2023-09-12T09:00:17,474 Created temporary directory: /tmp/pip-build-tracker-5_yokgeh 2023-09-12T09:00:17,476 Initialized build tracking at /tmp/pip-build-tracker-5_yokgeh 2023-09-12T09:00:17,476 Created build tracker: /tmp/pip-build-tracker-5_yokgeh 2023-09-12T09:00:17,477 Entered build tracker: /tmp/pip-build-tracker-5_yokgeh 2023-09-12T09:00:17,477 Created temporary directory: /tmp/pip-wheel-rbjky0ie 2023-09-12T09:00:17,481 Created temporary directory: /tmp/pip-ephem-wheel-cache-7uexnso3 2023-09-12T09:00:17,502 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-12T09:00:17,506 2 location(s) to search for versions of uta-align: 2023-09-12T09:00:17,506 * https://pypi.org/simple/uta-align/ 2023-09-12T09:00:17,506 * https://www.piwheels.org/simple/uta-align/ 2023-09-12T09:00:17,507 Fetching project page and analyzing links: https://pypi.org/simple/uta-align/ 2023-09-12T09:00:17,507 Getting page https://pypi.org/simple/uta-align/ 2023-09-12T09:00:17,509 Found index url https://pypi.org/simple/ 2023-09-12T09:00:17,725 Fetched page https://pypi.org/simple/uta-align/ as application/vnd.pypi.simple.v1+json 2023-09-12T09:00:17,730 Found link https://files.pythonhosted.org/packages/60/a2/47df4fbbbf9800199f0b9363ba2b02c7f234d074ad2693d09cb499a18b2f/uta-align-0.0.1dev-c749ca8b22a0.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.0.1dev-c749ca8b22a0 2023-09-12T09:00:17,731 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/08/ed/16116fd416d69101c3cda7290be8a3a4f82f9d3c9e7902c783633ed78f21/uta_align-0.0.1dev_c749ca8b22a0-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,732 Found link https://files.pythonhosted.org/packages/c5/c4/e4c65f29cdbcec6ec0269ae305bba6b2a228ff67699de315154dcda99f68/uta-align-0.1.0.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.1.0 2023-09-12T09:00:17,732 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/66/50/0cf3cc125b6ba7ad99012bedf436c15e56cdf19c677edd4d25f24c51cfe2/uta_align-0.1.0-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,733 Found link https://files.pythonhosted.org/packages/f5/7f/c7c7d3043fa52fe7d6c8d3a870409f9cc9126ca11c113ca05bcd889a123d/uta-align-0.1.2.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.1.2 2023-09-12T09:00:17,734 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/fe/38/a811e7ea2cfa3d1447302b1e0bf650a6b7394c85a308416ae9acbde5c0b9/uta_align-0.1.2-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,734 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/c8/ef/d709856489d8883fa96dfa2732a7cdf33a2b6eb7319e2d8f245e1fbe299a/uta_align-0.1.4-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,735 Found link https://files.pythonhosted.org/packages/4f/98/6c282d715088d99d0e4ad4574bd7ae06ae0157f9b4c94843bf215a2b13fd/uta-align-0.1.5.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.1.5 2023-09-12T09:00:17,736 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/d3/86/7a17a92e6730db93d570dde8d4f6ed2ebde235a4a2b1067fe41aa73e6d56/uta_align-0.1.5-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,736 Found link https://files.pythonhosted.org/packages/20/a0/944d267127f1cc2b188f8afbc3684232ebd576ccad97cec399179f29ada3/uta-align-0.1.6.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.1.6 2023-09-12T09:00:17,737 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/8a/79/ab5ccbbf4854c8dc038871306dccb76e18680581267e876528f829089b6a/uta_align-0.1.6-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,738 Found link https://files.pythonhosted.org/packages/42/c0/9999b551deffc63c27066cffdac0c2bdd6413d3741b775a6f0441ce82c94/uta-align-0.1.7.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.1.7 2023-09-12T09:00:17,738 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/8a/fc/a620e23d04f03f60881831b48f4e05e3fbd8b8cd9c797b06245f7783d8b4/uta_align-0.1.7-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,739 Found link https://files.pythonhosted.org/packages/f1/f2/ae2c44e1009a4c94be0a228a17ba41327cbb14ca4d205b9d30a6d03907e0/uta-align-0.1.8.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.1.8 2023-09-12T09:00:17,740 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/0a/e1/dfb0593828e024c1a8c1b40539a892d613a52221deec59e1916e6271c49d/uta_align-0.1.8-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,740 Found link https://files.pythonhosted.org/packages/53/9a/f8e1cab0dc5e7f59277cad128fcead3897c03c74c743b6ef05927a49914e/uta-align-0.1.9.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.1.9 2023-09-12T09:00:17,741 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/12/b6/bedbe1aa646f76d72de5a2e269b0771d04704ab97be399ebe34a7b4a31ac/uta_align-0.1.9-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,741 Found link https://files.pythonhosted.org/packages/94/6b/0b73dc6d3391468e9d5229a262129763672296d41f1a26d4f128c66a99dd/uta-align-0.1.10.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.1.10 2023-09-12T09:00:17,742 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/af/ec/2ec104fea2c5ad78e85b77df92d92a77c75fca18b9fd5efe75e970c4d6ed/uta_align-0.1.10-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,742 Found link https://files.pythonhosted.org/packages/46/1c/47de77a2b89f0339022a5ae5a03f4a919f1afa18d47b5640c3e87c0f5e68/uta-align-0.1.11.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.1.11 2023-09-12T09:00:17,743 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/dd/a7/46496d2d48416e55e45b4f7a77103d53a80f9165552d81ffba27e51ff99b/uta_align-0.1.11-py2.7-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,744 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/0f/7c/ffe50738dd367f7378193f892584392015f4b62aa3ebce7ff721b0cddbc4/uta_align-0.1.11-py3.6-linux-x86_64.egg (from https://pypi.org/simple/uta-align/) 2023-09-12T09:00:17,744 Found link https://files.pythonhosted.org/packages/0f/a2/e6bdd37d746c294c7a6374664078ecf2d34677b52c5267ff0576f669eb15/uta-align-0.2.0a1.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.2.0a1 2023-09-12T09:00:17,745 Found link https://files.pythonhosted.org/packages/7c/07/3d0483101728198e619f9d45552d2d50dc90fc2937964a899e6fe3908687/uta-align-0.2.0a2.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.2.0a2 2023-09-12T09:00:17,745 Found link https://files.pythonhosted.org/packages/d6/4e/c15fb32400d949bcfd2078c9a7ad9944c8f59603e2504e40b6f2a7c79980/uta-align-0.2.0a3.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.2.0a3 2023-09-12T09:00:17,746 Found link https://files.pythonhosted.org/packages/64/bc/5306c731e7d4d304e9d1f7fee2a8fa1d79640626ccaac9f9df660078893c/uta-align-0.2.0.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.2.0 2023-09-12T09:00:17,747 Fetching project page and analyzing links: https://www.piwheels.org/simple/uta-align/ 2023-09-12T09:00:17,747 Getting page https://www.piwheels.org/simple/uta-align/ 2023-09-12T09:00:17,749 Found index url https://www.piwheels.org/simple/ 2023-09-12T09:00:22,317 Fetched page https://www.piwheels.org/simple/uta-align/ as text/html 2023-09-12T09:00:22,335 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.1.11-cp39-cp39-linux_armv6l.whl#sha256=827c85ef70c500f1f1043097ddab023e02a866f3aa00719c37f486bb07bdc76f (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,336 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.1.11-cp39-cp39-linux_armv7l.whl#sha256=827c85ef70c500f1f1043097ddab023e02a866f3aa00719c37f486bb07bdc76f (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,337 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0-cp35-cp35m-linux_armv6l.whl#sha256=dae4936aefa1312d72056637cd86114fe7343d74171802cfd626b4df74e3fc1e (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,339 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0-cp35-cp35m-linux_armv7l.whl#sha256=dae4936aefa1312d72056637cd86114fe7343d74171802cfd626b4df74e3fc1e (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,340 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0-cp37-cp37m-linux_armv6l.whl#sha256=42d546e097c14adde7bcdc285512044c928ccf557dc96029a4205f3c86f271a3 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,340 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0-cp37-cp37m-linux_armv7l.whl#sha256=42d546e097c14adde7bcdc285512044c928ccf557dc96029a4205f3c86f271a3 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,341 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0-cp39-cp39-linux_armv6l.whl#sha256=63c55627e235d6e95ecee14361b3e51f02fc7dbe1257875f66bd870a2d86e251 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,342 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0-cp39-cp39-linux_armv7l.whl#sha256=63c55627e235d6e95ecee14361b3e51f02fc7dbe1257875f66bd870a2d86e251 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,343 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a1-cp35-cp35m-linux_armv6l.whl#sha256=9557dfb5280a0929438f9a71f5bf321a29ce6a090b4e6242baf364fa80204c54 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,344 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a1-cp35-cp35m-linux_armv7l.whl#sha256=9557dfb5280a0929438f9a71f5bf321a29ce6a090b4e6242baf364fa80204c54 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,345 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a1-cp37-cp37m-linux_armv6l.whl#sha256=66ebdb1248c86c01cc3714d7c0ec736ebf9c6934dd3ae0c581b54d58d3088331 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,346 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a1-cp37-cp37m-linux_armv7l.whl#sha256=66ebdb1248c86c01cc3714d7c0ec736ebf9c6934dd3ae0c581b54d58d3088331 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,347 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a1-cp39-cp39-linux_armv6l.whl#sha256=18908072448c5f15e1b8cefb1071b1b6782fe15aca7f97830a79a154fb4d9e19 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,348 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a1-cp39-cp39-linux_armv7l.whl#sha256=18908072448c5f15e1b8cefb1071b1b6782fe15aca7f97830a79a154fb4d9e19 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,349 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a2-cp35-cp35m-linux_armv6l.whl#sha256=8792ceb53aedebed753c74410a34ed1c5ad088acc434f4527f4158c05e1f6033 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,350 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a2-cp35-cp35m-linux_armv7l.whl#sha256=8792ceb53aedebed753c74410a34ed1c5ad088acc434f4527f4158c05e1f6033 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,351 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a2-cp37-cp37m-linux_armv6l.whl#sha256=0decd7a6fdbfca278e7d48d0c4365fe413ba471b43c3e9c8ad023bf91157be34 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,352 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a2-cp37-cp37m-linux_armv7l.whl#sha256=0decd7a6fdbfca278e7d48d0c4365fe413ba471b43c3e9c8ad023bf91157be34 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,353 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a2-cp39-cp39-linux_armv6l.whl#sha256=fc0523694bebe8202661746996848de4787dd23c86aedac17cc56d3958f26d54 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,354 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a2-cp39-cp39-linux_armv7l.whl#sha256=fc0523694bebe8202661746996848de4787dd23c86aedac17cc56d3958f26d54 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,355 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a3-cp35-cp35m-linux_armv6l.whl#sha256=3cb8658cec7e6bb1820937b5b58d040d7bcdafeae9fd8d1d0efe5f32c532e4cf (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,356 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a3-cp35-cp35m-linux_armv7l.whl#sha256=3cb8658cec7e6bb1820937b5b58d040d7bcdafeae9fd8d1d0efe5f32c532e4cf (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,356 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a3-cp37-cp37m-linux_armv6l.whl#sha256=b6eb04dfeab677556b95759aee55039d3e8d1bc2a65eaa0b266248cfd5300992 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,357 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a3-cp37-cp37m-linux_armv7l.whl#sha256=b6eb04dfeab677556b95759aee55039d3e8d1bc2a65eaa0b266248cfd5300992 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,358 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a3-cp39-cp39-linux_armv6l.whl#sha256=f07b67d97fc9a29b300ced5f81b287e6a0fd8638ce93e936705a2c184af86865 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,359 Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.2.0a3-cp39-cp39-linux_armv7l.whl#sha256=f07b67d97fc9a29b300ced5f81b287e6a0fd8638ce93e936705a2c184af86865 (from https://www.piwheels.org/simple/uta-align/) 2023-09-12T09:00:22,360 Skipping link: not a file: https://www.piwheels.org/simple/uta-align/ 2023-09-12T09:00:22,361 Skipping link: not a file: https://pypi.org/simple/uta-align/ 2023-09-12T09:00:22,409 Given no hashes to check 1 links for project 'uta-align': discarding no candidates 2023-09-12T09:00:22,427 Collecting uta-align==0.2.0a1 2023-09-12T09:00:22,430 Created temporary directory: /tmp/pip-unpack-o1f1q_cf 2023-09-12T09:00:23,273 Downloading uta-align-0.2.0a1.tar.gz (266 kB) 2023-09-12T09:00:23,523 Added uta-align==0.2.0a1 from https://files.pythonhosted.org/packages/0f/a2/e6bdd37d746c294c7a6374664078ecf2d34677b52c5267ff0576f669eb15/uta-align-0.2.0a1.tar.gz to build tracker '/tmp/pip-build-tracker-5_yokgeh' 2023-09-12T09:00:23,532 Created temporary directory: /tmp/pip-build-env-_w_3349q 2023-09-12T09:00:23,537 Installing build dependencies: started 2023-09-12T09:00:23,538 Running command pip subprocess to install build dependencies 2023-09-12T09:00:24,894 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-12T09:00:25,431 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-12T09:00:32,986 Collecting cython>=0.29 2023-09-12T09:00:32,987 Obtaining dependency information for cython>=0.29 from https://files.pythonhosted.org/packages/03/e9/9cc0c4f0d8a566089d096254cd25168a0db02dd047863a7f995d8d3eefa7/Cython-3.0.2-py2.py3-none-any.whl.metadata 2023-09-12T09:00:32,993 Using cached Cython-3.0.2-py2.py3-none-any.whl.metadata (3.1 kB) 2023-09-12T09:00:38,701 Collecting cython-setuptools 2023-09-12T09:00:38,711 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /simple/cython-setuptools/cython_setuptools-0.2.3-py3-none-any.whl 2023-09-12T09:00:43,605 Downloading https://www.piwheels.org/simple/cython-setuptools/cython_setuptools-0.2.3-py3-none-any.whl (9.7 kB) 2023-09-12T09:00:49,085 Collecting pysam>=0.15 2023-09-12T09:00:49,227 Downloading pysam-0.21.0.tar.gz (4.1 MB) 2023-09-12T09:00:49,635 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.1/4.1 MB 10.1 MB/s eta 0:00:00 2023-09-12T09:00:51,680 Installing build dependencies: started 2023-09-12T09:00:51,681 Running command pip subprocess to install build dependencies 2023-09-12T09:00:53,419 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-12T09:01:02,337 Collecting setuptools>=59.0 2023-09-12T09:01:02,338 Obtaining dependency information for setuptools>=59.0 from https://files.pythonhosted.org/packages/95/79/6b47c6a872b40743a480687dc0c79ffb4202710789f3e4d54a84fff8b550/setuptools-68.2.1-py3-none-any.whl.metadata 2023-09-12T09:01:02,345 Using cached setuptools-68.2.1-py3-none-any.whl.metadata (6.3 kB) 2023-09-12T09:01:02,557 Collecting wheel 2023-09-12T09:01:02,576 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-12T09:01:12,006 Collecting Cython<3.0,>=0.29.30 2023-09-12T09:01:12,008 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 2023-09-12T09:01:12,013 Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB) 2023-09-12T09:01:12,197 Using cached setuptools-68.2.1-py3-none-any.whl (807 kB) 2023-09-12T09:01:12,236 Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB) 2023-09-12T09:01:14,751 Installing collected packages: wheel, setuptools, Cython 2023-09-12T09:01:19,877 Successfully installed Cython-0.29.36 setuptools-68.2.1 wheel-0.41.2 2023-09-12T09:01:20,536 Installing build dependencies: finished with status 'done' 2023-09-12T09:01:20,539 Getting requirements to build wheel: started 2023-09-12T09:01:20,540 Running command Getting requirements to build wheel 2023-09-12T09:01:21,222 # pysam: cython is available - using cythonize if necessary 2023-09-12T09:01:21,224 # pysam: htslib mode is shared 2023-09-12T09:01:21,225 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2023-09-12T09:01:21,226 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc 2023-09-12T09:01:21,228 # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-12T09:01:21,229 # pysam: (sysconfig) LDFLAGS= -g -fwrapv -O2 2023-09-12T09:01:21,521 checking for gcc... arm-linux-gnueabihf-gcc 2023-09-12T09:01:21,789 checking whether the C compiler works... yes 2023-09-12T09:01:21,790 checking for C compiler default output file name... a.out 2023-09-12T09:01:21,989 checking for suffix of executables... 2023-09-12T09:01:22,198 checking whether we are cross compiling... no 2023-09-12T09:01:22,285 checking for suffix of object files... o 2023-09-12T09:01:22,362 checking whether we are using the GNU C compiler... yes 2023-09-12T09:01:22,434 checking whether arm-linux-gnueabihf-gcc accepts -g... yes 2023-09-12T09:01:22,565 checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed 2023-09-12T09:01:22,568 checking for ranlib... ranlib 2023-09-12T09:01:22,576 checking for grep that handles long lines and -e... /usr/bin/grep 2023-09-12T09:01:22,650 checking for C compiler warning flags... -Wall 2023-09-12T09:01:22,660 configure: Default CFLAGS_ARM/X86: -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-12T09:01:22,732 checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no 2023-09-12T09:01:22,805 checking whether C compiler accepts -mavx2... no 2023-09-12T09:01:22,887 checking whether C compiler accepts -mavx512f... no 2023-09-12T09:01:23,374 checking whether C compiler supports ARM Neon... no 2023-09-12T09:01:23,378 checking for pkg-config... /usr/bin/pkg-config 2023-09-12T09:01:23,384 checking pkg-config is at least version 0.9.0... yes 2023-09-12T09:01:23,386 checking for special C compiler options needed for large files... no 2023-09-12T09:01:23,573 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-09-12T09:01:23,588 checking shared library type for unknown-Linux... plain .so 2023-09-12T09:01:23,700 checking whether the linker supports versioned symbols... no 2023-09-12T09:01:23,875 checking whether the compiler accepts -fvisibility=hidden... yes 2023-09-12T09:01:23,984 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E 2023-09-12T09:01:24,098 checking for egrep... /usr/bin/grep -E 2023-09-12T09:01:24,610 checking for ANSI C header files... yes 2023-09-12T09:01:24,733 checking for sys/types.h... yes 2023-09-12T09:01:24,871 checking for sys/stat.h... yes 2023-09-12T09:01:25,010 checking for stdlib.h... yes 2023-09-12T09:01:25,156 checking for string.h... yes 2023-09-12T09:01:25,333 checking for memory.h... yes 2023-09-12T09:01:25,478 checking for strings.h... yes 2023-09-12T09:01:25,844 checking for inttypes.h... yes 2023-09-12T09:01:25,992 checking for stdint.h... yes 2023-09-12T09:01:26,187 checking for unistd.h... yes 2023-09-12T09:01:26,211 checking for stdlib.h... (cached) yes 2023-09-12T09:01:26,234 checking for unistd.h... (cached) yes 2023-09-12T09:01:26,413 checking for sys/param.h... yes 2023-09-12T09:01:26,620 checking for getpagesize... yes 2023-09-12T09:01:26,961 checking for working mmap... yes 2023-09-12T09:01:27,160 checking for gmtime_r... yes 2023-09-12T09:01:27,366 checking for fsync... yes 2023-09-12T09:01:27,581 checking for drand48... yes 2023-09-12T09:01:27,857 checking for srand48_deterministic... no 2023-09-12T09:01:28,029 checking whether fdatasync is declared... yes 2023-09-12T09:01:28,212 checking for fdatasync... yes 2023-09-12T09:01:28,653 checking for library containing log... -lm 2023-09-12T09:01:28,766 checking for zlib.h... yes 2023-09-12T09:01:28,952 checking for inflate in -lz... yes 2023-09-12T09:01:29,146 checking for library containing recv... none required 2023-09-12T09:01:29,241 checking for bzlib.h... yes 2023-09-12T09:01:29,474 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-09-12T09:01:29,731 checking for lzma.h... yes 2023-09-12T09:01:29,927 checking for lzma_easy_buffer_encode in -llzma... yes 2023-09-12T09:01:29,933 checking whether htscodecs files are present... yes 2023-09-12T09:01:30,014 checking for libdeflate.h... yes 2023-09-12T09:01:30,242 checking for libdeflate_deflate_compress in -ldeflate... yes 2023-09-12T09:01:30,402 checking for curl/curl.h... yes 2023-09-12T09:01:30,777 checking for curl_easy_pause in -lcurl... yes 2023-09-12T09:01:31,023 checking for CCHmac... no 2023-09-12T09:01:31,631 checking for library containing HMAC... -lcrypto 2023-09-12T09:01:31,825 checking for library containing regcomp... none required 2023-09-12T09:01:31,951 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2023-09-12T09:01:32,019 configure: creating ./config.status 2023-09-12T09:01:32,334 config.status: creating config.mk 2023-09-12T09:01:32,377 config.status: creating htslib.pc.tmp 2023-09-12T09:01:32,440 config.status: creating config.h 2023-09-12T09:01:32,490 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-09-12T09:01:33,144 # pysam: htslib configure options: --enable-libcurl 2023-09-12T09:01:33,150 # pysam: htslib_config HTS_CFLAGS_AVX2= 2023-09-12T09:01:33,152 # pysam: htslib_config HTS_CFLAGS_AVX512= 2023-09-12T09:01:33,153 # pysam: htslib_config HTS_CFLAGS_SSE4= 2023-09-12T09:01:33,154 # pysam: htslib_config HTS_HAVE_NEON= 2023-09-12T09:01:33,154 # 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 2023-09-12T09:01:33,155 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2023-09-12T09:01:33,155 # pysam: htslib_config PLATFORM=default 2023-09-12T09:01:33,156 # pysam: config_option: ENABLE_GCS=1 2023-09-12T09:01:33,156 # pysam: config_option: ENABLE_PLUGINS=0 2023-09-12T09:01:33,157 # pysam: config_option: ENABLE_S3=1 2023-09-12T09:01:33,158 # pysam: config_option: HAVE_COMMONCRYPTO=0 2023-09-12T09:01:33,158 # pysam: config_option: HAVE_HMAC=1 2023-09-12T09:01:33,159 # pysam: config_option: HAVE_LIBBZ2=1 2023-09-12T09:01:33,159 # pysam: config_option: HAVE_LIBCURL=1 2023-09-12T09:01:33,160 # pysam: config_option: HAVE_LIBDEFLATE=1 2023-09-12T09:01:33,160 # pysam: config_option: HAVE_LIBLZMA=1 2023-09-12T09:01:33,161 # pysam: config_option: HAVE_MMAP=1 2023-09-12T09:01:33,162 running egg_info 2023-09-12T09:01:33,162 writing pysam.egg-info/PKG-INFO 2023-09-12T09:01:33,167 writing dependency_links to pysam.egg-info/dependency_links.txt 2023-09-12T09:01:33,168 writing requirements to pysam.egg-info/requires.txt 2023-09-12T09:01:33,170 writing top-level names to pysam.egg-info/top_level.txt 2023-09-12T09:01:33,209 reading manifest file 'pysam.egg-info/SOURCES.txt' 2023-09-12T09:01:33,234 reading manifest template 'MANIFEST.in' 2023-09-12T09:01:33,236 warning: no files found matching 'KNOWN_BUGS' 2023-09-12T09:01:33,237 warning: no files found matching 'THANKS' 2023-09-12T09:01:33,245 no previously-included directories found matching 'tests/' 2023-09-12T09:01:33,361 adding license file 'COPYING' 2023-09-12T09:01:33,361 adding license file 'AUTHORS' 2023-09-12T09:01:33,384 writing manifest file 'pysam.egg-info/SOURCES.txt' 2023-09-12T09:01:33,506 Getting requirements to build wheel: finished with status 'done' 2023-09-12T09:01:33,518 Preparing metadata (pyproject.toml): started 2023-09-12T09:01:33,518 Running command Preparing metadata (pyproject.toml) 2023-09-12T09:01:34,189 # pysam: cython is available - using cythonize if necessary 2023-09-12T09:01:34,190 # pysam: htslib mode is shared 2023-09-12T09:01:34,191 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2023-09-12T09:01:34,191 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc 2023-09-12T09:01:34,192 # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-12T09:01:34,193 # pysam: (sysconfig) LDFLAGS= -g -fwrapv -O2 2023-09-12T09:01:34,494 checking for gcc... arm-linux-gnueabihf-gcc 2023-09-12T09:01:34,753 checking whether the C compiler works... yes 2023-09-12T09:01:34,754 checking for C compiler default output file name... a.out 2023-09-12T09:01:34,925 checking for suffix of executables... 2023-09-12T09:01:35,169 checking whether we are cross compiling... no 2023-09-12T09:01:35,256 checking for suffix of object files... o 2023-09-12T09:01:35,335 checking whether we are using the GNU C compiler... yes 2023-09-12T09:01:35,411 checking whether arm-linux-gnueabihf-gcc accepts -g... yes 2023-09-12T09:01:35,543 checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed 2023-09-12T09:01:35,546 checking for ranlib... ranlib 2023-09-12T09:01:35,554 checking for grep that handles long lines and -e... /usr/bin/grep 2023-09-12T09:01:35,630 checking for C compiler warning flags... -Wall 2023-09-12T09:01:35,640 configure: Default CFLAGS_ARM/X86: -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-12T09:01:35,699 checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no 2023-09-12T09:01:35,750 checking whether C compiler accepts -mavx2... no 2023-09-12T09:01:35,805 checking whether C compiler accepts -mavx512f... no 2023-09-12T09:01:36,296 checking whether C compiler supports ARM Neon... no 2023-09-12T09:01:36,299 checking for pkg-config... /usr/bin/pkg-config 2023-09-12T09:01:36,304 checking pkg-config is at least version 0.9.0... yes 2023-09-12T09:01:36,307 checking for special C compiler options needed for large files... no 2023-09-12T09:01:36,496 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-09-12T09:01:36,511 checking shared library type for unknown-Linux... plain .so 2023-09-12T09:01:36,621 checking whether the linker supports versioned symbols... no 2023-09-12T09:01:36,798 checking whether the compiler accepts -fvisibility=hidden... yes 2023-09-12T09:01:36,908 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E 2023-09-12T09:01:37,023 checking for egrep... /usr/bin/grep -E 2023-09-12T09:01:37,562 checking for ANSI C header files... yes 2023-09-12T09:01:37,685 checking for sys/types.h... yes 2023-09-12T09:01:37,821 checking for sys/stat.h... yes 2023-09-12T09:01:37,958 checking for stdlib.h... yes 2023-09-12T09:01:38,100 checking for string.h... yes 2023-09-12T09:01:38,241 checking for memory.h... yes 2023-09-12T09:01:38,411 checking for strings.h... yes 2023-09-12T09:01:38,558 checking for inttypes.h... yes 2023-09-12T09:01:38,712 checking for stdint.h... yes 2023-09-12T09:01:38,870 checking for unistd.h... yes 2023-09-12T09:01:38,895 checking for stdlib.h... (cached) yes 2023-09-12T09:01:38,918 checking for unistd.h... (cached) yes 2023-09-12T09:01:39,106 checking for sys/param.h... yes 2023-09-12T09:01:39,348 checking for getpagesize... yes 2023-09-12T09:01:39,691 checking for working mmap... yes 2023-09-12T09:01:39,892 checking for gmtime_r... yes 2023-09-12T09:01:40,128 checking for fsync... yes 2023-09-12T09:01:40,336 checking for drand48... yes 2023-09-12T09:01:40,562 checking for srand48_deterministic... no 2023-09-12T09:01:40,737 checking whether fdatasync is declared... yes 2023-09-12T09:01:40,960 checking for fdatasync... yes 2023-09-12T09:01:41,623 checking for library containing log... -lm 2023-09-12T09:01:41,788 checking for zlib.h... yes 2023-09-12T09:01:41,974 checking for inflate in -lz... yes 2023-09-12T09:01:42,165 checking for library containing recv... none required 2023-09-12T09:01:42,257 checking for bzlib.h... yes 2023-09-12T09:01:42,442 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-09-12T09:01:42,689 checking for lzma.h... yes 2023-09-12T09:01:42,878 checking for lzma_easy_buffer_encode in -llzma... yes 2023-09-12T09:01:42,884 checking whether htscodecs files are present... yes 2023-09-12T09:01:42,962 checking for libdeflate.h... yes 2023-09-12T09:01:43,147 checking for libdeflate_deflate_compress in -ldeflate... yes 2023-09-12T09:01:43,298 checking for curl/curl.h... yes 2023-09-12T09:01:43,661 checking for curl_easy_pause in -lcurl... yes 2023-09-12T09:01:43,870 checking for CCHmac... no 2023-09-12T09:01:44,503 checking for library containing HMAC... -lcrypto 2023-09-12T09:01:44,695 checking for library containing regcomp... none required 2023-09-12T09:01:44,816 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2023-09-12T09:01:44,876 configure: creating ./config.status 2023-09-12T09:01:45,557 config.status: creating config.mk 2023-09-12T09:01:45,614 config.status: creating htslib.pc.tmp 2023-09-12T09:01:45,676 config.status: creating config.h 2023-09-12T09:01:45,704 config.status: config.h is unchanged 2023-09-12T09:01:45,713 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-09-12T09:01:46,260 # pysam: htslib configure options: --enable-libcurl 2023-09-12T09:01:46,261 # pysam: htslib_config HTS_CFLAGS_AVX2= 2023-09-12T09:01:46,262 # pysam: htslib_config HTS_CFLAGS_AVX512= 2023-09-12T09:01:46,263 # pysam: htslib_config HTS_CFLAGS_SSE4= 2023-09-12T09:01:46,264 # pysam: htslib_config HTS_HAVE_NEON= 2023-09-12T09:01:46,265 # 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 2023-09-12T09:01:46,266 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2023-09-12T09:01:46,267 # pysam: htslib_config PLATFORM=default 2023-09-12T09:01:46,268 # pysam: config_option: ENABLE_GCS=1 2023-09-12T09:01:46,269 # pysam: config_option: ENABLE_PLUGINS=0 2023-09-12T09:01:46,270 # pysam: config_option: ENABLE_S3=1 2023-09-12T09:01:46,271 # pysam: config_option: HAVE_COMMONCRYPTO=0 2023-09-12T09:01:46,272 # pysam: config_option: HAVE_HMAC=1 2023-09-12T09:01:46,273 # pysam: config_option: HAVE_LIBBZ2=1 2023-09-12T09:01:46,274 # pysam: config_option: HAVE_LIBCURL=1 2023-09-12T09:01:46,275 # pysam: config_option: HAVE_LIBDEFLATE=1 2023-09-12T09:01:46,276 # pysam: config_option: HAVE_LIBLZMA=1 2023-09-12T09:01:46,277 # pysam: config_option: HAVE_MMAP=1 2023-09-12T09:01:46,278 running dist_info 2023-09-12T09:01:46,279 creating /tmp/pip-modern-metadata-mrydwgtx/pysam.egg-info 2023-09-12T09:01:46,279 writing /tmp/pip-modern-metadata-mrydwgtx/pysam.egg-info/PKG-INFO 2023-09-12T09:01:46,280 writing dependency_links to /tmp/pip-modern-metadata-mrydwgtx/pysam.egg-info/dependency_links.txt 2023-09-12T09:01:46,281 writing requirements to /tmp/pip-modern-metadata-mrydwgtx/pysam.egg-info/requires.txt 2023-09-12T09:01:46,282 writing top-level names to /tmp/pip-modern-metadata-mrydwgtx/pysam.egg-info/top_level.txt 2023-09-12T09:01:46,284 writing manifest file '/tmp/pip-modern-metadata-mrydwgtx/pysam.egg-info/SOURCES.txt' 2023-09-12T09:01:46,355 reading manifest file '/tmp/pip-modern-metadata-mrydwgtx/pysam.egg-info/SOURCES.txt' 2023-09-12T09:01:46,357 reading manifest template 'MANIFEST.in' 2023-09-12T09:01:46,359 warning: no files found matching 'KNOWN_BUGS' 2023-09-12T09:01:46,360 warning: no files found matching 'THANKS' 2023-09-12T09:01:46,370 no previously-included directories found matching 'tests/' 2023-09-12T09:01:46,494 adding license file 'COPYING' 2023-09-12T09:01:46,495 adding license file 'AUTHORS' 2023-09-12T09:01:46,512 writing manifest file '/tmp/pip-modern-metadata-mrydwgtx/pysam.egg-info/SOURCES.txt' 2023-09-12T09:01:46,514 creating '/tmp/pip-modern-metadata-mrydwgtx/pysam-0.21.0.dist-info' 2023-09-12T09:01:46,670 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-12T09:01:54,374 Collecting setuptools>=45 2023-09-12T09:01:54,375 Obtaining dependency information for setuptools>=45 from https://files.pythonhosted.org/packages/95/79/6b47c6a872b40743a480687dc0c79ffb4202710789f3e4d54a84fff8b550/setuptools-68.2.1-py3-none-any.whl.metadata 2023-09-12T09:01:54,380 Using cached setuptools-68.2.1-py3-none-any.whl.metadata (6.3 kB) 2023-09-12T09:02:00,666 Collecting setuptools_scm 2023-09-12T09:02:06,451 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-7.1.0-py3-none-any.whl (43 kB) 2023-09-12T09:02:10,977 Collecting tox 2023-09-12T09:02:10,978 Obtaining dependency information for tox from https://files.pythonhosted.org/packages/f5/f9/963052e8b825645c54262dce7b7c88691505e3b9ee10a3e3667711eaaf21/tox-4.11.3-py3-none-any.whl.metadata 2023-09-12T09:02:10,986 Downloading tox-4.11.3-py3-none-any.whl.metadata (5.0 kB) 2023-09-12T09:02:13,913 Collecting wheel 2023-09-12T09:02:14,152 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /simple/wheel/wheel-0.41.2-py3-none-any.whl 2023-09-12T09:02:22,434 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-12T09:02:22,691 Collecting click (from cython-setuptools) 2023-09-12T09:02:22,701 Downloading https://www.piwheels.org/simple/click/click-8.1.7-py3-none-any.whl (97 kB) 2023-09-12T09:02:22,723 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 6.1 MB/s eta 0:00:00 2023-09-12T09:02:23,124 Collecting packaging>=20.0 (from setuptools_scm) 2023-09-12T09:02:23,145 Using cached https://www.piwheels.org/simple/packaging/packaging-23.1-py3-none-any.whl (48 kB) 2023-09-12T09:02:23,257 Collecting typing-extensions (from setuptools_scm) 2023-09-12T09:02:23,273 Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.7.1-py3-none-any.whl (33 kB) 2023-09-12T09:02:23,524 Collecting cachetools>=5.3.1 (from tox) 2023-09-12T09:02:24,354 Downloading https://www.piwheels.org/simple/cachetools/cachetools-5.3.1-py3-none-any.whl (9.3 kB) 2023-09-12T09:02:24,522 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /simple/chardet/ 2023-09-12T09:02:26,104 Collecting chardet>=5.2 (from tox) 2023-09-12T09:02:26,118 Downloading https://www.piwheels.org/simple/chardet/chardet-5.2.0-py3-none-any.whl (199 kB) 2023-09-12T09:02:26,151 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 199.4/199.4 kB 7.9 MB/s eta 0:00:00 2023-09-12T09:02:26,287 Collecting colorama>=0.4.6 (from tox) 2023-09-12T09:02:26,296 Downloading https://www.piwheels.org/simple/colorama/colorama-0.4.6-py2.py3-none-any.whl (25 kB) 2023-09-12T09:02:26,378 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))': /simple/filelock/ 2023-09-12T09:02:30,517 Collecting filelock>=3.12.3 (from tox) 2023-09-12T09:02:30,535 Using cached https://www.piwheels.org/simple/filelock/filelock-3.12.3-py3-none-any.whl (11 kB) 2023-09-12T09:02:30,684 Collecting platformdirs>=3.10 (from tox) 2023-09-12T09:02:30,725 Using cached https://www.piwheels.org/simple/platformdirs/platformdirs-3.10.0-py3-none-any.whl (17 kB) 2023-09-12T09:02:30,836 Collecting pluggy>=1.3 (from tox) 2023-09-12T09:02:30,917 Using cached https://www.piwheels.org/simple/pluggy/pluggy-1.3.0-py3-none-any.whl (18 kB) 2023-09-12T09:02:31,092 Collecting pyproject-api>=1.6.1 (from tox) 2023-09-12T09:02:31,174 Downloading https://www.piwheels.org/simple/pyproject-api/pyproject_api-1.6.1-py3-none-any.whl (12 kB) 2023-09-12T09:02:38,978 Collecting virtualenv>=20.24.3 (from tox) 2023-09-12T09:02:38,979 Obtaining dependency information for virtualenv>=20.24.3 from https://files.pythonhosted.org/packages/4e/8b/f0d3a468c0186c603217a6656ea4f49259630e8ed99558501d92f6ff7dc3/virtualenv-20.24.5-py3-none-any.whl.metadata 2023-09-12T09:02:38,984 Using cached virtualenv-20.24.5-py3-none-any.whl.metadata (4.5 kB) 2023-09-12T09:02:42,385 Collecting distlib<1,>=0.3.7 (from virtualenv>=20.24.3->tox) 2023-09-12T09:02:42,438 Using cached https://www.piwheels.org/simple/distlib/distlib-0.3.7-py2.py3-none-any.whl (468 kB) 2023-09-12T09:02:42,569 Using cached Cython-3.0.2-py2.py3-none-any.whl (1.2 MB) 2023-09-12T09:02:42,614 Using cached setuptools-68.2.1-py3-none-any.whl (807 kB) 2023-09-12T09:02:42,636 Downloading tox-4.11.3-py3-none-any.whl (153 kB) 2023-09-12T09:02:42,662 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 153.8/153.8 kB 7.7 MB/s eta 0:00:00 2023-09-12T09:02:42,720 Using cached virtualenv-20.24.5-py3-none-any.whl (3.7 MB) 2023-09-12T09:02:42,882 Building wheels for collected packages: pysam 2023-09-12T09:02:42,887 Building wheel for pysam (pyproject.toml): started 2023-09-12T09:02:42,888 Running command Building wheel for pysam (pyproject.toml) 2023-09-12T09:02:43,589 # pysam: cython is available - using cythonize if necessary 2023-09-12T09:02:43,590 # pysam: htslib mode is shared 2023-09-12T09:02:43,591 # pysam: HTSLIB_CONFIGURE_OPTIONS=None 2023-09-12T09:02:43,591 # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc 2023-09-12T09:02:43,592 # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-12T09:02:43,593 # pysam: (sysconfig) LDFLAGS= -g -fwrapv -O2 2023-09-12T09:02:43,884 checking for gcc... arm-linux-gnueabihf-gcc 2023-09-12T09:02:44,140 checking whether the C compiler works... yes 2023-09-12T09:02:44,141 checking for C compiler default output file name... a.out 2023-09-12T09:02:44,311 checking for suffix of executables... 2023-09-12T09:02:44,515 checking whether we are cross compiling... no 2023-09-12T09:02:44,602 checking for suffix of object files... o 2023-09-12T09:02:44,687 checking whether we are using the GNU C compiler... yes 2023-09-12T09:02:44,781 checking whether arm-linux-gnueabihf-gcc accepts -g... yes 2023-09-12T09:02:44,910 checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed 2023-09-12T09:02:44,913 checking for ranlib... ranlib 2023-09-12T09:02:44,921 checking for grep that handles long lines and -e... /usr/bin/grep 2023-09-12T09:02:44,994 checking for C compiler warning flags... -Wall 2023-09-12T09:02:45,005 configure: Default CFLAGS_ARM/X86: -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC 2023-09-12T09:02:45,061 checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no 2023-09-12T09:02:45,108 checking whether C compiler accepts -mavx2... no 2023-09-12T09:02:45,161 checking whether C compiler accepts -mavx512f... no 2023-09-12T09:02:45,617 checking whether C compiler supports ARM Neon... no 2023-09-12T09:02:45,621 checking for pkg-config... /usr/bin/pkg-config 2023-09-12T09:02:45,627 checking pkg-config is at least version 0.9.0... yes 2023-09-12T09:02:45,630 checking for special C compiler options needed for large files... no 2023-09-12T09:02:45,823 checking for _FILE_OFFSET_BITS value needed for large files... 64 2023-09-12T09:02:45,838 checking shared library type for unknown-Linux... plain .so 2023-09-12T09:02:45,958 checking whether the linker supports versioned symbols... no 2023-09-12T09:02:46,134 checking whether the compiler accepts -fvisibility=hidden... yes 2023-09-12T09:02:46,267 checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E 2023-09-12T09:02:46,379 checking for egrep... /usr/bin/grep -E 2023-09-12T09:02:46,845 checking for ANSI C header files... yes 2023-09-12T09:02:46,965 checking for sys/types.h... yes 2023-09-12T09:02:47,129 checking for sys/stat.h... yes 2023-09-12T09:02:47,269 checking for stdlib.h... yes 2023-09-12T09:02:47,409 checking for string.h... yes 2023-09-12T09:02:47,550 checking for memory.h... yes 2023-09-12T09:02:47,690 checking for strings.h... yes 2023-09-12T09:02:47,851 checking for inttypes.h... yes 2023-09-12T09:02:48,033 checking for stdint.h... yes 2023-09-12T09:02:48,191 checking for unistd.h... yes 2023-09-12T09:02:48,216 checking for stdlib.h... (cached) yes 2023-09-12T09:02:48,238 checking for unistd.h... (cached) yes 2023-09-12T09:02:48,630 checking for sys/param.h... yes 2023-09-12T09:02:48,875 checking for getpagesize... yes 2023-09-12T09:02:49,222 checking for working mmap... yes 2023-09-12T09:02:49,419 checking for gmtime_r... yes 2023-09-12T09:02:49,621 checking for fsync... yes 2023-09-12T09:02:49,827 checking for drand48... yes 2023-09-12T09:02:50,049 checking for srand48_deterministic... no 2023-09-12T09:02:50,219 checking whether fdatasync is declared... yes 2023-09-12T09:02:50,435 checking for fdatasync... yes 2023-09-12T09:02:50,837 checking for library containing log... -lm 2023-09-12T09:02:50,943 checking for zlib.h... yes 2023-09-12T09:02:51,125 checking for inflate in -lz... yes 2023-09-12T09:02:51,615 checking for library containing recv... none required 2023-09-12T09:02:51,702 checking for bzlib.h... yes 2023-09-12T09:02:51,885 checking for BZ2_bzBuffToBuffCompress in -lbz2... yes 2023-09-12T09:02:52,113 checking for lzma.h... yes 2023-09-12T09:02:52,526 checking for lzma_easy_buffer_encode in -llzma... yes 2023-09-12T09:02:52,532 checking whether htscodecs files are present... yes 2023-09-12T09:02:52,609 checking for libdeflate.h... yes 2023-09-12T09:02:52,816 checking for libdeflate_deflate_compress in -ldeflate... yes 2023-09-12T09:02:52,980 checking for curl/curl.h... yes 2023-09-12T09:02:53,344 checking for curl_easy_pause in -lcurl... yes 2023-09-12T09:02:53,561 checking for CCHmac... no 2023-09-12T09:02:54,188 checking for library containing HMAC... -lcrypto 2023-09-12T09:02:54,380 checking for library containing regcomp... none required 2023-09-12T09:02:54,505 checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes 2023-09-12T09:02:54,571 configure: creating ./config.status 2023-09-12T09:02:54,864 config.status: creating config.mk 2023-09-12T09:02:54,906 config.status: creating htslib.pc.tmp 2023-09-12T09:02:54,950 config.status: creating config.h 2023-09-12T09:02:54,969 config.status: config.h is unchanged 2023-09-12T09:02:54,974 config.status: linking htscodecs_bundled.mk to htscodecs.mk 2023-09-12T09:02:55,476 # pysam: htslib configure options: --enable-libcurl 2023-09-12T09:02:55,477 # pysam: htslib_config HTS_CFLAGS_AVX2= 2023-09-12T09:02:55,478 # pysam: htslib_config HTS_CFLAGS_AVX512= 2023-09-12T09:02:55,479 # pysam: htslib_config HTS_CFLAGS_SSE4= 2023-09-12T09:02:55,480 # pysam: htslib_config HTS_HAVE_NEON= 2023-09-12T09:02:55,481 # 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 2023-09-12T09:02:55,482 # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto 2023-09-12T09:02:55,483 # pysam: htslib_config PLATFORM=default 2023-09-12T09:02:55,484 # pysam: config_option: ENABLE_GCS=1 2023-09-12T09:02:55,485 # pysam: config_option: ENABLE_PLUGINS=0 2023-09-12T09:02:55,486 # pysam: config_option: ENABLE_S3=1 2023-09-12T09:02:55,487 # pysam: config_option: HAVE_COMMONCRYPTO=0 2023-09-12T09:02:55,488 # pysam: config_option: HAVE_HMAC=1 2023-09-12T09:02:55,489 # pysam: config_option: HAVE_LIBBZ2=1 2023-09-12T09:02:55,490 # pysam: config_option: HAVE_LIBCURL=1 2023-09-12T09:02:55,491 # pysam: config_option: HAVE_LIBDEFLATE=1 2023-09-12T09:02:55,492 # pysam: config_option: HAVE_LIBLZMA=1 2023-09-12T09:02:55,493 # pysam: config_option: HAVE_MMAP=1 2023-09-12T09:02:55,494 running bdist_wheel 2023-09-12T09:02:55,495 running build 2023-09-12T09:02:55,496 running build_py 2023-09-12T09:02:55,498 creating build 2023-09-12T09:02:55,499 creating build/lib.linux-armv7l-cpython-311 2023-09-12T09:02:55,500 creating build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,501 copying pysam/config.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,503 copying pysam/samtools.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,506 copying pysam/__init__.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,508 copying pysam/version.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,510 copying pysam/utils.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,512 copying pysam/Pileup.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,514 copying pysam/bcftools.py -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,517 creating build/lib.linux-armv7l-cpython-311/pysam/include 2023-09-12T09:02:55,518 copying pysam/include/__init__.py -> build/lib.linux-armv7l-cpython-311/pysam/include 2023-09-12T09:02:55,522 running egg_info 2023-09-12T09:02:55,528 writing pysam.egg-info/PKG-INFO 2023-09-12T09:02:55,531 writing dependency_links to pysam.egg-info/dependency_links.txt 2023-09-12T09:02:55,532 writing requirements to pysam.egg-info/requires.txt 2023-09-12T09:02:55,533 writing top-level names to pysam.egg-info/top_level.txt 2023-09-12T09:02:55,596 reading manifest file 'pysam.egg-info/SOURCES.txt' 2023-09-12T09:02:55,635 reading manifest template 'MANIFEST.in' 2023-09-12T09:02:55,636 warning: no files found matching 'KNOWN_BUGS' 2023-09-12T09:02:55,638 warning: no files found matching 'THANKS' 2023-09-12T09:02:55,644 no previously-included directories found matching 'tests/' 2023-09-12T09:02:55,756 adding license file 'COPYING' 2023-09-12T09:02:55,757 adding license file 'AUTHORS' 2023-09-12T09:02:55,779 writing manifest file 'pysam.egg-info/SOURCES.txt' 2023-09-12T09:02:55,785 /tmp/pip-build-env-ye63whao/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. 2023-09-12T09:02:55,786 !! 2023-09-12T09:02:55,788 ******************************************************************************** 2023-09-12T09:02:55,789 ############################ 2023-09-12T09:02:55,790 # Package would be ignored # 2023-09-12T09:02:55,790 ############################ 2023-09-12T09:02:55,791 Python recognizes 'pysam.include.htslib.cram' as an importable package[^1], 2023-09-12T09:02:55,792 but it is absent from setuptools' `packages` configuration. 2023-09-12T09:02:55,794 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-12T09:02:55,795 package, please make sure that 'pysam.include.htslib.cram' is explicitly added 2023-09-12T09:02:55,798 to the `packages` configuration field. 2023-09-12T09:02:55,799 Alternatively, you can also rely on setuptools' discovery methods 2023-09-12T09:02:55,800 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-12T09:02:55,801 instead of `find_packages(...)`/`find:`). 2023-09-12T09:02:55,805 You can read more about "package discovery" on setuptools documentation page: 2023-09-12T09:02:55,806 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-12T09:02:55,807 If you don't want 'pysam.include.htslib.cram' to be distributed and are 2023-09-12T09:02:55,808 already explicitly excluding 'pysam.include.htslib.cram' via 2023-09-12T09:02:55,809 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-12T09:02:55,809 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-12T09:02:55,810 combination with a more fine grained `package-data` configuration. 2023-09-12T09:02:55,811 You can read more about "package data files" on setuptools documentation page: 2023-09-12T09:02:55,812 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-12T09:02:55,814 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-12T09:02:55,814 even if it does not contain any `.py` files. 2023-09-12T09:02:55,815 On the other hand, currently there is no concept of package data 2023-09-12T09:02:55,816 directory, all directories are treated like packages. 2023-09-12T09:02:55,816 ******************************************************************************** 2023-09-12T09:02:55,818 !! 2023-09-12T09:02:55,818 check.warn(importable) 2023-09-12T09:02:55,819 /tmp/pip-build-env-ye63whao/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. 2023-09-12T09:02:55,820 !! 2023-09-12T09:02:55,821 ******************************************************************************** 2023-09-12T09:02:55,822 ############################ 2023-09-12T09:02:55,823 # Package would be ignored # 2023-09-12T09:02:55,824 ############################ 2023-09-12T09:02:55,824 Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package[^1], 2023-09-12T09:02:55,825 but it is absent from setuptools' `packages` configuration. 2023-09-12T09:02:55,827 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-12T09:02:55,828 package, please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is explicitly added 2023-09-12T09:02:55,829 to the `packages` configuration field. 2023-09-12T09:02:55,831 Alternatively, you can also rely on setuptools' discovery methods 2023-09-12T09:02:55,832 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-12T09:02:55,833 instead of `find_packages(...)`/`find:`). 2023-09-12T09:02:55,834 You can read more about "package discovery" on setuptools documentation page: 2023-09-12T09:02:55,836 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-12T09:02:55,837 If you don't want 'pysam.include.htslib.htscodecs.htscodecs' to be distributed and are 2023-09-12T09:02:55,838 already explicitly excluding 'pysam.include.htslib.htscodecs.htscodecs' via 2023-09-12T09:02:55,839 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-12T09:02:55,840 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-12T09:02:55,840 combination with a more fine grained `package-data` configuration. 2023-09-12T09:02:55,842 You can read more about "package data files" on setuptools documentation page: 2023-09-12T09:02:55,843 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-12T09:02:55,846 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-12T09:02:55,846 even if it does not contain any `.py` files. 2023-09-12T09:02:55,847 On the other hand, currently there is no concept of package data 2023-09-12T09:02:55,848 directory, all directories are treated like packages. 2023-09-12T09:02:55,849 ******************************************************************************** 2023-09-12T09:02:55,850 !! 2023-09-12T09:02:55,851 check.warn(importable) 2023-09-12T09:02:55,851 /tmp/pip-build-env-ye63whao/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. 2023-09-12T09:02:55,852 !! 2023-09-12T09:02:55,854 ******************************************************************************** 2023-09-12T09:02:55,855 ############################ 2023-09-12T09:02:55,857 # Package would be ignored # 2023-09-12T09:02:55,861 ############################ 2023-09-12T09:02:55,867 Python recognizes 'pysam.include.htslib.m4' as an importable package[^1], 2023-09-12T09:02:55,877 but it is absent from setuptools' `packages` configuration. 2023-09-12T09:02:55,902 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-12T09:02:55,904 package, please make sure that 'pysam.include.htslib.m4' is explicitly added 2023-09-12T09:02:55,904 to the `packages` configuration field. 2023-09-12T09:02:55,906 Alternatively, you can also rely on setuptools' discovery methods 2023-09-12T09:02:55,906 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-12T09:02:55,907 instead of `find_packages(...)`/`find:`). 2023-09-12T09:02:55,908 You can read more about "package discovery" on setuptools documentation page: 2023-09-12T09:02:55,909 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-12T09:02:55,911 If you don't want 'pysam.include.htslib.m4' to be distributed and are 2023-09-12T09:02:55,911 already explicitly excluding 'pysam.include.htslib.m4' via 2023-09-12T09:02:55,912 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-12T09:02:55,913 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-12T09:02:55,913 combination with a more fine grained `package-data` configuration. 2023-09-12T09:02:55,915 You can read more about "package data files" on setuptools documentation page: 2023-09-12T09:02:55,916 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-12T09:02:55,918 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-12T09:02:55,919 even if it does not contain any `.py` files. 2023-09-12T09:02:55,920 On the other hand, currently there is no concept of package data 2023-09-12T09:02:55,920 directory, all directories are treated like packages. 2023-09-12T09:02:55,921 ******************************************************************************** 2023-09-12T09:02:55,922 !! 2023-09-12T09:02:55,922 check.warn(importable) 2023-09-12T09:02:55,923 /tmp/pip-build-env-ye63whao/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. 2023-09-12T09:02:55,923 !! 2023-09-12T09:02:55,924 ******************************************************************************** 2023-09-12T09:02:55,925 ############################ 2023-09-12T09:02:55,926 # Package would be ignored # 2023-09-12T09:02:55,926 ############################ 2023-09-12T09:02:55,927 Python recognizes 'pysam.include.htslib.os' as an importable package[^1], 2023-09-12T09:02:55,927 but it is absent from setuptools' `packages` configuration. 2023-09-12T09:02:55,928 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-12T09:02:55,929 package, please make sure that 'pysam.include.htslib.os' is explicitly added 2023-09-12T09:02:55,929 to the `packages` configuration field. 2023-09-12T09:02:55,931 Alternatively, you can also rely on setuptools' discovery methods 2023-09-12T09:02:55,931 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-12T09:02:55,932 instead of `find_packages(...)`/`find:`). 2023-09-12T09:02:55,933 You can read more about "package discovery" on setuptools documentation page: 2023-09-12T09:02:55,935 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-12T09:02:55,937 If you don't want 'pysam.include.htslib.os' to be distributed and are 2023-09-12T09:02:55,937 already explicitly excluding 'pysam.include.htslib.os' via 2023-09-12T09:02:55,938 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-12T09:02:55,939 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-12T09:02:55,939 combination with a more fine grained `package-data` configuration. 2023-09-12T09:02:55,941 You can read more about "package data files" on setuptools documentation page: 2023-09-12T09:02:55,942 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-12T09:02:55,944 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-12T09:02:55,945 even if it does not contain any `.py` files. 2023-09-12T09:02:55,945 On the other hand, currently there is no concept of package data 2023-09-12T09:02:55,950 directory, all directories are treated like packages. 2023-09-12T09:02:55,963 ******************************************************************************** 2023-09-12T09:02:55,967 !! 2023-09-12T09:02:55,968 check.warn(importable) 2023-09-12T09:02:55,968 /tmp/pip-build-env-ye63whao/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. 2023-09-12T09:02:55,969 !! 2023-09-12T09:02:55,970 ******************************************************************************** 2023-09-12T09:02:55,971 ############################ 2023-09-12T09:02:55,971 # Package would be ignored # 2023-09-12T09:02:55,972 ############################ 2023-09-12T09:02:55,974 Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], 2023-09-12T09:02:55,974 but it is absent from setuptools' `packages` configuration. 2023-09-12T09:02:55,975 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-12T09:02:55,975 package, please make sure that 'pysam.include.samtools.lz4' is explicitly added 2023-09-12T09:02:55,976 to the `packages` configuration field. 2023-09-12T09:02:55,978 Alternatively, you can also rely on setuptools' discovery methods 2023-09-12T09:02:55,978 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-12T09:02:55,979 instead of `find_packages(...)`/`find:`). 2023-09-12T09:02:55,980 You can read more about "package discovery" on setuptools documentation page: 2023-09-12T09:02:55,981 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-12T09:02:55,982 If you don't want 'pysam.include.samtools.lz4' to be distributed and are 2023-09-12T09:02:55,982 already explicitly excluding 'pysam.include.samtools.lz4' via 2023-09-12T09:02:55,983 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-12T09:02:55,984 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-12T09:02:55,984 combination with a more fine grained `package-data` configuration. 2023-09-12T09:02:55,985 You can read more about "package data files" on setuptools documentation page: 2023-09-12T09:02:55,986 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-12T09:02:55,988 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-12T09:02:55,988 even if it does not contain any `.py` files. 2023-09-12T09:02:55,989 On the other hand, currently there is no concept of package data 2023-09-12T09:02:55,990 directory, all directories are treated like packages. 2023-09-12T09:02:55,990 ******************************************************************************** 2023-09-12T09:02:55,992 !! 2023-09-12T09:02:55,992 check.warn(importable) 2023-09-12T09:02:55,993 copying pysam/cbcftools_util.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,994 copying pysam/csamtools_util.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,994 copying pysam/htslib_util.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,995 copying pysam/htslib_util.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,996 copying pysam/libcalignedsegment.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,996 copying pysam/libcalignedsegment.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,997 copying pysam/libcalignedsegment.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,997 copying pysam/libcalignedsegment.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,998 copying pysam/libcalignmentfile.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,998 copying pysam/libcalignmentfile.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:55,999 copying pysam/libcalignmentfile.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,000 copying pysam/libcalignmentfile.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,000 copying pysam/libcbcf.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,054 copying pysam/libcbcf.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,056 copying pysam/libcbcf.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,059 copying pysam/libcbcf.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,064 copying pysam/libcbcftools.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,068 copying pysam/libcbcftools.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,070 copying pysam/libcbcftools.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,072 copying pysam/libcbcftools.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,074 copying pysam/libcbgzf.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,082 copying pysam/libcbgzf.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,084 copying pysam/libcbgzf.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,087 copying pysam/libcfaidx.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,101 copying pysam/libcfaidx.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,103 copying pysam/libcfaidx.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,105 copying pysam/libcfaidx.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,108 copying pysam/libchtslib.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,123 copying pysam/libchtslib.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,127 copying pysam/libchtslib.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,130 copying pysam/libchtslib.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,133 copying pysam/libcsamfile.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,140 copying pysam/libcsamfile.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,142 copying pysam/libcsamfile.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,144 copying pysam/libcsamfile.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,146 copying pysam/libcsamtools.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,150 copying pysam/libcsamtools.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,152 copying pysam/libcsamtools.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,154 copying pysam/libcsamtools.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,156 copying pysam/libctabix.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,184 copying pysam/libctabix.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,186 copying pysam/libctabix.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,188 copying pysam/libctabix.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,192 copying pysam/libctabixproxies.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,232 copying pysam/libctabixproxies.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,235 copying pysam/libctabixproxies.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,238 copying pysam/libctabixproxies.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,241 copying pysam/libcutils.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,253 copying pysam/libcutils.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,255 copying pysam/libcutils.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,257 copying pysam/libcutils.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,261 copying pysam/libcvcf.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,291 copying pysam/libcvcf.pxd -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,293 copying pysam/libcvcf.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,296 copying pysam/libcvcf.pyx -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,300 copying pysam/py.typed -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,303 copying pysam/pysam_stream.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,305 copying pysam/pysam_util.c -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,308 copying pysam/pysam_util.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,310 copying pysam/version.h -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,313 copying pysam/version.pyi -> build/lib.linux-armv7l-cpython-311/pysam 2023-09-12T09:02:56,315 creating build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,316 copying samtools/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,320 copying samtools/README -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,323 copying samtools/amplicon_stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,328 copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,332 copying samtools/bam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,335 copying samtools/bam.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,338 copying samtools/bam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,341 copying samtools/bam2depth.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,344 copying samtools/bam2depth.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,347 copying samtools/bam_addrprg.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,349 copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,352 copying samtools/bam_ampliconclip.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,356 copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,360 copying samtools/bam_ampliconclip.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,362 copying samtools/bam_aux.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,364 copying samtools/bam_aux.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,367 copying samtools/bam_cat.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,370 copying samtools/bam_cat.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,373 copying samtools/bam_color.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,376 copying samtools/bam_color.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,378 copying samtools/bam_consensus.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,383 copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,387 copying samtools/bam_fastq.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,392 copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,399 copying samtools/bam_flags.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,406 copying samtools/bam_flags.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,414 copying samtools/bam_import.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,419 copying samtools/bam_import.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,421 copying samtools/bam_index.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,424 copying samtools/bam_index.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,427 copying samtools/bam_lpileup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,430 copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,432 copying samtools/bam_lpileup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,434 copying samtools/bam_markdup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,438 copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,442 copying samtools/bam_mate.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,445 copying samtools/bam_mate.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,448 copying samtools/bam_md.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,450 copying samtools/bam_md.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,453 copying samtools/bam_plbuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,455 copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,458 copying samtools/bam_plbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,460 copying samtools/bam_plcmd.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,464 copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,468 copying samtools/bam_quickcheck.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,471 copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,473 copying samtools/bam_reheader.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,476 copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,479 copying samtools/bam_rmdup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,481 copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,484 copying samtools/bam_rmdupse.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,487 copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,489 copying samtools/bam_samples.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,492 copying samtools/bam_samples.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,494 copying samtools/bam_sort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,499 copying samtools/bam_sort.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,504 copying samtools/bam_split.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,507 copying samtools/bam_split.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,510 copying samtools/bam_stat.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,512 copying samtools/bam_stat.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,516 copying samtools/bamshuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,523 copying samtools/bamshuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,526 copying samtools/bamtk.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,530 copying samtools/bamtk.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,533 copying samtools/bedcov.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,536 copying samtools/bedcov.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,539 copying samtools/bedidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,542 copying samtools/bedidx.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,546 copying samtools/bedidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,551 copying samtools/consensus_pileup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,557 copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,566 copying samtools/consensus_pileup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,577 copying samtools/coverage.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,589 copying samtools/coverage.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,602 copying samtools/cram_size.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,614 copying samtools/cram_size.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,626 copying samtools/cut_target.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,637 copying samtools/cut_target.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,649 copying samtools/dict.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,662 copying samtools/dict.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,677 copying samtools/faidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,681 copying samtools/faidx.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,686 copying samtools/padding.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,691 copying samtools/padding.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,696 copying samtools/phase.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,701 copying samtools/phase.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,707 copying samtools/reference.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,712 copying samtools/reference.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,716 copying samtools/reset.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,721 copying samtools/reset.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,726 copying samtools/sam_opts.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,731 copying samtools/sam_opts.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,735 copying samtools/sam_opts.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,740 copying samtools/sam_utils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,743 copying samtools/sam_utils.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,746 copying samtools/sam_utils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,750 copying samtools/sam_view.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,754 copying samtools/sam_view.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,759 copying samtools/sample.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,762 copying samtools/sample.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,764 copying samtools/sample.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,767 copying samtools/samtools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,769 copying samtools/samtools.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,772 copying samtools/samtools.pysam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,775 copying samtools/splaysort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,777 copying samtools/stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,781 copying samtools/stats.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,786 copying samtools/stats_isize.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,788 copying samtools/stats_isize.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,791 copying samtools/stats_isize.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,793 copying samtools/tmp_file.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,796 copying samtools/tmp_file.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,799 copying samtools/tmp_file.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,801 copying samtools/version.sh -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,803 creating build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4 2023-09-12T09:02:56,804 copying samtools/lz4/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4 2023-09-12T09:02:56,806 copying samtools/lz4/lz4.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4 2023-09-12T09:02:56,810 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4 2023-09-12T09:02:56,813 copying samtools/lz4/lz4.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4 2023-09-12T09:02:56,816 copying samtools/config.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools 2023-09-12T09:02:56,818 creating build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,819 copying bcftools/HMM.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,822 copying bcftools/HMM.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,825 copying bcftools/HMM.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,828 copying bcftools/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,831 copying bcftools/README -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,834 copying bcftools/abuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,837 copying bcftools/abuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,840 copying bcftools/abuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,842 copying bcftools/bam2bcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,845 copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,848 copying bcftools/bam2bcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,851 copying bcftools/bam2bcf_iaux.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,854 copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,857 copying bcftools/bam2bcf_indel.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,860 copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,863 copying bcftools/bam_sample.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,865 copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,868 copying bcftools/bam_sample.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,870 copying bcftools/bcftools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,872 copying bcftools/bcftools.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,875 copying bcftools/bcftools.pysam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,877 copying bcftools/bin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,879 copying bcftools/bin.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,881 copying bcftools/bin.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,884 copying bcftools/call.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,886 copying bcftools/ccall.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,889 copying bcftools/ccall.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,892 copying bcftools/cigar_state.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,894 copying bcftools/cols.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,897 copying bcftools/cols.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,899 copying bcftools/cols.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,901 copying bcftools/consensus.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,904 copying bcftools/consensus.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,908 copying bcftools/convert.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,911 copying bcftools/convert.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,915 copying bcftools/convert.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,917 copying bcftools/csq.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,923 copying bcftools/csq.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,928 copying bcftools/dbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,930 copying bcftools/dist.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,933 copying bcftools/dist.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,935 copying bcftools/dist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,938 copying bcftools/em.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,941 copying bcftools/em.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,945 copying bcftools/extsort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,949 copying bcftools/extsort.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,953 copying bcftools/extsort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,956 copying bcftools/filter.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,962 copying bcftools/filter.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,969 copying bcftools/filter.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,974 copying bcftools/gvcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,981 copying bcftools/gvcf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,988 copying bcftools/gvcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,991 copying bcftools/hclust.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,994 copying bcftools/hclust.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,996 copying bcftools/hclust.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:56,999 copying bcftools/hex.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,001 copying bcftools/khash_str2str.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,003 copying bcftools/kheap.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,006 copying bcftools/kmin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,008 copying bcftools/kmin.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,011 copying bcftools/kmin.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,013 copying bcftools/main.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,015 copying bcftools/main.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,018 copying bcftools/mcall.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,021 copying bcftools/mcall.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,025 copying bcftools/mpileup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,029 copying bcftools/mpileup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,033 copying bcftools/mw.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,036 copying bcftools/ploidy.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,039 copying bcftools/ploidy.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,042 copying bcftools/ploidy.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,045 copying bcftools/prob1.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,048 copying bcftools/prob1.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,050 copying bcftools/prob1.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,053 copying bcftools/rbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,056 copying bcftools/read_consensus.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,059 copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,061 copying bcftools/read_consensus.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,064 copying bcftools/regidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,067 copying bcftools/regidx.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,070 copying bcftools/regidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,072 copying bcftools/reheader.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,075 copying bcftools/reheader.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,078 copying bcftools/smpl_ilist.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,081 copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,083 copying bcftools/smpl_ilist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,086 copying bcftools/str_finder.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,088 copying bcftools/str_finder.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,091 copying bcftools/str_finder.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,093 copying bcftools/tabix.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,096 copying bcftools/tabix.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,098 copying bcftools/tsv2vcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,101 copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,103 copying bcftools/tsv2vcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,105 copying bcftools/utlist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,109 copying bcftools/variantkey.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,112 copying bcftools/vcfannotate.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,117 copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,122 copying bcftools/vcfbuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,124 copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,127 copying bcftools/vcfbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,130 copying bcftools/vcfcall.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,134 copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,136 copying bcftools/vcfcnv.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,140 copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,144 copying bcftools/vcfconcat.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,147 copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,150 copying bcftools/vcfconvert.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,154 copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,158 copying bcftools/vcffilter.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,162 copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,165 copying bcftools/vcfgtcheck.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,170 copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,174 copying bcftools/vcfhead.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,177 copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,179 copying bcftools/vcfindex.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,182 copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,185 copying bcftools/vcfisec.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,188 copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,192 copying bcftools/vcfmerge.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,198 copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,204 copying bcftools/vcfnorm.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,209 copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,214 copying bcftools/vcfplugin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,217 copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,220 copying bcftools/vcfquery.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,223 copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,225 copying bcftools/vcfroh.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,229 copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,232 copying bcftools/vcfsom.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,235 copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,239 copying bcftools/vcfsort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,242 copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,245 copying bcftools/vcfstats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,250 copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,255 copying bcftools/vcfview.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,258 copying bcftools/vcfview.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,261 copying bcftools/vcmp.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,264 copying bcftools/vcmp.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,266 copying bcftools/vcmp.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,268 copying bcftools/version.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,271 copying bcftools/version.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,273 copying bcftools/version.sh -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,276 copying bcftools/config.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools 2023-09-12T09:02:57,278 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,279 copying htslib/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,282 copying htslib/Makefile -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,285 copying htslib/README -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,287 copying htslib/bcf_sr_sort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,290 copying htslib/bcf_sr_sort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,292 copying htslib/bgzf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,297 copying htslib/bgzip.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,300 copying htslib/builddir_vars.mk.in -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,302 copying htslib/config.h.in -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,304 copying htslib/config.mk.in -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,306 copying htslib/configure -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,314 copying htslib/configure.ac -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,317 copying htslib/errmod.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,319 copying htslib/faidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,322 copying htslib/header.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,326 copying htslib/header.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,329 copying htslib/hfile.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,332 copying htslib/hfile_gcs.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,335 copying htslib/hfile_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,338 copying htslib/hfile_libcurl.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,341 copying htslib/hfile_s3.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,344 copying htslib/hfile_s3_write.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,347 copying htslib/hts.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,352 copying htslib/hts_expr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,355 copying htslib/hts_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,358 copying htslib/hts_os.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,360 copying htslib/hts_time_funcs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,363 copying htslib/htscodecs_bundled.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,365 copying htslib/htscodecs_external.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,368 copying htslib/htsfile.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,372 copying htslib/htslib.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,375 copying htslib/htslib.pc.in -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,378 copying htslib/htslib_vars.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,380 copying htslib/kfunc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,382 copying htslib/kstring.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,385 copying htslib/md5.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,387 copying htslib/multipart.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,390 copying htslib/plugin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,392 copying htslib/probaln.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,395 copying htslib/realn.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,398 copying htslib/regidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,401 copying htslib/region.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,403 copying htslib/sam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,409 copying htslib/sam_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,412 copying htslib/synced_bcf_reader.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,415 copying htslib/tabix.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,418 copying htslib/tbx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,420 copying htslib/textutils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,423 copying htslib/textutils_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,425 copying htslib/thread_pool.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,428 copying htslib/thread_pool_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,430 copying htslib/vcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,436 copying htslib/vcf_sweep.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,438 copying htslib/vcfutils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,441 copying htslib/version.sh -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,443 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,444 copying htslib/cram/cram.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,447 copying htslib/cram/cram_codecs.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,452 copying htslib/cram/cram_codecs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,455 copying htslib/cram/cram_decode.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,460 copying htslib/cram/cram_decode.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,463 copying htslib/cram/cram_encode.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,467 copying htslib/cram/cram_encode.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,470 copying htslib/cram/cram_external.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,472 copying htslib/cram/cram_index.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,475 copying htslib/cram/cram_index.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,477 copying htslib/cram/cram_io.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,483 copying htslib/cram/cram_io.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,486 copying htslib/cram/cram_samtools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,489 copying htslib/cram/cram_stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,492 copying htslib/cram/cram_stats.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,495 copying htslib/cram/cram_structs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,499 copying htslib/cram/mFILE.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,502 copying htslib/cram/mFILE.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,505 copying htslib/cram/misc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,508 copying htslib/cram/open_trace_file.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,511 copying htslib/cram/open_trace_file.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,514 copying htslib/cram/os.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,517 copying htslib/cram/pooled_alloc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,520 copying htslib/cram/pooled_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,523 copying htslib/cram/string_alloc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,526 copying htslib/cram/string_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram 2023-09-12T09:02:57,529 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs 2023-09-12T09:02:57,530 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,533 copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,535 copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,538 copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,540 copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,543 copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,548 copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,551 copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,554 copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,556 copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,560 copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,563 copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,567 copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,570 copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,573 copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,577 copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,580 copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,583 copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,586 copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,588 copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,591 copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,596 copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,598 copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,602 copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,606 copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,608 copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,612 copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,615 copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,617 copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,619 copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,623 copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,626 copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,628 copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,632 copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,635 copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,638 copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:02:57,640 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4 2023-09-12T09:02:57,642 copying htslib/m4/ax_check_compile_flag.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4 2023-09-12T09:02:57,646 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4 2023-09-12T09:02:57,651 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4 2023-09-12T09:02:57,655 copying htslib/m4/pkg.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4 2023-09-12T09:02:57,659 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os 2023-09-12T09:02:57,660 copying htslib/os/lzma_stub.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os 2023-09-12T09:02:57,663 copying htslib/os/rand.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os 2023-09-12T09:02:57,665 copying htslib/config.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib 2023-09-12T09:02:57,668 creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,669 copying htslib/htslib/bgzf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,672 copying htslib/htslib/cram.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,676 copying htslib/htslib/faidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,678 copying htslib/htslib/hfile.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,681 copying htslib/htslib/hts.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,685 copying htslib/htslib/hts_defs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,687 copying htslib/htslib/hts_endian.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,690 copying htslib/htslib/hts_expr.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,692 copying htslib/htslib/hts_log.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,694 copying htslib/htslib/hts_os.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,697 copying htslib/htslib/kbitset.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,699 copying htslib/htslib/kfunc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,701 copying htslib/htslib/khash.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,704 copying htslib/htslib/khash_str2int.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,706 copying htslib/htslib/klist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,708 copying htslib/htslib/knetfile.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,710 copying htslib/htslib/kroundup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,713 copying htslib/htslib/kseq.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,715 copying htslib/htslib/ksort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,718 copying htslib/htslib/kstring.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,720 copying htslib/htslib/regidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,722 copying htslib/htslib/sam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,727 copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,730 copying htslib/htslib/tbx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,733 copying htslib/htslib/thread_pool.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,735 copying htslib/htslib/vcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,739 copying htslib/htslib/vcf_sweep.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,742 copying htslib/htslib/vcfutils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib 2023-09-12T09:02:57,749 running build_ext 2023-09-12T09:02:57,814 skipping 'pysam/libchtslib.c' Cython extension (up-to-date) 2023-09-12T09:02:57,815 skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) 2023-09-12T09:02:57,816 skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) 2023-09-12T09:02:57,817 skipping 'pysam/libcutils.c' Cython extension (up-to-date) 2023-09-12T09:02:57,817 skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) 2023-09-12T09:02:57,818 skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) 2023-09-12T09:02:57,819 skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) 2023-09-12T09:02:57,820 skipping 'pysam/libctabix.c' Cython extension (up-to-date) 2023-09-12T09:02:57,821 skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) 2023-09-12T09:02:57,822 skipping 'pysam/libcbcf.c' Cython extension (up-to-date) 2023-09-12T09:02:57,822 skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) 2023-09-12T09:02:57,823 skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) 2023-09-12T09:02:57,824 skipping 'pysam/libcvcf.c' Cython extension (up-to-date) 2023-09-12T09:02:57,825 creating htslib/config_vars.h for 'pysam.libchtslib' extension 2023-09-12T09:02:57,826 building 'libhts.a' 2023-09-12T09:02:57,879 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 2023-09-12T09:02:58,342 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 2023-09-12T09:02:59,196 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 2023-09-12T09:03:01,755 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 bgzf.o bgzf.c 2023-09-12T09:03:04,994 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 2023-09-12T09:03:05,667 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 faidx.o faidx.c 2023-09-12T09:03:07,620 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 2023-09-12T09:03:12,152 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 2023-09-12T09:03:13,986 echo '#define HTS_VERSION_TEXT "1.17"' > version.h 2023-09-12T09:03:13,993 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 2023-09-12T09:03:22,533 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 hts_expr.o hts_expr.c 2023-09-12T09:03:24,494 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 2023-09-12T09:03:24,829 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 2023-09-12T09:03:25,486 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 2023-09-12T09:03:26,245 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 2023-09-12T09:03:26,987 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 2023-09-12T09:03:27,913 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 2023-09-12T09:03:29,506 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 2023-09-12T09:03:30,306 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 2023-09-12T09:03:44,766 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 2023-09-12T09:03:48,066 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 2023-09-12T09:03:48,502 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 2023-09-12T09:03:49,344 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 2023-09-12T09:03:50,392 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 2023-09-12T09:03:51,580 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 2023-09-12T09:04:06,181 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 2023-09-12T09:04:09,432 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 2023-09-12T09:04:15,003 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 2023-09-12T09:04:21,272 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 2023-09-12T09:04:29,388 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 2023-09-12T09:04:30,538 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 2023-09-12T09:04:31,867 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 2023-09-12T09:04:39,583 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 2023-09-12T09:04:40,323 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 2023-09-12T09:04:40,991 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 2023-09-12T09:04:41,522 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 2023-09-12T09:04:41,707 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 2023-09-12T09:04:41,908 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 2023-09-12T09:04:45,694 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 2023-09-12T09:04:49,763 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 2023-09-12T09:04:49,830 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 2023-09-12T09:04:50,628 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 2023-09-12T09:04:55,521 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 2023-09-12T09:04:58,726 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 2023-09-12T09:05:00,826 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 2023-09-12T09:05:01,301 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 2023-09-12T09:05:04,605 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 2023-09-12T09:05:05,941 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 2023-09-12T09:05:06,401 hfile_libcurl.c: In function ‘libcurl_open’: 2023-09-12T09:05:06,402 hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 2023-09-12T09:05:06,403 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, 2023-09-12T09:05:06,404 | ^~ 2023-09-12T09:05:06,405 In file included from hfile_libcurl.c:47: 2023-09-12T09:05:06,405 /usr/include/arm-linux-gnueabihf/curl/curl.h:2858:3: note: declared here 2023-09-12T09:05:06,406 2858 | CURLINFO_CONTENT_LENGTH_DOWNLOAD 2023-09-12T09:05:06,407 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:05:08,468 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 2023-09-12T09:05:08,952 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 2023-09-12T09:05:11,955 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 2023-09-12T09:05:13,398 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 2023-09-12T09:05:13,742 ranlib libhts.a 2023-09-12T09:05:14,046 building 'pysam.libchtslib' extension 2023-09-12T09:05:14,047 creating build/temp.linux-armv7l-cpython-311 2023-09-12T09:05:14,048 creating build/temp.linux-armv7l-cpython-311/pysam 2023-09-12T09:05:14,050 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:14,362 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:29,562 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:30,175 creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension 2023-09-12T09:05:30,178 building 'pysam.libcsamtools' extension 2023-09-12T09:05:30,179 creating build/temp.linux-armv7l-cpython-311/samtools 2023-09-12T09:05:30,182 creating build/temp.linux-armv7l-cpython-311/samtools/lz4 2023-09-12T09:05:30,184 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:31,233 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:35,386 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:35,969 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-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:38,508 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:39,234 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:41,208 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:41,429 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:42,217 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:42,507 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:45,633 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:47,003 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:47,244 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:48,225 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:48,692 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:49,308 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:54,278 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:55,865 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:56,948 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:57,157 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:59,611 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:05:59,962 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:00,782 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:02,252 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:03,465 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:04,303 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:13,600 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:14,909 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:15,711 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:18,018 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:18,759 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:19,861 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:21,646 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:22,287 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:23,428 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:23,621 samtools/cram_size.c.pysam.c: In function ‘cram_size’: 2023-09-12T09:06:23,622 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=] 2023-09-12T09:06:23,623 563 | fprintf(outfp, "Total file size %18"PRId64"\n", end); 2023-09-12T09:06:23,624 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ 2023-09-12T09:06:23,625 | | 2023-09-12T09:06:23,626 | off_t {aka long int} 2023-09-12T09:06:23,627 In file included from /tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib/htslib/hts.h:33, 2023-09-12T09:06:23,628 from /tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib/htslib/sam.h:33, 2023-09-12T09:06:23,629 from samtools/cram_size.c.pysam.c:39: 2023-09-12T09:06:23,630 /usr/include/inttypes.h:57:41: note: format string is defined here 2023-09-12T09:06:23,631 57 | # define PRId64 __PRI64_PREFIX "d" 2023-09-12T09:06:23,633 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=] 2023-09-12T09:06:23,634 564 | fprintf(outfp, "Format overhead size %18"PRId64"\n", end - tot_size); 2023-09-12T09:06:23,635 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ 2023-09-12T09:06:23,636 | | 2023-09-12T09:06:23,637 | off_t {aka long int} 2023-09-12T09:06:23,638 /usr/include/inttypes.h:57:41: note: format string is defined here 2023-09-12T09:06:23,639 57 | # define PRId64 __PRI64_PREFIX "d" 2023-09-12T09:06:24,503 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:25,161 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:26,204 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:26,824 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:33,041 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:34,378 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:37,552 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:38,552 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:39,607 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:39,924 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:40,499 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-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:43,607 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:44,406 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:44,612 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:49,778 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:50,428 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:50,897 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:51,278 building 'pysam.libcbcftools' extension 2023-09-12T09:06:51,279 creating build/temp.linux-armv7l-cpython-311/bcftools 2023-09-12T09:06:51,282 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:52,337 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:55,115 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:57,640 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:06:59,306 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:01,794 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:03,718 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:03,918 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:04,233 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:04,984 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:05,212 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:07,676 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:13,864 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:23,009 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:23,271 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:23,834 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:24,374 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:38,352 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:38,952 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:39,582 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:40,025 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:40,353 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:44,231 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:46,890 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:47,981 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:49,588 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:51,469 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:52,886 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:56,071 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:56,554 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:57,218 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:57,581 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:07:57,985 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:07,543 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:09,162 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:11,877 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:13,994 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:16,659 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:20,274 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:21,845 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:24,909 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:25,295 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:25,939 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:27,686 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:30,118 bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: 2023-09-12T09:08:30,119 bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2023-09-12T09:08:30,120 751 | 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 2023-09-12T09:08:30,121 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:08:30,122 In file included from /tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib/htslib/kstring.h:30, 2023-09-12T09:08:30,123 from /tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib/htslib/hts.h:37, 2023-09-12T09:08:30,124 from /tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib/htslib/vcf.h:39, 2023-09-12T09:08:30,125 from bcftools/vcfmerge.c.pysam.c:35: 2023-09-12T09:08:30,126 /usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’ declared here 2023-09-12T09:08:30,127 556 | extern void *calloc (size_t __nmemb, size_t __size) 2023-09-12T09:08:30,128 | ^~~~~~ 2023-09-12T09:08:39,044 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:47,625 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:47,884 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:49,159 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:51,796 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:53,159 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:53,956 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:08:58,420 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:09:00,420 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:09:00,861 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:09:01,201 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:09:02,312 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:09:02,761 building 'pysam.libcutils' extension 2023-09-12T09:09:02,762 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:09:15,047 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:09:15,199 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:09:15,381 building 'pysam.libcalignmentfile' extension 2023-09-12T09:09:15,383 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:09:20,174 pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: 2023-09-12T09:09:20,203 pysam/libcalignmentfile.c:28658:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-12T09:09:20,205 28658 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); 2023-09-12T09:09:20,206 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:09:20,405 pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: 2023-09-12T09:09:20,420 pysam/libcalignmentfile.c:14341:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-12T09:09:20,421 14341 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); 2023-09-12T09:09:20,422 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:10:01,331 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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,$ORIGIN 2023-09-12T09:10:01,559 building 'pysam.libcsamfile' extension 2023-09-12T09:10:01,560 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-armv7l-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-12T09:10:04,211 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcsamfile.o -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-12T09:10:04,374 building 'pysam.libcalignedsegment' extension 2023-09-12T09:10:04,375 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:10:13,564 pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: 2023-09-12T09:10:13,579 pysam/libcalignedsegment.c:14415:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-12T09:10:13,580 14415 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); 2023-09-12T09:10:13,581 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:11:07,028 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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,$ORIGIN 2023-09-12T09:11:07,306 building 'pysam.libctabix' extension 2023-09-12T09:11:07,307 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-armv7l-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement 2023-09-12T09:11:30,956 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libctabix.o -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN 2023-09-12T09:11:31,147 building 'pysam.libcfaidx' extension 2023-09-12T09:11:31,148 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:11:45,692 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:11:45,874 building 'pysam.libcbcf' extension 2023-09-12T09:11:45,875 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:11:56,372 pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: 2023-09-12T09:11:56,440 pysam/libcbcf.c:67371:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-12T09:11:56,441 67371 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); 2023-09-12T09:11:56,441 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:11:56,454 pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: 2023-09-12T09:11:56,519 pysam/libcbcf.c:67096:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-12T09:11:56,520 67096 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); 2023-09-12T09:11:56,521 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:11:56,525 pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: 2023-09-12T09:11:56,588 pysam/libcbcf.c:72230:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-12T09:11:56,589 72230 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); 2023-09-12T09:11:56,590 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:11:57,395 pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: 2023-09-12T09:11:57,429 pysam/libcbcf.c:35394:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-12T09:11:57,430 35394 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); 2023-09-12T09:11:57,431 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:11:57,460 pysam/libcbcf.c:35420:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2023-09-12T09:11:57,460 35420 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); 2023-09-12T09:11:57,461 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:13:11,663 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:13:11,984 building 'pysam.libcbgzf' extension 2023-09-12T09:13:11,986 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:13:17,813 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:13:17,981 building 'pysam.libctabixproxies' extension 2023-09-12T09:13:17,981 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:13:38,535 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:13:38,720 building 'pysam.libcvcf' extension 2023-09-12T09:13:38,721 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/htslib -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/samtools/lz4 -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/bcftools -I/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:14:18,196 pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’: 2023-09-12T09:14:18,222 pysam/libcvcf.c:25833:15: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-12T09:14:18,223 25833 | __pyx_t_8 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 873, __pyx_L1_error) 2023-09-12T09:14:18,224 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-12T09:14:18,245 pysam/libcvcf.c:20265:10: note: ‘__pyx_v_qual’ was declared here 2023-09-12T09:14:18,246 20265 | double __pyx_v_qual; 2023-09-12T09:14:18,247 | ^~~~~~~~~~~~ 2023-09-12T09:14:45,492 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-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3/pysam -L/tmp/pip-install-379l8vub/pysam_81cde9bd34054e79995da3b278c257a3 -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 2023-09-12T09:14:46,756 installing to build/bdist.linux-armv7l/wheel 2023-09-12T09:14:46,758 running install 2023-09-12T09:14:46,783 running install_lib 2023-09-12T09:14:46,788 creating build/bdist.linux-armv7l 2023-09-12T09:14:46,789 creating build/bdist.linux-armv7l/wheel 2023-09-12T09:14:46,792 creating build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,794 copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,809 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,811 copying build/lib.linux-armv7l-cpython-311/pysam/py.typed -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,813 copying build/lib.linux-armv7l-cpython-311/pysam/pysam_stream.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,815 copying build/lib.linux-armv7l-cpython-311/pysam/config.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,818 copying build/lib.linux-armv7l-cpython-311/pysam/pysam_util.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,820 copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,822 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,828 copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,831 copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,833 copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,841 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,844 copying build/lib.linux-armv7l-cpython-311/pysam/cbcftools_util.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,847 copying build/lib.linux-armv7l-cpython-311/pysam/pysam_util.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,849 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,852 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,861 copying build/lib.linux-armv7l-cpython-311/pysam/csamtools_util.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,864 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,866 copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,868 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,874 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,877 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,929 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,978 copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,987 copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,989 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,992 copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:46,994 copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,075 copying build/lib.linux-armv7l-cpython-311/pysam/samtools.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,078 copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,091 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,095 copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,100 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,102 copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,122 copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,163 copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,194 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,253 copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:47,256 creating build/bdist.linux-armv7l/wheel/pysam/include 2023-09-12T09:14:47,259 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,261 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/kstring.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,265 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,266 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,270 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/khash_str2int.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,272 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcf_sweep.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,274 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/bgzf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,276 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_expr.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,279 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/cram.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,281 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_endian.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,284 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kroundup.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,286 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_log.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,288 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/tbx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,290 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kbitset.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,292 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcfutils.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,295 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,297 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_os.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,299 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_defs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,301 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/klist.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,304 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kstring.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,306 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,309 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/synced_bcf_reader.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,312 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kfunc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,314 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/ksort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,317 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kseq.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,319 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/knetfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,322 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/faidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,324 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,328 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/khash.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,330 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/thread_pool.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,333 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/sam.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib 2023-09-12T09:14:47,337 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/tbx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,339 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs_external.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,341 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/probaln.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,344 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/Makefile -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,347 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,352 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/configure.ac -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,355 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib_vars.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,357 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/header.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,361 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/os 2023-09-12T09:14:47,362 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os/rand.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/os 2023-09-12T09:14:47,365 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os/lzma_stub.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/os 2023-09-12T09:14:47,368 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.h.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,371 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/realn.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,373 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bcf_sr_sort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,376 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/header.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,378 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,383 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/sam.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,389 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/md5.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,392 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,393 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_decode.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,396 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/mFILE.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,399 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_io.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,402 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,404 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,407 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/open_trace_file.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,409 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_stats.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,412 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/pooled_alloc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,414 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_encode.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,419 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/mFILE.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,422 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_external.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,424 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_codecs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,429 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_index.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,432 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_encode.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,434 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/string_alloc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,436 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_samtools.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,438 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/pooled_alloc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,441 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/os.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,443 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_io.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,449 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_index.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,451 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_codecs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,454 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/misc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,456 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/string_alloc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,459 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_structs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,462 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/open_trace_file.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,464 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_decode.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram 2023-09-12T09:14:47,469 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,473 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/configure -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,479 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/textutils_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,482 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/multipart.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,484 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/tabix.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,488 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/kfunc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,490 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/plugin.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,493 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_s3_write.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,495 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/regidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,498 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/textutils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,500 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,503 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bgzf.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,508 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/builddir_vars.mk.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,510 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htsfile.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,512 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/thread_pool.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,516 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib.pc.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,517 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcf_sweep.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,521 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4 2023-09-12T09:14:47,523 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4/pkg.m4 -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4 2023-09-12T09:14:47,525 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 2023-09-12T09:14:47,527 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 2023-09-12T09:14:47,530 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 2023-09-12T09:14:47,532 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_libcurl.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,536 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_s3.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,538 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,540 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,543 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.mk.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,545 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_expr.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,548 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs 2023-09-12T09:14:47,549 creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,551 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rle.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,553 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 2023-09-12T09:14:47,555 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/utils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,558 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 2023-09-12T09:14:47,560 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rle.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,562 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 2023-09-12T09:14:47,564 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,566 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 2023-09-12T09:14:47,569 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/varint.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,571 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/permute.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,573 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 2023-09-12T09:14:47,576 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 2023-09-12T09:14:47,580 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 2023-09-12T09:14:47,584 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 2023-09-12T09:14:47,588 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 2023-09-12T09:14:47,590 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pack.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,592 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 2023-09-12T09:14:47,595 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 2023-09-12T09:14:47,597 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 2023-09-12T09:14:47,600 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 2023-09-12T09:14:47,602 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 2023-09-12T09:14:47,605 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,607 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 2023-09-12T09:14:47,609 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,612 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 2023-09-12T09:14:47,614 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pack.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,617 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 2023-09-12T09:14:47,619 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 2023-09-12T09:14:47,621 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/utils.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,624 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/version.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs 2023-09-12T09:14:47,625 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 2023-09-12T09:14:47,627 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 2023-09-12T09:14:47,630 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 2023-09-12T09:14:47,633 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 2023-09-12T09:14:47,635 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 2023-09-12T09:14:47,637 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/region.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,639 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bcf_sr_sort.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,642 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/README -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,644 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcfutils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,646 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs_bundled.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,648 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,651 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_os.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,652 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_time_funcs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,654 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_gcs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,657 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,659 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,661 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/errmod.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,663 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bgzip.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,665 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/thread_pool_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,667 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/faidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,670 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/sam_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,672 copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/synced_bcf_reader.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib 2023-09-12T09:14:47,677 creating build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,678 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reference.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,680 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,683 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,686 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,688 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_markdup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,691 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_cat.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,694 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,696 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_markdup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,700 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,703 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,705 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,710 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plcmd.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,714 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_stat.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,716 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,718 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,721 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,723 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,725 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamshuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,728 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,730 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,732 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_fastq.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,735 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamshuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,738 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdupse.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,740 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_flags.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,742 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,744 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,746 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,748 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,751 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,753 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_samples.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,756 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/coverage.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,758 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedcov.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,760 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,763 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cram_size.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,765 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/amplicon_stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,769 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reference.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,772 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,775 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_cat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,777 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,779 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,781 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,783 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,787 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,789 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,793 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,795 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_split.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,797 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/phase.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,800 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cut_target.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,802 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_fastq.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,805 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,807 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,809 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reset.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,812 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_mate.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,814 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_import.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,817 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdupse.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,819 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/dict.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,821 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_mate.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,824 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_sort.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,828 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_addrprg.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,830 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_index.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,833 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_addrprg.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,835 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_color.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,838 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,840 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cut_target.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,843 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,846 creating build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4 2023-09-12T09:14:47,848 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4 2023-09-12T09:14:47,851 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4 2023-09-12T09:14:47,855 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4 2023-09-12T09:14:47,858 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4 2023-09-12T09:14:47,861 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,863 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_reheader.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,866 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_reheader.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,869 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_split.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,871 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/faidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,874 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_quickcheck.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,876 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,878 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_color.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,880 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/amplicon_stats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,884 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_view.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,888 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,890 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/coverage.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,893 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reset.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,896 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,898 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_samples.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,901 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_flags.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,903 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_md.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,906 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_index.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,908 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_md.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,910 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cram_size.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,913 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,916 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam2depth.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,918 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plcmd.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,921 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,924 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_import.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,927 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,931 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_quickcheck.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,934 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamtk.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,937 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_aux.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,940 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,943 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,946 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/README -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,949 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/padding.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,953 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,955 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/dict.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,958 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam2depth.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,960 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,963 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_sort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,968 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,970 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedcov.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,972 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/phase.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,975 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,977 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/faidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,980 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_view.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,984 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamtk.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,987 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_stat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,989 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/splaysort.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,992 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/padding.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,994 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:47,998 copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_aux.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools 2023-09-12T09:14:48,001 copying build/lib.linux-armv7l-cpython-311/pysam/include/__init__.py -> build/bdist.linux-armv7l/wheel/pysam/include 2023-09-12T09:14:48,005 creating build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,006 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfstats.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,010 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfannotate.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,016 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,018 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/reheader.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,021 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfmerge.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,026 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,028 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/reheader.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,031 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,033 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,036 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,039 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconcat.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,042 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,044 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,047 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfquery.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,050 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,052 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,054 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconvert.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,057 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,060 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,062 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_indel.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,065 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,068 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconvert.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,072 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,075 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,077 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,079 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,081 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,083 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kheap.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,086 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfindex.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,088 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,090 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfhead.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,092 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,095 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,097 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,099 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,101 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfquery.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,104 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mpileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,108 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/variantkey.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,111 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfannotate.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,117 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,119 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/khash_str2str.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,121 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfnorm.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,127 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,129 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfisec.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,133 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/rbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,135 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,139 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/csq.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,145 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,148 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mpileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,151 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/em.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,154 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,156 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tabix.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,159 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,161 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfmerge.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,166 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,168 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,170 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfplugin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,173 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfroh.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,177 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsort.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,179 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,183 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,185 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,188 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,190 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,193 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,195 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mw.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,199 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfroh.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,202 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,204 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,207 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,248 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/main.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,250 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mcall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,253 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,256 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,258 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,261 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,263 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,266 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcffilter.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,269 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mcall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,272 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,275 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,277 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cigar_state.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,280 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ccall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,282 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfgtcheck.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,286 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,288 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/main.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,290 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcnv.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,293 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/call.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,296 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,298 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,301 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,303 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,305 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,308 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/csq.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,314 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfplugin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,318 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,320 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfnorm.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,324 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfview.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,327 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,330 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,333 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfindex.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,336 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/em.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,338 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,340 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,342 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/README -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,344 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsom.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,346 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,349 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,354 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,356 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfstats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,360 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,363 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,365 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hex.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,367 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/utlist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,371 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconcat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,374 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,377 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,380 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,382 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcnv.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,386 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,389 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,392 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,394 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,397 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,400 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,403 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,407 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfhead.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,409 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,413 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcffilter.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,417 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,420 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,422 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tabix.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,425 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,428 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfisec.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,432 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,435 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,438 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfview.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,441 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,445 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,450 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,453 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,457 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ccall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,461 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsom.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,466 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,470 copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools 2023-09-12T09:14:48,474 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,477 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,482 copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,487 copying build/lib.linux-armv7l-cpython-311/pysam/__init__.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,490 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,493 copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,496 copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,498 copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,501 copying build/lib.linux-armv7l-cpython-311/pysam/version.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,503 copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,525 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,528 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,531 copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,559 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,601 copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,603 copying build/lib.linux-armv7l-cpython-311/pysam/utils.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,606 copying build/lib.linux-armv7l-cpython-311/pysam/version.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,609 copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,612 copying build/lib.linux-armv7l-cpython-311/pysam/Pileup.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,615 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,663 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,666 copying build/lib.linux-armv7l-cpython-311/pysam/bcftools.py -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,669 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,734 copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,736 copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,749 copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,767 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,821 copying build/lib.linux-armv7l-cpython-311/pysam/version.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,824 copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pxd -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,826 copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,829 copying build/lib.linux-armv7l-cpython-311/pysam/htslib_util.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,832 copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,835 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,882 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,887 copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,892 copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,894 copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,913 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,915 copying build/lib.linux-armv7l-cpython-311/pysam/htslib_util.h -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,918 copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,920 copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.c -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,931 copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pyx -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,933 copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pyi -> build/bdist.linux-armv7l/wheel/pysam 2023-09-12T09:14:48,935 running install_egg_info 2023-09-12T09:14:48,940 Copying pysam.egg-info to build/bdist.linux-armv7l/wheel/pysam-0.21.0-py3.11.egg-info 2023-09-12T09:14:48,953 running install_scripts 2023-09-12T09:14:49,013 creating build/bdist.linux-armv7l/wheel/pysam-0.21.0.dist-info/WHEEL 2023-09-12T09:14:49,016 creating '/tmp/pip-wheel-84cbchuu/.tmp-b0zpdb1i/pysam-0.21.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-12T09:14:49,020 adding 'pysam/Pileup.py' 2023-09-12T09:14:49,022 adding 'pysam/__init__.py' 2023-09-12T09:14:49,024 adding 'pysam/bcftools.py' 2023-09-12T09:14:49,026 adding 'pysam/cbcftools_util.h' 2023-09-12T09:14:49,027 adding 'pysam/config.py' 2023-09-12T09:14:49,029 adding 'pysam/csamtools_util.h' 2023-09-12T09:14:49,031 adding 'pysam/htslib_util.c' 2023-09-12T09:14:49,033 adding 'pysam/htslib_util.h' 2023-09-12T09:14:49,218 adding 'pysam/libcalignedsegment.c' 2023-09-12T09:14:49,850 adding 'pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:49,876 adding 'pysam/libcalignedsegment.pxd' 2023-09-12T09:14:49,878 adding 'pysam/libcalignedsegment.pyi' 2023-09-12T09:14:49,891 adding 'pysam/libcalignedsegment.pyx' 2023-09-12T09:14:50,024 adding 'pysam/libcalignmentfile.c' 2023-09-12T09:14:50,499 adding 'pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:50,520 adding 'pysam/libcalignmentfile.pxd' 2023-09-12T09:14:50,522 adding 'pysam/libcalignmentfile.pyi' 2023-09-12T09:14:50,535 adding 'pysam/libcalignmentfile.pyx' 2023-09-12T09:14:50,768 adding 'pysam/libcbcf.c' 2023-09-12T09:14:51,571 adding 'pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:51,606 adding 'pysam/libcbcf.pxd' 2023-09-12T09:14:51,609 adding 'pysam/libcbcf.pyi' 2023-09-12T09:14:51,623 adding 'pysam/libcbcf.pyx' 2023-09-12T09:14:51,635 adding 'pysam/libcbcftools.c' 2023-09-12T09:14:52,448 adding 'pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:52,478 adding 'pysam/libcbcftools.pxd' 2023-09-12T09:14:52,480 adding 'pysam/libcbcftools.pyi' 2023-09-12T09:14:52,482 adding 'pysam/libcbcftools.pyx' 2023-09-12T09:14:52,512 adding 'pysam/libcbgzf.c' 2023-09-12T09:14:52,585 adding 'pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:52,589 adding 'pysam/libcbgzf.pyi' 2023-09-12T09:14:52,592 adding 'pysam/libcbgzf.pyx' 2023-09-12T09:14:52,644 adding 'pysam/libcfaidx.c' 2023-09-12T09:14:52,816 adding 'pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:52,824 adding 'pysam/libcfaidx.pxd' 2023-09-12T09:14:52,826 adding 'pysam/libcfaidx.pyi' 2023-09-12T09:14:52,830 adding 'pysam/libcfaidx.pyx' 2023-09-12T09:14:52,886 adding 'pysam/libchtslib.c' 2023-09-12T09:14:53,964 adding 'pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:54,017 adding 'pysam/libchtslib.pxd' 2023-09-12T09:14:54,020 adding 'pysam/libchtslib.pyi' 2023-09-12T09:14:54,023 adding 'pysam/libchtslib.pyx' 2023-09-12T09:14:54,045 adding 'pysam/libcsamfile.c' 2023-09-12T09:14:54,071 adding 'pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:54,074 adding 'pysam/libcsamfile.pxd' 2023-09-12T09:14:54,076 adding 'pysam/libcsamfile.pyi' 2023-09-12T09:14:54,077 adding 'pysam/libcsamfile.pyx' 2023-09-12T09:14:54,088 adding 'pysam/libcsamtools.c' 2023-09-12T09:14:54,654 adding 'pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:54,675 adding 'pysam/libcsamtools.pxd' 2023-09-12T09:14:54,677 adding 'pysam/libcsamtools.pyi' 2023-09-12T09:14:54,679 adding 'pysam/libcsamtools.pyx' 2023-09-12T09:14:54,752 adding 'pysam/libctabix.c' 2023-09-12T09:14:55,003 adding 'pysam/libctabix.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:55,015 adding 'pysam/libctabix.pxd' 2023-09-12T09:14:55,017 adding 'pysam/libctabix.pyi' 2023-09-12T09:14:55,022 adding 'pysam/libctabix.pyx' 2023-09-12T09:14:55,097 adding 'pysam/libctabixproxies.c' 2023-09-12T09:14:55,348 adding 'pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:55,359 adding 'pysam/libctabixproxies.pxd' 2023-09-12T09:14:55,361 adding 'pysam/libctabixproxies.pyi' 2023-09-12T09:14:55,365 adding 'pysam/libctabixproxies.pyx' 2023-09-12T09:14:55,409 adding 'pysam/libcutils.c' 2023-09-12T09:14:55,546 adding 'pysam/libcutils.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:55,553 adding 'pysam/libcutils.pxd' 2023-09-12T09:14:55,555 adding 'pysam/libcutils.pyi' 2023-09-12T09:14:55,557 adding 'pysam/libcutils.pyx' 2023-09-12T09:14:55,687 adding 'pysam/libcvcf.c' 2023-09-12T09:14:56,247 adding 'pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so' 2023-09-12T09:14:56,269 adding 'pysam/libcvcf.pxd' 2023-09-12T09:14:56,271 adding 'pysam/libcvcf.pyi' 2023-09-12T09:14:56,276 adding 'pysam/libcvcf.pyx' 2023-09-12T09:14:56,278 adding 'pysam/py.typed' 2023-09-12T09:14:56,280 adding 'pysam/pysam_stream.h' 2023-09-12T09:14:56,281 adding 'pysam/pysam_util.c' 2023-09-12T09:14:56,283 adding 'pysam/pysam_util.h' 2023-09-12T09:14:56,284 adding 'pysam/samtools.py' 2023-09-12T09:14:56,286 adding 'pysam/utils.py' 2023-09-12T09:14:56,287 adding 'pysam/version.h' 2023-09-12T09:14:56,289 adding 'pysam/version.py' 2023-09-12T09:14:56,291 adding 'pysam/version.pyi' 2023-09-12T09:14:56,292 adding 'pysam/include/__init__.py' 2023-09-12T09:14:56,297 adding 'pysam/include/bcftools/HMM.c' 2023-09-12T09:14:56,300 adding 'pysam/include/bcftools/HMM.c.pysam.c' 2023-09-12T09:14:56,301 adding 'pysam/include/bcftools/HMM.h' 2023-09-12T09:14:56,308 adding 'pysam/include/bcftools/LICENSE' 2023-09-12T09:14:56,310 adding 'pysam/include/bcftools/README' 2023-09-12T09:14:56,314 adding 'pysam/include/bcftools/abuf.c' 2023-09-12T09:14:56,318 adding 'pysam/include/bcftools/abuf.c.pysam.c' 2023-09-12T09:14:56,319 adding 'pysam/include/bcftools/abuf.h' 2023-09-12T09:14:56,325 adding 'pysam/include/bcftools/bam2bcf.c' 2023-09-12T09:14:56,331 adding 'pysam/include/bcftools/bam2bcf.c.pysam.c' 2023-09-12T09:14:56,333 adding 'pysam/include/bcftools/bam2bcf.h' 2023-09-12T09:14:56,337 adding 'pysam/include/bcftools/bam2bcf_iaux.c' 2023-09-12T09:14:56,341 adding 'pysam/include/bcftools/bam2bcf_iaux.c.pysam.c' 2023-09-12T09:14:56,346 adding 'pysam/include/bcftools/bam2bcf_indel.c' 2023-09-12T09:14:56,351 adding 'pysam/include/bcftools/bam2bcf_indel.c.pysam.c' 2023-09-12T09:14:56,354 adding 'pysam/include/bcftools/bam_sample.c' 2023-09-12T09:14:56,356 adding 'pysam/include/bcftools/bam_sample.c.pysam.c' 2023-09-12T09:14:56,358 adding 'pysam/include/bcftools/bam_sample.h' 2023-09-12T09:14:56,359 adding 'pysam/include/bcftools/bcftools.h' 2023-09-12T09:14:56,361 adding 'pysam/include/bcftools/bcftools.pysam.c' 2023-09-12T09:14:56,362 adding 'pysam/include/bcftools/bcftools.pysam.h' 2023-09-12T09:14:56,364 adding 'pysam/include/bcftools/bin.c' 2023-09-12T09:14:56,365 adding 'pysam/include/bcftools/bin.c.pysam.c' 2023-09-12T09:14:56,367 adding 'pysam/include/bcftools/bin.h' 2023-09-12T09:14:56,368 adding 'pysam/include/bcftools/call.h' 2023-09-12T09:14:56,371 adding 'pysam/include/bcftools/ccall.c' 2023-09-12T09:14:56,373 adding 'pysam/include/bcftools/ccall.c.pysam.c' 2023-09-12T09:14:56,375 adding 'pysam/include/bcftools/cigar_state.h' 2023-09-12T09:14:56,376 adding 'pysam/include/bcftools/cols.c' 2023-09-12T09:14:56,378 adding 'pysam/include/bcftools/cols.c.pysam.c' 2023-09-12T09:14:56,379 adding 'pysam/include/bcftools/cols.h' 2023-09-12T09:14:56,381 adding 'pysam/include/bcftools/config.h' 2023-09-12T09:14:56,386 adding 'pysam/include/bcftools/consensus.c' 2023-09-12T09:14:56,392 adding 'pysam/include/bcftools/consensus.c.pysam.c' 2023-09-12T09:14:56,398 adding 'pysam/include/bcftools/convert.c' 2023-09-12T09:14:56,405 adding 'pysam/include/bcftools/convert.c.pysam.c' 2023-09-12T09:14:56,407 adding 'pysam/include/bcftools/convert.h' 2023-09-12T09:14:56,426 adding 'pysam/include/bcftools/csq.c' 2023-09-12T09:14:56,446 adding 'pysam/include/bcftools/csq.c.pysam.c' 2023-09-12T09:14:56,449 adding 'pysam/include/bcftools/dbuf.h' 2023-09-12T09:14:56,451 adding 'pysam/include/bcftools/dist.c' 2023-09-12T09:14:56,452 adding 'pysam/include/bcftools/dist.c.pysam.c' 2023-09-12T09:14:56,454 adding 'pysam/include/bcftools/dist.h' 2023-09-12T09:14:56,455 adding 'pysam/include/bcftools/em.c' 2023-09-12T09:14:56,457 adding 'pysam/include/bcftools/em.c.pysam.c' 2023-09-12T09:14:56,459 adding 'pysam/include/bcftools/extsort.c' 2023-09-12T09:14:56,461 adding 'pysam/include/bcftools/extsort.c.pysam.c' 2023-09-12T09:14:56,463 adding 'pysam/include/bcftools/extsort.h' 2023-09-12T09:14:56,476 adding 'pysam/include/bcftools/filter.c' 2023-09-12T09:14:56,491 adding 'pysam/include/bcftools/filter.c.pysam.c' 2023-09-12T09:14:56,493 adding 'pysam/include/bcftools/filter.h' 2023-09-12T09:14:56,495 adding 'pysam/include/bcftools/gvcf.c' 2023-09-12T09:14:56,497 adding 'pysam/include/bcftools/gvcf.c.pysam.c' 2023-09-12T09:14:56,498 adding 'pysam/include/bcftools/gvcf.h' 2023-09-12T09:14:56,501 adding 'pysam/include/bcftools/hclust.c' 2023-09-12T09:14:56,503 adding 'pysam/include/bcftools/hclust.c.pysam.c' 2023-09-12T09:14:56,504 adding 'pysam/include/bcftools/hclust.h' 2023-09-12T09:14:56,506 adding 'pysam/include/bcftools/hex.h' 2023-09-12T09:14:56,507 adding 'pysam/include/bcftools/khash_str2str.h' 2023-09-12T09:14:56,509 adding 'pysam/include/bcftools/kheap.h' 2023-09-12T09:14:56,511 adding 'pysam/include/bcftools/kmin.c' 2023-09-12T09:14:56,513 adding 'pysam/include/bcftools/kmin.c.pysam.c' 2023-09-12T09:14:56,515 adding 'pysam/include/bcftools/kmin.h' 2023-09-12T09:14:56,517 adding 'pysam/include/bcftools/main.c' 2023-09-12T09:14:56,519 adding 'pysam/include/bcftools/main.c.pysam.c' 2023-09-12T09:14:56,527 adding 'pysam/include/bcftools/mcall.c' 2023-09-12T09:14:56,535 adding 'pysam/include/bcftools/mcall.c.pysam.c' 2023-09-12T09:14:56,543 adding 'pysam/include/bcftools/mpileup.c' 2023-09-12T09:14:56,552 adding 'pysam/include/bcftools/mpileup.c.pysam.c' 2023-09-12T09:14:56,555 adding 'pysam/include/bcftools/mw.h' 2023-09-12T09:14:56,558 adding 'pysam/include/bcftools/ploidy.c' 2023-09-12T09:14:56,560 adding 'pysam/include/bcftools/ploidy.c.pysam.c' 2023-09-12T09:14:56,561 adding 'pysam/include/bcftools/ploidy.h' 2023-09-12T09:14:56,564 adding 'pysam/include/bcftools/prob1.c' 2023-09-12T09:14:56,568 adding 'pysam/include/bcftools/prob1.c.pysam.c' 2023-09-12T09:14:56,570 adding 'pysam/include/bcftools/prob1.h' 2023-09-12T09:14:56,571 adding 'pysam/include/bcftools/rbuf.h' 2023-09-12T09:14:56,575 adding 'pysam/include/bcftools/read_consensus.c' 2023-09-12T09:14:56,579 adding 'pysam/include/bcftools/read_consensus.c.pysam.c' 2023-09-12T09:14:56,581 adding 'pysam/include/bcftools/read_consensus.h' 2023-09-12T09:14:56,584 adding 'pysam/include/bcftools/regidx.c' 2023-09-12T09:14:56,586 adding 'pysam/include/bcftools/regidx.c.pysam.c' 2023-09-12T09:14:56,588 adding 'pysam/include/bcftools/regidx.h' 2023-09-12T09:14:56,592 adding 'pysam/include/bcftools/reheader.c' 2023-09-12T09:14:56,595 adding 'pysam/include/bcftools/reheader.c.pysam.c' 2023-09-12T09:14:56,597 adding 'pysam/include/bcftools/smpl_ilist.c' 2023-09-12T09:14:56,599 adding 'pysam/include/bcftools/smpl_ilist.c.pysam.c' 2023-09-12T09:14:56,600 adding 'pysam/include/bcftools/smpl_ilist.h' 2023-09-12T09:14:56,602 adding 'pysam/include/bcftools/str_finder.c' 2023-09-12T09:14:56,604 adding 'pysam/include/bcftools/str_finder.c.pysam.c' 2023-09-12T09:14:56,606 adding 'pysam/include/bcftools/str_finder.h' 2023-09-12T09:14:56,607 adding 'pysam/include/bcftools/tabix.c' 2023-09-12T09:14:56,609 adding 'pysam/include/bcftools/tabix.c.pysam.c' 2023-09-12T09:14:56,611 adding 'pysam/include/bcftools/tsv2vcf.c' 2023-09-12T09:14:56,613 adding 'pysam/include/bcftools/tsv2vcf.c.pysam.c' 2023-09-12T09:14:56,614 adding 'pysam/include/bcftools/tsv2vcf.h' 2023-09-12T09:14:56,618 adding 'pysam/include/bcftools/utlist.h' 2023-09-12T09:14:56,621 adding 'pysam/include/bcftools/variantkey.h' 2023-09-12T09:14:56,636 adding 'pysam/include/bcftools/vcfannotate.c' 2023-09-12T09:14:56,652 adding 'pysam/include/bcftools/vcfannotate.c.pysam.c' 2023-09-12T09:14:56,655 adding 'pysam/include/bcftools/vcfbuf.c' 2023-09-12T09:14:56,658 adding 'pysam/include/bcftools/vcfbuf.c.pysam.c' 2023-09-12T09:14:56,660 adding 'pysam/include/bcftools/vcfbuf.h' 2023-09-12T09:14:56,665 adding 'pysam/include/bcftools/vcfcall.c' 2023-09-12T09:14:56,671 adding 'pysam/include/bcftools/vcfcall.c.pysam.c' 2023-09-12T09:14:56,677 adding 'pysam/include/bcftools/vcfcnv.c' 2023-09-12T09:14:56,684 adding 'pysam/include/bcftools/vcfcnv.c.pysam.c' 2023-09-12T09:14:56,690 adding 'pysam/include/bcftools/vcfconcat.c' 2023-09-12T09:14:56,695 adding 'pysam/include/bcftools/vcfconcat.c.pysam.c' 2023-09-12T09:14:56,702 adding 'pysam/include/bcftools/vcfconvert.c' 2023-09-12T09:14:56,710 adding 'pysam/include/bcftools/vcfconvert.c.pysam.c' 2023-09-12T09:14:56,714 adding 'pysam/include/bcftools/vcffilter.c' 2023-09-12T09:14:56,718 adding 'pysam/include/bcftools/vcffilter.c.pysam.c' 2023-09-12T09:14:56,724 adding 'pysam/include/bcftools/vcfgtcheck.c' 2023-09-12T09:14:56,729 adding 'pysam/include/bcftools/vcfgtcheck.c.pysam.c' 2023-09-12T09:14:56,732 adding 'pysam/include/bcftools/vcfhead.c' 2023-09-12T09:14:56,733 adding 'pysam/include/bcftools/vcfhead.c.pysam.c' 2023-09-12T09:14:56,735 adding 'pysam/include/bcftools/vcfindex.c' 2023-09-12T09:14:56,738 adding 'pysam/include/bcftools/vcfindex.c.pysam.c' 2023-09-12T09:14:56,741 adding 'pysam/include/bcftools/vcfisec.c' 2023-09-12T09:14:56,744 adding 'pysam/include/bcftools/vcfisec.c.pysam.c' 2023-09-12T09:14:56,759 adding 'pysam/include/bcftools/vcfmerge.c' 2023-09-12T09:14:56,774 adding 'pysam/include/bcftools/vcfmerge.c.pysam.c' 2023-09-12T09:14:56,784 adding 'pysam/include/bcftools/vcfnorm.c' 2023-09-12T09:14:56,794 adding 'pysam/include/bcftools/vcfnorm.c.pysam.c' 2023-09-12T09:14:56,798 adding 'pysam/include/bcftools/vcfplugin.c' 2023-09-12T09:14:56,802 adding 'pysam/include/bcftools/vcfplugin.c.pysam.c' 2023-09-12T09:14:56,805 adding 'pysam/include/bcftools/vcfquery.c' 2023-09-12T09:14:56,807 adding 'pysam/include/bcftools/vcfquery.c.pysam.c' 2023-09-12T09:14:56,813 adding 'pysam/include/bcftools/vcfroh.c' 2023-09-12T09:14:56,819 adding 'pysam/include/bcftools/vcfroh.c.pysam.c' 2023-09-12T09:14:56,822 adding 'pysam/include/bcftools/vcfsom.c' 2023-09-12T09:14:56,826 adding 'pysam/include/bcftools/vcfsom.c.pysam.c' 2023-09-12T09:14:56,828 adding 'pysam/include/bcftools/vcfsort.c' 2023-09-12T09:14:56,831 adding 'pysam/include/bcftools/vcfsort.c.pysam.c' 2023-09-12T09:14:56,839 adding 'pysam/include/bcftools/vcfstats.c' 2023-09-12T09:14:56,848 adding 'pysam/include/bcftools/vcfstats.c.pysam.c' 2023-09-12T09:14:56,852 adding 'pysam/include/bcftools/vcfview.c' 2023-09-12T09:14:56,857 adding 'pysam/include/bcftools/vcfview.c.pysam.c' 2023-09-12T09:14:56,859 adding 'pysam/include/bcftools/vcmp.c' 2023-09-12T09:14:56,860 adding 'pysam/include/bcftools/vcmp.c.pysam.c' 2023-09-12T09:14:56,862 adding 'pysam/include/bcftools/vcmp.h' 2023-09-12T09:14:56,863 adding 'pysam/include/bcftools/version.c' 2023-09-12T09:14:56,865 adding 'pysam/include/bcftools/version.c.pysam.c' 2023-09-12T09:14:56,866 adding 'pysam/include/bcftools/version.sh' 2023-09-12T09:14:56,869 adding 'pysam/include/htslib/LICENSE' 2023-09-12T09:14:56,874 adding 'pysam/include/htslib/Makefile' 2023-09-12T09:14:56,876 adding 'pysam/include/htslib/README' 2023-09-12T09:14:56,879 adding 'pysam/include/htslib/bcf_sr_sort.c' 2023-09-12T09:14:56,880 adding 'pysam/include/htslib/bcf_sr_sort.h' 2023-09-12T09:14:56,890 adding 'pysam/include/htslib/bgzf.c' 2023-09-12T09:14:56,893 adding 'pysam/include/htslib/bgzip.c' 2023-09-12T09:14:56,895 adding 'pysam/include/htslib/builddir_vars.mk.in' 2023-09-12T09:14:56,896 adding 'pysam/include/htslib/config.h' 2023-09-12T09:14:56,898 adding 'pysam/include/htslib/config.h.in' 2023-09-12T09:14:56,899 adding 'pysam/include/htslib/config.mk.in' 2023-09-12T09:14:56,921 adding 'pysam/include/htslib/configure' 2023-09-12T09:14:56,925 adding 'pysam/include/htslib/configure.ac' 2023-09-12T09:14:56,927 adding 'pysam/include/htslib/errmod.c' 2023-09-12T09:14:56,931 adding 'pysam/include/htslib/faidx.c' 2023-09-12T09:14:56,940 adding 'pysam/include/htslib/header.c' 2023-09-12T09:14:56,943 adding 'pysam/include/htslib/header.h' 2023-09-12T09:14:56,948 adding 'pysam/include/htslib/hfile.c' 2023-09-12T09:14:56,950 adding 'pysam/include/htslib/hfile_gcs.c' 2023-09-12T09:14:56,952 adding 'pysam/include/htslib/hfile_internal.h' 2023-09-12T09:14:56,958 adding 'pysam/include/htslib/hfile_libcurl.c' 2023-09-12T09:14:56,963 adding 'pysam/include/htslib/hfile_s3.c' 2023-09-12T09:14:56,966 adding 'pysam/include/htslib/hfile_s3_write.c' 2023-09-12T09:14:56,984 adding 'pysam/include/htslib/hts.c' 2023-09-12T09:14:56,988 adding 'pysam/include/htslib/hts_expr.c' 2023-09-12T09:14:56,990 adding 'pysam/include/htslib/hts_internal.h' 2023-09-12T09:14:56,992 adding 'pysam/include/htslib/hts_os.c' 2023-09-12T09:14:56,994 adding 'pysam/include/htslib/hts_time_funcs.h' 2023-09-12T09:14:56,996 adding 'pysam/include/htslib/htscodecs_bundled.mk' 2023-09-12T09:14:56,997 adding 'pysam/include/htslib/htscodecs_external.mk' 2023-09-12T09:14:56,999 adding 'pysam/include/htslib/htsfile.c' 2023-09-12T09:14:57,001 adding 'pysam/include/htslib/htslib.mk' 2023-09-12T09:14:57,003 adding 'pysam/include/htslib/htslib.pc.in' 2023-09-12T09:14:57,004 adding 'pysam/include/htslib/htslib_vars.mk' 2023-09-12T09:14:57,006 adding 'pysam/include/htslib/kfunc.c' 2023-09-12T09:14:57,008 adding 'pysam/include/htslib/kstring.c' 2023-09-12T09:14:57,010 adding 'pysam/include/htslib/md5.c' 2023-09-12T09:14:57,012 adding 'pysam/include/htslib/multipart.c' 2023-09-12T09:14:57,014 adding 'pysam/include/htslib/plugin.c' 2023-09-12T09:14:57,016 adding 'pysam/include/htslib/probaln.c' 2023-09-12T09:14:57,019 adding 'pysam/include/htslib/realn.c' 2023-09-12T09:14:57,022 adding 'pysam/include/htslib/regidx.c' 2023-09-12T09:14:57,023 adding 'pysam/include/htslib/region.c' 2023-09-12T09:14:57,048 adding 'pysam/include/htslib/sam.c' 2023-09-12T09:14:57,051 adding 'pysam/include/htslib/sam_internal.h' 2023-09-12T09:14:57,057 adding 'pysam/include/htslib/synced_bcf_reader.c' 2023-09-12T09:14:57,060 adding 'pysam/include/htslib/tabix.c' 2023-09-12T09:14:57,063 adding 'pysam/include/htslib/tbx.c' 2023-09-12T09:14:57,065 adding 'pysam/include/htslib/textutils.c' 2023-09-12T09:14:57,068 adding 'pysam/include/htslib/textutils_internal.h' 2023-09-12T09:14:57,073 adding 'pysam/include/htslib/thread_pool.c' 2023-09-12T09:14:57,075 adding 'pysam/include/htslib/thread_pool_internal.h' 2023-09-12T09:14:57,095 adding 'pysam/include/htslib/vcf.c' 2023-09-12T09:14:57,099 adding 'pysam/include/htslib/vcf_sweep.c' 2023-09-12T09:14:57,102 adding 'pysam/include/htslib/vcfutils.c' 2023-09-12T09:14:57,103 adding 'pysam/include/htslib/version.sh' 2023-09-12T09:14:57,106 adding 'pysam/include/htslib/cram/cram.h' 2023-09-12T09:14:57,117 adding 'pysam/include/htslib/cram/cram_codecs.c' 2023-09-12T09:14:57,120 adding 'pysam/include/htslib/cram/cram_codecs.h' 2023-09-12T09:14:57,132 adding 'pysam/include/htslib/cram/cram_decode.c' 2023-09-12T09:14:57,135 adding 'pysam/include/htslib/cram/cram_decode.h' 2023-09-12T09:14:57,149 adding 'pysam/include/htslib/cram/cram_encode.c' 2023-09-12T09:14:57,151 adding 'pysam/include/htslib/cram/cram_encode.h' 2023-09-12T09:14:57,155 adding 'pysam/include/htslib/cram/cram_external.c' 2023-09-12T09:14:57,158 adding 'pysam/include/htslib/cram/cram_index.c' 2023-09-12T09:14:57,160 adding 'pysam/include/htslib/cram/cram_index.h' 2023-09-12T09:14:57,179 adding 'pysam/include/htslib/cram/cram_io.c' 2023-09-12T09:14:57,183 adding 'pysam/include/htslib/cram/cram_io.h' 2023-09-12T09:14:57,184 adding 'pysam/include/htslib/cram/cram_samtools.h' 2023-09-12T09:14:57,187 adding 'pysam/include/htslib/cram/cram_stats.c' 2023-09-12T09:14:57,188 adding 'pysam/include/htslib/cram/cram_stats.h' 2023-09-12T09:14:57,192 adding 'pysam/include/htslib/cram/cram_structs.h' 2023-09-12T09:14:57,195 adding 'pysam/include/htslib/cram/mFILE.c' 2023-09-12T09:14:57,197 adding 'pysam/include/htslib/cram/mFILE.h' 2023-09-12T09:14:57,198 adding 'pysam/include/htslib/cram/misc.h' 2023-09-12T09:14:57,200 adding 'pysam/include/htslib/cram/open_trace_file.c' 2023-09-12T09:14:57,202 adding 'pysam/include/htslib/cram/open_trace_file.h' 2023-09-12T09:14:57,204 adding 'pysam/include/htslib/cram/os.h' 2023-09-12T09:14:57,205 adding 'pysam/include/htslib/cram/pooled_alloc.c' 2023-09-12T09:14:57,207 adding 'pysam/include/htslib/cram/pooled_alloc.h' 2023-09-12T09:14:57,209 adding 'pysam/include/htslib/cram/string_alloc.c' 2023-09-12T09:14:57,210 adding 'pysam/include/htslib/cram/string_alloc.h' 2023-09-12T09:14:57,216 adding 'pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c' 2023-09-12T09:14:57,217 adding 'pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h' 2023-09-12T09:14:57,219 adding 'pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h' 2023-09-12T09:14:57,220 adding 'pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h' 2023-09-12T09:14:57,226 adding 'pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c' 2023-09-12T09:14:57,228 adding 'pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h' 2023-09-12T09:14:57,230 adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs.c' 2023-09-12T09:14:57,231 adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs.h' 2023-09-12T09:14:57,233 adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h' 2023-09-12T09:14:57,234 adding 'pysam/include/htslib/htscodecs/htscodecs/pack.c' 2023-09-12T09:14:57,236 adding 'pysam/include/htslib/htscodecs/htscodecs/pack.h' 2023-09-12T09:14:57,239 adding 'pysam/include/htslib/htscodecs/htscodecs/permute.h' 2023-09-12T09:14:57,240 adding 'pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h' 2023-09-12T09:14:57,243 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h' 2023-09-12T09:14:57,246 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static.c' 2023-09-12T09:14:57,248 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static.h' 2023-09-12T09:14:57,251 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h' 2023-09-12T09:14:57,254 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c' 2023-09-12T09:14:57,256 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h' 2023-09-12T09:14:57,261 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c' 2023-09-12T09:14:57,265 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c' 2023-09-12T09:14:57,272 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c' 2023-09-12T09:14:57,278 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c' 2023-09-12T09:14:57,280 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h' 2023-09-12T09:14:57,286 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c' 2023-09-12T09:14:57,289 adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_word.h' 2023-09-12T09:14:57,290 adding 'pysam/include/htslib/htscodecs/htscodecs/rle.c' 2023-09-12T09:14:57,292 adding 'pysam/include/htslib/htscodecs/htscodecs/rle.h' 2023-09-12T09:14:57,298 adding 'pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c' 2023-09-12T09:14:57,300 adding 'pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h' 2023-09-12T09:14:57,302 adding 'pysam/include/htslib/htscodecs/htscodecs/utils.c' 2023-09-12T09:14:57,304 adding 'pysam/include/htslib/htscodecs/htscodecs/utils.h' 2023-09-12T09:14:57,307 adding 'pysam/include/htslib/htscodecs/htscodecs/varint.h' 2023-09-12T09:14:57,309 adding 'pysam/include/htslib/htscodecs/htscodecs/varint2.h' 2023-09-12T09:14:57,310 adding 'pysam/include/htslib/htscodecs/htscodecs/version.h' 2023-09-12T09:14:57,313 adding 'pysam/include/htslib/htslib/bgzf.h' 2023-09-12T09:14:57,316 adding 'pysam/include/htslib/htslib/cram.h' 2023-09-12T09:14:57,319 adding 'pysam/include/htslib/htslib/faidx.h' 2023-09-12T09:14:57,321 adding 'pysam/include/htslib/htslib/hfile.h' 2023-09-12T09:14:57,329 adding 'pysam/include/htslib/htslib/hts.h' 2023-09-12T09:14:57,331 adding 'pysam/include/htslib/htslib/hts_defs.h' 2023-09-12T09:14:57,333 adding 'pysam/include/htslib/htslib/hts_endian.h' 2023-09-12T09:14:57,335 adding 'pysam/include/htslib/htslib/hts_expr.h' 2023-09-12T09:14:57,336 adding 'pysam/include/htslib/htslib/hts_log.h' 2023-09-12T09:14:57,338 adding 'pysam/include/htslib/htslib/hts_os.h' 2023-09-12T09:14:57,340 adding 'pysam/include/htslib/htslib/kbitset.h' 2023-09-12T09:14:57,341 adding 'pysam/include/htslib/htslib/kfunc.h' 2023-09-12T09:14:57,344 adding 'pysam/include/htslib/htslib/khash.h' 2023-09-12T09:14:57,346 adding 'pysam/include/htslib/htslib/khash_str2int.h' 2023-09-12T09:14:57,347 adding 'pysam/include/htslib/htslib/klist.h' 2023-09-12T09:14:57,349 adding 'pysam/include/htslib/htslib/knetfile.h' 2023-09-12T09:14:57,350 adding 'pysam/include/htslib/htslib/kroundup.h' 2023-09-12T09:14:57,352 adding 'pysam/include/htslib/htslib/kseq.h' 2023-09-12T09:14:57,354 adding 'pysam/include/htslib/htslib/ksort.h' 2023-09-12T09:14:57,357 adding 'pysam/include/htslib/htslib/kstring.h' 2023-09-12T09:14:57,359 adding 'pysam/include/htslib/htslib/regidx.h' 2023-09-12T09:14:57,370 adding 'pysam/include/htslib/htslib/sam.h' 2023-09-12T09:14:57,373 adding 'pysam/include/htslib/htslib/synced_bcf_reader.h' 2023-09-12T09:14:57,375 adding 'pysam/include/htslib/htslib/tbx.h' 2023-09-12T09:14:57,377 adding 'pysam/include/htslib/htslib/thread_pool.h' 2023-09-12T09:14:57,386 adding 'pysam/include/htslib/htslib/vcf.h' 2023-09-12T09:14:57,388 adding 'pysam/include/htslib/htslib/vcf_sweep.h' 2023-09-12T09:14:57,390 adding 'pysam/include/htslib/htslib/vcfutils.h' 2023-09-12T09:14:57,392 adding 'pysam/include/htslib/m4/ax_check_compile_flag.m4' 2023-09-12T09:14:57,393 adding 'pysam/include/htslib/m4/hts_hide_dynamic_syms.m4' 2023-09-12T09:14:57,395 adding 'pysam/include/htslib/m4/hts_prog_cc_warnings.m4' 2023-09-12T09:14:57,397 adding 'pysam/include/htslib/m4/pkg.m4' 2023-09-12T09:14:57,399 adding 'pysam/include/htslib/os/lzma_stub.h' 2023-09-12T09:14:57,401 adding 'pysam/include/htslib/os/rand.c' 2023-09-12T09:14:57,404 adding 'pysam/include/samtools/LICENSE' 2023-09-12T09:14:57,406 adding 'pysam/include/samtools/README' 2023-09-12T09:14:57,413 adding 'pysam/include/samtools/amplicon_stats.c' 2023-09-12T09:14:57,421 adding 'pysam/include/samtools/amplicon_stats.c.pysam.c' 2023-09-12T09:14:57,423 adding 'pysam/include/samtools/bam.c' 2023-09-12T09:14:57,425 adding 'pysam/include/samtools/bam.c.pysam.c' 2023-09-12T09:14:57,427 adding 'pysam/include/samtools/bam.h' 2023-09-12T09:14:57,431 adding 'pysam/include/samtools/bam2depth.c' 2023-09-12T09:14:57,435 adding 'pysam/include/samtools/bam2depth.c.pysam.c' 2023-09-12T09:14:57,438 adding 'pysam/include/samtools/bam_addrprg.c' 2023-09-12T09:14:57,440 adding 'pysam/include/samtools/bam_addrprg.c.pysam.c' 2023-09-12T09:14:57,444 adding 'pysam/include/samtools/bam_ampliconclip.c' 2023-09-12T09:14:57,448 adding 'pysam/include/samtools/bam_ampliconclip.c.pysam.c' 2023-09-12T09:14:57,450 adding 'pysam/include/samtools/bam_ampliconclip.h' 2023-09-12T09:14:57,451 adding 'pysam/include/samtools/bam_aux.c' 2023-09-12T09:14:57,453 adding 'pysam/include/samtools/bam_aux.c.pysam.c' 2023-09-12T09:14:57,455 adding 'pysam/include/samtools/bam_cat.c' 2023-09-12T09:14:57,458 adding 'pysam/include/samtools/bam_cat.c.pysam.c' 2023-09-12T09:14:57,460 adding 'pysam/include/samtools/bam_color.c' 2023-09-12T09:14:57,462 adding 'pysam/include/samtools/bam_color.c.pysam.c' 2023-09-12T09:14:57,473 adding 'pysam/include/samtools/bam_consensus.c' 2023-09-12T09:14:57,485 adding 'pysam/include/samtools/bam_consensus.c.pysam.c' 2023-09-12T09:14:57,490 adding 'pysam/include/samtools/bam_fastq.c' 2023-09-12T09:14:57,494 adding 'pysam/include/samtools/bam_fastq.c.pysam.c' 2023-09-12T09:14:57,496 adding 'pysam/include/samtools/bam_flags.c' 2023-09-12T09:14:57,497 adding 'pysam/include/samtools/bam_flags.c.pysam.c' 2023-09-12T09:14:57,500 adding 'pysam/include/samtools/bam_import.c' 2023-09-12T09:14:57,502 adding 'pysam/include/samtools/bam_import.c.pysam.c' 2023-09-12T09:14:57,504 adding 'pysam/include/samtools/bam_index.c' 2023-09-12T09:14:57,507 adding 'pysam/include/samtools/bam_index.c.pysam.c' 2023-09-12T09:14:57,508 adding 'pysam/include/samtools/bam_lpileup.c' 2023-09-12T09:14:57,511 adding 'pysam/include/samtools/bam_lpileup.c.pysam.c' 2023-09-12T09:14:57,512 adding 'pysam/include/samtools/bam_lpileup.h' 2023-09-12T09:14:57,521 adding 'pysam/include/samtools/bam_markdup.c' 2023-09-12T09:14:57,530 adding 'pysam/include/samtools/bam_markdup.c.pysam.c' 2023-09-12T09:14:57,534 adding 'pysam/include/samtools/bam_mate.c' 2023-09-12T09:14:57,538 adding 'pysam/include/samtools/bam_mate.c.pysam.c' 2023-09-12T09:14:57,541 adding 'pysam/include/samtools/bam_md.c' 2023-09-12T09:14:57,543 adding 'pysam/include/samtools/bam_md.c.pysam.c' 2023-09-12T09:14:57,545 adding 'pysam/include/samtools/bam_plbuf.c' 2023-09-12T09:14:57,547 adding 'pysam/include/samtools/bam_plbuf.c.pysam.c' 2023-09-12T09:14:57,548 adding 'pysam/include/samtools/bam_plbuf.h' 2023-09-12T09:14:57,553 adding 'pysam/include/samtools/bam_plcmd.c' 2023-09-12T09:14:57,558 adding 'pysam/include/samtools/bam_plcmd.c.pysam.c' 2023-09-12T09:14:57,561 adding 'pysam/include/samtools/bam_quickcheck.c' 2023-09-12T09:14:57,562 adding 'pysam/include/samtools/bam_quickcheck.c.pysam.c' 2023-09-12T09:14:57,565 adding 'pysam/include/samtools/bam_reheader.c' 2023-09-12T09:14:57,568 adding 'pysam/include/samtools/bam_reheader.c.pysam.c' 2023-09-12T09:14:57,570 adding 'pysam/include/samtools/bam_rmdup.c' 2023-09-12T09:14:57,572 adding 'pysam/include/samtools/bam_rmdup.c.pysam.c' 2023-09-12T09:14:57,574 adding 'pysam/include/samtools/bam_rmdupse.c' 2023-09-12T09:14:57,576 adding 'pysam/include/samtools/bam_rmdupse.c.pysam.c' 2023-09-12T09:14:57,578 adding 'pysam/include/samtools/bam_samples.c' 2023-09-12T09:14:57,581 adding 'pysam/include/samtools/bam_samples.c.pysam.c' 2023-09-12T09:14:57,595 adding 'pysam/include/samtools/bam_sort.c' 2023-09-12T09:14:57,609 adding 'pysam/include/samtools/bam_sort.c.pysam.c' 2023-09-12T09:14:57,613 adding 'pysam/include/samtools/bam_split.c' 2023-09-12T09:14:57,616 adding 'pysam/include/samtools/bam_split.c.pysam.c' 2023-09-12T09:14:57,618 adding 'pysam/include/samtools/bam_stat.c' 2023-09-12T09:14:57,620 adding 'pysam/include/samtools/bam_stat.c.pysam.c' 2023-09-12T09:14:57,623 adding 'pysam/include/samtools/bamshuf.c' 2023-09-12T09:14:57,626 adding 'pysam/include/samtools/bamshuf.c.pysam.c' 2023-09-12T09:14:57,628 adding 'pysam/include/samtools/bamtk.c' 2023-09-12T09:14:57,631 adding 'pysam/include/samtools/bamtk.c.pysam.c' 2023-09-12T09:14:57,633 adding 'pysam/include/samtools/bedcov.c' 2023-09-12T09:14:57,635 adding 'pysam/include/samtools/bedcov.c.pysam.c' 2023-09-12T09:14:57,638 adding 'pysam/include/samtools/bedidx.c' 2023-09-12T09:14:57,641 adding 'pysam/include/samtools/bedidx.c.pysam.c' 2023-09-12T09:14:57,642 adding 'pysam/include/samtools/bedidx.h' 2023-09-12T09:14:57,644 adding 'pysam/include/samtools/config.h' 2023-09-12T09:14:57,646 adding 'pysam/include/samtools/consensus_pileup.c' 2023-09-12T09:14:57,649 adding 'pysam/include/samtools/consensus_pileup.c.pysam.c' 2023-09-12T09:14:57,650 adding 'pysam/include/samtools/consensus_pileup.h' 2023-09-12T09:14:57,654 adding 'pysam/include/samtools/coverage.c' 2023-09-12T09:14:57,658 adding 'pysam/include/samtools/coverage.c.pysam.c' 2023-09-12T09:14:57,661 adding 'pysam/include/samtools/cram_size.c' 2023-09-12T09:14:57,664 adding 'pysam/include/samtools/cram_size.c.pysam.c' 2023-09-12T09:14:57,666 adding 'pysam/include/samtools/cut_target.c' 2023-09-12T09:14:57,668 adding 'pysam/include/samtools/cut_target.c.pysam.c' 2023-09-12T09:14:57,670 adding 'pysam/include/samtools/dict.c' 2023-09-12T09:14:57,671 adding 'pysam/include/samtools/dict.c.pysam.c' 2023-09-12T09:14:57,674 adding 'pysam/include/samtools/faidx.c' 2023-09-12T09:14:57,676 adding 'pysam/include/samtools/faidx.c.pysam.c' 2023-09-12T09:14:57,680 adding 'pysam/include/samtools/padding.c' 2023-09-12T09:14:57,683 adding 'pysam/include/samtools/padding.c.pysam.c' 2023-09-12T09:14:57,687 adding 'pysam/include/samtools/phase.c' 2023-09-12T09:14:57,691 adding 'pysam/include/samtools/phase.c.pysam.c' 2023-09-12T09:14:57,694 adding 'pysam/include/samtools/reference.c' 2023-09-12T09:14:57,697 adding 'pysam/include/samtools/reference.c.pysam.c' 2023-09-12T09:14:57,700 adding 'pysam/include/samtools/reset.c' 2023-09-12T09:14:57,703 adding 'pysam/include/samtools/reset.c.pysam.c' 2023-09-12T09:14:57,705 adding 'pysam/include/samtools/sam_opts.c' 2023-09-12T09:14:57,706 adding 'pysam/include/samtools/sam_opts.c.pysam.c' 2023-09-12T09:14:57,708 adding 'pysam/include/samtools/sam_opts.h' 2023-09-12T09:14:57,710 adding 'pysam/include/samtools/sam_utils.c' 2023-09-12T09:14:57,712 adding 'pysam/include/samtools/sam_utils.c.pysam.c' 2023-09-12T09:14:57,713 adding 'pysam/include/samtools/sam_utils.h' 2023-09-12T09:14:57,720 adding 'pysam/include/samtools/sam_view.c' 2023-09-12T09:14:57,728 adding 'pysam/include/samtools/sam_view.c.pysam.c' 2023-09-12T09:14:57,730 adding 'pysam/include/samtools/sample.c' 2023-09-12T09:14:57,731 adding 'pysam/include/samtools/sample.c.pysam.c' 2023-09-12T09:14:57,733 adding 'pysam/include/samtools/sample.h' 2023-09-12T09:14:57,734 adding 'pysam/include/samtools/samtools.h' 2023-09-12T09:14:57,736 adding 'pysam/include/samtools/samtools.pysam.c' 2023-09-12T09:14:57,737 adding 'pysam/include/samtools/samtools.pysam.h' 2023-09-12T09:14:57,739 adding 'pysam/include/samtools/splaysort.h' 2023-09-12T09:14:57,750 adding 'pysam/include/samtools/stats.c' 2023-09-12T09:14:57,763 adding 'pysam/include/samtools/stats.c.pysam.c' 2023-09-12T09:14:57,766 adding 'pysam/include/samtools/stats_isize.c' 2023-09-12T09:14:57,768 adding 'pysam/include/samtools/stats_isize.c.pysam.c' 2023-09-12T09:14:57,770 adding 'pysam/include/samtools/stats_isize.h' 2023-09-12T09:14:57,773 adding 'pysam/include/samtools/tmp_file.c' 2023-09-12T09:14:57,775 adding 'pysam/include/samtools/tmp_file.c.pysam.c' 2023-09-12T09:14:57,777 adding 'pysam/include/samtools/tmp_file.h' 2023-09-12T09:14:57,778 adding 'pysam/include/samtools/version.sh' 2023-09-12T09:14:57,780 adding 'pysam/include/samtools/lz4/LICENSE' 2023-09-12T09:14:57,786 adding 'pysam/include/samtools/lz4/lz4.c' 2023-09-12T09:14:57,793 adding 'pysam/include/samtools/lz4/lz4.c.pysam.c' 2023-09-12T09:14:57,796 adding 'pysam/include/samtools/lz4/lz4.h' 2023-09-12T09:14:57,799 adding 'pysam-0.21.0.dist-info/AUTHORS' 2023-09-12T09:14:57,800 adding 'pysam-0.21.0.dist-info/COPYING' 2023-09-12T09:14:57,802 adding 'pysam-0.21.0.dist-info/METADATA' 2023-09-12T09:14:57,803 adding 'pysam-0.21.0.dist-info/WHEEL' 2023-09-12T09:14:57,804 adding 'pysam-0.21.0.dist-info/top_level.txt' 2023-09-12T09:14:57,812 adding 'pysam-0.21.0.dist-info/RECORD' 2023-09-12T09:14:57,997 removing build/bdist.linux-armv7l/wheel 2023-09-12T09:14:58,263 Building wheel for pysam (pyproject.toml): finished with status 'done' 2023-09-12T09:14:58,842 Created wheel for pysam: filename=pysam-0.21.0-cp311-cp311-linux_armv7l.whl size=16179704 sha256=1eb79947613ba9cd3763d2d6ab16c955dae6ba4c7296cd5fc0ee685d9605cbd7 2023-09-12T09:14:58,843 Stored in directory: /home/piwheels/.cache/pip/wheels/52/2d/ed/b1e5c4ad36c535940dc1b1da900d05f571f88ff26f7be95f4c 2023-09-12T09:14:58,861 Successfully built pysam 2023-09-12T09:15:01,596 Installing collected packages: distlib, wheel, typing-extensions, setuptools, pluggy, platformdirs, packaging, filelock, cython, colorama, click, chardet, cachetools, virtualenv, setuptools_scm, pysam, pyproject-api, cython-setuptools, tox 2023-09-12T09:15:02,157 Creating /tmp/pip-build-env-_w_3349q/overlay/local/bin 2023-09-12T09:15:02,159 changing mode of /tmp/pip-build-env-_w_3349q/overlay/local/bin/wheel to 755 2023-09-12T09:15:07,767 changing mode of /tmp/pip-build-env-_w_3349q/overlay/local/bin/cygdb to 755 2023-09-12T09:15:07,769 changing mode of /tmp/pip-build-env-_w_3349q/overlay/local/bin/cython to 755 2023-09-12T09:15:07,771 changing mode of /tmp/pip-build-env-_w_3349q/overlay/local/bin/cythonize to 755 2023-09-12T09:15:08,970 changing mode of /tmp/pip-build-env-_w_3349q/overlay/local/bin/chardetect to 755 2023-09-12T09:15:09,790 changing mode of /tmp/pip-build-env-_w_3349q/overlay/local/bin/virtualenv to 755 2023-09-12T09:15:12,280 changing mode of /tmp/pip-build-env-_w_3349q/overlay/local/bin/cython-setuptools to 755 2023-09-12T09:15:13,001 changing mode of /tmp/pip-build-env-_w_3349q/overlay/local/bin/tox to 755 2023-09-12T09:15:13,267 Successfully installed cachetools-5.3.1 chardet-5.2.0 click-8.1.7 colorama-0.4.6 cython-3.0.2 cython-setuptools-0.2.3 distlib-0.3.7 filelock-3.12.3 packaging-23.1 platformdirs-3.10.0 pluggy-1.3.0 pyproject-api-1.6.1 pysam-0.21.0 setuptools-68.2.1 setuptools_scm-7.1.0 tox-4.11.3 typing-extensions-4.7.1 virtualenv-20.24.5 wheel-0.41.2 2023-09-12T09:15:14,576 Installing build dependencies: finished with status 'done' 2023-09-12T09:15:14,580 Getting requirements to build wheel: started 2023-09-12T09:15:14,581 Running command Getting requirements to build wheel 2023-09-12T09:15:25,339 warning: uta_align/align/cigar_utils.pyx:23:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310 2023-09-12T09:15:25,340 warning: uta_align/align/cigar_utils.pyx:24:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310 2023-09-12T09:15:25,635 Error compiling Cython file: 2023-09-12T09:15:25,635 ------------------------------------------------------------ 2023-09-12T09:15:25,636 ... 2023-09-12T09:15:25,637 INSERTION.inverse = DELETION 2023-09-12T09:15:25,637 DELETION.inverse = INSERTION 2023-09-12T09:15:25,638 SEQ_MATCH.inverse = SEQ_MATCH 2023-09-12T09:15:25,638 SEQ_MISMATCH.inverse = SEQ_MISMATCH 2023-09-12T09:15:25,639 cpdef tuple BAM_OPS = (MATCH, INSERTION, DELETION, SKIPPED, SOFT_CLIP, HARD_CLIP, PADDING, SEQ_MATCH, SEQ_MISMATCH) 2023-09-12T09:15:25,639 ^ 2023-09-12T09:15:25,640 ------------------------------------------------------------ 2023-09-12T09:15:25,641 uta_align/align/cigar_utils.pyx:62:6: Variables cannot be declared with 'cpdef'. Use 'cdef' instead. 2023-09-12T09:15:25,642 Error compiling Cython file: 2023-09-12T09:15:25,643 ------------------------------------------------------------ 2023-09-12T09:15:25,643 ... 2023-09-12T09:15:25,644 # Create mapping from ord(char_op) to op 2023-09-12T09:15:25,644 _temp_map = [None]*256 2023-09-12T09:15:25,645 for _op in BAM_OPS: 2023-09-12T09:15:25,645 _temp_map[_op.code] = _op 2023-09-12T09:15:25,646 cpdef tuple BAM_OP_CHAR_MAP = tuple(_temp_map) 2023-09-12T09:15:25,647 ^ 2023-09-12T09:15:25,647 ------------------------------------------------------------ 2023-09-12T09:15:25,648 uta_align/align/cigar_utils.pyx:69:6: Variables cannot be declared with 'cpdef'. Use 'cdef' instead. 2023-09-12T09:15:26,178 Compiling uta_align/align/algorithms.pyx because it changed. 2023-09-12T09:15:26,178 Compiling uta_align/align/cigar_utils.pyx because it changed. 2023-09-12T09:15:26,179 [1/2] Cythonizing uta_align/align/algorithms.pyx 2023-09-12T09:15:26,180 [2/2] Cythonizing uta_align/align/cigar_utils.pyx 2023-09-12T09:15:26,180 Traceback (most recent call last): 2023-09-12T09:15:26,181 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in 2023-09-12T09:15:26,181 main() 2023-09-12T09:15:26,182 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main 2023-09-12T09:15:26,182 json_out['return_val'] = hook(**hook_input['kwargs']) 2023-09-12T09:15:26,183 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,184 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel 2023-09-12T09:15:26,184 return hook(config_settings) 2023-09-12T09:15:26,185 ^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,185 File "/tmp/pip-build-env-_w_3349q/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 355, in get_requires_for_build_wheel 2023-09-12T09:15:26,186 return self._get_build_requires(config_settings, requirements=['wheel']) 2023-09-12T09:15:26,187 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,188 File "/tmp/pip-build-env-_w_3349q/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 325, in _get_build_requires 2023-09-12T09:15:26,189 self.run_setup() 2023-09-12T09:15:26,189 File "/tmp/pip-build-env-_w_3349q/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 341, in run_setup 2023-09-12T09:15:26,190 exec(code, locals()) 2023-09-12T09:15:26,191 File "", line 52, in 2023-09-12T09:15:26,192 File "/tmp/pip-build-env-_w_3349q/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1134, in cythonize 2023-09-12T09:15:26,194 cythonize_one(*args) 2023-09-12T09:15:26,195 File "/tmp/pip-build-env-_w_3349q/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one 2023-09-12T09:15:26,196 raise CompileError(None, pyx_file) 2023-09-12T09:15:26,197 Cython.Compiler.Errors.CompileError: uta_align/align/cigar_utils.pyx 2023-09-12T09:15:26,601 ERROR: [present-rich] Getting requirements to build wheel exited with 1 2023-09-12T09:15:26,614 [bold magenta]full command[/]: [blue]/usr/bin/python3 /usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py get_requires_for_build_wheel /tmp/tmpwi36wme4[/] 2023-09-12T09:15:26,615 [bold magenta]cwd[/]: /tmp/pip-wheel-rbjky0ie/uta-align_e9dcb470382545c9af83a1648402e2ff 2023-09-12T09:15:26,615 Getting requirements to build wheel: finished with status 'error' 2023-09-12T09:15:26,618 ERROR: [present-rich] Getting requirements to build wheel exited with 1 2023-09-12T09:15:26,623 Exception information: 2023-09-12T09:15:26,623 Traceback (most recent call last): 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-12T09:15:26,623 status = run_func(*args) 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-12T09:15:26,623 return func(self, options, args) 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 147, in run 2023-09-12T09:15:26,623 requirement_set = resolver.resolve(reqs, check_supported_wheels=True) 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 92, in resolve 2023-09-12T09:15:26,623 result = self._result = resolver.resolve( 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve 2023-09-12T09:15:26,623 state = resolution.resolve(requirements, max_rounds=max_rounds) 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 397, in resolve 2023-09-12T09:15:26,623 self._add_to_criteria(self.state.criteria, r, parent=None) 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria 2023-09-12T09:15:26,623 if not criterion.candidates: 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/structs.py", line 156, in __bool__ 2023-09-12T09:15:26,623 return bool(self._sequence) 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in __bool__ 2023-09-12T09:15:26,623 return any(self) 2023-09-12T09:15:26,623 ^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in 2023-09-12T09:15:26,623 return (c for c in iterator if id(c) not in self._incompatible_ids) 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built 2023-09-12T09:15:26,623 candidate = func() 2023-09-12T09:15:26,623 ^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link 2023-09-12T09:15:26,623 self._link_candidate_cache[link] = LinkCandidate( 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__ 2023-09-12T09:15:26,623 super().__init__( 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ 2023-09-12T09:15:26,623 self.dist = self._prepare() 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare 2023-09-12T09:15:26,623 dist = self._prepare_distribution() 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution 2023-09-12T09:15:26,623 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 538, in prepare_linked_requirement 2023-09-12T09:15:26,623 return self._prepare_linked_requirement(req, parallel_builds) 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 653, in _prepare_linked_requirement 2023-09-12T09:15:26,623 dist = _get_prepared_distribution( 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution 2023-09-12T09:15:26,623 abstract_dist.prepare_distribution_metadata( 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 48, in prepare_distribution_metadata 2023-09-12T09:15:26,623 self._install_build_reqs(finder) 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 118, in _install_build_reqs 2023-09-12T09:15:26,623 build_reqs = self._get_build_requires_wheel() 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 95, in _get_build_requires_wheel 2023-09-12T09:15:26,623 return backend.get_requires_for_build_wheel() 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/misc.py", line 697, in get_requires_for_build_wheel 2023-09-12T09:15:26,623 return super().get_requires_for_build_wheel(config_settings=cs) 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_impl.py", line 166, in get_requires_for_build_wheel 2023-09-12T09:15:26,623 return self._call_hook('get_requires_for_build_wheel', { 2023-09-12T09:15:26,623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook 2023-09-12T09:15:26,623 self._subprocess_runner( 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/subprocess.py", line 252, in runner 2023-09-12T09:15:26,623 call_subprocess( 2023-09-12T09:15:26,623 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess 2023-09-12T09:15:26,623 raise error 2023-09-12T09:15:26,623 pip._internal.exceptions.InstallationSubprocessError: Getting requirements to build wheel exited with 1 2023-09-12T09:15:26,638 Removed uta-align==0.2.0a1 from https://files.pythonhosted.org/packages/0f/a2/e6bdd37d746c294c7a6374664078ecf2d34677b52c5267ff0576f669eb15/uta-align-0.2.0a1.tar.gz from build tracker '/tmp/pip-build-tracker-5_yokgeh' 2023-09-12T09:15:26,639 Removed build tracker: '/tmp/pip-build-tracker-5_yokgeh'