there is no concept of package data 2023-09-14T00:11:06,772 directory, all directories are treated like packages. 2023-09-14T00:11:06,773 ******************************************************************************** 2023-09-14T00:11:06,775 !! 2023-09-14T00:11:06,776 check.warn(importable) 2023-09-14T00:11:06,777 /tmp/pip-build-env-2_kbmfrk/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pysam.include.htslib.m4' is absent from the `packages` configuration. 2023-09-14T00:11:06,785 !! 2023-09-14T00:11:06,813 ******************************************************************************** 2023-09-14T00:11:06,815 ############################ 2023-09-14T00:11:06,816 # Package would be ignored # 2023-09-14T00:11:06,816 ############################ 2023-09-14T00:11:06,817 Python recognizes 'pysam.include.htslib.m4' as an importable package[^1], 2023-09-14T00:11:06,817 but it is absent from setuptools' `packages` configuration. 2023-09-14T00:11:06,819 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T00:11:06,819 package, please make sure that 'pysam.include.htslib.m4' is explicitly added 2023-09-14T00:11:06,820 to the `packages` configuration field. 2023-09-14T00:11:06,821 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T00:11:06,822 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T00:11:06,823 instead of `find_packages(...)`/`find:`). 2023-09-14T00:11:06,824 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T00:11:06,826 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T00:11:06,828 If you don't want 'pysam.include.htslib.m4' to be distributed and are 2023-09-14T00:11:06,829 already explicitly excluding 'pysam.include.htslib.m4' via 2023-09-14T00:11:06,830 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T00:11:06,831 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T00:11:06,841 combination with a more fine grained `package-data` configuration. 2023-09-14T00:11:06,842 You can read more about "package data files" on setuptools documentation page: 2023-09-14T00:11:06,844 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T00:11:06,846 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T00:11:06,846 even if it does not contain any `.py` files. 2023-09-14T00:11:06,847 On the other hand, currently there is no concept of package data 2023-09-14T00:11:06,848 directory, all directories are treated like packages. 2023-09-14T00:11:06,848 ******************************************************************************** 2023-09-14T00:11:06,850 !! 2023-09-14T00:11:06,850 check.warn(importable) 2023-09-14T00:11:06,851 /tmp/pip-build-env-2_kbmfrk/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pysam.include.htslib.os' is absent from the `packages` configuration. 2023-09-14T00:11:06,852 !! 2023-09-14T00:11:06,853 ******************************************************************************** 2023-09-14T00:11:06,854 ############################ 2023-09-14T00:11:06,855 # Package would be ignored # 2023-09-14T00:11:06,856 ############################ 2023-09-14T00:11:06,857 Python recognizes 'pysam.include.htslib.os' as an importable package[^1], 2023-09-14T00:11:06,857 but it is absent from setuptools' `packages` configuration. 2023-09-14T00:11:06,858 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T00:11:06,859 package, please make sure that 'pysam.include.htslib.os' is explicitly added 2023-09-14T00:11:06,871 to the `packages` configuration field. 2023-09-14T00:11:06,876 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T00:11:06,881 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T00:11:06,882 instead of `find_packages(...)`/`find:`). 2023-09-14T00:11:06,883 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T00:11:06,884 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T00:11:06,885 If you don't want 'pysam.include.htslib.os' to be distributed and are 2023-09-14T00:11:06,886 already explicitly excluding 'pysam.include.htslib.os' via 2023-09-14T00:11:06,887 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T00:11:06,887 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T00:11:06,888 combination with a more fine grained `package-data` configuration. 2023-09-14T00:11:06,889 You can read more about "package data files" on setuptools documentation page: 2023-09-14T00:11:06,892 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T00:11:06,894 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T00:11:06,894 even if it does not contain any `.py` files. 2023-09-14T00:11:06,895 On the other hand, currently there is no concept of package data 2023-09-14T00:11:06,897 directory, all directories are treated like packages. 2023-09-14T00:11:06,900 ******************************************************************************** 2023-09-14T00:11:06,902 !! 2023-09-14T00:11:06,903 check.warn(importable) 2023-09-14T00:11:06,904 /tmp/pip-build-env-2_kbmfrk/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. 2023-09-14T00:11:06,905 !! 2023-09-14T00:11:06,907 ******************************************************************************** 2023-09-14T00:11:06,910 ############################ 2023-09-14T00:11:06,911 # Package would be ignored # 2023-09-14T00:11:06,918 ############################ 2023-09-14T00:11:06,923 Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], 2023-09-14T00:11:06,923 but it is absent from setuptools' `packages` configuration. 2023-09-14T00:11:06,931 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T00:11:06,932 package, please make sure that 'pysam.include.samtools.lz4' is explicitly added 2023-09-14T00:11:06,933 to the `packages` configuration field. 2023-09-14T00:11:06,934 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T00:11:06,934 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T00:11:06,935 instead of `find_packages(...)`/`find:`). 2023-09-14T00:11:06,936 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T00:11:06,937 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T00:11:06,939 If you don't want 'pysam.include.samtools.lz4' to be distributed and are 2023-09-14T00:11:06,939 already explicitly excluding 'pysam.include.samtools.lz4' via 2023-09-14T00:11:06,940 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T00:11:06,941 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T00:11:06,941 combination with a more fine grained `package-data` configuration. 2023-09-14T00:11:06,942 You can read more about "package data files" on setuptools documentation page: 2023-09-14T00:11:06,944 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T00:11:06,945 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T00:11:06,946 even if it does not contain any `.py` files. 2023-09-14T00:11:06,947 On the other hand, currently there is no concept of package data 2023-09-14T00:11:06,947 directory, all directories are treated like packages. 2023-09-14T00:11:06,948 ******************************************************************************** 2023-09-14T00:11:06,949 !! 2023-09-14T00:11:06,951 check.warn(importable) 2023-09-14T00:11:06,952 copying pysam/cbcftools_util.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,952 copying pysam/csamtools_util.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,953 copying pysam/htslib_util.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,955 copying pysam/htslib_util.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,959 copying pysam/libcalignedsegment.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,964 copying pysam/libcalignedsegment.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,968 copying pysam/libcalignedsegment.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,970 copying pysam/libcalignedsegment.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,971 copying pysam/libcalignmentfile.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,971 copying pysam/libcalignmentfile.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,972 copying pysam/libcalignmentfile.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,973 copying pysam/libcalignmentfile.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:06,980 copying pysam/libcbcf.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,065 copying pysam/libcbcf.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,068 copying pysam/libcbcf.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,070 copying pysam/libcbcf.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,075 copying pysam/libcbcftools.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,079 copying pysam/libcbcftools.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,081 copying pysam/libcbcftools.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,083 copying pysam/libcbcftools.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,086 copying pysam/libcbgzf.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,093 copying pysam/libcbgzf.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,095 copying pysam/libcbgzf.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,098 copying pysam/libcfaidx.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,116 copying pysam/libcfaidx.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,119 copying pysam/libcfaidx.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,121 copying pysam/libcfaidx.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,125 copying pysam/libchtslib.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,144 copying pysam/libchtslib.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,149 copying pysam/libchtslib.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,152 copying pysam/libchtslib.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,155 copying pysam/libcsamfile.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,164 copying pysam/libcsamfile.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,166 copying pysam/libcsamfile.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,168 copying pysam/libcsamfile.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,171 copying pysam/libcsamtools.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,176 copying pysam/libcsamtools.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,178 copying pysam/libcsamtools.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,180 copying pysam/libcsamtools.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,182 copying pysam/libctabix.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,207 copying pysam/libctabix.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,209 copying pysam/libctabix.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,211 copying pysam/libctabix.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,214 copying pysam/libctabixproxies.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,232 copying pysam/libctabixproxies.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,235 copying pysam/libctabixproxies.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,239 copying pysam/libctabixproxies.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,242 copying pysam/libcutils.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,253 copying pysam/libcutils.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,256 copying pysam/libcutils.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,259 copying pysam/libcutils.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,263 copying pysam/libcvcf.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,302 copying pysam/libcvcf.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,306 copying pysam/libcvcf.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,308 copying pysam/libcvcf.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,313 copying pysam/py.typed -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,315 copying pysam/pysam_stream.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,317 copying pysam/pysam_util.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,320 copying pysam/pysam_util.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,322 copying pysam/version.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,324 copying pysam/version.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-14T00:11:07,326 creating build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,327 copying samtools/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,330 copying samtools/README -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,332 copying samtools/amplicon_stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,336 copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,340 copying samtools/bam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,344 copying samtools/bam.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,347 copying samtools/bam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,349 copying samtools/bam2depth.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,352 copying samtools/bam2depth.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,356 copying samtools/bam_addrprg.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,359 copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,362 copying samtools/bam_ampliconclip.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,365 copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,368 copying samtools/bam_ampliconclip.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,370 copying samtools/bam_aux.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,373 copying samtools/bam_aux.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,375 copying samtools/bam_cat.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,378 copying samtools/bam_cat.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,381 copying samtools/bam_color.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,384 copying samtools/bam_color.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,386 copying samtools/bam_consensus.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,391 copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,395 copying samtools/bam_fastq.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,398 copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,401 copying samtools/bam_flags.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,404 copying samtools/bam_flags.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,406 copying samtools/bam_import.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,409 copying samtools/bam_import.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,412 copying samtools/bam_index.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,414 copying samtools/bam_index.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,417 copying samtools/bam_lpileup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,420 copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,423 copying samtools/bam_lpileup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,425 copying samtools/bam_markdup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,430 copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,434 copying samtools/bam_mate.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,437 copying samtools/bam_mate.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,439 copying samtools/bam_md.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,443 copying samtools/bam_md.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,446 copying samtools/bam_plbuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,448 copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,450 copying samtools/bam_plbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,453 copying samtools/bam_plcmd.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,456 copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,459 copying samtools/bam_quickcheck.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,462 copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,466 copying samtools/bam_reheader.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,469 copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,472 copying samtools/bam_rmdup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,474 copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,477 copying samtools/bam_rmdupse.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,479 copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,482 copying samtools/bam_samples.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,485 copying samtools/bam_samples.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,488 copying samtools/bam_sort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,493 copying samtools/bam_sort.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,498 copying samtools/bam_split.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,502 copying samtools/bam_split.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,506 copying samtools/bam_stat.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,508 copying samtools/bam_stat.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,512 copying samtools/bamshuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,515 copying samtools/bamshuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,519 copying samtools/bamtk.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,522 copying samtools/bamtk.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,525 copying samtools/bedcov.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,527 copying samtools/bedcov.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,530 copying samtools/bedidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,533 copying samtools/bedidx.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,535 copying samtools/bedidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,538 copying samtools/consensus_pileup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,540 copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,543 copying samtools/consensus_pileup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,546 copying samtools/coverage.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,548 copying samtools/coverage.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,551 copying samtools/cram_size.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,554 copying samtools/cram_size.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,557 copying samtools/cut_target.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,559 copying samtools/cut_target.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,562 copying samtools/dict.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,564 copying samtools/dict.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,567 copying samtools/faidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,572 copying samtools/faidx.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,574 copying samtools/padding.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,578 copying samtools/padding.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,581 copying samtools/phase.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,584 copying samtools/phase.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,587 copying samtools/reference.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,589 copying samtools/reference.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,592 copying samtools/reset.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,594 copying samtools/reset.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,597 copying samtools/sam_opts.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,600 copying samtools/sam_opts.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,602 copying samtools/sam_opts.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,605 copying samtools/sam_utils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,607 copying samtools/sam_utils.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,609 copying samtools/sam_utils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,612 copying samtools/sam_view.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,615 copying samtools/sam_view.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,618 copying samtools/sample.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,621 copying samtools/sample.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,623 copying samtools/sample.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,626 copying samtools/samtools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,628 copying samtools/samtools.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,630 copying samtools/samtools.pysam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,632 copying samtools/splaysort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,635 copying samtools/stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,640 copying samtools/stats.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,645 copying samtools/stats_isize.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,647 copying samtools/stats_isize.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,650 copying samtools/stats_isize.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,652 copying samtools/tmp_file.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,655 copying samtools/tmp_file.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,658 copying samtools/tmp_file.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,660 copying samtools/version.sh -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,662 creating build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4 2023-09-14T00:11:07,663 copying samtools/lz4/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4 2023-09-14T00:11:07,666 copying samtools/lz4/lz4.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4 2023-09-14T00:11:07,670 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4 2023-09-14T00:11:07,674 copying samtools/lz4/lz4.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4 2023-09-14T00:11:07,677 copying samtools/config.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-14T00:11:07,679 creating build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,680 copying bcftools/HMM.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,683 copying bcftools/HMM.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,686 copying bcftools/HMM.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,689 copying bcftools/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,693 copying bcftools/README -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,695 copying bcftools/abuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,698 copying bcftools/abuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,702 copying bcftools/abuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,704 copying bcftools/bam2bcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,707 copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,711 copying bcftools/bam2bcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,714 copying bcftools/bam2bcf_iaux.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,718 copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,721 copying bcftools/bam2bcf_indel.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,725 copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,729 copying bcftools/bam_sample.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,732 copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,736 copying bcftools/bam_sample.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,738 copying bcftools/bcftools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,742 copying bcftools/bcftools.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,744 copying bcftools/bcftools.pysam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,747 copying bcftools/bin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,750 copying bcftools/bin.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,753 copying bcftools/bin.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,754 copying bcftools/call.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,757 copying bcftools/ccall.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,759 copying bcftools/ccall.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,762 copying bcftools/cigar_state.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,764 copying bcftools/cols.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,767 copying bcftools/cols.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,769 copying bcftools/cols.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,771 copying bcftools/consensus.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,774 copying bcftools/consensus.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,778 copying bcftools/convert.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,781 copying bcftools/convert.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,784 copying bcftools/convert.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,786 copying bcftools/csq.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,792 copying bcftools/csq.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,798 copying bcftools/dbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,801 copying bcftools/dist.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,804 copying bcftools/dist.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,807 copying bcftools/dist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,810 copying bcftools/em.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,813 copying bcftools/em.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,816 copying bcftools/extsort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,818 copying bcftools/extsort.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,821 copying bcftools/extsort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,823 copying bcftools/filter.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,828 copying bcftools/filter.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,835 copying bcftools/filter.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,838 copying bcftools/gvcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,841 copying bcftools/gvcf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,843 copying bcftools/gvcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,846 copying bcftools/hclust.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,848 copying bcftools/hclust.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,851 copying bcftools/hclust.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,854 copying bcftools/hex.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,856 copying bcftools/khash_str2str.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,858 copying bcftools/kheap.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,861 copying bcftools/kmin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,863 copying bcftools/kmin.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,866 copying bcftools/kmin.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,868 copying bcftools/main.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,871 copying bcftools/main.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,874 copying bcftools/mcall.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,878 copying bcftools/mcall.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,882 copying bcftools/mpileup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,887 copying bcftools/mpileup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,893 copying bcftools/mw.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,898 copying bcftools/ploidy.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,902 copying bcftools/ploidy.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,905 copying bcftools/ploidy.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,908 copying bcftools/prob1.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,912 copying bcftools/prob1.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,916 copying bcftools/prob1.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,919 copying bcftools/rbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,922 copying bcftools/read_consensus.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,927 copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,932 copying bcftools/read_consensus.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,935 copying bcftools/regidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,939 copying bcftools/regidx.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,943 copying bcftools/regidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,947 copying bcftools/reheader.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,951 copying bcftools/reheader.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,956 copying bcftools/smpl_ilist.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,960 copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,963 copying bcftools/smpl_ilist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,966 copying bcftools/str_finder.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,970 copying bcftools/str_finder.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,974 copying bcftools/str_finder.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,978 copying bcftools/tabix.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,981 copying bcftools/tabix.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,985 copying bcftools/tsv2vcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,989 copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,992 copying bcftools/tsv2vcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:07,996 copying bcftools/utlist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,001 copying bcftools/variantkey.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,006 copying bcftools/vcfannotate.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,014 copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,023 copying bcftools/vcfbuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,026 copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,029 copying bcftools/vcfbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,032 copying bcftools/vcfcall.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,035 copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,039 copying bcftools/vcfcnv.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,043 copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,047 copying bcftools/vcfconcat.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,050 copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,053 copying bcftools/vcfconvert.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,058 copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,062 copying bcftools/vcffilter.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,066 copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,071 copying bcftools/vcfgtcheck.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,086 copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,092 copying bcftools/vcfhead.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,095 copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,099 copying bcftools/vcfindex.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,103 copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,107 copying bcftools/vcfisec.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,111 copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,115 copying bcftools/vcfmerge.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,121 copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,128 copying bcftools/vcfnorm.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,134 copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,140 copying bcftools/vcfplugin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,144 copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,147 copying bcftools/vcfquery.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,150 copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,153 copying bcftools/vcfroh.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,157 copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,161 copying bcftools/vcfsom.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,164 copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,168 copying bcftools/vcfsort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,171 copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,175 copying bcftools/vcfstats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,179 copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,184 copying bcftools/vcfview.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,188 copying bcftools/vcfview.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,192 copying bcftools/vcmp.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,196 copying bcftools/vcmp.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,200 copying bcftools/vcmp.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,203 copying bcftools/version.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,206 copying bcftools/version.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,209 copying bcftools/version.sh -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,212 copying bcftools/config.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-14T00:11:08,215 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,216 copying htslib/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,220 copying htslib/Makefile -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,224 copying htslib/README -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,228 copying htslib/bcf_sr_sort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,231 copying htslib/bcf_sr_sort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,235 copying htslib/bgzf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,240 copying htslib/bgzip.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,244 copying htslib/builddir_vars.mk.in -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,247 copying htslib/config.h.in -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,251 copying htslib/config.mk.in -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,253 copying htslib/configure -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,261 copying htslib/configure.ac -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,266 copying htslib/errmod.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,271 copying htslib/faidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,275 copying htslib/header.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,282 copying htslib/header.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,285 copying htslib/hfile.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,289 copying htslib/hfile_gcs.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,292 copying htslib/hfile_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,295 copying htslib/hfile_libcurl.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,299 copying htslib/hfile_s3.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,302 copying htslib/hfile_s3_write.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,305 copying htslib/hts.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,312 copying htslib/hts_expr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,316 copying htslib/hts_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,319 copying htslib/hts_os.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,322 copying htslib/hts_time_funcs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,324 copying htslib/htscodecs_bundled.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,327 copying htslib/htscodecs_external.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,329 copying htslib/htsfile.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,332 copying htslib/htslib.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,335 copying htslib/htslib.pc.in -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,338 copying htslib/htslib_vars.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,340 copying htslib/kfunc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,343 copying htslib/kstring.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,346 copying htslib/md5.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,348 copying htslib/multipart.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,351 copying htslib/plugin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,355 copying htslib/probaln.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,358 copying htslib/realn.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,361 copying htslib/regidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,365 copying htslib/region.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,368 copying htslib/sam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,374 copying htslib/sam_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,376 copying htslib/synced_bcf_reader.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,380 copying htslib/tabix.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,384 copying htslib/tbx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,387 copying htslib/textutils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,389 copying htslib/textutils_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,392 copying htslib/thread_pool.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,396 copying htslib/thread_pool_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,399 copying htslib/vcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,405 copying htslib/vcf_sweep.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,408 copying htslib/vcfutils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,412 copying htslib/version.sh -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,414 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,415 copying htslib/cram/cram.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,419 copying htslib/cram/cram_codecs.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,424 copying htslib/cram/cram_codecs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,427 copying htslib/cram/cram_decode.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,431 copying htslib/cram/cram_decode.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,434 copying htslib/cram/cram_encode.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,439 copying htslib/cram/cram_encode.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,442 copying htslib/cram/cram_external.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,445 copying htslib/cram/cram_index.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,449 copying htslib/cram/cram_index.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,452 copying htslib/cram/cram_io.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,459 copying htslib/cram/cram_io.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,462 copying htslib/cram/cram_samtools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,465 copying htslib/cram/cram_stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,468 copying htslib/cram/cram_stats.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,472 copying htslib/cram/cram_structs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,475 copying htslib/cram/mFILE.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,479 copying htslib/cram/mFILE.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,481 copying htslib/cram/misc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,483 copying htslib/cram/open_trace_file.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,487 copying htslib/cram/open_trace_file.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,489 copying htslib/cram/os.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,492 copying htslib/cram/pooled_alloc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,494 copying htslib/cram/pooled_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,496 copying htslib/cram/string_alloc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,499 copying htslib/cram/string_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-14T00:11:08,501 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs 2023-09-14T00:11:08,503 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,504 copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,507 copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,509 copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,511 copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,514 copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,517 copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,520 copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,522 copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,525 copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,527 copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,530 copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,532 copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,535 copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,537 copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,540 copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,544 copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,546 copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,550 copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,554 copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,557 copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,562 copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,565 copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,570 copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,576 copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,579 copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,583 copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,586 copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,589 copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,592 copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,595 copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,598 copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,602 copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,605 copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,609 copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,613 copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:11:08,616 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4 2023-09-14T00:11:08,617 copying htslib/m4/ax_check_compile_flag.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4 2023-09-14T00:11:08,619 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4 2023-09-14T00:11:08,621 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4 2023-09-14T00:11:08,624 copying htslib/m4/pkg.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4 2023-09-14T00:11:08,627 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os 2023-09-14T00:11:08,628 copying htslib/os/lzma_stub.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os 2023-09-14T00:11:08,630 copying htslib/os/rand.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os 2023-09-14T00:11:08,633 copying htslib/config.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-14T00:11:08,635 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,636 copying htslib/htslib/bgzf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,639 copying htslib/htslib/cram.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,642 copying htslib/htslib/faidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,645 copying htslib/htslib/hfile.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,648 copying htslib/htslib/hts.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,651 copying htslib/htslib/hts_defs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,654 copying htslib/htslib/hts_endian.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,656 copying htslib/htslib/hts_expr.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,659 copying htslib/htslib/hts_log.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,662 copying htslib/htslib/hts_os.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,664 copying htslib/htslib/kbitset.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,667 copying htslib/htslib/kfunc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,669 copying htslib/htslib/khash.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,672 copying htslib/htslib/khash_str2int.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,674 copying htslib/htslib/klist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,677 copying htslib/htslib/knetfile.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,679 copying htslib/htslib/kroundup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,682 copying htslib/htslib/kseq.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,684 copying htslib/htslib/ksort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,687 copying htslib/htslib/kstring.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,690 copying htslib/htslib/regidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,692 copying htslib/htslib/sam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,696 copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,701 copying htslib/htslib/tbx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,704 copying htslib/htslib/thread_pool.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,706 copying htslib/htslib/vcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,710 copying htslib/htslib/vcf_sweep.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,712 copying htslib/htslib/vcfutils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-14T00:11:08,719 running build_ext 2023-09-14T00:11:08,785 skipping 'pysam/libchtslib.c' Cython extension (up-to-date) 2023-09-14T00:11:08,787 skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) 2023-09-14T00:11:08,788 skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) 2023-09-14T00:11:08,789 skipping 'pysam/libcutils.c' Cython extension (up-to-date) 2023-09-14T00:11:08,790 skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) 2023-09-14T00:11:08,791 skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) 2023-09-14T00:11:08,793 skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) 2023-09-14T00:11:08,794 skipping 'pysam/libctabix.c' Cython extension (up-to-date) 2023-09-14T00:11:08,795 skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) 2023-09-14T00:11:08,797 skipping 'pysam/libcbcf.c' Cython extension (up-to-date) 2023-09-14T00:11:08,798 skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) 2023-09-14T00:11:08,799 skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) 2023-09-14T00:11:08,800 skipping 'pysam/libcvcf.c' Cython extension (up-to-date) 2023-09-14T00:11:08,801 creating htslib/config_vars.h for 'pysam.libchtslib' extension 2023-09-14T00:11:08,803 building 'libhts.a' 2023-09-14T00:11:08,849 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kfunc.o kfunc.c 2023-09-14T00:11:09,345 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kstring.o kstring.c 2023-09-14T00:11:10,198 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bcf_sr_sort.o bcf_sr_sort.c 2023-09-14T00:11:12,794 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bgzf.o bgzf.c 2023-09-14T00:11:16,134 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o errmod.o errmod.c 2023-09-14T00:11:16,847 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o faidx.o faidx.c 2023-09-14T00:11:18,809 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o header.o header.c 2023-09-14T00:11:23,352 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile.o hfile.c 2023-09-14T00:11:25,040 echo '#define HTS_VERSION_TEXT "1.17"' > version.h 2023-09-14T00:11:25,046 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts.o hts.c 2023-09-14T00:11:33,667 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_expr.o hts_expr.c 2023-09-14T00:11:35,626 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_os.o hts_os.c 2023-09-14T00:11:35,736 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o md5.o md5.c 2023-09-14T00:11:36,390 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o multipart.o multipart.c 2023-09-14T00:11:37,167 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o probaln.o probaln.c 2023-09-14T00:11:37,910 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o realn.o realn.c 2023-09-14T00:11:38,840 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o regidx.o regidx.c 2023-09-14T00:11:40,352 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o region.o region.c 2023-09-14T00:11:41,012 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam.o sam.c 2023-09-14T00:11:55,155 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o synced_bcf_reader.o synced_bcf_reader.c 2023-09-14T00:11:57,926 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf_sweep.o vcf_sweep.c 2023-09-14T00:11:58,304 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o tbx.o tbx.c 2023-09-14T00:11:59,212 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o textutils.o textutils.c 2023-09-14T00:12:00,188 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o thread_pool.o thread_pool.c 2023-09-14T00:12:01,119 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf.o vcf.c 2023-09-14T00:12:15,742 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcfutils.o vcfutils.c 2023-09-14T00:12:18,995 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_codecs.o cram/cram_codecs.c 2023-09-14T00:12:24,594 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_decode.o cram/cram_decode.c 2023-09-14T00:12:30,886 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_encode.o cram/cram_encode.c 2023-09-14T00:12:39,084 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_external.o cram/cram_external.c 2023-09-14T00:12:40,250 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_index.o cram/cram_index.c 2023-09-14T00:12:41,584 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_io.o cram/cram_io.c 2023-09-14T00:12:49,559 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_stats.o cram/cram_stats.c 2023-09-14T00:12:50,312 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/mFILE.o cram/mFILE.c 2023-09-14T00:12:50,988 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/open_trace_file.o cram/open_trace_file.c 2023-09-14T00:12:51,533 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/pooled_alloc.o cram/pooled_alloc.c 2023-09-14T00:12:51,932 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/string_alloc.o cram/string_alloc.c 2023-09-14T00:12:52,132 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c 2023-09-14T00:12:55,909 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c 2023-09-14T00:12:59,940 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c 2023-09-14T00:13:00,008 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c 2023-09-14T00:13:00,846 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c 2023-09-14T00:13:05,755 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c 2023-09-14T00:13:08,998 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c 2023-09-14T00:13:11,102 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c 2023-09-14T00:13:11,576 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c 2023-09-14T00:13:14,525 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c 2023-09-14T00:13:14,818 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile_libcurl.o hfile_libcurl.c 2023-09-14T00:13:15,268 hfile_libcurl.c: In function ‘libcurl_open’: 2023-09-14T00:13:15,270 hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 2023-09-14T00:13:15,271 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, 2023-09-14T00:13:15,272 | ^~ 2023-09-14T00:13:15,274 In file included from hfile_libcurl.c:47: 2023-09-14T00:13:15,274 /usr/include/arm-linux-gnueabihf/curl/curl.h:2858:3: note: declared here 2023-09-14T00:13:15,275 2858 | CURLINFO_CONTENT_LENGTH_DOWNLOAD 2023-09-14T00:13:15,276 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:13:17,341 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile_gcs.o hfile_gcs.c 2023-09-14T00:13:17,833 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile_s3.o hfile_s3.c 2023-09-14T00:13:20,816 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile_s3_write.o hfile_s3_write.c 2023-09-14T00:13:22,303 ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o 2023-09-14T00:13:22,668 ranlib libhts.a 2023-09-14T00:13:22,962 building 'pysam.libchtslib' extension 2023-09-14T00:13:22,963 creating build/temp.linux-armv7l-cpython-311 2023-09-14T00:13:22,963 creating build/temp.linux-armv7l-cpython-311/pysam 2023-09-14T00:13:22,964 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/htslib_util.c -o build/temp.linux-armv7l-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:23,275 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libchtslib.c -o build/temp.linux-armv7l-cpython-311/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:38,864 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/htslib_util.o build/temp.linux-armv7l-cpython-311/pysam/libchtslib.o htslib/kfunc.o htslib/kstring.o htslib/bcf_sr_sort.o htslib/bgzf.o htslib/errmod.o htslib/faidx.o htslib/header.o htslib/hfile.o htslib/hts.o htslib/hts_expr.o htslib/hts_os.o htslib/md5.o htslib/multipart.o htslib/probaln.o htslib/realn.o htslib/regidx.o htslib/region.o htslib/sam.o htslib/synced_bcf_reader.o htslib/vcf_sweep.o htslib/tbx.o htslib/textutils.o htslib/thread_pool.o htslib/vcf.o htslib/vcfutils.o htslib/cram/cram_codecs.o htslib/cram/cram_decode.o htslib/cram/cram_encode.o htslib/cram/cram_external.o htslib/cram/cram_index.o htslib/cram/cram_io.o htslib/cram/cram_stats.o htslib/cram/mFILE.o htslib/cram/open_trace_file.o htslib/cram/pooled_alloc.o htslib/cram/string_alloc.o htslib/htscodecs/htscodecs/arith_dynamic.o htslib/htscodecs/htscodecs/fqzcomp_qual.o htslib/htscodecs/htscodecs/htscodecs.o htslib/htscodecs/htscodecs/pack.o htslib/htscodecs/htscodecs/rANS_static4x16pr.o htslib/htscodecs/htscodecs/rANS_static32x16pr.o htslib/htscodecs/htscodecs/rANS_static.o htslib/htscodecs/htscodecs/rle.o htslib/htscodecs/htscodecs/tokenise_name3.o htslib/htscodecs/htscodecs/utils.o htslib/hfile_libcurl.o htslib/hfile_gcs.o htslib/hfile_s3.o htslib/hfile_s3_write.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -o build/lib.linux-armv7l-cpython-311/pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:13:39,463 creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension 2023-09-14T00:13:39,466 building 'pysam.libcsamtools' extension 2023-09-14T00:13:39,467 creating build/temp.linux-armv7l-cpython-311/samtools 2023-09-14T00:13:39,470 creating build/temp.linux-armv7l-cpython-311/samtools/lz4 2023-09-14T00:13:39,472 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libcsamtools.c -o build/temp.linux-armv7l-cpython-311/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:40,606 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:44,796 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:45,376 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:47,912 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:48,646 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:50,623 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:50,885 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:51,675 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:51,964 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:55,094 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:56,465 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:56,709 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:57,690 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:58,145 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:13:58,800 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:03,815 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:05,402 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:06,527 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:06,749 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:09,199 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:09,555 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:10,339 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:11,833 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:13,079 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:13,948 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:23,244 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:25,023 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:25,825 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:28,121 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:28,617 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:29,729 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:31,513 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:32,152 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/coverage.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:33,296 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/cram_size.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:33,745 samtools/cram_size.c.pysam.c: In function ‘cram_size’: 2023-09-14T00:14:33,746 samtools/cram_size.c.pysam.c:563:20: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘off_t’ {aka ‘long int’} [-Wformat=] 2023-09-14T00:14:33,747 563 | fprintf(outfp, "Total file size %18"PRId64"\n", end); 2023-09-14T00:14:33,748 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ 2023-09-14T00:14:33,749 | | 2023-09-14T00:14:33,749 | off_t {aka long int} 2023-09-14T00:14:33,750 In file included from /tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib/htslib/hts.h:33, 2023-09-14T00:14:33,751 from /tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib/htslib/sam.h:33, 2023-09-14T00:14:33,753 from samtools/cram_size.c.pysam.c:39: 2023-09-14T00:14:33,754 /usr/include/inttypes.h:57:41: note: format string is defined here 2023-09-14T00:14:33,755 57 | # define PRId64 __PRI64_PREFIX "d" 2023-09-14T00:14:33,758 samtools/cram_size.c.pysam.c:564:20: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘off_t’ {aka ‘long int’} [-Wformat=] 2023-09-14T00:14:33,759 564 | fprintf(outfp, "Format overhead size %18"PRId64"\n", end - tot_size); 2023-09-14T00:14:33,760 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ 2023-09-14T00:14:33,761 | | 2023-09-14T00:14:33,763 | off_t {aka long int} 2023-09-14T00:14:33,764 /usr/include/inttypes.h:57:41: note: format string is defined here 2023-09-14T00:14:33,765 57 | # define PRId64 __PRI64_PREFIX "d" 2023-09-14T00:14:34,633 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:35,296 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/dict.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:36,341 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:36,958 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/lz4/lz4.c -o build/temp.linux-armv7l-cpython-311/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:43,166 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:44,536 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:47,718 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/reference.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:48,742 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/reset.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:49,815 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:50,135 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:50,648 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:53,742 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:54,545 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/samtools.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:14:54,751 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:00,147 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:00,802 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armv7l-cpython-311/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:01,278 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcsamtools.o build/temp.linux-armv7l-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_samples.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bamtk.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/coverage.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/cram_size.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/dict.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/faidx.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/lz4/lz4.o build/temp.linux-armv7l-cpython-311/samtools/padding.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/phase.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/reference.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/reset.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/sam_opts.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/sam_utils.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/sample.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/samtools.pysam.o build/temp.linux-armv7l-cpython-311/samtools/stats.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-cpython-311/samtools/tmp_file.c.pysam.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:15:02,164 building 'pysam.libcbcftools' extension 2023-09-14T00:15:02,167 creating build/temp.linux-armv7l-cpython-311/bcftools 2023-09-14T00:15:02,169 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:03,202 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/abuf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:06,030 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:08,575 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:10,240 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:12,743 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:14,704 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/bcftools.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:15,094 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/bin.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:15,421 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:16,188 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/cols.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:16,771 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:19,532 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/convert.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:25,754 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/csq.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:34,964 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/dist.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:35,236 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/em.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:36,016 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/extsort.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:36,555 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/filter.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:50,564 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:51,168 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:51,835 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:52,273 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/main.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:52,604 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:56,521 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:15:59,189 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:00,254 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:01,855 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:03,728 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:05,154 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:08,331 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:08,832 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:09,271 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:09,637 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:10,024 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:19,581 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:20,958 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:23,653 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:25,777 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:28,457 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:32,079 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:33,661 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:36,722 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:37,076 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:37,756 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:39,501 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:41,952 bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: 2023-09-14T00:16:41,954 bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-09-14T00:16:41,955 751 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n 2023-09-14T00:16:41,956 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:16:41,957 In file included from /tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib/htslib/kstring.h:30, 2023-09-14T00:16:41,958 from /tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib/htslib/hts.h:37, 2023-09-14T00:16:41,958 from /tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib/htslib/vcf.h:39, 2023-09-14T00:16:41,959 from bcftools/vcfmerge.c.pysam.c:35: 2023-09-14T00:16:41,960 /usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’ declared here 2023-09-14T00:16:41,961 556 | extern void *calloc (size_t __nmemb, size_t __size) 2023-09-14T00:16:41,962 | ^~~~~~ 2023-09-14T00:16:50,920 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:59,510 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:16:59,770 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:01,048 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:03,697 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:05,059 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:05,862 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:10,342 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:12,404 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:13,117 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c bcftools/version.c.pysam.c -o build/temp.linux-armv7l-cpython-311/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:13,755 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libcbcftools.c -o build/temp.linux-armv7l-cpython-311/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:14,830 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/bcftools/HMM.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/abuf.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bcftools.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/bin.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/ccall.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/cols.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/consensus.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/convert.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/csq.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/dist.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/em.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/extsort.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/filter.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/gvcf.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/hclust.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/kmin.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/main.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/mcall.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/mpileup.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/ploidy.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/prob1.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/read_consensus.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/regidx.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/reheader.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/str_finder.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/tabix.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfplugin.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcfview.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/vcmp.c.pysam.o build/temp.linux-armv7l-cpython-311/bcftools/version.c.pysam.o build/temp.linux-armv7l-cpython-311/pysam/libcbcftools.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:17:15,297 building 'pysam.libcutils' extension 2023-09-14T00:17:15,299 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libcutils.c -o build/temp.linux-armv7l-cpython-311/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:27,576 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/pysam_util.c -o build/temp.linux-armv7l-cpython-311/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:27,728 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcutils.o build/temp.linux-armv7l-cpython-311/pysam/pysam_util.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcsamtools.cpython-311-arm-linux-gnueabihf -lcbcftools.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcutils.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:17:27,922 building 'pysam.libcalignmentfile' extension 2023-09-14T00:17:27,923 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libcalignmentfile.c -o build/temp.linux-armv7l-cpython-311/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:17:32,738 pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: 2023-09-14T00:17:32,768 pysam/libcalignmentfile.c:28658:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-14T00:17:32,769 28658 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); 2023-09-14T00:17:32,769 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:17:32,971 pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: 2023-09-14T00:17:32,986 pysam/libcalignmentfile.c:14341:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-14T00:17:32,987 14341 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); 2023-09-14T00:17:32,988 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:18:14,013 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcalignmentfile.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:18:14,243 building 'pysam.libcsamfile' extension 2023-09-14T00:18:14,244 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-armv7l-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:18:16,600 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcsamfile.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:18:16,755 building 'pysam.libcalignedsegment' extension 2023-09-14T00:18:16,756 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libcalignedsegment.c -o build/temp.linux-armv7l-cpython-311/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:18:25,518 pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: 2023-09-14T00:18:25,533 pysam/libcalignedsegment.c:14415:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-14T00:18:25,534 14415 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); 2023-09-14T00:18:25,535 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:19:19,055 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcalignedsegment.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:19:19,343 building 'pysam.libctabix' extension 2023-09-14T00:19:19,343 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-armv7l-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:19:43,069 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libctabix.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:19:43,266 building 'pysam.libcfaidx' extension 2023-09-14T00:19:43,267 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libcfaidx.c -o build/temp.linux-armv7l-cpython-311/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:19:57,896 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcfaidx.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:19:58,076 building 'pysam.libcbcf' extension 2023-09-14T00:19:58,077 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libcbcf.c -o build/temp.linux-armv7l-cpython-311/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:20:08,905 pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: 2023-09-14T00:20:08,972 pysam/libcbcf.c:67371:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-14T00:20:08,973 67371 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); 2023-09-14T00:20:08,973 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:20:08,984 pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: 2023-09-14T00:20:09,050 pysam/libcbcf.c:67096:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-14T00:20:09,051 67096 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); 2023-09-14T00:20:09,052 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:20:09,057 pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: 2023-09-14T00:20:09,121 pysam/libcbcf.c:72230:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-14T00:20:09,121 72230 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); 2023-09-14T00:20:09,122 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:20:09,931 pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: 2023-09-14T00:20:09,966 pysam/libcbcf.c:35394:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-14T00:20:09,967 35394 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); 2023-09-14T00:20:09,967 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:20:09,999 pysam/libcbcf.c:35420:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-14T00:20:10,000 35420 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); 2023-09-14T00:20:10,001 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:21:24,328 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcbcf.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:21:24,877 building 'pysam.libcbgzf' extension 2023-09-14T00:21:24,878 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libcbgzf.c -o build/temp.linux-armv7l-cpython-311/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:21:30,984 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcbgzf.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:21:31,153 building 'pysam.libctabixproxies' extension 2023-09-14T00:21:31,154 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libctabixproxies.c -o build/temp.linux-armv7l-cpython-311/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:21:51,835 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libctabixproxies.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:21:52,019 building 'pysam.libcvcf' extension 2023-09-14T00:21:52,020 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/htslib -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/samtools/lz4 -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/bcftools -I/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -I/usr/include/python3.11 -c pysam/libcvcf.c -o build/temp.linux-armv7l-cpython-311/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-14T00:22:31,812 pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’: 2023-09-14T00:22:31,839 pysam/libcvcf.c:25833:15: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-14T00:22:31,840 25833 | __pyx_t_8 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 873, __pyx_L1_error) 2023-09-14T00:22:31,841 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:22:31,862 pysam/libcvcf.c:20265:10: note: ‘__pyx_v_qual’ was declared here 2023-09-14T00:22:31,863 20265 | double __pyx_v_qual; 2023-09-14T00:22:31,864 | ^~~~~~~~~~~~ 2023-09-14T00:22:59,260 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcvcf.o -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb/pysam -L/tmp/pip-install-916oge9o/pysam_0266b074f26e45208eff85fd12bd4abb -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-14T00:23:00,466 installing to build/bdist.linux-armv7l/wheel 2023-09-14T00:23:00,467 running install 2023-09-14T00:23:00,493 running install_lib 2023-09-14T00:23:00,499 creating build/bdist.linux-armv7l 2023-09-14T00:23:00,500 creating build/bdist.linux-armv7l/wheel 2023-09-14T00:23:00,504 creating build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:00,506 copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:00,520 copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:00,550 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:00,553 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:00,556 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:00,561 creating build/bdist.linux-armv7l/wheel/pysam/include 2023-09-14T00:23:00,565 creating build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,568 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/phase.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,572 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reference.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,576 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam2depth.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,580 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,583 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,586 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/amplicon_stats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,594 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cut_target.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,598 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_stat.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,601 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,604 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,607 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamshuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,611 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,614 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_stat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,616 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,621 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_fastq.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,623 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamshuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,626 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,630 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_mate.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,633 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,635 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,638 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,640 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_view.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,643 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_flags.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,645 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_import.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,648 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdupse.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,650 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,653 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_aux.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,655 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/padding.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,658 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/dict.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,660 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_reheader.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,662 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/faidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,665 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_sort.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,669 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_samples.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,672 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,674 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,677 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedcov.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,680 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_reheader.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,682 creating build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4 2023-09-14T00:23:00,683 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4 2023-09-14T00:23:00,686 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4 2023-09-14T00:23:00,690 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4 2023-09-14T00:23:00,693 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4 2023-09-14T00:23:00,695 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,698 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,700 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_quickcheck.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,702 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_color.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,704 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_index.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,706 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,709 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,711 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/dict.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,713 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/coverage.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,716 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,718 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,720 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_markdup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,724 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_cat.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,727 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,730 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_index.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,734 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_import.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,737 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,740 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,743 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,745 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,748 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,751 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reset.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,753 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/padding.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,756 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,758 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,762 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,764 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_aux.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,766 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,768 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_mate.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,771 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,773 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_cat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,775 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reference.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,778 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,781 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cram_size.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,786 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_md.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,794 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,798 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_split.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,801 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/README -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,803 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam2depth.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,805 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plcmd.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,809 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cut_target.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,811 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_addrprg.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,814 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cram_size.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,816 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_sort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,821 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/coverage.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,824 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_samples.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,826 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_color.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,829 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamtk.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,831 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/amplicon_stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,834 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdupse.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,838 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_flags.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,841 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,844 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,850 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,854 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_view.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,858 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_markdup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,863 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,866 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamtk.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,869 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,872 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,875 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,878 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reset.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,882 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_split.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,885 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,889 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_md.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,892 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,895 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_quickcheck.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,898 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,900 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_fastq.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,905 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plcmd.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,908 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,911 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,913 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedcov.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,916 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,919 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/phase.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,922 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/splaysort.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,926 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/faidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,929 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_addrprg.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-14T00:23:00,933 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:00,934 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htsfile.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:00,938 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,939 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_codecs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,943 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/string_alloc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,945 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/pooled_alloc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,947 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_codecs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,953 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_io.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,956 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_encode.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,958 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_index.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,962 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_decode.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,969 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/mFILE.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,971 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_samtools.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,974 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,977 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/mFILE.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,980 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/pooled_alloc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,983 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_index.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,986 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,988 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/misc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,991 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/os.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,993 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_stats.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,996 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_structs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:00,999 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/open_trace_file.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:01,001 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_encode.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:01,007 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_decode.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:01,010 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/open_trace_file.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:01,013 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_external.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:01,016 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_io.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:01,022 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/string_alloc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-14T00:23:01,025 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,031 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs_external.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,033 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bcf_sr_sort.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,036 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs_bundled.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,039 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/plugin.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,041 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_time_funcs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,043 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_os.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,046 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4 2023-09-14T00:23:01,047 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4/pkg.m4 -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4 2023-09-14T00:23:01,049 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4/hts_prog_cc_warnings.m4 -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4 2023-09-14T00:23:01,052 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4/ax_check_compile_flag.m4 -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4 2023-09-14T00:23:01,054 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4/hts_hide_dynamic_syms.m4 -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4 2023-09-14T00:23:01,056 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bgzip.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,058 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/realn.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,061 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,063 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_s3_write.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,065 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/faidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,068 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_expr.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,071 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_libcurl.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,074 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_s3.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,077 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/synced_bcf_reader.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,081 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bcf_sr_sort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,083 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/textutils_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,085 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/builddir_vars.mk.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,087 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,092 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/configure -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,097 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,099 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/multipart.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,102 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/regidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,104 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/sam.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,111 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcfutils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,115 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,117 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kseq.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,120 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kroundup.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,123 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/bgzf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,126 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcf_sweep.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,129 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_log.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,132 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/khash.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,135 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/khash_str2int.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,138 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/klist.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,141 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/tbx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,144 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,147 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_expr.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,149 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/ksort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,153 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_defs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,155 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/synced_bcf_reader.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,158 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcfutils.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,161 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kstring.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,164 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/thread_pool.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,168 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/cram.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,171 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,174 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,178 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/faidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,182 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_endian.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,185 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/sam.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,190 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/knetfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,193 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_os.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,195 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kbitset.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,197 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kfunc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,199 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-14T00:23:01,202 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/os 2023-09-14T00:23:01,203 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os/rand.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/os 2023-09-14T00:23:01,205 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os/lzma_stub.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/os 2023-09-14T00:23:01,208 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/kstring.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,210 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/kfunc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,212 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/tbx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,214 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcf_sweep.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,216 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,219 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/Makefile -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,222 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/errmod.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,224 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/thread_pool_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,226 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/thread_pool.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,229 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,231 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/README -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,234 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs 2023-09-14T00:23:01,235 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,237 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,239 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,242 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,245 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/permute.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,248 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,250 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,252 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,254 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,256 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_word.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,259 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,261 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,265 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/varint.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,267 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,270 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,272 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/version.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,274 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/utils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,276 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,278 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,281 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,284 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rle.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,286 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,290 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,292 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pack.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,295 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,297 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,299 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pack.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,301 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,304 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,306 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,308 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,310 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/utils.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,312 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rle.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,315 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,316 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,318 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-14T00:23:01,321 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/configure.ac -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,324 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/probaln.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,326 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/textutils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,329 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/md5.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,331 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib_vars.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,334 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,336 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/sam_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,338 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.mk.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,339 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.h.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,342 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/header.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,346 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/tabix.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,348 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/header.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,351 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bgzf.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,354 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_gcs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,357 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/region.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,359 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,361 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,363 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib.pc.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-14T00:23:01,365 copying build/lib.linux-armv7l-cpython-311/pysam/include/__init__.py -> build/bdist.linux-armv7l/wheel/pysam/include 2023-09-14T00:23:01,369 creating build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,369 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ccall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,372 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfmerge.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,377 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,379 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,381 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconcat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,384 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mpileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,387 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/utlist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,390 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,392 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,395 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsom.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,398 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfmerge.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,403 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,406 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,408 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/csq.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,415 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/reheader.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,417 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfnorm.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,423 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfisec.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,425 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfnorm.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,431 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,432 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/reheader.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,435 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,438 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,440 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/rbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,442 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfroh.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,446 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_indel.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,448 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,451 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,454 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tabix.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,457 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/em.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,458 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/csq.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,464 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,466 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,468 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,471 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,474 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,475 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,478 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfquery.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,481 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,482 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,484 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,487 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,489 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,491 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconvert.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,495 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,497 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,499 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,502 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,506 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,509 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/main.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,512 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/variantkey.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,514 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,518 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,520 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,521 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kheap.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,524 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,526 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,528 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcnv.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,531 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/em.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,534 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfplugin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,537 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,539 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,541 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,543 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,545 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,548 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,550 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfplugin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,552 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfstats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,556 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/main.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,559 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,562 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,564 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,566 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfisec.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,569 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,571 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/call.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,574 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hex.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,576 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,578 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,581 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mcall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,585 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcnv.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,588 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsort.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,590 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,593 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsom.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,595 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,597 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,601 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,602 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,606 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/README -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,608 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mpileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,612 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcffilter.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,614 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,616 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,618 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,620 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconcat.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,623 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cigar_state.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,626 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,628 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,631 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,634 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,636 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfgtcheck.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,639 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfroh.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,642 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ccall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,645 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcffilter.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,648 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,650 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mcall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,654 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfview.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,657 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfhead.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,659 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,662 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfstats.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,666 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfhead.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,668 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfindex.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,670 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,672 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,675 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,677 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,679 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfindex.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,682 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,683 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,685 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfannotate.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,690 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,692 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,694 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfannotate.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,700 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/khash_str2str.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,702 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,704 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,707 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,712 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,715 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,717 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tabix.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,719 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfview.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,722 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,725 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mw.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,728 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,732 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,734 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconvert.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,738 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,741 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,744 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,746 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,748 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,751 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,754 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,764 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfquery.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,774 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,784 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,787 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-14T00:23:01,789 copying build/lib.linux-armv7l-cpython-311/pysam/pysam_util.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,791 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,869 copying build/lib.linux-armv7l-cpython-311/pysam/version.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,871 copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,874 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,877 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,880 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,882 copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,884 copying build/lib.linux-armv7l-cpython-311/pysam/samtools.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,887 copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,889 copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,908 copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,916 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,921 copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,936 copying build/lib.linux-armv7l-cpython-311/pysam/csamtools_util.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,938 copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,941 copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,951 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,953 copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,955 copying build/lib.linux-armv7l-cpython-311/pysam/config.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,957 copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,959 copying build/lib.linux-armv7l-cpython-311/pysam/version.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,961 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,965 copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,967 copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,971 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,973 copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,974 copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:01,988 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,048 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,051 copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,054 copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,072 copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,123 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,170 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,208 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,251 copying build/lib.linux-armv7l-cpython-311/pysam/bcftools.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,254 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,262 copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,332 copying build/lib.linux-armv7l-cpython-311/pysam/__init__.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,334 copying build/lib.linux-armv7l-cpython-311/pysam/version.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,336 copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,338 copying build/lib.linux-armv7l-cpython-311/pysam/htslib_util.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,340 copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,343 copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,345 copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,355 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,360 copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,363 copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,365 copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,367 copying build/lib.linux-armv7l-cpython-311/pysam/utils.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,369 copying build/lib.linux-armv7l-cpython-311/pysam/cbcftools_util.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,371 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,375 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,438 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,441 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,479 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,482 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,519 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,521 copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,523 copying build/lib.linux-armv7l-cpython-311/pysam/py.typed -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,525 copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,527 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,529 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,534 copying build/lib.linux-armv7l-cpython-311/pysam/pysam_util.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,536 copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,559 copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,561 copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,568 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,569 copying build/lib.linux-armv7l-cpython-311/pysam/htslib_util.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,571 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,573 copying build/lib.linux-armv7l-cpython-311/pysam/pysam_stream.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,575 copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,577 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,579 copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,604 copying build/lib.linux-armv7l-cpython-311/pysam/Pileup.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-14T00:23:02,609 running install_egg_info 2023-09-14T00:23:02,614 Copying pysam.egg-info to build/bdist.linux-armv7l/wheel/pysam-0.21.0-py3.11.egg-info 2023-09-14T00:23:02,626 running install_scripts 2023-09-14T00:23:02,678 creating build/bdist.linux-armv7l/wheel/pysam-0.21.0.dist-info/WHEEL 2023-09-14T00:23:02,682 creating '/tmp/pip-wheel-dr6nia5_/.tmp-zirbv46u/pysam-0.21.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-14T00:23:02,687 adding 'pysam/Pileup.py' 2023-09-14T00:23:02,690 adding 'pysam/__init__.py' 2023-09-14T00:23:02,692 adding 'pysam/bcftools.py' 2023-09-14T00:23:02,693 adding 'pysam/cbcftools_util.h' 2023-09-14T00:23:02,694 adding 'pysam/config.py' 2023-09-14T00:23:02,696 adding 'pysam/csamtools_util.h' 2023-09-14T00:23:02,697 adding 'pysam/htslib_util.c' 2023-09-14T00:23:02,699 adding 'pysam/htslib_util.h' 2023-09-14T00:23:02,884 adding 'pysam/libcalignedsegment.c' 2023-09-14T00:23:03,516 adding 'pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:03,542 adding 'pysam/libcalignedsegment.pxd' 2023-09-14T00:23:03,543 adding 'pysam/libcalignedsegment.pyi' 2023-09-14T00:23:03,556 adding 'pysam/libcalignedsegment.pyx' 2023-09-14T00:23:03,689 adding 'pysam/libcalignmentfile.c' 2023-09-14T00:23:04,167 adding 'pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:04,186 adding 'pysam/libcalignmentfile.pxd' 2023-09-14T00:23:04,188 adding 'pysam/libcalignmentfile.pyi' 2023-09-14T00:23:04,200 adding 'pysam/libcalignmentfile.pyx' 2023-09-14T00:23:04,433 adding 'pysam/libcbcf.c' 2023-09-14T00:23:05,239 adding 'pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:05,274 adding 'pysam/libcbcf.pxd' 2023-09-14T00:23:05,276 adding 'pysam/libcbcf.pyi' 2023-09-14T00:23:05,290 adding 'pysam/libcbcf.pyx' 2023-09-14T00:23:05,302 adding 'pysam/libcbcftools.c' 2023-09-14T00:23:06,116 adding 'pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:06,145 adding 'pysam/libcbcftools.pxd' 2023-09-14T00:23:06,147 adding 'pysam/libcbcftools.pyi' 2023-09-14T00:23:06,148 adding 'pysam/libcbcftools.pyx' 2023-09-14T00:23:06,178 adding 'pysam/libcbgzf.c' 2023-09-14T00:23:06,251 adding 'pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:06,255 adding 'pysam/libcbgzf.pyi' 2023-09-14T00:23:06,258 adding 'pysam/libcbgzf.pyx' 2023-09-14T00:23:06,310 adding 'pysam/libcfaidx.c' 2023-09-14T00:23:06,482 adding 'pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:06,490 adding 'pysam/libcfaidx.pxd' 2023-09-14T00:23:06,491 adding 'pysam/libcfaidx.pyi' 2023-09-14T00:23:06,494 adding 'pysam/libcfaidx.pyx' 2023-09-14T00:23:06,550 adding 'pysam/libchtslib.c' 2023-09-14T00:23:07,629 adding 'pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:07,682 adding 'pysam/libchtslib.pxd' 2023-09-14T00:23:07,684 adding 'pysam/libchtslib.pyi' 2023-09-14T00:23:07,687 adding 'pysam/libchtslib.pyx' 2023-09-14T00:23:07,709 adding 'pysam/libcsamfile.c' 2023-09-14T00:23:07,736 adding 'pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:07,738 adding 'pysam/libcsamfile.pxd' 2023-09-14T00:23:07,740 adding 'pysam/libcsamfile.pyi' 2023-09-14T00:23:07,741 adding 'pysam/libcsamfile.pyx' 2023-09-14T00:23:07,752 adding 'pysam/libcsamtools.c' 2023-09-14T00:23:08,317 adding 'pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:08,338 adding 'pysam/libcsamtools.pxd' 2023-09-14T00:23:08,340 adding 'pysam/libcsamtools.pyi' 2023-09-14T00:23:08,341 adding 'pysam/libcsamtools.pyx' 2023-09-14T00:23:08,414 adding 'pysam/libctabix.c' 2023-09-14T00:23:08,667 adding 'pysam/libctabix.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:08,678 adding 'pysam/libctabix.pxd' 2023-09-14T00:23:08,680 adding 'pysam/libctabix.pyi' 2023-09-14T00:23:08,684 adding 'pysam/libctabix.pyx' 2023-09-14T00:23:08,759 adding 'pysam/libctabixproxies.c' 2023-09-14T00:23:09,010 adding 'pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:09,020 adding 'pysam/libctabixproxies.pxd' 2023-09-14T00:23:09,022 adding 'pysam/libctabixproxies.pyi' 2023-09-14T00:23:09,025 adding 'pysam/libctabixproxies.pyx' 2023-09-14T00:23:09,067 adding 'pysam/libcutils.c' 2023-09-14T00:23:09,204 adding 'pysam/libcutils.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:09,210 adding 'pysam/libcutils.pxd' 2023-09-14T00:23:09,212 adding 'pysam/libcutils.pyi' 2023-09-14T00:23:09,214 adding 'pysam/libcutils.pyx' 2023-09-14T00:23:09,344 adding 'pysam/libcvcf.c' 2023-09-14T00:23:09,907 adding 'pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:23:09,929 adding 'pysam/libcvcf.pxd' 2023-09-14T00:23:09,931 adding 'pysam/libcvcf.pyi' 2023-09-14T00:23:09,936 adding 'pysam/libcvcf.pyx' 2023-09-14T00:23:09,938 adding 'pysam/py.typed' 2023-09-14T00:23:09,939 adding 'pysam/pysam_stream.h' 2023-09-14T00:23:09,941 adding 'pysam/pysam_util.c' 2023-09-14T00:23:09,942 adding 'pysam/pysam_util.h' 2023-09-14T00:23:09,943 adding 'pysam/samtools.py' 2023-09-14T00:23:09,945 adding 'pysam/utils.py' 2023-09-14T00:23:09,946 adding 'pysam/version.h' 2023-09-14T00:23:09,948 adding 'pysam/version.py' 2023-09-14T00:23:09,949 adding 'pysam/version.pyi' 2023-09-14T00:23:09,951 adding 'pysam/include/__init__.py' 2023-09-14T00:23:09,956 adding 'pysam/include/bcftools/HMM.c' 2023-09-14T00:23:09,958 adding 'pysam/include/bcftools/HMM.c.pysam.c' 2023-09-14T00:23:09,960 adding 'pysam/include/bcftools/HMM.h' 2023-09-14T00:23:09,967 adding 'pysam/include/bcftools/LICENSE' 2023-09-14T00:23:09,968 adding 'pysam/include/bcftools/README' 2023-09-14T00:23:09,972 adding 'pysam/include/bcftools/abuf.c' 2023-09-14T00:23:09,976 adding 'pysam/include/bcftools/abuf.c.pysam.c' 2023-09-14T00:23:09,978 adding 'pysam/include/bcftools/abuf.h' 2023-09-14T00:23:09,983 adding 'pysam/include/bcftools/bam2bcf.c' 2023-09-14T00:23:09,989 adding 'pysam/include/bcftools/bam2bcf.c.pysam.c' 2023-09-14T00:23:09,992 adding 'pysam/include/bcftools/bam2bcf.h' 2023-09-14T00:23:09,996 adding 'pysam/include/bcftools/bam2bcf_iaux.c' 2023-09-14T00:23:10,000 adding 'pysam/include/bcftools/bam2bcf_iaux.c.pysam.c' 2023-09-14T00:23:10,005 adding 'pysam/include/bcftools/bam2bcf_indel.c' 2023-09-14T00:23:10,010 adding 'pysam/include/bcftools/bam2bcf_indel.c.pysam.c' 2023-09-14T00:23:10,012 adding 'pysam/include/bcftools/bam_sample.c' 2023-09-14T00:23:10,014 adding 'pysam/include/bcftools/bam_sample.c.pysam.c' 2023-09-14T00:23:10,016 adding 'pysam/include/bcftools/bam_sample.h' 2023-09-14T00:23:10,017 adding 'pysam/include/bcftools/bcftools.h' 2023-09-14T00:23:10,019 adding 'pysam/include/bcftools/bcftools.pysam.c' 2023-09-14T00:23:10,020 adding 'pysam/include/bcftools/bcftools.pysam.h' 2023-09-14T00:23:10,021 adding 'pysam/include/bcftools/bin.c' 2023-09-14T00:23:10,023 adding 'pysam/include/bcftools/bin.c.pysam.c' 2023-09-14T00:23:10,024 adding 'pysam/include/bcftools/bin.h' 2023-09-14T00:23:10,026 adding 'pysam/include/bcftools/call.h' 2023-09-14T00:23:10,028 adding 'pysam/include/bcftools/ccall.c' 2023-09-14T00:23:10,030 adding 'pysam/include/bcftools/ccall.c.pysam.c' 2023-09-14T00:23:10,032 adding 'pysam/include/bcftools/cigar_state.h' 2023-09-14T00:23:10,033 adding 'pysam/include/bcftools/cols.c' 2023-09-14T00:23:10,035 adding 'pysam/include/bcftools/cols.c.pysam.c' 2023-09-14T00:23:10,036 adding 'pysam/include/bcftools/cols.h' 2023-09-14T00:23:10,037 adding 'pysam/include/bcftools/config.h' 2023-09-14T00:23:10,043 adding 'pysam/include/bcftools/consensus.c' 2023-09-14T00:23:10,049 adding 'pysam/include/bcftools/consensus.c.pysam.c' 2023-09-14T00:23:10,055 adding 'pysam/include/bcftools/convert.c' 2023-09-14T00:23:10,062 adding 'pysam/include/bcftools/convert.c.pysam.c' 2023-09-14T00:23:10,064 adding 'pysam/include/bcftools/convert.h' 2023-09-14T00:23:10,083 adding 'pysam/include/bcftools/csq.c' 2023-09-14T00:23:10,103 adding 'pysam/include/bcftools/csq.c.pysam.c' 2023-09-14T00:23:10,105 adding 'pysam/include/bcftools/dbuf.h' 2023-09-14T00:23:10,107 adding 'pysam/include/bcftools/dist.c' 2023-09-14T00:23:10,108 adding 'pysam/include/bcftools/dist.c.pysam.c' 2023-09-14T00:23:10,110 adding 'pysam/include/bcftools/dist.h' 2023-09-14T00:23:10,112 adding 'pysam/include/bcftools/em.c' 2023-09-14T00:23:10,113 adding 'pysam/include/bcftools/em.c.pysam.c' 2023-09-14T00:23:10,115 adding 'pysam/include/bcftools/extsort.c' 2023-09-14T00:23:10,117 adding 'pysam/include/bcftools/extsort.c.pysam.c' 2023-09-14T00:23:10,118 adding 'pysam/include/bcftools/extsort.h' 2023-09-14T00:23:10,132 adding 'pysam/include/bcftools/filter.c' 2023-09-14T00:23:10,146 adding 'pysam/include/bcftools/filter.c.pysam.c' 2023-09-14T00:23:10,149 adding 'pysam/include/bcftools/filter.h' 2023-09-14T00:23:10,150 adding 'pysam/include/bcftools/gvcf.c' 2023-09-14T00:23:10,152 adding 'pysam/include/bcftools/gvcf.c.pysam.c' 2023-09-14T00:23:10,154 adding 'pysam/include/bcftools/gvcf.h' 2023-09-14T00:23:10,156 adding 'pysam/include/bcftools/hclust.c' 2023-09-14T00:23:10,158 adding 'pysam/include/bcftools/hclust.c.pysam.c' 2023-09-14T00:23:10,159 adding 'pysam/include/bcftools/hclust.h' 2023-09-14T00:23:10,161 adding 'pysam/include/bcftools/hex.h' 2023-09-14T00:23:10,162 adding 'pysam/include/bcftools/khash_str2str.h' 2023-09-14T00:23:10,164 adding 'pysam/include/bcftools/kheap.h' 2023-09-14T00:23:10,166 adding 'pysam/include/bcftools/kmin.c' 2023-09-14T00:23:10,168 adding 'pysam/include/bcftools/kmin.c.pysam.c' 2023-09-14T00:23:10,169 adding 'pysam/include/bcftools/kmin.h' 2023-09-14T00:23:10,171 adding 'pysam/include/bcftools/main.c' 2023-09-14T00:23:10,173 adding 'pysam/include/bcftools/main.c.pysam.c' 2023-09-14T00:23:10,180 adding 'pysam/include/bcftools/mcall.c' 2023-09-14T00:23:10,188 adding 'pysam/include/bcftools/mcall.c.pysam.c' 2023-09-14T00:23:10,197 adding 'pysam/include/bcftools/mpileup.c' 2023-09-14T00:23:10,205 adding 'pysam/include/bcftools/mpileup.c.pysam.c' 2023-09-14T00:23:10,209 adding 'pysam/include/bcftools/mw.h' 2023-09-14T00:23:10,211 adding 'pysam/include/bcftools/ploidy.c' 2023-09-14T00:23:10,213 adding 'pysam/include/bcftools/ploidy.c.pysam.c' 2023-09-14T00:23:10,214 adding 'pysam/include/bcftools/ploidy.h' 2023-09-14T00:23:10,217 adding 'pysam/include/bcftools/prob1.c' 2023-09-14T00:23:10,220 adding 'pysam/include/bcftools/prob1.c.pysam.c' 2023-09-14T00:23:10,222 adding 'pysam/include/bcftools/prob1.h' 2023-09-14T00:23:10,224 adding 'pysam/include/bcftools/rbuf.h' 2023-09-14T00:23:10,227 adding 'pysam/include/bcftools/read_consensus.c' 2023-09-14T00:23:10,231 adding 'pysam/include/bcftools/read_consensus.c.pysam.c' 2023-09-14T00:23:10,233 adding 'pysam/include/bcftools/read_consensus.h' 2023-09-14T00:23:10,236 adding 'pysam/include/bcftools/regidx.c' 2023-09-14T00:23:10,238 adding 'pysam/include/bcftools/regidx.c.pysam.c' 2023-09-14T00:23:10,240 adding 'pysam/include/bcftools/regidx.h' 2023-09-14T00:23:10,243 adding 'pysam/include/bcftools/reheader.c' 2023-09-14T00:23:10,247 adding 'pysam/include/bcftools/reheader.c.pysam.c' 2023-09-14T00:23:10,249 adding 'pysam/include/bcftools/smpl_ilist.c' 2023-09-14T00:23:10,250 adding 'pysam/include/bcftools/smpl_ilist.c.pysam.c' 2023-09-14T00:23:10,252 adding 'pysam/include/bcftools/smpl_ilist.h' 2023-09-14T00:23:10,253 adding 'pysam/include/bcftools/str_finder.c' 2023-09-14T00:23:10,255 adding 'pysam/include/bcftools/str_finder.c.pysam.c' 2023-09-14T00:23:10,257 adding 'pysam/include/bcftools/str_finder.h' 2023-09-14T00:23:10,258 adding 'pysam/include/bcftools/tabix.c' 2023-09-14T00:23:10,260 adding 'pysam/include/bcftools/tabix.c.pysam.c' 2023-09-14T00:23:10,261 adding 'pysam/include/bcftools/tsv2vcf.c' 2023-09-14T00:23:10,263 adding 'pysam/include/bcftools/tsv2vcf.c.pysam.c' 2023-09-14T00:23:10,264 adding 'pysam/include/bcftools/tsv2vcf.h' 2023-09-14T00:23:10,267 adding 'pysam/include/bcftools/utlist.h' 2023-09-14T00:23:10,270 adding 'pysam/include/bcftools/variantkey.h' 2023-09-14T00:23:10,285 adding 'pysam/include/bcftools/vcfannotate.c' 2023-09-14T00:23:10,301 adding 'pysam/include/bcftools/vcfannotate.c.pysam.c' 2023-09-14T00:23:10,305 adding 'pysam/include/bcftools/vcfbuf.c' 2023-09-14T00:23:10,307 adding 'pysam/include/bcftools/vcfbuf.c.pysam.c' 2023-09-14T00:23:10,309 adding 'pysam/include/bcftools/vcfbuf.h' 2023-09-14T00:23:10,314 adding 'pysam/include/bcftools/vcfcall.c' 2023-09-14T00:23:10,320 adding 'pysam/include/bcftools/vcfcall.c.pysam.c' 2023-09-14T00:23:10,326 adding 'pysam/include/bcftools/vcfcnv.c' 2023-09-14T00:23:10,333 adding 'pysam/include/bcftools/vcfcnv.c.pysam.c' 2023-09-14T00:23:10,338 adding 'pysam/include/bcftools/vcfconcat.c' 2023-09-14T00:23:10,344 adding 'pysam/include/bcftools/vcfconcat.c.pysam.c' 2023-09-14T00:23:10,351 adding 'pysam/include/bcftools/vcfconvert.c' 2023-09-14T00:23:10,359 adding 'pysam/include/bcftools/vcfconvert.c.pysam.c' 2023-09-14T00:23:10,363 adding 'pysam/include/bcftools/vcffilter.c' 2023-09-14T00:23:10,367 adding 'pysam/include/bcftools/vcffilter.c.pysam.c' 2023-09-14T00:23:10,372 adding 'pysam/include/bcftools/vcfgtcheck.c' 2023-09-14T00:23:10,378 adding 'pysam/include/bcftools/vcfgtcheck.c.pysam.c' 2023-09-14T00:23:10,380 adding 'pysam/include/bcftools/vcfhead.c' 2023-09-14T00:23:10,382 adding 'pysam/include/bcftools/vcfhead.c.pysam.c' 2023-09-14T00:23:10,384 adding 'pysam/include/bcftools/vcfindex.c' 2023-09-14T00:23:10,386 adding 'pysam/include/bcftools/vcfindex.c.pysam.c' 2023-09-14T00:23:10,389 adding 'pysam/include/bcftools/vcfisec.c' 2023-09-14T00:23:10,393 adding 'pysam/include/bcftools/vcfisec.c.pysam.c' 2023-09-14T00:23:10,407 adding 'pysam/include/bcftools/vcfmerge.c' 2023-09-14T00:23:10,423 adding 'pysam/include/bcftools/vcfmerge.c.pysam.c' 2023-09-14T00:23:10,433 adding 'pysam/include/bcftools/vcfnorm.c' 2023-09-14T00:23:10,442 adding 'pysam/include/bcftools/vcfnorm.c.pysam.c' 2023-09-14T00:23:10,447 adding 'pysam/include/bcftools/vcfplugin.c' 2023-09-14T00:23:10,450 adding 'pysam/include/bcftools/vcfplugin.c.pysam.c' 2023-09-14T00:23:10,453 adding 'pysam/include/bcftools/vcfquery.c' 2023-09-14T00:23:10,455 adding 'pysam/include/bcftools/vcfquery.c.pysam.c' 2023-09-14T00:23:10,461 adding 'pysam/include/bcftools/vcfroh.c' 2023-09-14T00:23:10,467 adding 'pysam/include/bcftools/vcfroh.c.pysam.c' 2023-09-14T00:23:10,470 adding 'pysam/include/bcftools/vcfsom.c' 2023-09-14T00:23:10,474 adding 'pysam/include/bcftools/vcfsom.c.pysam.c' 2023-09-14T00:23:10,476 adding 'pysam/include/bcftools/vcfsort.c' 2023-09-14T00:23:10,479 adding 'pysam/include/bcftools/vcfsort.c.pysam.c' 2023-09-14T00:23:10,487 adding 'pysam/include/bcftools/vcfstats.c' 2023-09-14T00:23:10,496 adding 'pysam/include/bcftools/vcfstats.c.pysam.c' 2023-09-14T00:23:10,500 adding 'pysam/include/bcftools/vcfview.c' 2023-09-14T00:23:10,505 adding 'pysam/include/bcftools/vcfview.c.pysam.c' 2023-09-14T00:23:10,506 adding 'pysam/include/bcftools/vcmp.c' 2023-09-14T00:23:10,508 adding 'pysam/include/bcftools/vcmp.c.pysam.c' 2023-09-14T00:23:10,509 adding 'pysam/include/bcftools/vcmp.h' 2023-09-14T00:23:10,511 adding 'pysam/include/bcftools/version.c' 2023-09-14T00:23:10,512 adding 'pysam/include/bcftools/version.c.pysam.c' 2023-09-14T00:23:10,514 adding 'pysam/include/bcftools/version.sh' 2023-09-14T00:23:10,517 adding 'pysam/include/htslib/LICENSE' 2023-09-14T00:23:10,521 adding 'pysam/include/htslib/Makefile' 2023-09-14T00:23:10,523 adding 'pysam/include/htslib/README' 2023-09-14T00:23:10,526 adding 'pysam/include/htslib/bcf_sr_sort.c' 2023-09-14T00:23:10,528 adding 'pysam/include/htslib/bcf_sr_sort.h' 2023-09-14T00:23:10,538 adding 'pysam/include/htslib/bgzf.c' 2023-09-14T00:23:10,541 adding 'pysam/include/htslib/bgzip.c' 2023-09-14T00:23:10,543 adding 'pysam/include/htslib/builddir_vars.mk.in' 2023-09-14T00:23:10,544 adding 'pysam/include/htslib/config.h' 2023-09-14T00:23:10,545 adding 'pysam/include/htslib/config.h.in' 2023-09-14T00:23:10,547 adding 'pysam/include/htslib/config.mk.in' 2023-09-14T00:23:10,569 adding 'pysam/include/htslib/configure' 2023-09-14T00:23:10,573 adding 'pysam/include/htslib/configure.ac' 2023-09-14T00:23:10,575 adding 'pysam/include/htslib/errmod.c' 2023-09-14T00:23:10,578 adding 'pysam/include/htslib/faidx.c' 2023-09-14T00:23:10,587 adding 'pysam/include/htslib/header.c' 2023-09-14T00:23:10,590 adding 'pysam/include/htslib/header.h' 2023-09-14T00:23:10,595 adding 'pysam/include/htslib/hfile.c' 2023-09-14T00:23:10,597 adding 'pysam/include/htslib/hfile_gcs.c' 2023-09-14T00:23:10,599 adding 'pysam/include/htslib/hfile_internal.h' 2023-09-14T00:23:10,605 adding 'pysam/include/htslib/hfile_libcurl.c' 2023-09-14T00:23:10,610 adding 'pysam/include/htslib/hfile_s3.c' 2023-09-14T00:23:10,613 adding 'pysam/include/htslib/hfile_s3_write.c' 2023-09-14T00:23:10,631 adding 'pysam/include/htslib/hts.c' 2023-09-14T00:23:10,635 adding 'pysam/include/htslib/hts_expr.c' 2023-09-14T00:23:10,637 adding 'pysam/include/htslib/hts_internal.h' 2023-09-14T00:23:10,638 adding 'pysam/include/htslib/hts_os.c' 2023-09-14T00:23:10,640 adding 'pysam/include/htslib/hts_time_funcs.h' 2023-09-14T00:23:10,641 adding 'pysam/include/htslib/htscodecs_bundled.mk' 2023-09-14T00:23:10,642 adding 'pysam/include/htslib/htscodecs_external.mk' 2023-09-14T00:23:10,644 adding 'pysam/include/htslib/htsfile.c' 2023-09-14T00:23:10,646 adding 'pysam/include/htslib/htslib.mk' 2023-09-14T00:23:10,647 adding 'pysam/include/htslib/htslib.pc.in' 2023-09-14T00:23:10,648 adding 'pysam/include/htslib/htslib_vars.mk' 2023-09-14T00:23:10,650 adding 'pysam/include/htslib/kfunc.c' 2023-09-14T00:23:10,652 adding 'pysam/include/htslib/kstring.c' 2023-09-14T00:23:10,654 adding 'pysam/include/htslib/md5.c' 2023-09-14T00:23:10,657 adding 'pysam/include/htslib/multipart.c' 2023-09-14T00:23:10,658 adding 'pysam/include/htslib/plugin.c' 2023-09-14T00:23:10,661 adding 'pysam/include/htslib/probaln.c' 2023-09-14T00:23:10,663 adding 'pysam/include/htslib/realn.c' 2023-09-14T00:23:10,666 adding 'pysam/include/htslib/regidx.c' 2023-09-14T00:23:10,668 adding 'pysam/include/htslib/region.c' 2023-09-14T00:23:10,693 adding 'pysam/include/htslib/sam.c' 2023-09-14T00:23:10,696 adding 'pysam/include/htslib/sam_internal.h' 2023-09-14T00:23:10,702 adding 'pysam/include/htslib/synced_bcf_reader.c' 2023-09-14T00:23:10,705 adding 'pysam/include/htslib/tabix.c' 2023-09-14T00:23:10,708 adding 'pysam/include/htslib/tbx.c' 2023-09-14T00:23:10,710 adding 'pysam/include/htslib/textutils.c' 2023-09-14T00:23:10,712 adding 'pysam/include/htslib/textutils_internal.h' 2023-09-14T00:23:10,718 adding 'pysam/include/htslib/thread_pool.c' 2023-09-14T00:23:10,720 adding 'pysam/include/htslib/thread_pool_internal.h' 2023-09-14T00:23:10,740 adding 'pysam/include/htslib/vcf.c' 2023-09-14T00:23:10,743 adding 'pysam/include/htslib/vcf_sweep.c' 2023-09-14T00:23:10,746 adding 'pysam/include/htslib/vcfutils.c' 2023-09-14T00:23:10,748 adding 'pysam/include/htslib/version.sh' 2023-09-14T00:23:10,750 adding 'pysam/include/htslib/cram/cram.h' 2023-09-14T00:23:10,762 adding 'pysam/include/htslib/cram/cram_codecs.c' 2023-09-14T00:23:10,764 adding 'pysam/include/htslib/cram/cram_codecs.h' 2023-09-14T00:23:10,776 adding 'pysam/include/htslib/cram/cram_decode.c' 2023-09-14T00:23:10,779 adding 'pysam/include/htslib/cram/cram_decode.h' 2023-09-14T00:23:10,793 adding 'pysam/include/htslib/cram/cram_encode.c' 2023-09-14T00:23:10,795 adding 'pysam/include/htslib/cram/cram_encode.h' 2023-09-14T00:23:10,799 adding 'pysam/include/htslib/cram/cram_external.c' 2023-09-14T00:23:10,802 adding 'pysam/include/htslib/cram/cram_index.c' 2023-09-14T00:23:10,804 adding 'pysam/include/htslib/cram/cram_index.h' 2023-09-14T00:23:10,823 adding 'pysam/include/htslib/cram/cram_io.c' 2023-09-14T00:23:10,826 adding 'pysam/include/htslib/cram/cram_io.h' 2023-09-14T00:23:10,828 adding 'pysam/include/htslib/cram/cram_samtools.h' 2023-09-14T00:23:10,830 adding 'pysam/include/htslib/cram/cram_stats.c' 2023-09-14T00:23:10,831 adding 'pysam/include/htslib/cram/cram_stats.h' 2023-09-14T00:23:10,835 adding 'pysam/include/htslib/cram/cram_structs.h' 2023-09-14T00:23:10,838 adding 'pysam/include/htslib/cram/mFILE.c' 2023-09-14T00:23:10,840 adding 'pysam/include/htslib/cram/mFILE.h' 2023-09-14T00:23:10,841 adding 'pysam/include/htslib/cram/misc.h' 2023-09-14T00:23:10,843 adding 'pysam/include/htslib/cram/open_trace_file.c' 2023-09-14T00:23:10,845 adding 'pysam/include/htslib/cram/open_trace_file.h' 2023-09-14T00:23:10,846 adding 'pysam/include/htslib/cram/os.h' 2023-09-14T00:23:10,848 adding 'pysam/include/htslib/cram/pooled_alloc.c' 2023-09-14T00:23:10,849 adding 'pysam/include/htslib/cram/pooled_alloc.h' 2023-09-14T00:23:10,851 adding 'pysam/include/htslib/cram/string_alloc.c' 2023-09-14T00:23:10,852 adding 'pysam/include/htslib/cram/string_alloc.h' 2023-09-14T00:23:10,858 adding 'pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c' 2023-09-14T00:23:10,859 adding 'pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h' 2023-09-14T00:23:10,860 adding 'pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h' 2023-09-14T00:23:10,862 adding 'pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h' 2023-09-14T00:23:10,868 adding 'pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c' 2023-09-14T00:23:10,870 adding 'pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h' 2023-09-14T00:23:10,871 adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs.c' 2023-09-14T00:23:10,872 adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs.h' 2023-09-14T00:23:10,874 adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h' 2023-09-14T00:23:10,876 adding 'pysam/include/htslib/htscodecs/htscodecs/pack.c' 2023-09-14T00:23:10,877 adding 'pysam/include/htslib/htscodecs/htscodecs/pack.h' 2023-09-14T00:23:10,880 adding 'pysam/include/htslib/htscodecs/htscodecs/permute.h' 2023-09-14T00:23:10,881 adding 'pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h' 2023-09-14T00:23:10,884 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h' 2023-09-14T00:23:10,887 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static.c' 2023-09-14T00:23:10,889 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static.h' 2023-09-14T00:23:10,891 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h' 2023-09-14T00:23:10,894 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c' 2023-09-14T00:23:10,896 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h' 2023-09-14T00:23:10,901 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c' 2023-09-14T00:23:10,905 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c' 2023-09-14T00:23:10,912 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c' 2023-09-14T00:23:10,918 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c' 2023-09-14T00:23:10,920 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h' 2023-09-14T00:23:10,926 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c' 2023-09-14T00:23:10,929 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_word.h' 2023-09-14T00:23:10,931 adding 'pysam/include/htslib/htscodecs/htscodecs/rle.c' 2023-09-14T00:23:10,932 adding 'pysam/include/htslib/htscodecs/htscodecs/rle.h' 2023-09-14T00:23:10,938 adding 'pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c' 2023-09-14T00:23:10,940 adding 'pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h' 2023-09-14T00:23:10,942 adding 'pysam/include/htslib/htscodecs/htscodecs/utils.c' 2023-09-14T00:23:10,944 adding 'pysam/include/htslib/htscodecs/htscodecs/utils.h' 2023-09-14T00:23:10,946 adding 'pysam/include/htslib/htscodecs/htscodecs/varint.h' 2023-09-14T00:23:10,948 adding 'pysam/include/htslib/htscodecs/htscodecs/varint2.h' 2023-09-14T00:23:10,949 adding 'pysam/include/htslib/htscodecs/htscodecs/version.h' 2023-09-14T00:23:10,952 adding 'pysam/include/htslib/htslib/bgzf.h' 2023-09-14T00:23:10,955 adding 'pysam/include/htslib/htslib/cram.h' 2023-09-14T00:23:10,958 adding 'pysam/include/htslib/htslib/faidx.h' 2023-09-14T00:23:10,960 adding 'pysam/include/htslib/htslib/hfile.h' 2023-09-14T00:23:10,968 adding 'pysam/include/htslib/htslib/hts.h' 2023-09-14T00:23:10,970 adding 'pysam/include/htslib/htslib/hts_defs.h' 2023-09-14T00:23:10,971 adding 'pysam/include/htslib/htslib/hts_endian.h' 2023-09-14T00:23:10,973 adding 'pysam/include/htslib/htslib/hts_expr.h' 2023-09-14T00:23:10,975 adding 'pysam/include/htslib/htslib/hts_log.h' 2023-09-14T00:23:10,976 adding 'pysam/include/htslib/htslib/hts_os.h' 2023-09-14T00:23:10,978 adding 'pysam/include/htslib/htslib/kbitset.h' 2023-09-14T00:23:10,979 adding 'pysam/include/htslib/htslib/kfunc.h' 2023-09-14T00:23:10,982 adding 'pysam/include/htslib/htslib/khash.h' 2023-09-14T00:23:10,983 adding 'pysam/include/htslib/htslib/khash_str2int.h' 2023-09-14T00:23:10,985 adding 'pysam/include/htslib/htslib/klist.h' 2023-09-14T00:23:10,986 adding 'pysam/include/htslib/htslib/knetfile.h' 2023-09-14T00:23:10,988 adding 'pysam/include/htslib/htslib/kroundup.h' 2023-09-14T00:23:10,989 adding 'pysam/include/htslib/htslib/kseq.h' 2023-09-14T00:23:10,991 adding 'pysam/include/htslib/htslib/ksort.h' 2023-09-14T00:23:10,994 adding 'pysam/include/htslib/htslib/kstring.h' 2023-09-14T00:23:10,996 adding 'pysam/include/htslib/htslib/regidx.h' 2023-09-14T00:23:11,007 adding 'pysam/include/htslib/htslib/sam.h' 2023-09-14T00:23:11,010 adding 'pysam/include/htslib/htslib/synced_bcf_reader.h' 2023-09-14T00:23:11,012 adding 'pysam/include/htslib/htslib/tbx.h' 2023-09-14T00:23:11,014 adding 'pysam/include/htslib/htslib/thread_pool.h' 2023-09-14T00:23:11,023 adding 'pysam/include/htslib/htslib/vcf.h' 2023-09-14T00:23:11,025 adding 'pysam/include/htslib/htslib/vcf_sweep.h' 2023-09-14T00:23:11,026 adding 'pysam/include/htslib/htslib/vcfutils.h' 2023-09-14T00:23:11,028 adding 'pysam/include/htslib/m4/ax_check_compile_flag.m4' 2023-09-14T00:23:11,030 adding 'pysam/include/htslib/m4/hts_hide_dynamic_syms.m4' 2023-09-14T00:23:11,031 adding 'pysam/include/htslib/m4/hts_prog_cc_warnings.m4' 2023-09-14T00:23:11,033 adding 'pysam/include/htslib/m4/pkg.m4' 2023-09-14T00:23:11,035 adding 'pysam/include/htslib/os/lzma_stub.h' 2023-09-14T00:23:11,037 adding 'pysam/include/htslib/os/rand.c' 2023-09-14T00:23:11,040 adding 'pysam/include/samtools/LICENSE' 2023-09-14T00:23:11,042 adding 'pysam/include/samtools/README' 2023-09-14T00:23:11,049 adding 'pysam/include/samtools/amplicon_stats.c' 2023-09-14T00:23:11,057 adding 'pysam/include/samtools/amplicon_stats.c.pysam.c' 2023-09-14T00:23:11,059 adding 'pysam/include/samtools/bam.c' 2023-09-14T00:23:11,061 adding 'pysam/include/samtools/bam.c.pysam.c' 2023-09-14T00:23:11,063 adding 'pysam/include/samtools/bam.h' 2023-09-14T00:23:11,067 adding 'pysam/include/samtools/bam2depth.c' 2023-09-14T00:23:11,071 adding 'pysam/include/samtools/bam2depth.c.pysam.c' 2023-09-14T00:23:11,074 adding 'pysam/include/samtools/bam_addrprg.c' 2023-09-14T00:23:11,076 adding 'pysam/include/samtools/bam_addrprg.c.pysam.c' 2023-09-14T00:23:11,080 adding 'pysam/include/samtools/bam_ampliconclip.c' 2023-09-14T00:23:11,084 adding 'pysam/include/samtools/bam_ampliconclip.c.pysam.c' 2023-09-14T00:23:11,086 adding 'pysam/include/samtools/bam_ampliconclip.h' 2023-09-14T00:23:11,087 adding 'pysam/include/samtools/bam_aux.c' 2023-09-14T00:23:11,089 adding 'pysam/include/samtools/bam_aux.c.pysam.c' 2023-09-14T00:23:11,092 adding 'pysam/include/samtools/bam_cat.c' 2023-09-14T00:23:11,095 adding 'pysam/include/samtools/bam_cat.c.pysam.c' 2023-09-14T00:23:11,096 adding 'pysam/include/samtools/bam_color.c' 2023-09-14T00:23:11,098 adding 'pysam/include/samtools/bam_color.c.pysam.c' 2023-09-14T00:23:11,110 adding 'pysam/include/samtools/bam_consensus.c' 2023-09-14T00:23:11,122 adding 'pysam/include/samtools/bam_consensus.c.pysam.c' 2023-09-14T00:23:11,127 adding 'pysam/include/samtools/bam_fastq.c' 2023-09-14T00:23:11,131 adding 'pysam/include/samtools/bam_fastq.c.pysam.c' 2023-09-14T00:23:11,133 adding 'pysam/include/samtools/bam_flags.c' 2023-09-14T00:23:11,134 adding 'pysam/include/samtools/bam_flags.c.pysam.c' 2023-09-14T00:23:11,137 adding 'pysam/include/samtools/bam_import.c' 2023-09-14T00:23:11,139 adding 'pysam/include/samtools/bam_import.c.pysam.c' 2023-09-14T00:23:11,142 adding 'pysam/include/samtools/bam_index.c' 2023-09-14T00:23:11,144 adding 'pysam/include/samtools/bam_index.c.pysam.c' 2023-09-14T00:23:11,146 adding 'pysam/include/samtools/bam_lpileup.c' 2023-09-14T00:23:11,147 adding 'pysam/include/samtools/bam_lpileup.c.pysam.c' 2023-09-14T00:23:11,149 adding 'pysam/include/samtools/bam_lpileup.h' 2023-09-14T00:23:11,158 adding 'pysam/include/samtools/bam_markdup.c' 2023-09-14T00:23:11,167 adding 'pysam/include/samtools/bam_markdup.c.pysam.c' 2023-09-14T00:23:11,172 adding 'pysam/include/samtools/bam_mate.c' 2023-09-14T00:23:11,175 adding 'pysam/include/samtools/bam_mate.c.pysam.c' 2023-09-14T00:23:11,178 adding 'pysam/include/samtools/bam_md.c' 2023-09-14T00:23:11,181 adding 'pysam/include/samtools/bam_md.c.pysam.c' 2023-09-14T00:23:11,182 adding 'pysam/include/samtools/bam_plbuf.c' 2023-09-14T00:23:11,184 adding 'pysam/include/samtools/bam_plbuf.c.pysam.c' 2023-09-14T00:23:11,185 adding 'pysam/include/samtools/bam_plbuf.h' 2023-09-14T00:23:11,191 adding 'pysam/include/samtools/bam_plcmd.c' 2023-09-14T00:23:11,196 adding 'pysam/include/samtools/bam_plcmd.c.pysam.c' 2023-09-14T00:23:11,198 adding 'pysam/include/samtools/bam_quickcheck.c' 2023-09-14T00:23:11,200 adding 'pysam/include/samtools/bam_quickcheck.c.pysam.c' 2023-09-14T00:23:11,202 adding 'pysam/include/samtools/bam_reheader.c' 2023-09-14T00:23:11,205 adding 'pysam/include/samtools/bam_reheader.c.pysam.c' 2023-09-14T00:23:11,207 adding 'pysam/include/samtools/bam_rmdup.c' 2023-09-14T00:23:11,209 adding 'pysam/include/samtools/bam_rmdup.c.pysam.c' 2023-09-14T00:23:11,211 adding 'pysam/include/samtools/bam_rmdupse.c' 2023-09-14T00:23:11,213 adding 'pysam/include/samtools/bam_rmdupse.c.pysam.c' 2023-09-14T00:23:11,215 adding 'pysam/include/samtools/bam_samples.c' 2023-09-14T00:23:11,217 adding 'pysam/include/samtools/bam_samples.c.pysam.c' 2023-09-14T00:23:11,231 adding 'pysam/include/samtools/bam_sort.c' 2023-09-14T00:23:11,246 adding 'pysam/include/samtools/bam_sort.c.pysam.c' 2023-09-14T00:23:11,250 adding 'pysam/include/samtools/bam_split.c' 2023-09-14T00:23:11,252 adding 'pysam/include/samtools/bam_split.c.pysam.c' 2023-09-14T00:23:11,254 adding 'pysam/include/samtools/bam_stat.c' 2023-09-14T00:23:11,256 adding 'pysam/include/samtools/bam_stat.c.pysam.c' 2023-09-14T00:23:11,259 adding 'pysam/include/samtools/bamshuf.c' 2023-09-14T00:23:11,262 adding 'pysam/include/samtools/bamshuf.c.pysam.c' 2023-09-14T00:23:11,264 adding 'pysam/include/samtools/bamtk.c' 2023-09-14T00:23:11,266 adding 'pysam/include/samtools/bamtk.c.pysam.c' 2023-09-14T00:23:11,268 adding 'pysam/include/samtools/bedcov.c' 2023-09-14T00:23:11,271 adding 'pysam/include/samtools/bedcov.c.pysam.c' 2023-09-14T00:23:11,273 adding 'pysam/include/samtools/bedidx.c' 2023-09-14T00:23:11,276 adding 'pysam/include/samtools/bedidx.c.pysam.c' 2023-09-14T00:23:11,278 adding 'pysam/include/samtools/bedidx.h' 2023-09-14T00:23:11,279 adding 'pysam/include/samtools/config.h' 2023-09-14T00:23:11,281 adding 'pysam/include/samtools/consensus_pileup.c' 2023-09-14T00:23:11,284 adding 'pysam/include/samtools/consensus_pileup.c.pysam.c' 2023-09-14T00:23:11,286 adding 'pysam/include/samtools/consensus_pileup.h' 2023-09-14T00:23:11,289 adding 'pysam/include/samtools/coverage.c' 2023-09-14T00:23:11,293 adding 'pysam/include/samtools/coverage.c.pysam.c' 2023-09-14T00:23:11,296 adding 'pysam/include/samtools/cram_size.c' 2023-09-14T00:23:11,299 adding 'pysam/include/samtools/cram_size.c.pysam.c' 2023-09-14T00:23:11,301 adding 'pysam/include/samtools/cut_target.c' 2023-09-14T00:23:11,303 adding 'pysam/include/samtools/cut_target.c.pysam.c' 2023-09-14T00:23:11,304 adding 'pysam/include/samtools/dict.c' 2023-09-14T00:23:11,306 adding 'pysam/include/samtools/dict.c.pysam.c' 2023-09-14T00:23:11,308 adding 'pysam/include/samtools/faidx.c' 2023-09-14T00:23:11,311 adding 'pysam/include/samtools/faidx.c.pysam.c' 2023-09-14T00:23:11,314 adding 'pysam/include/samtools/padding.c' 2023-09-14T00:23:11,317 adding 'pysam/include/samtools/padding.c.pysam.c' 2023-09-14T00:23:11,321 adding 'pysam/include/samtools/phase.c' 2023-09-14T00:23:11,325 adding 'pysam/include/samtools/phase.c.pysam.c' 2023-09-14T00:23:11,328 adding 'pysam/include/samtools/reference.c' 2023-09-14T00:23:11,331 adding 'pysam/include/samtools/reference.c.pysam.c' 2023-09-14T00:23:11,334 adding 'pysam/include/samtools/reset.c' 2023-09-14T00:23:11,336 adding 'pysam/include/samtools/reset.c.pysam.c' 2023-09-14T00:23:11,338 adding 'pysam/include/samtools/sam_opts.c' 2023-09-14T00:23:11,340 adding 'pysam/include/samtools/sam_opts.c.pysam.c' 2023-09-14T00:23:11,341 adding 'pysam/include/samtools/sam_opts.h' 2023-09-14T00:23:11,343 adding 'pysam/include/samtools/sam_utils.c' 2023-09-14T00:23:11,345 adding 'pysam/include/samtools/sam_utils.c.pysam.c' 2023-09-14T00:23:11,347 adding 'pysam/include/samtools/sam_utils.h' 2023-09-14T00:23:11,353 adding 'pysam/include/samtools/sam_view.c' 2023-09-14T00:23:11,360 adding 'pysam/include/samtools/sam_view.c.pysam.c' 2023-09-14T00:23:11,362 adding 'pysam/include/samtools/sample.c' 2023-09-14T00:23:11,364 adding 'pysam/include/samtools/sample.c.pysam.c' 2023-09-14T00:23:11,365 adding 'pysam/include/samtools/sample.h' 2023-09-14T00:23:11,366 adding 'pysam/include/samtools/samtools.h' 2023-09-14T00:23:11,368 adding 'pysam/include/samtools/samtools.pysam.c' 2023-09-14T00:23:11,369 adding 'pysam/include/samtools/samtools.pysam.h' 2023-09-14T00:23:11,371 adding 'pysam/include/samtools/splaysort.h' 2023-09-14T00:23:11,382 adding 'pysam/include/samtools/stats.c' 2023-09-14T00:23:11,395 adding 'pysam/include/samtools/stats.c.pysam.c' 2023-09-14T00:23:11,397 adding 'pysam/include/samtools/stats_isize.c' 2023-09-14T00:23:11,399 adding 'pysam/include/samtools/stats_isize.c.pysam.c' 2023-09-14T00:23:11,401 adding 'pysam/include/samtools/stats_isize.h' 2023-09-14T00:23:11,403 adding 'pysam/include/samtools/tmp_file.c' 2023-09-14T00:23:11,405 adding 'pysam/include/samtools/tmp_file.c.pysam.c' 2023-09-14T00:23:11,406 adding 'pysam/include/samtools/tmp_file.h' 2023-09-14T00:23:11,408 adding 'pysam/include/samtools/version.sh' 2023-09-14T00:23:11,410 adding 'pysam/include/samtools/lz4/LICENSE' 2023-09-14T00:23:11,416 adding 'pysam/include/samtools/lz4/lz4.c' 2023-09-14T00:23:11,422 adding 'pysam/include/samtools/lz4/lz4.c.pysam.c' 2023-09-14T00:23:11,426 adding 'pysam/include/samtools/lz4/lz4.h' 2023-09-14T00:23:11,428 adding 'pysam-0.21.0.dist-info/AUTHORS' 2023-09-14T00:23:11,429 adding 'pysam-0.21.0.dist-info/COPYING' 2023-09-14T00:23:11,431 adding 'pysam-0.21.0.dist-info/METADATA' 2023-09-14T00:23:11,432 adding 'pysam-0.21.0.dist-info/WHEEL' 2023-09-14T00:23:11,433 adding 'pysam-0.21.0.dist-info/top_level.txt' 2023-09-14T00:23:11,440 adding 'pysam-0.21.0.dist-info/RECORD' 2023-09-14T00:23:11,616 removing build/bdist.linux-armv7l/wheel 2023-09-14T00:23:11,879 Building wheel for pysam (pyproject.toml): finished with status 'done' 2023-09-14T00:23:12,503 Created wheel for pysam: filename=pysam-0.21.0-cp311-cp311-linux_armv7l.whl size=16179569 sha256=eb6339b5a1b549be24fdfbbb646449212b6e7b5026c858a7c535d3ba8fa27931 2023-09-14T00:23:12,503 Stored in directory: /home/piwheels/.cache/pip/wheels/52/2d/ed/b1e5c4ad36c535940dc1b1da900d05f571f88ff26f7be95f4c 2023-09-14T00:23:12,523 Successfully built pysam 2023-09-14T00:23:14,938 Installing collected packages: wheel, setuptools, numpy, cython, pysam 2023-09-14T00:23:15,155 Creating /tmp/pip-build-env-81o70t3g/overlay/local/bin 2023-09-14T00:23:15,157 changing mode of /tmp/pip-build-env-81o70t3g/overlay/local/bin/wheel to 755 2023-09-14T00:23:26,271 changing mode of /tmp/pip-build-env-81o70t3g/overlay/local/bin/f2py to 755 2023-09-14T00:23:26,273 changing mode of /tmp/pip-build-env-81o70t3g/overlay/local/bin/f2py3 to 755 2023-09-14T00:23:26,275 changing mode of /tmp/pip-build-env-81o70t3g/overlay/local/bin/f2py3.11 to 755 2023-09-14T00:23:29,884 changing mode of /tmp/pip-build-env-81o70t3g/overlay/local/bin/cygdb to 755 2023-09-14T00:23:29,887 changing mode of /tmp/pip-build-env-81o70t3g/overlay/local/bin/cython to 755 2023-09-14T00:23:29,889 changing mode of /tmp/pip-build-env-81o70t3g/overlay/local/bin/cythonize to 755 2023-09-14T00:23:33,315 Successfully installed cython-3.0.2 numpy-1.25.2 pysam-0.21.0 setuptools-68.2.2 wheel-0.41.2 2023-09-14T00:23:34,600 Installing build dependencies: finished with status 'done' 2023-09-14T00:23:34,604 Getting requirements to build wheel: started 2023-09-14T00:23:34,605 Running command Getting requirements to build wheel 2023-09-14T00:24:11,159 Compiling indelpost/variant.pyx because it changed. 2023-09-14T00:24:11,159 Compiling indelpost/utilities.pyx because it changed. 2023-09-14T00:24:11,160 Compiling indelpost/pileup.pyx because it changed. 2023-09-14T00:24:11,161 Compiling indelpost/varaln.pyx because it changed. 2023-09-14T00:24:11,161 Compiling indelpost/contig.pyx because it changed. 2023-09-14T00:24:11,162 Compiling indelpost/softclip.pyx because it changed. 2023-09-14T00:24:11,162 Compiling indelpost/localn.pyx because it changed. 2023-09-14T00:24:11,163 Compiling indelpost/gappedaln.pyx because it changed. 2023-09-14T00:24:11,163 [1/8] Cythonizing indelpost/contig.pyx 2023-09-14T00:24:11,164 [2/8] Cythonizing indelpost/gappedaln.pyx 2023-09-14T00:24:11,164 [3/8] Cythonizing indelpost/localn.pyx 2023-09-14T00:24:11,165 [4/8] Cythonizing indelpost/pileup.pyx 2023-09-14T00:24:11,165 [5/8] Cythonizing indelpost/softclip.pyx 2023-09-14T00:24:11,165 [6/8] Cythonizing indelpost/utilities.pyx 2023-09-14T00:24:11,166 [7/8] Cythonizing indelpost/varaln.pyx 2023-09-14T00:24:11,166 [8/8] Cythonizing indelpost/variant.pyx 2023-09-14T00:24:11,231 running egg_info 2023-09-14T00:24:11,237 writing indelpost.egg-info/PKG-INFO 2023-09-14T00:24:11,239 writing dependency_links to indelpost.egg-info/dependency_links.txt 2023-09-14T00:24:11,241 writing requirements to indelpost.egg-info/requires.txt 2023-09-14T00:24:11,242 writing top-level names to indelpost.egg-info/top_level.txt 2023-09-14T00:24:11,268 reading manifest file 'indelpost.egg-info/SOURCES.txt' 2023-09-14T00:24:11,271 reading manifest template 'MANIFEST.in' 2023-09-14T00:24:11,275 writing manifest file 'indelpost.egg-info/SOURCES.txt' 2023-09-14T00:24:11,938 Getting requirements to build wheel: finished with status 'done' 2023-09-14T00:24:11,947 Created temporary directory: /tmp/pip-modern-metadata-808dn1xf 2023-09-14T00:24:11,949 Preparing metadata (pyproject.toml): started 2023-09-14T00:24:11,951 Running command Preparing metadata (pyproject.toml) 2023-09-14T00:24:13,935 running dist_info 2023-09-14T00:24:13,954 creating /tmp/pip-modern-metadata-808dn1xf/indelpost.egg-info 2023-09-14T00:24:13,959 writing /tmp/pip-modern-metadata-808dn1xf/indelpost.egg-info/PKG-INFO 2023-09-14T00:24:13,962 writing dependency_links to /tmp/pip-modern-metadata-808dn1xf/indelpost.egg-info/dependency_links.txt 2023-09-14T00:24:13,964 writing requirements to /tmp/pip-modern-metadata-808dn1xf/indelpost.egg-info/requires.txt 2023-09-14T00:24:13,965 writing top-level names to /tmp/pip-modern-metadata-808dn1xf/indelpost.egg-info/top_level.txt 2023-09-14T00:24:13,966 writing manifest file '/tmp/pip-modern-metadata-808dn1xf/indelpost.egg-info/SOURCES.txt' 2023-09-14T00:24:13,988 reading manifest file '/tmp/pip-modern-metadata-808dn1xf/indelpost.egg-info/SOURCES.txt' 2023-09-14T00:24:13,990 reading manifest template 'MANIFEST.in' 2023-09-14T00:24:13,995 writing manifest file '/tmp/pip-modern-metadata-808dn1xf/indelpost.egg-info/SOURCES.txt' 2023-09-14T00:24:13,996 creating '/tmp/pip-modern-metadata-808dn1xf/indelpost-0.0.4.dist-info' 2023-09-14T00:24:14,206 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-14T00:24:14,210 Source in /tmp/pip-wheel-4f52la9s/indelpost_254b58e7693542a0a94733fce1cad1b9 has version 0.0.4, which satisfies requirement indelpost==0.0.4 from https://files.pythonhosted.org/packages/ef/04/6d459daa1e4c992bc65ee1bedd624a7c061e7026df01e2f835591a205a54/indelpost-0.0.4.tar.gz 2023-09-14T00:24:14,211 Removed indelpost==0.0.4 from https://files.pythonhosted.org/packages/ef/04/6d459daa1e4c992bc65ee1bedd624a7c061e7026df01e2f835591a205a54/indelpost-0.0.4.tar.gz from build tracker '/tmp/pip-build-tracker-397bmtav' 2023-09-14T00:24:14,215 Created temporary directory: /tmp/pip-unpack-nbxo93jt 2023-09-14T00:24:14,216 Created temporary directory: /tmp/pip-unpack-w7tyf2k1 2023-09-14T00:24:14,223 Building wheels for collected packages: indelpost 2023-09-14T00:24:14,227 Created temporary directory: /tmp/pip-wheel-0zqzcclq 2023-09-14T00:24:14,227 Destination directory: /tmp/pip-wheel-0zqzcclq 2023-09-14T00:24:14,229 Building wheel for indelpost (pyproject.toml): started 2023-09-14T00:24:14,231 Running command Building wheel for indelpost (pyproject.toml) 2023-09-14T00:24:16,199 running bdist_wheel 2023-09-14T00:24:16,232 running build 2023-09-14T00:24:16,232 running build_py 2023-09-14T00:24:16,240 creating build 2023-09-14T00:24:16,241 creating build/lib.linux-armv7l-cpython-311 2023-09-14T00:24:16,242 creating build/lib.linux-armv7l-cpython-311/indelpost 2023-09-14T00:24:16,243 copying indelpost/chromosomes.py -> build/lib.linux-armv7l-cpython-311/indelpost 2023-09-14T00:24:16,245 copying indelpost/alleles.py -> build/lib.linux-armv7l-cpython-311/indelpost 2023-09-14T00:24:16,247 copying indelpost/consensus.py -> build/lib.linux-armv7l-cpython-311/indelpost 2023-09-14T00:24:16,249 copying indelpost/__init__.py -> build/lib.linux-armv7l-cpython-311/indelpost 2023-09-14T00:24:16,251 copying indelpost/version.py -> build/lib.linux-armv7l-cpython-311/indelpost 2023-09-14T00:24:16,253 running build_ext 2023-09-14T00:24:16,264 building 'indelpost.variant' extension 2023-09-14T00:24:16,265 creating build/temp.linux-armv7l-cpython-311 2023-09-14T00:24:16,265 creating build/temp.linux-armv7l-cpython-311/indelpost 2023-09-14T00:24:16,266 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c indelpost/variant.c -o build/temp.linux-armv7l-cpython-311/indelpost/variant.o 2023-09-14T00:24:18,877 In file included from /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:4, 2023-09-14T00:24:18,878 from indelpost/variant.c:1224: 2023-09-14T00:24:18,878 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:185:19: warning: ‘kseq_read’ defined but not used [-Wunused-function] 2023-09-14T00:24:18,879 185 | SCOPE int kseq_read(kseq_t *seq) \ 2023-09-14T00:24:18,880 | ^~~~~~~~~ 2023-09-14T00:24:18,880 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:238:9: note: in expansion of macro ‘__KSEQ_READ’ 2023-09-14T00:24:18,881 238 | __KSEQ_READ(SCOPE) 2023-09-14T00:24:18,882 | ^~~~~~~~~~~ 2023-09-14T00:24:18,882 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:24:18,883 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:24:18,884 | ^~~~~~~~~~ 2023-09-14T00:24:18,884 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:24:18,885 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:24:18,886 | ^~~~~~~~~ 2023-09-14T00:24:18,886 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:171:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] 2023-09-14T00:24:18,887 171 | SCOPE void kseq_destroy(kseq_t *ks) \ 2023-09-14T00:24:18,888 | ^~~~~~~~~~~~ 2023-09-14T00:24:18,888 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:24:18,889 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:24:18,889 | ^~~~~~~~~~~~ 2023-09-14T00:24:18,890 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:24:18,891 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:24:18,892 | ^~~~~~~~~~ 2023-09-14T00:24:18,892 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:24:18,893 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:24:18,894 | ^~~~~~~~~ 2023-09-14T00:24:18,894 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:165:23: warning: ‘kseq_init’ defined but not used [-Wunused-function] 2023-09-14T00:24:18,895 165 | SCOPE kseq_t *kseq_init(type_t fd) \ 2023-09-14T00:24:18,896 | ^~~~~~~~~ 2023-09-14T00:24:18,897 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:24:18,897 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:24:18,898 | ^~~~~~~~~~~~ 2023-09-14T00:24:18,899 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:24:18,900 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:24:18,901 | ^~~~~~~~~~ 2023-09-14T00:24:18,901 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:24:18,902 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:24:18,902 | ^~~~~~~~~ 2023-09-14T00:24:54,488 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/indelpost/variant.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/indelpost/variant.cpython-311-arm-linux-gnueabihf.so 2023-09-14T00:24:54,634 building 'indelpost.utilities' extension 2023-09-14T00:24:54,634 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c indelpost/utilities.c -o build/temp.linux-armv7l-cpython-311/indelpost/utilities.o 2023-09-14T00:24:58,955 In file included from /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:4, 2023-09-14T00:24:58,956 from indelpost/utilities.c:1224: 2023-09-14T00:24:58,957 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:185:19: warning: ‘kseq_read’ defined but not used [-Wunused-function] 2023-09-14T00:24:58,958 185 | SCOPE int kseq_read(kseq_t *seq) \ 2023-09-14T00:24:58,958 | ^~~~~~~~~ 2023-09-14T00:24:58,959 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:238:9: note: in expansion of macro ‘__KSEQ_READ’ 2023-09-14T00:24:58,959 238 | __KSEQ_READ(SCOPE) 2023-09-14T00:24:58,960 | ^~~~~~~~~~~ 2023-09-14T00:24:58,960 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:24:58,961 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:24:58,962 | ^~~~~~~~~~ 2023-09-14T00:24:58,962 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:24:58,963 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:24:58,964 | ^~~~~~~~~ 2023-09-14T00:24:58,964 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:171:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] 2023-09-14T00:24:58,965 171 | SCOPE void kseq_destroy(kseq_t *ks) \ 2023-09-14T00:24:58,966 | ^~~~~~~~~~~~ 2023-09-14T00:24:58,967 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:24:58,967 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:24:58,968 | ^~~~~~~~~~~~ 2023-09-14T00:24:58,968 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:24:58,968 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:24:58,969 | ^~~~~~~~~~ 2023-09-14T00:24:58,969 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:24:58,970 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:24:58,970 | ^~~~~~~~~ 2023-09-14T00:24:58,971 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:165:23: warning: ‘kseq_init’ defined but not used [-Wunused-function] 2023-09-14T00:24:58,971 165 | SCOPE kseq_t *kseq_init(type_t fd) \ 2023-09-14T00:24:58,971 | ^~~~~~~~~ 2023-09-14T00:24:58,972 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:24:58,972 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:24:58,973 | ^~~~~~~~~~~~ 2023-09-14T00:24:58,974 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:24:58,974 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:24:58,975 | ^~~~~~~~~~ 2023-09-14T00:24:58,976 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:24:58,976 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:24:58,977 | ^~~~~~~~~ 2023-09-14T00:25:45,095 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/indelpost/utilities.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/indelpost/utilities.cpython-311-arm-linux-gnueabihf.so 2023-09-14T00:25:45,260 building 'indelpost.pileup' extension 2023-09-14T00:25:45,261 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c indelpost/pileup.c -o build/temp.linux-armv7l-cpython-311/indelpost/pileup.o 2023-09-14T00:25:48,930 indelpost/pileup.c:11293:18: warning: ‘__pyx_f_9indelpost_6pileup_leftalign_cigar’ defined but not used [-Wunused-function] 2023-09-14T00:25:48,931 11293 | static PyObject *__pyx_f_9indelpost_6pileup_leftalign_cigar(PyObject *__pyx_v_cigarstring, struct __pyx_obj_9indelpost_7variant_Variant *__pyx_v_target, int __pyx_v_read_start) { 2023-09-14T00:25:48,932 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-14T00:25:48,932 In file included from /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:4, 2023-09-14T00:25:48,933 from indelpost/pileup.c:1224: 2023-09-14T00:25:48,934 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:185:19: warning: ‘kseq_read’ defined but not used [-Wunused-function] 2023-09-14T00:25:48,934 185 | SCOPE int kseq_read(kseq_t *seq) \ 2023-09-14T00:25:48,935 | ^~~~~~~~~ 2023-09-14T00:25:48,935 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:238:9: note: in expansion of macro ‘__KSEQ_READ’ 2023-09-14T00:25:48,936 238 | __KSEQ_READ(SCOPE) 2023-09-14T00:25:48,936 | ^~~~~~~~~~~ 2023-09-14T00:25:48,937 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:25:48,937 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:25:48,938 | ^~~~~~~~~~ 2023-09-14T00:25:48,938 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:25:48,939 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:25:48,939 | ^~~~~~~~~ 2023-09-14T00:25:48,940 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:171:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] 2023-09-14T00:25:48,940 171 | SCOPE void kseq_destroy(kseq_t *ks) \ 2023-09-14T00:25:48,941 | ^~~~~~~~~~~~ 2023-09-14T00:25:48,941 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:25:48,942 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:25:48,943 | ^~~~~~~~~~~~ 2023-09-14T00:25:48,943 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:25:48,944 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:25:48,944 | ^~~~~~~~~~ 2023-09-14T00:25:48,945 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:25:48,946 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:25:48,947 | ^~~~~~~~~ 2023-09-14T00:25:48,947 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:165:23: warning: ‘kseq_init’ defined but not used [-Wunused-function] 2023-09-14T00:25:48,948 165 | SCOPE kseq_t *kseq_init(type_t fd) \ 2023-09-14T00:25:48,949 | ^~~~~~~~~ 2023-09-14T00:25:48,950 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:25:48,951 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:25:48,952 | ^~~~~~~~~~~~ 2023-09-14T00:25:48,953 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:25:48,953 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:25:48,954 | ^~~~~~~~~~ 2023-09-14T00:25:48,955 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:25:48,956 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:25:48,957 | ^~~~~~~~~ 2023-09-14T00:26:50,899 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/indelpost/pileup.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/indelpost/pileup.cpython-311-arm-linux-gnueabihf.so 2023-09-14T00:26:51,064 building 'indelpost.varaln' extension 2023-09-14T00:26:51,065 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c indelpost/varaln.c -o build/temp.linux-armv7l-cpython-311/indelpost/varaln.o 2023-09-14T00:26:54,010 In file included from /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:4, 2023-09-14T00:26:54,011 from indelpost/varaln.c:1224: 2023-09-14T00:26:54,012 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:185:19: warning: ‘kseq_read’ defined but not used [-Wunused-function] 2023-09-14T00:26:54,012 185 | SCOPE int kseq_read(kseq_t *seq) \ 2023-09-14T00:26:54,013 | ^~~~~~~~~ 2023-09-14T00:26:54,013 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:238:9: note: in expansion of macro ‘__KSEQ_READ’ 2023-09-14T00:26:54,014 238 | __KSEQ_READ(SCOPE) 2023-09-14T00:26:54,014 | ^~~~~~~~~~~ 2023-09-14T00:26:54,015 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:26:54,016 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:26:54,016 | ^~~~~~~~~~ 2023-09-14T00:26:54,017 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:26:54,017 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:26:54,018 | ^~~~~~~~~ 2023-09-14T00:26:54,019 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:171:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] 2023-09-14T00:26:54,019 171 | SCOPE void kseq_destroy(kseq_t *ks) \ 2023-09-14T00:26:54,020 | ^~~~~~~~~~~~ 2023-09-14T00:26:54,021 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:26:54,021 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:26:54,022 | ^~~~~~~~~~~~ 2023-09-14T00:26:54,022 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:26:54,023 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:26:54,024 | ^~~~~~~~~~ 2023-09-14T00:26:54,024 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:26:54,025 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:26:54,026 | ^~~~~~~~~ 2023-09-14T00:26:54,027 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:165:23: warning: ‘kseq_init’ defined but not used [-Wunused-function] 2023-09-14T00:26:54,028 165 | SCOPE kseq_t *kseq_init(type_t fd) \ 2023-09-14T00:26:54,029 | ^~~~~~~~~ 2023-09-14T00:26:54,030 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:26:54,030 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:26:54,031 | ^~~~~~~~~~~~ 2023-09-14T00:26:54,032 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:26:54,032 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:26:54,033 | ^~~~~~~~~~ 2023-09-14T00:26:54,033 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:26:54,034 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:26:54,034 | ^~~~~~~~~ 2023-09-14T00:27:36,815 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/indelpost/varaln.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/indelpost/varaln.cpython-311-arm-linux-gnueabihf.so 2023-09-14T00:27:36,968 building 'indelpost.contig' extension 2023-09-14T00:27:36,969 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c indelpost/contig.c -o build/temp.linux-armv7l-cpython-311/indelpost/contig.o 2023-09-14T00:27:39,586 In file included from /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:4, 2023-09-14T00:27:39,587 from indelpost/contig.c:1224: 2023-09-14T00:27:39,588 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:185:19: warning: ‘kseq_read’ defined but not used [-Wunused-function] 2023-09-14T00:27:39,588 185 | SCOPE int kseq_read(kseq_t *seq) \ 2023-09-14T00:27:39,589 | ^~~~~~~~~ 2023-09-14T00:27:39,590 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:238:9: note: in expansion of macro ‘__KSEQ_READ’ 2023-09-14T00:27:39,590 238 | __KSEQ_READ(SCOPE) 2023-09-14T00:27:39,591 | ^~~~~~~~~~~ 2023-09-14T00:27:39,592 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:27:39,592 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:27:39,593 | ^~~~~~~~~~ 2023-09-14T00:27:39,593 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:27:39,594 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:27:39,595 | ^~~~~~~~~ 2023-09-14T00:27:39,595 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:171:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] 2023-09-14T00:27:39,596 171 | SCOPE void kseq_destroy(kseq_t *ks) \ 2023-09-14T00:27:39,597 | ^~~~~~~~~~~~ 2023-09-14T00:27:39,597 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:27:39,598 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:27:39,598 | ^~~~~~~~~~~~ 2023-09-14T00:27:39,599 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:27:39,599 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:27:39,600 | ^~~~~~~~~~ 2023-09-14T00:27:39,600 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:27:39,601 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:27:39,601 | ^~~~~~~~~ 2023-09-14T00:27:39,601 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:165:23: warning: ‘kseq_init’ defined but not used [-Wunused-function] 2023-09-14T00:27:39,602 165 | SCOPE kseq_t *kseq_init(type_t fd) \ 2023-09-14T00:27:39,603 | ^~~~~~~~~ 2023-09-14T00:27:39,603 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:27:39,604 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:27:39,604 | ^~~~~~~~~~~~ 2023-09-14T00:27:39,605 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:27:39,605 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:27:39,606 | ^~~~~~~~~~ 2023-09-14T00:27:39,607 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:27:39,608 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:27:39,609 | ^~~~~~~~~ 2023-09-14T00:28:08,919 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/indelpost/contig.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/indelpost/contig.cpython-311-arm-linux-gnueabihf.so 2023-09-14T00:28:09,075 building 'indelpost.softclip' extension 2023-09-14T00:28:09,076 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c indelpost/softclip.c -o build/temp.linux-armv7l-cpython-311/indelpost/softclip.o 2023-09-14T00:28:10,184 In file included from /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:4, 2023-09-14T00:28:10,185 from indelpost/softclip.c:1224: 2023-09-14T00:28:10,185 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:185:19: warning: ‘kseq_read’ defined but not used [-Wunused-function] 2023-09-14T00:28:10,186 185 | SCOPE int kseq_read(kseq_t *seq) \ 2023-09-14T00:28:10,187 | ^~~~~~~~~ 2023-09-14T00:28:10,188 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:238:9: note: in expansion of macro ‘__KSEQ_READ’ 2023-09-14T00:28:10,188 238 | __KSEQ_READ(SCOPE) 2023-09-14T00:28:10,189 | ^~~~~~~~~~~ 2023-09-14T00:28:10,190 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:28:10,190 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:28:10,191 | ^~~~~~~~~~ 2023-09-14T00:28:10,191 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:28:10,192 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:28:10,192 | ^~~~~~~~~ 2023-09-14T00:28:10,193 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:171:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] 2023-09-14T00:28:10,193 171 | SCOPE void kseq_destroy(kseq_t *ks) \ 2023-09-14T00:28:10,194 | ^~~~~~~~~~~~ 2023-09-14T00:28:10,195 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:28:10,196 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:28:10,197 | ^~~~~~~~~~~~ 2023-09-14T00:28:10,197 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:28:10,198 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:28:10,199 | ^~~~~~~~~~ 2023-09-14T00:28:10,200 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:28:10,200 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:28:10,201 | ^~~~~~~~~ 2023-09-14T00:28:10,201 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:165:23: warning: ‘kseq_init’ defined but not used [-Wunused-function] 2023-09-14T00:28:10,202 165 | SCOPE kseq_t *kseq_init(type_t fd) \ 2023-09-14T00:28:10,202 | ^~~~~~~~~ 2023-09-14T00:28:10,203 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:28:10,204 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:28:10,204 | ^~~~~~~~~~~~ 2023-09-14T00:28:10,205 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:28:10,205 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:28:10,206 | ^~~~~~~~~~ 2023-09-14T00:28:10,207 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:28:10,207 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:28:10,208 | ^~~~~~~~~ 2023-09-14T00:28:19,380 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/indelpost/softclip.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/indelpost/softclip.cpython-311-arm-linux-gnueabihf.so 2023-09-14T00:28:19,498 building 'indelpost.localn' extension 2023-09-14T00:28:19,499 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c indelpost/localn.c -o build/temp.linux-armv7l-cpython-311/indelpost/localn.o 2023-09-14T00:28:21,297 In file included from /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:4, 2023-09-14T00:28:21,298 from indelpost/localn.c:1224: 2023-09-14T00:28:21,298 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:185:19: warning: ‘kseq_read’ defined but not used [-Wunused-function] 2023-09-14T00:28:21,299 185 | SCOPE int kseq_read(kseq_t *seq) \ 2023-09-14T00:28:21,299 | ^~~~~~~~~ 2023-09-14T00:28:21,300 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:238:9: note: in expansion of macro ‘__KSEQ_READ’ 2023-09-14T00:28:21,300 238 | __KSEQ_READ(SCOPE) 2023-09-14T00:28:21,301 | ^~~~~~~~~~~ 2023-09-14T00:28:21,301 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:28:21,302 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:28:21,302 | ^~~~~~~~~~ 2023-09-14T00:28:21,303 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:28:21,303 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:28:21,304 | ^~~~~~~~~ 2023-09-14T00:28:21,305 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:171:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] 2023-09-14T00:28:21,306 171 | SCOPE void kseq_destroy(kseq_t *ks) \ 2023-09-14T00:28:21,306 | ^~~~~~~~~~~~ 2023-09-14T00:28:21,307 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:28:21,308 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:28:21,309 | ^~~~~~~~~~~~ 2023-09-14T00:28:21,310 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:28:21,311 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:28:21,312 | ^~~~~~~~~~ 2023-09-14T00:28:21,313 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:28:21,313 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:28:21,314 | ^~~~~~~~~ 2023-09-14T00:28:21,314 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:165:23: warning: ‘kseq_init’ defined but not used [-Wunused-function] 2023-09-14T00:28:21,315 165 | SCOPE kseq_t *kseq_init(type_t fd) \ 2023-09-14T00:28:21,316 | ^~~~~~~~~ 2023-09-14T00:28:21,316 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:28:21,317 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:28:21,318 | ^~~~~~~~~~~~ 2023-09-14T00:28:21,318 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:28:21,319 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:28:21,320 | ^~~~~~~~~~ 2023-09-14T00:28:21,321 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:28:21,321 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:28:21,322 | ^~~~~~~~~ 2023-09-14T00:28:46,917 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/indelpost/localn.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/indelpost/localn.cpython-311-arm-linux-gnueabihf.so 2023-09-14T00:28:47,038 building 'indelpost.gappedaln' extension 2023-09-14T00:28:47,039 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c indelpost/gappedaln.c -o build/temp.linux-armv7l-cpython-311/indelpost/gappedaln.o 2023-09-14T00:28:48,594 In file included from /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:4, 2023-09-14T00:28:48,595 from indelpost/gappedaln.c:1224: 2023-09-14T00:28:48,595 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:185:19: warning: ‘kseq_read’ defined but not used [-Wunused-function] 2023-09-14T00:28:48,596 185 | SCOPE int kseq_read(kseq_t *seq) \ 2023-09-14T00:28:48,596 | ^~~~~~~~~ 2023-09-14T00:28:48,597 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:238:9: note: in expansion of macro ‘__KSEQ_READ’ 2023-09-14T00:28:48,598 238 | __KSEQ_READ(SCOPE) 2023-09-14T00:28:48,599 | ^~~~~~~~~~~ 2023-09-14T00:28:48,599 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:28:48,600 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:28:48,601 | ^~~~~~~~~~ 2023-09-14T00:28:48,601 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:28:48,602 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:28:48,602 | ^~~~~~~~~ 2023-09-14T00:28:48,603 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:171:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] 2023-09-14T00:28:48,604 171 | SCOPE void kseq_destroy(kseq_t *ks) \ 2023-09-14T00:28:48,605 | ^~~~~~~~~~~~ 2023-09-14T00:28:48,606 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:28:48,607 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:28:48,607 | ^~~~~~~~~~~~ 2023-09-14T00:28:48,608 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:28:48,609 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:28:48,609 | ^~~~~~~~~~ 2023-09-14T00:28:48,610 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:28:48,611 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:28:48,611 | ^~~~~~~~~ 2023-09-14T00:28:48,612 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:165:23: warning: ‘kseq_init’ defined but not used [-Wunused-function] 2023-09-14T00:28:48,612 165 | SCOPE kseq_t *kseq_init(type_t fd) \ 2023-09-14T00:28:48,613 | ^~~~~~~~~ 2023-09-14T00:28:48,613 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:237:9: note: in expansion of macro ‘__KSEQ_BASIC’ 2023-09-14T00:28:48,614 237 | __KSEQ_BASIC(SCOPE, type_t) \ 2023-09-14T00:28:48,614 | ^~~~~~~~~~~~ 2023-09-14T00:28:48,615 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:240:35: note: in expansion of macro ‘KSEQ_INIT2’ 2023-09-14T00:28:48,615 240 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) 2023-09-14T00:28:48,616 | ^~~~~~~~~~ 2023-09-14T00:28:48,616 /tmp/pip-build-env-81o70t3g/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’ 2023-09-14T00:28:48,617 9 | KSEQ_INIT(BGZF *, bgzf_read) 2023-09-14T00:28:48,617 | ^~~~~~~~~ 2023-09-14T00:29:09,841 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/indelpost/gappedaln.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/indelpost/gappedaln.cpython-311-arm-linux-gnueabihf.so 2023-09-14T00:29:09,985 installing to build/bdist.linux-armv7l/wheel 2023-09-14T00:29:09,986 running install 2023-09-14T00:29:10,010 running install_lib 2023-09-14T00:29:10,018 creating build/bdist.linux-armv7l 2023-09-14T00:29:10,019 creating build/bdist.linux-armv7l/wheel 2023-09-14T00:29:10,021 creating build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,022 copying build/lib.linux-armv7l-cpython-311/indelpost/softclip.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,034 copying build/lib.linux-armv7l-cpython-311/indelpost/contig.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,055 copying build/lib.linux-armv7l-cpython-311/indelpost/gappedaln.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,074 copying build/lib.linux-armv7l-cpython-311/indelpost/pileup.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,104 copying build/lib.linux-armv7l-cpython-311/indelpost/chromosomes.py -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,106 copying build/lib.linux-armv7l-cpython-311/indelpost/alleles.py -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,109 copying build/lib.linux-armv7l-cpython-311/indelpost/localn.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,123 copying build/lib.linux-armv7l-cpython-311/indelpost/consensus.py -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,125 copying build/lib.linux-armv7l-cpython-311/indelpost/__init__.py -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,127 copying build/lib.linux-armv7l-cpython-311/indelpost/version.py -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,129 copying build/lib.linux-armv7l-cpython-311/indelpost/varaln.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,152 copying build/lib.linux-armv7l-cpython-311/indelpost/variant.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,174 copying build/lib.linux-armv7l-cpython-311/indelpost/utilities.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/indelpost 2023-09-14T00:29:10,199 running install_egg_info 2023-09-14T00:29:10,214 running egg_info 2023-09-14T00:29:10,220 writing indelpost.egg-info/PKG-INFO 2023-09-14T00:29:10,223 writing dependency_links to indelpost.egg-info/dependency_links.txt 2023-09-14T00:29:10,224 writing requirements to indelpost.egg-info/requires.txt 2023-09-14T00:29:10,226 writing top-level names to indelpost.egg-info/top_level.txt 2023-09-14T00:29:10,235 reading manifest file 'indelpost.egg-info/SOURCES.txt' 2023-09-14T00:29:10,239 reading manifest template 'MANIFEST.in' 2023-09-14T00:29:10,244 writing manifest file 'indelpost.egg-info/SOURCES.txt' 2023-09-14T00:29:10,246 Copying indelpost.egg-info to build/bdist.linux-armv7l/wheel/indelpost-0.0.4-py3.11.egg-info 2023-09-14T00:29:10,255 running install_scripts 2023-09-14T00:29:10,300 creating build/bdist.linux-armv7l/wheel/indelpost-0.0.4.dist-info/WHEEL 2023-09-14T00:29:10,303 creating '/tmp/pip-wheel-0zqzcclq/.tmp-0omrzddk/indelpost-0.0.4-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-14T00:29:10,306 adding 'indelpost/__init__.py' 2023-09-14T00:29:10,309 adding 'indelpost/alleles.py' 2023-09-14T00:29:10,311 adding 'indelpost/chromosomes.py' 2023-09-14T00:29:10,313 adding 'indelpost/consensus.py' 2023-09-14T00:29:10,560 adding 'indelpost/contig.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:29:10,729 adding 'indelpost/gappedaln.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:29:10,899 adding 'indelpost/localn.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:29:11,278 adding 'indelpost/pileup.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:29:11,380 adding 'indelpost/softclip.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:29:11,753 adding 'indelpost/utilities.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:29:12,065 adding 'indelpost/varaln.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:29:12,348 adding 'indelpost/variant.cpython-311-arm-linux-gnueabihf.so' 2023-09-14T00:29:12,359 adding 'indelpost/version.py' 2023-09-14T00:29:12,361 adding 'indelpost-0.0.4.dist-info/METADATA' 2023-09-14T00:29:12,363 adding 'indelpost-0.0.4.dist-info/WHEEL' 2023-09-14T00:29:12,364 adding 'indelpost-0.0.4.dist-info/top_level.txt' 2023-09-14T00:29:12,365 adding 'indelpost-0.0.4.dist-info/RECORD' 2023-09-14T00:29:12,406 removing build/bdist.linux-armv7l/wheel 2023-09-14T00:29:12,558 Building wheel for indelpost (pyproject.toml): finished with status 'done' 2023-09-14T00:29:12,651 Created wheel for indelpost: filename=indelpost-0.0.4-cp311-cp311-linux_armv7l.whl size=3955004 sha256=26c0ffb0dc998c5ca1e7a54c3eb1cbf7bdf3ba245fb5d0efde084ab2b501dd97 2023-09-14T00:29:12,652 Stored in directory: /tmp/pip-ephem-wheel-cache-dxyfgmqc/wheels/9a/46/7b/4bc42bfbb7cc49b8f988832665ba2b975ead953a6640156dcb 2023-09-14T00:29:12,663 Successfully built indelpost 2023-09-14T00:29:12,779 Removed build tracker: '/tmp/pip-build-tracker-397bmtav'