2023-09-12T10:22:32,413 Created temporary directory: /tmp/pip-build-tracker-ugq70naj
2023-09-12T10:22:32,415 Initialized build tracking at /tmp/pip-build-tracker-ugq70naj
2023-09-12T10:22:32,415 Created build tracker: /tmp/pip-build-tracker-ugq70naj
2023-09-12T10:22:32,416 Entered build tracker: /tmp/pip-build-tracker-ugq70naj
2023-09-12T10:22:32,417 Created temporary directory: /tmp/pip-wheel-1vk64f1r
2023-09-12T10:22:32,420 Created temporary directory: /tmp/pip-ephem-wheel-cache-dt_7e6tn
2023-09-12T10:22:32,445 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-12T10:22:32,448 2 location(s) to search for versions of uta-align:
2023-09-12T10:22:32,448 * https://pypi.org/simple/uta-align/
2023-09-12T10:22:32,448 * https://www.piwheels.org/simple/uta-align/
2023-09-12T10:22:32,449 Fetching project page and analyzing links: https://pypi.org/simple/uta-align/
2023-09-12T10:22:32,450 Getting page https://pypi.org/simple/uta-align/
2023-09-12T10:22:32,451 Found index url https://pypi.org/simple/
2023-09-12T10:22:32,591 Fetched page https://pypi.org/simple/uta-align/ as application/vnd.pypi.simple.v1+json
2023-09-12T10:22:32,597   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
2023-09-12T10:22:32,597   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/)
2023-09-12T10:22:32,598   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
2023-09-12T10:22:32,599   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/)
2023-09-12T10:22:32,599   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
2023-09-12T10:22:32,600   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/)
2023-09-12T10:22:32,601   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/)
2023-09-12T10:22:32,601   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
2023-09-12T10:22:32,602   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/)
2023-09-12T10:22:32,603   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
2023-09-12T10:22:32,603   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/)
2023-09-12T10:22:32,604   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
2023-09-12T10:22:32,605   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/)
2023-09-12T10:22:32,605   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
2023-09-12T10:22:32,606   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/)
2023-09-12T10:22:32,606   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
2023-09-12T10:22:32,607   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/)
2023-09-12T10:22:32,607   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
2023-09-12T10:22:32,608   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/)
2023-09-12T10:22:32,608   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
2023-09-12T10:22:32,609   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/)
2023-09-12T10:22:32,610   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/)
2023-09-12T10:22:32,610   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
2023-09-12T10:22:32,611   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
2023-09-12T10:22:32,612   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
2023-09-12T10:22:32,613   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
2023-09-12T10:22:32,613 Fetching project page and analyzing links: https://www.piwheels.org/simple/uta-align/
2023-09-12T10:22:32,614 Getting page https://www.piwheels.org/simple/uta-align/
2023-09-12T10:22:32,615 Found index url https://www.piwheels.org/simple/
2023-09-12T10:22:33,852 Fetched page https://www.piwheels.org/simple/uta-align/ as text/html
2023-09-12T10:22:33,867   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/)
2023-09-12T10:22:33,868   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/)
2023-09-12T10:22:33,869   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/)
2023-09-12T10:22:33,871   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/)
2023-09-12T10:22:33,871   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/)
2023-09-12T10:22:33,872   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/)
2023-09-12T10:22:33,873   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/)
2023-09-12T10:22:33,874   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/)
2023-09-12T10:22:33,874   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/)
2023-09-12T10:22:33,875   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/)
2023-09-12T10:22:33,876   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/)
2023-09-12T10:22:33,877   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/)
2023-09-12T10:22:33,878   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/)
2023-09-12T10:22:33,879   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/)
2023-09-12T10:22:33,880   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/)
2023-09-12T10:22:33,880   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/)
2023-09-12T10:22:33,881   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/)
2023-09-12T10:22:33,883   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/)
2023-09-12T10:22:33,883   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/)
2023-09-12T10:22:33,884   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/)
2023-09-12T10:22:33,885   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/)
2023-09-12T10:22:33,886   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/)
2023-09-12T10:22:33,887   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/)
2023-09-12T10:22:33,887   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/)
2023-09-12T10:22:33,888   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/)
2023-09-12T10:22:33,889   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/)
2023-09-12T10:22:33,890 Skipping link: not a file: https://www.piwheels.org/simple/uta-align/
2023-09-12T10:22:33,891 Skipping link: not a file: https://pypi.org/simple/uta-align/
2023-09-12T10:22:33,932 Given no hashes to check 1 links for project 'uta-align': discarding no candidates
2023-09-12T10:22:33,951 Collecting uta-align==0.2.0
2023-09-12T10:22:33,953   Created temporary directory: /tmp/pip-unpack-a4dl5nxr
2023-09-12T10:22:34,307   Downloading uta-align-0.2.0.tar.gz (268 kB)
2023-09-12T10:22:34,497   Added uta-align==0.2.0 from https://files.pythonhosted.org/packages/64/bc/5306c731e7d4d304e9d1f7fee2a8fa1d79640626ccaac9f9df660078893c/uta-align-0.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-ugq70naj'
2023-09-12T10:22:34,507   Created temporary directory: /tmp/pip-build-env-i12qz61r
2023-09-12T10:22:34,511   Installing build dependencies: started
2023-09-12T10:22:34,512   Running command pip subprocess to install build dependencies
2023-09-12T10:22:35,671   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-09-12T10:22:36,162   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-12T10:22:37,992   Collecting cython>=0.29
2023-09-12T10:22:37,994     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
2023-09-12T10:22:38,000     Using cached Cython-3.0.2-py2.py3-none-any.whl.metadata (3.1 kB)
2023-09-12T10:22:38,554   Collecting cython-setuptools
2023-09-12T10:22:38,564     Downloading https://www.piwheels.org/simple/cython-setuptools/cython_setuptools-0.2.3-py3-none-any.whl (9.7 kB)
2023-09-12T10:22:38,790   Collecting pysam>=0.15
2023-09-12T10:22:38,930     Downloading pysam-0.21.0.tar.gz (4.1 MB)
2023-09-12T10:22:39,307        ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.1/4.1 MB 11.0 MB/s eta 0:00:00
2023-09-12T10:22:41,254     Installing build dependencies: started
2023-09-12T10:22:41,256     Running command pip subprocess to install build dependencies
2023-09-12T10:22:42,900     Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-12T10:22:44,537     Collecting setuptools>=59.0
2023-09-12T10:22:44,539       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
2023-09-12T10:22:44,544       Using cached setuptools-68.2.1-py3-none-any.whl.metadata (6.3 kB)
2023-09-12T10:22:44,748     Collecting wheel
2023-09-12T10:22:44,764       Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB)
2023-09-12T10:22:46,140     Collecting Cython<3.0,>=0.29.30
2023-09-12T10:22:46,141       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
2023-09-12T10:22:46,148       Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB)
2023-09-12T10:22:46,326     Using cached setuptools-68.2.1-py3-none-any.whl (807 kB)
2023-09-12T10:22:46,360     Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB)
2023-09-12T10:22:48,852     Installing collected packages: wheel, setuptools, Cython
2023-09-12T10:22:53,943     Successfully installed Cython-0.29.36 setuptools-68.2.1 wheel-0.41.2
2023-09-12T10:22:54,554     Installing build dependencies: finished with status 'done'
2023-09-12T10:22:54,557     Getting requirements to build wheel: started
2023-09-12T10:22:54,557     Running command Getting requirements to build wheel
2023-09-12T10:22:55,249     # pysam: cython is available - using cythonize if necessary
2023-09-12T10:22:55,250     # pysam: htslib mode is shared
2023-09-12T10:22:55,251     # pysam: HTSLIB_CONFIGURE_OPTIONS=None
2023-09-12T10:22:55,251     # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc
2023-09-12T10:22:55,252     # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:22:55,253     # pysam: (sysconfig) LDFLAGS=  -g -fwrapv -O2
2023-09-12T10:22:55,546     checking for gcc... arm-linux-gnueabihf-gcc
2023-09-12T10:22:55,825     checking whether the C compiler works... yes
2023-09-12T10:22:55,826     checking for C compiler default output file name... a.out
2023-09-12T10:22:55,997     checking for suffix of executables...
2023-09-12T10:22:56,197     checking whether we are cross compiling... no
2023-09-12T10:22:56,281     checking for suffix of object files... o
2023-09-12T10:22:56,358     checking whether we are using the GNU C compiler... yes
2023-09-12T10:22:56,431     checking whether arm-linux-gnueabihf-gcc accepts -g... yes
2023-09-12T10:22:56,562     checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed
2023-09-12T10:22:56,566     checking for ranlib... ranlib
2023-09-12T10:22:56,578     checking for grep that handles long lines and -e... /usr/bin/grep
2023-09-12T10:22:56,676     checking for C compiler warning flags... -Wall
2023-09-12T10:22:56,686     configure: Default CFLAGS_ARM/X86:  -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:22:56,744     checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no
2023-09-12T10:22:56,791     checking whether C compiler accepts -mavx2... no
2023-09-12T10:22:56,845     checking whether C compiler accepts -mavx512f... no
2023-09-12T10:22:57,308     checking whether C compiler supports ARM Neon... no
2023-09-12T10:22:57,312     checking for pkg-config... /usr/bin/pkg-config
2023-09-12T10:22:57,318     checking pkg-config is at least version 0.9.0... yes
2023-09-12T10:22:57,320     checking for special C compiler options needed for large files... no
2023-09-12T10:22:57,505     checking for _FILE_OFFSET_BITS value needed for large files... 64
2023-09-12T10:22:57,519     checking shared library type for unknown-Linux... plain .so
2023-09-12T10:22:57,629     checking whether the linker supports versioned symbols... no
2023-09-12T10:22:57,799     checking whether the compiler accepts -fvisibility=hidden... yes
2023-09-12T10:22:57,905     checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E
2023-09-12T10:22:58,016     checking for egrep... /usr/bin/grep -E
2023-09-12T10:22:58,510     checking for ANSI C header files... yes
2023-09-12T10:22:58,629     checking for sys/types.h... yes
2023-09-12T10:22:58,762     checking for sys/stat.h... yes
2023-09-12T10:22:58,894     checking for stdlib.h... yes
2023-09-12T10:22:59,036     checking for string.h... yes
2023-09-12T10:22:59,177     checking for memory.h... yes
2023-09-12T10:22:59,316     checking for strings.h... yes
2023-09-12T10:22:59,459     checking for inttypes.h... yes
2023-09-12T10:22:59,603     checking for stdint.h... yes
2023-09-12T10:22:59,762     checking for unistd.h... yes
2023-09-12T10:22:59,787     checking for stdlib.h... (cached) yes
2023-09-12T10:22:59,810     checking for unistd.h... (cached) yes
2023-09-12T10:22:59,988     checking for sys/param.h... yes
2023-09-12T10:23:00,189     checking for getpagesize... yes
2023-09-12T10:23:00,567     checking for working mmap... yes
2023-09-12T10:23:00,764     checking for gmtime_r... yes
2023-09-12T10:23:00,970     checking for fsync... yes
2023-09-12T10:23:01,205     checking for drand48... yes
2023-09-12T10:23:01,426     checking for srand48_deterministic... no
2023-09-12T10:23:01,597     checking whether fdatasync is declared... yes
2023-09-12T10:23:01,779     checking for fdatasync... yes
2023-09-12T10:23:02,213     checking for library containing log... -lm
2023-09-12T10:23:02,319     checking for zlib.h... yes
2023-09-12T10:23:02,499     checking for inflate in -lz... yes
2023-09-12T10:23:02,685     checking for library containing recv... none required
2023-09-12T10:23:02,805     checking for bzlib.h... yes
2023-09-12T10:23:02,992     checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
2023-09-12T10:23:03,205     checking for lzma.h... yes
2023-09-12T10:23:03,396     checking for lzma_easy_buffer_encode in -llzma... yes
2023-09-12T10:23:03,402     checking whether htscodecs files are present... yes
2023-09-12T10:23:03,485     checking for libdeflate.h... yes
2023-09-12T10:23:03,704     checking for libdeflate_deflate_compress in -ldeflate... yes
2023-09-12T10:23:03,858     checking for curl/curl.h... yes
2023-09-12T10:23:04,228     checking for curl_easy_pause in -lcurl... yes
2023-09-12T10:23:04,466     checking for CCHmac... no
2023-09-12T10:23:05,067     checking for library containing HMAC... -lcrypto
2023-09-12T10:23:05,257     checking for library containing regcomp... none required
2023-09-12T10:23:05,380     checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
2023-09-12T10:23:05,446     configure: creating ./config.status
2023-09-12T10:23:05,742     config.status: creating config.mk
2023-09-12T10:23:05,783     config.status: creating htslib.pc.tmp
2023-09-12T10:23:05,828     config.status: creating config.h
2023-09-12T10:23:05,864     config.status: linking htscodecs_bundled.mk to htscodecs.mk
2023-09-12T10:23:06,485     # pysam: htslib configure options: --enable-libcurl
2023-09-12T10:23:06,485     # pysam: htslib_config HTS_CFLAGS_AVX2=
2023-09-12T10:23:06,486     # pysam: htslib_config HTS_CFLAGS_AVX512=
2023-09-12T10:23:06,487     # pysam: htslib_config HTS_CFLAGS_SSE4=
2023-09-12T10:23:06,487     # pysam: htslib_config HTS_HAVE_NEON=
2023-09-12T10:23:06,488     # 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
2023-09-12T10:23:06,489     # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
2023-09-12T10:23:06,490     # pysam: htslib_config PLATFORM=default
2023-09-12T10:23:06,490     # pysam: config_option: ENABLE_GCS=1
2023-09-12T10:23:06,491     # pysam: config_option: ENABLE_PLUGINS=0
2023-09-12T10:23:06,492     # pysam: config_option: ENABLE_S3=1
2023-09-12T10:23:06,493     # pysam: config_option: HAVE_COMMONCRYPTO=0
2023-09-12T10:23:06,493     # pysam: config_option: HAVE_HMAC=1
2023-09-12T10:23:06,494     # pysam: config_option: HAVE_LIBBZ2=1
2023-09-12T10:23:06,495     # pysam: config_option: HAVE_LIBCURL=1
2023-09-12T10:23:06,496     # pysam: config_option: HAVE_LIBDEFLATE=1
2023-09-12T10:23:06,497     # pysam: config_option: HAVE_LIBLZMA=1
2023-09-12T10:23:06,498     # pysam: config_option: HAVE_MMAP=1
2023-09-12T10:23:06,498     running egg_info
2023-09-12T10:23:06,500     writing pysam.egg-info/PKG-INFO
2023-09-12T10:23:06,503     writing dependency_links to pysam.egg-info/dependency_links.txt
2023-09-12T10:23:06,505     writing requirements to pysam.egg-info/requires.txt
2023-09-12T10:23:06,507     writing top-level names to pysam.egg-info/top_level.txt
2023-09-12T10:23:06,545     reading manifest file 'pysam.egg-info/SOURCES.txt'
2023-09-12T10:23:06,570     reading manifest template 'MANIFEST.in'
2023-09-12T10:23:06,571     warning: no files found matching 'KNOWN_BUGS'
2023-09-12T10:23:06,573     warning: no files found matching 'THANKS'
2023-09-12T10:23:06,581     no previously-included directories found matching 'tests/'
2023-09-12T10:23:06,700     adding license file 'COPYING'
2023-09-12T10:23:06,701     adding license file 'AUTHORS'
2023-09-12T10:23:06,723     writing manifest file 'pysam.egg-info/SOURCES.txt'
2023-09-12T10:23:06,846     Getting requirements to build wheel: finished with status 'done'
2023-09-12T10:23:06,858     Preparing metadata (pyproject.toml): started
2023-09-12T10:23:06,859     Running command Preparing metadata (pyproject.toml)
2023-09-12T10:23:07,493     # pysam: cython is available - using cythonize if necessary
2023-09-12T10:23:07,494     # pysam: htslib mode is shared
2023-09-12T10:23:07,495     # pysam: HTSLIB_CONFIGURE_OPTIONS=None
2023-09-12T10:23:07,496     # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc
2023-09-12T10:23:07,498     # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:23:07,499     # pysam: (sysconfig) LDFLAGS=  -g -fwrapv -O2
2023-09-12T10:23:07,790     checking for gcc... arm-linux-gnueabihf-gcc
2023-09-12T10:23:08,045     checking whether the C compiler works... yes
2023-09-12T10:23:08,046     checking for C compiler default output file name... a.out
2023-09-12T10:23:08,212     checking for suffix of executables...
2023-09-12T10:23:08,429     checking whether we are cross compiling... no
2023-09-12T10:23:08,525     checking for suffix of object files... o
2023-09-12T10:23:08,625     checking whether we are using the GNU C compiler... yes
2023-09-12T10:23:08,705     checking whether arm-linux-gnueabihf-gcc accepts -g... yes
2023-09-12T10:23:08,947     checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed
2023-09-12T10:23:08,952     checking for ranlib... ranlib
2023-09-12T10:23:08,966     checking for grep that handles long lines and -e... /usr/bin/grep
2023-09-12T10:23:09,076     checking for C compiler warning flags... -Wall
2023-09-12T10:23:09,093     configure: Default CFLAGS_ARM/X86:  -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:23:09,172     checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no
2023-09-12T10:23:09,265     checking whether C compiler accepts -mavx2... no
2023-09-12T10:23:09,356     checking whether C compiler accepts -mavx512f... no
2023-09-12T10:23:10,029     checking whether C compiler supports ARM Neon... no
2023-09-12T10:23:10,032     checking for pkg-config... /usr/bin/pkg-config
2023-09-12T10:23:10,038     checking pkg-config is at least version 0.9.0... yes
2023-09-12T10:23:10,043     checking for special C compiler options needed for large files... no
2023-09-12T10:23:10,351     checking for _FILE_OFFSET_BITS value needed for large files... 64
2023-09-12T10:23:10,368     checking shared library type for unknown-Linux... plain .so
2023-09-12T10:23:10,496     checking whether the linker supports versioned symbols... no
2023-09-12T10:23:10,681     checking whether the compiler accepts -fvisibility=hidden... yes
2023-09-12T10:23:10,797     checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E
2023-09-12T10:23:10,940     checking for egrep... /usr/bin/grep -E
2023-09-12T10:23:11,508     checking for ANSI C header files... yes
2023-09-12T10:23:11,635     checking for sys/types.h... yes
2023-09-12T10:23:11,774     checking for sys/stat.h... yes
2023-09-12T10:23:11,938     checking for stdlib.h... yes
2023-09-12T10:23:12,079     checking for string.h... yes
2023-09-12T10:23:12,220     checking for memory.h... yes
2023-09-12T10:23:12,361     checking for strings.h... yes
2023-09-12T10:23:12,506     checking for inttypes.h... yes
2023-09-12T10:23:12,649     checking for stdint.h... yes
2023-09-12T10:23:12,806     checking for unistd.h... yes
2023-09-12T10:23:12,830     checking for stdlib.h... (cached) yes
2023-09-12T10:23:12,854     checking for unistd.h... (cached) yes
2023-09-12T10:23:13,028     checking for sys/param.h... yes
2023-09-12T10:23:13,223     checking for getpagesize... yes
2023-09-12T10:23:13,596     checking for working mmap... yes
2023-09-12T10:23:13,791     checking for gmtime_r... yes
2023-09-12T10:23:13,994     checking for fsync... yes
2023-09-12T10:23:14,232     checking for drand48... yes
2023-09-12T10:23:14,454     checking for srand48_deterministic... no
2023-09-12T10:23:14,625     checking whether fdatasync is declared... yes
2023-09-12T10:23:14,809     checking for fdatasync... yes
2023-09-12T10:23:15,234     checking for library containing log... -lm
2023-09-12T10:23:15,341     checking for zlib.h... yes
2023-09-12T10:23:15,523     checking for inflate in -lz... yes
2023-09-12T10:23:15,706     checking for library containing recv... none required
2023-09-12T10:23:15,813     checking for bzlib.h... yes
2023-09-12T10:23:16,002     checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
2023-09-12T10:23:16,182     checking for lzma.h... yes
2023-09-12T10:23:16,371     checking for lzma_easy_buffer_encode in -llzma... yes
2023-09-12T10:23:16,377     checking whether htscodecs files are present... yes
2023-09-12T10:23:16,454     checking for libdeflate.h... yes
2023-09-12T10:23:16,670     checking for libdeflate_deflate_compress in -ldeflate... yes
2023-09-12T10:23:16,819     checking for curl/curl.h... yes
2023-09-12T10:23:17,176     checking for curl_easy_pause in -lcurl... yes
2023-09-12T10:23:17,396     checking for CCHmac... no
2023-09-12T10:23:18,011     checking for library containing HMAC... -lcrypto
2023-09-12T10:23:18,197     checking for library containing regcomp... none required
2023-09-12T10:23:18,319     checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
2023-09-12T10:23:18,384     configure: creating ./config.status
2023-09-12T10:23:18,672     config.status: creating config.mk
2023-09-12T10:23:18,713     config.status: creating htslib.pc.tmp
2023-09-12T10:23:18,756     config.status: creating config.h
2023-09-12T10:23:18,775     config.status: config.h is unchanged
2023-09-12T10:23:18,781     config.status: linking htscodecs_bundled.mk to htscodecs.mk
2023-09-12T10:23:19,283     # pysam: htslib configure options: --enable-libcurl
2023-09-12T10:23:19,284     # pysam: htslib_config HTS_CFLAGS_AVX2=
2023-09-12T10:23:19,285     # pysam: htslib_config HTS_CFLAGS_AVX512=
2023-09-12T10:23:19,285     # pysam: htslib_config HTS_CFLAGS_SSE4=
2023-09-12T10:23:19,286     # pysam: htslib_config HTS_HAVE_NEON=
2023-09-12T10:23:19,287     # 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
2023-09-12T10:23:19,288     # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
2023-09-12T10:23:19,289     # pysam: htslib_config PLATFORM=default
2023-09-12T10:23:19,290     # pysam: config_option: ENABLE_GCS=1
2023-09-12T10:23:19,291     # pysam: config_option: ENABLE_PLUGINS=0
2023-09-12T10:23:19,292     # pysam: config_option: ENABLE_S3=1
2023-09-12T10:23:19,293     # pysam: config_option: HAVE_COMMONCRYPTO=0
2023-09-12T10:23:19,294     # pysam: config_option: HAVE_HMAC=1
2023-09-12T10:23:19,294     # pysam: config_option: HAVE_LIBBZ2=1
2023-09-12T10:23:19,295     # pysam: config_option: HAVE_LIBCURL=1
2023-09-12T10:23:19,296     # pysam: config_option: HAVE_LIBDEFLATE=1
2023-09-12T10:23:19,297     # pysam: config_option: HAVE_LIBLZMA=1
2023-09-12T10:23:19,298     # pysam: config_option: HAVE_MMAP=1
2023-09-12T10:23:19,299     running dist_info
2023-09-12T10:23:19,300     creating /tmp/pip-modern-metadata-qtgugs08/pysam.egg-info
2023-09-12T10:23:19,301     writing /tmp/pip-modern-metadata-qtgugs08/pysam.egg-info/PKG-INFO
2023-09-12T10:23:19,302     writing dependency_links to /tmp/pip-modern-metadata-qtgugs08/pysam.egg-info/dependency_links.txt
2023-09-12T10:23:19,303     writing requirements to /tmp/pip-modern-metadata-qtgugs08/pysam.egg-info/requires.txt
2023-09-12T10:23:19,304     writing top-level names to /tmp/pip-modern-metadata-qtgugs08/pysam.egg-info/top_level.txt
2023-09-12T10:23:19,305     writing manifest file '/tmp/pip-modern-metadata-qtgugs08/pysam.egg-info/SOURCES.txt'
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2023-09-12T10:23:19,368     reading manifest template 'MANIFEST.in'
2023-09-12T10:23:19,369     warning: no files found matching 'KNOWN_BUGS'
2023-09-12T10:23:19,370     warning: no files found matching 'THANKS'
2023-09-12T10:23:19,379     no previously-included directories found matching 'tests/'
2023-09-12T10:23:19,483     adding license file 'COPYING'
2023-09-12T10:23:19,484     adding license file 'AUTHORS'
2023-09-12T10:23:19,501     writing manifest file '/tmp/pip-modern-metadata-qtgugs08/pysam.egg-info/SOURCES.txt'
2023-09-12T10:23:19,502     creating '/tmp/pip-modern-metadata-qtgugs08/pysam-0.21.0.dist-info'
2023-09-12T10:23:19,655     Preparing metadata (pyproject.toml): finished with status 'done'
2023-09-12T10:23:21,197   Collecting setuptools>=45
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2023-09-12T10:23:25,558   Building wheels for collected packages: pysam
2023-09-12T10:23:25,563     Building wheel for pysam (pyproject.toml): started
2023-09-12T10:23:25,564     Running command Building wheel for pysam (pyproject.toml)
2023-09-12T10:23:26,183     # pysam: cython is available - using cythonize if necessary
2023-09-12T10:23:26,184     # pysam: htslib mode is shared
2023-09-12T10:23:26,185     # pysam: HTSLIB_CONFIGURE_OPTIONS=None
2023-09-12T10:23:26,186     # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc
2023-09-12T10:23:26,186     # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:23:26,187     # pysam: (sysconfig) LDFLAGS=  -g -fwrapv -O2
2023-09-12T10:23:26,477     checking for gcc... arm-linux-gnueabihf-gcc
2023-09-12T10:23:26,730     checking whether the C compiler works... yes
2023-09-12T10:23:26,731     checking for C compiler default output file name... a.out
2023-09-12T10:23:26,895     checking for suffix of executables...
2023-09-12T10:23:27,129     checking whether we are cross compiling... no
2023-09-12T10:23:27,214     checking for suffix of object files... o
2023-09-12T10:23:27,292     checking whether we are using the GNU C compiler... yes
2023-09-12T10:23:27,364     checking whether arm-linux-gnueabihf-gcc accepts -g... yes
2023-09-12T10:23:27,491     checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed
2023-09-12T10:23:27,493     checking for ranlib... ranlib
2023-09-12T10:23:27,501     checking for grep that handles long lines and -e... /usr/bin/grep
2023-09-12T10:23:27,574     checking for C compiler warning flags... -Wall
2023-09-12T10:23:27,584     configure: Default CFLAGS_ARM/X86:  -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:23:27,640     checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no
2023-09-12T10:23:27,688     checking whether C compiler accepts -mavx2... no
2023-09-12T10:23:27,760     checking whether C compiler accepts -mavx512f... no
2023-09-12T10:23:28,266     checking whether C compiler supports ARM Neon... no
2023-09-12T10:23:28,268     checking for pkg-config... /usr/bin/pkg-config
2023-09-12T10:23:28,273     checking pkg-config is at least version 0.9.0... yes
2023-09-12T10:23:28,275     checking for special C compiler options needed for large files... no
2023-09-12T10:23:28,462     checking for _FILE_OFFSET_BITS value needed for large files... 64
2023-09-12T10:23:28,476     checking shared library type for unknown-Linux... plain .so
2023-09-12T10:23:28,588     checking whether the linker supports versioned symbols... no
2023-09-12T10:23:28,759     checking whether the compiler accepts -fvisibility=hidden... yes
2023-09-12T10:23:28,865     checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E
2023-09-12T10:23:28,976     checking for egrep... /usr/bin/grep -E
2023-09-12T10:23:29,474     checking for ANSI C header files... yes
2023-09-12T10:23:29,594     checking for sys/types.h... yes
2023-09-12T10:23:29,729     checking for sys/stat.h... yes
2023-09-12T10:23:29,862     checking for stdlib.h... yes
2023-09-12T10:23:30,004     checking for string.h... yes
2023-09-12T10:23:30,146     checking for memory.h... yes
2023-09-12T10:23:30,286     checking for strings.h... yes
2023-09-12T10:23:30,430     checking for inttypes.h... yes
2023-09-12T10:23:30,575     checking for stdint.h... yes
2023-09-12T10:23:30,732     checking for unistd.h... yes
2023-09-12T10:23:30,756     checking for stdlib.h... (cached) yes
2023-09-12T10:23:30,779     checking for unistd.h... (cached) yes
2023-09-12T10:23:30,992     checking for sys/param.h... yes
2023-09-12T10:23:31,189     checking for getpagesize... yes
2023-09-12T10:23:31,529     checking for working mmap... yes
2023-09-12T10:23:31,753     checking for gmtime_r... yes
2023-09-12T10:23:31,956     checking for fsync... yes
2023-09-12T10:23:32,165     checking for drand48... yes
2023-09-12T10:23:32,386     checking for srand48_deterministic... no
2023-09-12T10:23:32,586     checking whether fdatasync is declared... yes
2023-09-12T10:23:32,768     checking for fdatasync... yes
2023-09-12T10:23:33,167     checking for library containing log... -lm
2023-09-12T10:23:33,273     checking for zlib.h... yes
2023-09-12T10:23:33,454     checking for inflate in -lz... yes
2023-09-12T10:23:33,637     checking for library containing recv... none required
2023-09-12T10:23:33,726     checking for bzlib.h... yes
2023-09-12T10:23:33,909     checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
2023-09-12T10:23:34,120     checking for lzma.h... yes
2023-09-12T10:23:34,307     checking for lzma_easy_buffer_encode in -llzma... yes
2023-09-12T10:23:34,312     checking whether htscodecs files are present... yes
2023-09-12T10:23:34,389     checking for libdeflate.h... yes
2023-09-12T10:23:34,572     checking for libdeflate_deflate_compress in -ldeflate... yes
2023-09-12T10:23:34,727     checking for curl/curl.h... yes
2023-09-12T10:23:35,122     checking for curl_easy_pause in -lcurl... yes
2023-09-12T10:23:35,330     checking for CCHmac... no
2023-09-12T10:23:35,930     checking for library containing HMAC... -lcrypto
2023-09-12T10:23:36,117     checking for library containing regcomp... none required
2023-09-12T10:23:36,240     checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
2023-09-12T10:23:36,306     configure: creating ./config.status
2023-09-12T10:23:36,598     config.status: creating config.mk
2023-09-12T10:23:36,639     config.status: creating htslib.pc.tmp
2023-09-12T10:23:36,683     config.status: creating config.h
2023-09-12T10:23:36,703     config.status: config.h is unchanged
2023-09-12T10:23:36,709     config.status: linking htscodecs_bundled.mk to htscodecs.mk
2023-09-12T10:23:37,183     # pysam: htslib configure options: --enable-libcurl
2023-09-12T10:23:37,184     # pysam: htslib_config HTS_CFLAGS_AVX2=
2023-09-12T10:23:37,185     # pysam: htslib_config HTS_CFLAGS_AVX512=
2023-09-12T10:23:37,186     # pysam: htslib_config HTS_CFLAGS_SSE4=
2023-09-12T10:23:37,186     # pysam: htslib_config HTS_HAVE_NEON=
2023-09-12T10:23:37,187     # 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
2023-09-12T10:23:37,188     # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
2023-09-12T10:23:37,188     # pysam: htslib_config PLATFORM=default
2023-09-12T10:23:37,189     # pysam: config_option: ENABLE_GCS=1
2023-09-12T10:23:37,190     # pysam: config_option: ENABLE_PLUGINS=0
2023-09-12T10:23:37,190     # pysam: config_option: ENABLE_S3=1
2023-09-12T10:23:37,191     # pysam: config_option: HAVE_COMMONCRYPTO=0
2023-09-12T10:23:37,191     # pysam: config_option: HAVE_HMAC=1
2023-09-12T10:23:37,192     # pysam: config_option: HAVE_LIBBZ2=1
2023-09-12T10:23:37,192     # pysam: config_option: HAVE_LIBCURL=1
2023-09-12T10:23:37,193     # pysam: config_option: HAVE_LIBDEFLATE=1
2023-09-12T10:23:37,193     # pysam: config_option: HAVE_LIBLZMA=1
2023-09-12T10:23:37,194     # pysam: config_option: HAVE_MMAP=1
2023-09-12T10:23:37,194     running bdist_wheel
2023-09-12T10:23:37,199     running build
2023-09-12T10:23:37,200     running build_py
2023-09-12T10:23:37,205     creating build
2023-09-12T10:23:37,207     creating build/lib.linux-armv7l-cpython-311
2023-09-12T10:23:37,208     creating build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,210     copying pysam/config.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,216     copying pysam/bcftools.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,217     copying pysam/Pileup.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,219     copying pysam/samtools.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,221     copying pysam/utils.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,223     copying pysam/version.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,226     copying pysam/__init__.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,229     creating build/lib.linux-armv7l-cpython-311/pysam/include
2023-09-12T10:23:37,230     copying pysam/include/__init__.py -> build/lib.linux-armv7l-cpython-311/pysam/include
2023-09-12T10:23:37,235     running egg_info
2023-09-12T10:23:37,241     writing pysam.egg-info/PKG-INFO
2023-09-12T10:23:37,244     writing dependency_links to pysam.egg-info/dependency_links.txt
2023-09-12T10:23:37,246     writing requirements to pysam.egg-info/requires.txt
2023-09-12T10:23:37,248     writing top-level names to pysam.egg-info/top_level.txt
2023-09-12T10:23:37,309     reading manifest file 'pysam.egg-info/SOURCES.txt'
2023-09-12T10:23:37,346     reading manifest template 'MANIFEST.in'
2023-09-12T10:23:37,348     warning: no files found matching 'KNOWN_BUGS'
2023-09-12T10:23:37,350     warning: no files found matching 'THANKS'
2023-09-12T10:23:37,358     no previously-included directories found matching 'tests/'
2023-09-12T10:23:37,460     adding license file 'COPYING'
2023-09-12T10:23:37,461     adding license file 'AUTHORS'
2023-09-12T10:23:37,485     writing manifest file 'pysam.egg-info/SOURCES.txt'
2023-09-12T10:23:37,490     /tmp/pip-build-env-32z5ywps/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.
2023-09-12T10:23:37,494     !!

2023-09-12T10:23:37,495             ********************************************************************************
2023-09-12T10:23:37,496             ############################
2023-09-12T10:23:37,496             # Package would be ignored #
2023-09-12T10:23:37,497             ############################
2023-09-12T10:23:37,497             Python recognizes 'pysam.include.htslib.cram' as an importable package[^1],
2023-09-12T10:23:37,498             but it is absent from setuptools' `packages` configuration.

2023-09-12T10:23:37,500             This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-12T10:23:37,501             package, please make sure that 'pysam.include.htslib.cram' is explicitly added
2023-09-12T10:23:37,502             to the `packages` configuration field.

2023-09-12T10:23:37,504             Alternatively, you can also rely on setuptools' discovery methods
2023-09-12T10:23:37,505             (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-12T10:23:37,506             instead of `find_packages(...)`/`find:`).

2023-09-12T10:23:37,508             You can read more about "package discovery" on setuptools documentation page:

2023-09-12T10:23:37,510             - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-12T10:23:37,511             If you don't want 'pysam.include.htslib.cram' to be distributed and are
2023-09-12T10:23:37,512             already explicitly excluding 'pysam.include.htslib.cram' via
2023-09-12T10:23:37,513             `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-12T10:23:37,514             you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-12T10:23:37,515             combination with a more fine grained `package-data` configuration.

2023-09-12T10:23:37,516             You can read more about "package data files" on setuptools documentation page:

2023-09-12T10:23:37,518             - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-12T10:23:37,521             [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-12T10:23:37,522                   even if it does not contain any `.py` files.
2023-09-12T10:23:37,523                   On the other hand, currently there is no concept of package data
2023-09-12T10:23:37,523                   directory, all directories are treated like packages.
2023-09-12T10:23:37,524             ********************************************************************************

2023-09-12T10:23:37,526     !!
2023-09-12T10:23:37,527       check.warn(importable)
2023-09-12T10:23:37,528     /tmp/pip-build-env-32z5ywps/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.
2023-09-12T10:23:37,529     !!

2023-09-12T10:23:37,531             ********************************************************************************
2023-09-12T10:23:37,532             ############################
2023-09-12T10:23:37,533             # Package would be ignored #
2023-09-12T10:23:37,534             ############################
2023-09-12T10:23:37,535             Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package[^1],
2023-09-12T10:23:37,536             but it is absent from setuptools' `packages` configuration.

2023-09-12T10:23:37,538             This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-12T10:23:37,539             package, please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is explicitly added
2023-09-12T10:23:37,541             to the `packages` configuration field.

2023-09-12T10:23:37,543             Alternatively, you can also rely on setuptools' discovery methods
2023-09-12T10:23:37,545             (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-12T10:23:37,546             instead of `find_packages(...)`/`find:`).

2023-09-12T10:23:37,548             You can read more about "package discovery" on setuptools documentation page:

2023-09-12T10:23:37,550             - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-12T10:23:37,551             If you don't want 'pysam.include.htslib.htscodecs.htscodecs' to be distributed and are
2023-09-12T10:23:37,552             already explicitly excluding 'pysam.include.htslib.htscodecs.htscodecs' via
2023-09-12T10:23:37,553             `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-12T10:23:37,554             you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-12T10:23:37,555             combination with a more fine grained `package-data` configuration.

2023-09-12T10:23:37,557             You can read more about "package data files" on setuptools documentation page:

2023-09-12T10:23:37,559             - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-12T10:23:37,568             [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-12T10:23:37,583                   even if it does not contain any `.py` files.
2023-09-12T10:23:37,593                   On the other hand, currently there is no concept of package data
2023-09-12T10:23:37,594                   directory, all directories are treated like packages.
2023-09-12T10:23:37,594             ********************************************************************************

2023-09-12T10:23:37,595     !!
2023-09-12T10:23:37,596       check.warn(importable)
2023-09-12T10:23:37,597     /tmp/pip-build-env-32z5ywps/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.
2023-09-12T10:23:37,597     !!

2023-09-12T10:23:37,598             ********************************************************************************
2023-09-12T10:23:37,599             ############################
2023-09-12T10:23:37,599             # Package would be ignored #
2023-09-12T10:23:37,600             ############################
2023-09-12T10:23:37,600             Python recognizes 'pysam.include.htslib.m4' as an importable package[^1],
2023-09-12T10:23:37,601             but it is absent from setuptools' `packages` configuration.

2023-09-12T10:23:37,602             This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-12T10:23:37,603             package, please make sure that 'pysam.include.htslib.m4' is explicitly added
2023-09-12T10:23:37,604             to the `packages` configuration field.

2023-09-12T10:23:37,605             Alternatively, you can also rely on setuptools' discovery methods
2023-09-12T10:23:37,605             (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-12T10:23:37,606             instead of `find_packages(...)`/`find:`).

2023-09-12T10:23:37,607             You can read more about "package discovery" on setuptools documentation page:

2023-09-12T10:23:37,609             - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-12T10:23:37,610             If you don't want 'pysam.include.htslib.m4' to be distributed and are
2023-09-12T10:23:37,611             already explicitly excluding 'pysam.include.htslib.m4' via
2023-09-12T10:23:37,612             `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-12T10:23:37,612             you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-12T10:23:37,613             combination with a more fine grained `package-data` configuration.

2023-09-12T10:23:37,615             You can read more about "package data files" on setuptools documentation page:

2023-09-12T10:23:37,616             - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-12T10:23:37,618             [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-12T10:23:37,619                   even if it does not contain any `.py` files.
2023-09-12T10:23:37,620                   On the other hand, currently there is no concept of package data
2023-09-12T10:23:37,621                   directory, all directories are treated like packages.
2023-09-12T10:23:37,621             ********************************************************************************

2023-09-12T10:23:37,623     !!
2023-09-12T10:23:37,623       check.warn(importable)
2023-09-12T10:23:37,624     /tmp/pip-build-env-32z5ywps/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.
2023-09-12T10:23:37,625     !!

2023-09-12T10:23:37,626             ********************************************************************************
2023-09-12T10:23:37,627             ############################
2023-09-12T10:23:37,628             # Package would be ignored #
2023-09-12T10:23:37,628             ############################
2023-09-12T10:23:37,629             Python recognizes 'pysam.include.htslib.os' as an importable package[^1],
2023-09-12T10:23:37,630             but it is absent from setuptools' `packages` configuration.

2023-09-12T10:23:37,631             This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-12T10:23:37,632             package, please make sure that 'pysam.include.htslib.os' is explicitly added
2023-09-12T10:23:37,632             to the `packages` configuration field.

2023-09-12T10:23:37,634             Alternatively, you can also rely on setuptools' discovery methods
2023-09-12T10:23:37,635             (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-12T10:23:37,635             instead of `find_packages(...)`/`find:`).

2023-09-12T10:23:37,636             You can read more about "package discovery" on setuptools documentation page:

2023-09-12T10:23:37,638             - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-12T10:23:37,639             If you don't want 'pysam.include.htslib.os' to be distributed and are
2023-09-12T10:23:37,640             already explicitly excluding 'pysam.include.htslib.os' via
2023-09-12T10:23:37,641             `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-12T10:23:37,641             you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-12T10:23:37,642             combination with a more fine grained `package-data` configuration.

2023-09-12T10:23:37,643             You can read more about "package data files" on setuptools documentation page:

2023-09-12T10:23:37,656             - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-12T10:23:37,660             [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-12T10:23:37,660                   even if it does not contain any `.py` files.
2023-09-12T10:23:37,661                   On the other hand, currently there is no concept of package data
2023-09-12T10:23:37,662                   directory, all directories are treated like packages.
2023-09-12T10:23:37,662             ********************************************************************************

2023-09-12T10:23:37,663     !!
2023-09-12T10:23:37,664       check.warn(importable)
2023-09-12T10:23:37,665     /tmp/pip-build-env-32z5ywps/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.
2023-09-12T10:23:37,665     !!

2023-09-12T10:23:37,666             ********************************************************************************
2023-09-12T10:23:37,669             ############################
2023-09-12T10:23:37,669             # Package would be ignored #
2023-09-12T10:23:37,670             ############################
2023-09-12T10:23:37,671             Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1],
2023-09-12T10:23:37,671             but it is absent from setuptools' `packages` configuration.

2023-09-12T10:23:37,672             This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-12T10:23:37,673             package, please make sure that 'pysam.include.samtools.lz4' is explicitly added
2023-09-12T10:23:37,674             to the `packages` configuration field.

2023-09-12T10:23:37,675             Alternatively, you can also rely on setuptools' discovery methods
2023-09-12T10:23:37,676             (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-12T10:23:37,676             instead of `find_packages(...)`/`find:`).

2023-09-12T10:23:37,678             You can read more about "package discovery" on setuptools documentation page:

2023-09-12T10:23:37,679             - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-12T10:23:37,681             If you don't want 'pysam.include.samtools.lz4' to be distributed and are
2023-09-12T10:23:37,682             already explicitly excluding 'pysam.include.samtools.lz4' via
2023-09-12T10:23:37,682             `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-12T10:23:37,683             you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-12T10:23:37,684             combination with a more fine grained `package-data` configuration.

2023-09-12T10:23:37,685             You can read more about "package data files" on setuptools documentation page:

2023-09-12T10:23:37,686             - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-12T10:23:37,688             [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-12T10:23:37,688                   even if it does not contain any `.py` files.
2023-09-12T10:23:37,689                   On the other hand, currently there is no concept of package data
2023-09-12T10:23:37,696                   directory, all directories are treated like packages.
2023-09-12T10:23:37,703             ********************************************************************************

2023-09-12T10:23:37,726     !!
2023-09-12T10:23:37,732       check.warn(importable)
2023-09-12T10:23:37,733     copying pysam/cbcftools_util.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,733     copying pysam/csamtools_util.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,734     copying pysam/htslib_util.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,734     copying pysam/htslib_util.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,734     copying pysam/libcalignedsegment.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,735     copying pysam/libcalignedsegment.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,735     copying pysam/libcalignedsegment.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,736     copying pysam/libcalignedsegment.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,736     copying pysam/libcalignmentfile.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,737     copying pysam/libcalignmentfile.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,738     copying pysam/libcalignmentfile.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,738     copying pysam/libcalignmentfile.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,738     copying pysam/libcbcf.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,739     copying pysam/libcbcf.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,740     copying pysam/libcbcf.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,742     copying pysam/libcbcf.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,746     copying pysam/libcbcftools.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,751     copying pysam/libcbcftools.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,753     copying pysam/libcbcftools.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,756     copying pysam/libcbcftools.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,757     copying pysam/libcbgzf.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,765     copying pysam/libcbgzf.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,768     copying pysam/libcbgzf.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,770     copying pysam/libcfaidx.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,785     copying pysam/libcfaidx.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,788     copying pysam/libcfaidx.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,791     copying pysam/libcfaidx.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,794     copying pysam/libchtslib.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,809     copying pysam/libchtslib.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,814     copying pysam/libchtslib.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,816     copying pysam/libchtslib.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,818     copying pysam/libcsamfile.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,825     copying pysam/libcsamfile.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,827     copying pysam/libcsamfile.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,829     copying pysam/libcsamfile.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,831     copying pysam/libcsamtools.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,835     copying pysam/libcsamtools.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,837     copying pysam/libcsamtools.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,839     copying pysam/libcsamtools.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,841     copying pysam/libctabix.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,860     copying pysam/libctabix.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,862     copying pysam/libctabix.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,864     copying pysam/libctabix.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,867     copying pysam/libctabixproxies.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,887     copying pysam/libctabixproxies.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,889     copying pysam/libctabixproxies.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,890     copying pysam/libctabixproxies.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,893     copying pysam/libcutils.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,904     copying pysam/libcutils.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,906     copying pysam/libcutils.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,908     copying pysam/libcutils.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,910     copying pysam/libcvcf.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,940     copying pysam/libcvcf.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,942     copying pysam/libcvcf.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,944     copying pysam/libcvcf.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,947     copying pysam/py.typed -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,949     copying pysam/pysam_stream.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,951     copying pysam/pysam_util.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,953     copying pysam/pysam_util.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,955     copying pysam/version.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,957     copying pysam/version.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:37,958     creating build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,959     copying samtools/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,962     copying samtools/README -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,964     copying samtools/amplicon_stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,969     copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,972     copying samtools/bam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,975     copying samtools/bam.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,978     copying samtools/bam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,980     copying samtools/bam2depth.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,983     copying samtools/bam2depth.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,987     copying samtools/bam_addrprg.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,989     copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,992     copying samtools/bam_ampliconclip.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,996     copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:37,999     copying samtools/bam_ampliconclip.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,001     copying samtools/bam_aux.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,003     copying samtools/bam_aux.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,005     copying samtools/bam_cat.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,008     copying samtools/bam_cat.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,011     copying samtools/bam_color.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,014     copying samtools/bam_color.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,016     copying samtools/bam_consensus.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,020     copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,025     copying samtools/bam_fastq.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,028     copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,031     copying samtools/bam_flags.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,033     copying samtools/bam_flags.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,036     copying samtools/bam_import.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,038     copying samtools/bam_import.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,041     copying samtools/bam_index.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,044     copying samtools/bam_index.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,047     copying samtools/bam_lpileup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,049     copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,052     copying samtools/bam_lpileup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,054     copying samtools/bam_markdup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,058     copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,062     copying samtools/bam_mate.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,065     copying samtools/bam_mate.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,067     copying samtools/bam_md.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,070     copying samtools/bam_md.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,073     copying samtools/bam_plbuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,075     copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,077     copying samtools/bam_plbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,079     copying samtools/bam_plcmd.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,082     copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,086     copying samtools/bam_quickcheck.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,088     copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,091     copying samtools/bam_reheader.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,094     copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,096     copying samtools/bam_rmdup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,099     copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,101     copying samtools/bam_rmdupse.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,104     copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,106     copying samtools/bam_samples.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,109     copying samtools/bam_samples.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,112     copying samtools/bam_sort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,116     copying samtools/bam_sort.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,121     copying samtools/bam_split.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,124     copying samtools/bam_split.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,126     copying samtools/bam_stat.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,129     copying samtools/bam_stat.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,131     copying samtools/bamshuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,134     copying samtools/bamshuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,137     copying samtools/bamtk.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,139     copying samtools/bamtk.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,142     copying samtools/bedcov.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,145     copying samtools/bedcov.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,147     copying samtools/bedidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,150     copying samtools/bedidx.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,153     copying samtools/bedidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,155     copying samtools/consensus_pileup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,158     copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,161     copying samtools/consensus_pileup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,163     copying samtools/coverage.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,166     copying samtools/coverage.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,169     copying samtools/cram_size.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,172     copying samtools/cram_size.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,174     copying samtools/cut_target.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,177     copying samtools/cut_target.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,180     copying samtools/dict.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,182     copying samtools/dict.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,185     copying samtools/faidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,187     copying samtools/faidx.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,190     copying samtools/padding.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,193     copying samtools/padding.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,197     copying samtools/phase.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,200     copying samtools/phase.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,202     copying samtools/reference.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,206     copying samtools/reference.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,208     copying samtools/reset.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,212     copying samtools/reset.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,215     copying samtools/sam_opts.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,218     copying samtools/sam_opts.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,220     copying samtools/sam_opts.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,223     copying samtools/sam_utils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,226     copying samtools/sam_utils.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,228     copying samtools/sam_utils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,230     copying samtools/sam_view.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,234     copying samtools/sam_view.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,238     copying samtools/sample.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,240     copying samtools/sample.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,243     copying samtools/sample.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,245     copying samtools/samtools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,248     copying samtools/samtools.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,250     copying samtools/samtools.pysam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,252     copying samtools/splaysort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,255     copying samtools/stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,260     copying samtools/stats.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,264     copying samtools/stats_isize.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,267     copying samtools/stats_isize.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,270     copying samtools/stats_isize.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,272     copying samtools/tmp_file.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,275     copying samtools/tmp_file.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,277     copying samtools/tmp_file.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,280     copying samtools/version.sh -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,282     creating build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4
2023-09-12T10:23:38,283     copying samtools/lz4/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4
2023-09-12T10:23:38,285     copying samtools/lz4/lz4.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4
2023-09-12T10:23:38,289     copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4
2023-09-12T10:23:38,293     copying samtools/lz4/lz4.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4
2023-09-12T10:23:38,296     copying samtools/config.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:38,298     creating build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,299     copying bcftools/HMM.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,302     copying bcftools/HMM.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,305     copying bcftools/HMM.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,308     copying bcftools/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,312     copying bcftools/README -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,314     copying bcftools/abuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,318     copying bcftools/abuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,321     copying bcftools/abuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,324     copying bcftools/bam2bcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,327     copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,331     copying bcftools/bam2bcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,334     copying bcftools/bam2bcf_iaux.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,337     copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,340     copying bcftools/bam2bcf_indel.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,343     copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,346     copying bcftools/bam_sample.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,349     copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,352     copying bcftools/bam_sample.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,354     copying bcftools/bcftools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,357     copying bcftools/bcftools.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,359     copying bcftools/bcftools.pysam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,362     copying bcftools/bin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,364     copying bcftools/bin.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,367     copying bcftools/bin.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,370     copying bcftools/call.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,373     copying bcftools/ccall.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,376     copying bcftools/ccall.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,378     copying bcftools/cigar_state.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,380     copying bcftools/cols.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,383     copying bcftools/cols.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,385     copying bcftools/cols.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,388     copying bcftools/consensus.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,392     copying bcftools/consensus.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,394     copying bcftools/convert.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,398     copying bcftools/convert.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,402     copying bcftools/convert.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,405     copying bcftools/csq.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,411     copying bcftools/csq.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,417     copying bcftools/dbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,420     copying bcftools/dist.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,423     copying bcftools/dist.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,426     copying bcftools/dist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,429     copying bcftools/em.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,432     copying bcftools/em.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,436     copying bcftools/extsort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,439     copying bcftools/extsort.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,442     copying bcftools/extsort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,445     copying bcftools/filter.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:38,451     copying bcftools/filter.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
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2023-09-12T10:23:38,788     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,789     copying htslib/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,792     copying htslib/Makefile -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,795     copying htslib/README -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
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2023-09-12T10:23:38,816     copying htslib/configure -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
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2023-09-12T10:23:38,825     copying htslib/errmod.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
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2023-09-12T10:23:38,836     copying htslib/hfile.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
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2023-09-12T10:23:38,857     copying htslib/hts.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,863     copying htslib/hts_expr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,866     copying htslib/hts_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,870     copying htslib/hts_os.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,872     copying htslib/hts_time_funcs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,876     copying htslib/htscodecs_bundled.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,878     copying htslib/htscodecs_external.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,881     copying htslib/htsfile.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,884     copying htslib/htslib.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,888     copying htslib/htslib.pc.in -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,890     copying htslib/htslib_vars.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,893     copying htslib/kfunc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
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2023-09-12T10:23:38,899     copying htslib/md5.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,902     copying htslib/multipart.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,906     copying htslib/plugin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,909     copying htslib/probaln.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,912     copying htslib/realn.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,915     copying htslib/regidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,919     copying htslib/region.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,922     copying htslib/sam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,928     copying htslib/sam_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,931     copying htslib/synced_bcf_reader.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,936     copying htslib/tabix.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,939     copying htslib/tbx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,943     copying htslib/textutils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,946     copying htslib/textutils_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,950     copying htslib/thread_pool.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,954     copying htslib/thread_pool_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,957     copying htslib/vcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,964     copying htslib/vcf_sweep.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,967     copying htslib/vcfutils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,971     copying htslib/version.sh -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:38,974     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:38,976     copying htslib/cram/cram.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:38,979     copying htslib/cram/cram_codecs.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:38,985     copying htslib/cram/cram_codecs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:38,988     copying htslib/cram/cram_decode.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:38,994     copying htslib/cram/cram_decode.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:38,997     copying htslib/cram/cram_encode.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,003     copying htslib/cram/cram_encode.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,006     copying htslib/cram/cram_external.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,010     copying htslib/cram/cram_index.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,013     copying htslib/cram/cram_index.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,016     copying htslib/cram/cram_io.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,023     copying htslib/cram/cram_io.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,027     copying htslib/cram/cram_samtools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,030     copying htslib/cram/cram_stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,033     copying htslib/cram/cram_stats.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,036     copying htslib/cram/cram_structs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,040     copying htslib/cram/mFILE.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,043     copying htslib/cram/mFILE.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,046     copying htslib/cram/misc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,049     copying htslib/cram/open_trace_file.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,053     copying htslib/cram/open_trace_file.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,056     copying htslib/cram/os.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,059     copying htslib/cram/pooled_alloc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,062     copying htslib/cram/pooled_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,065     copying htslib/cram/string_alloc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,068     copying htslib/cram/string_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:39,071     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs
2023-09-12T10:23:39,073     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,075     copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,079     copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,082     copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,085     copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,088     copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,092     copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,095     copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,098     copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,101     copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,104     copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,107     copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,110     copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,113     copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,117     copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,120     copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,123     copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,125     copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,128     copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,131     copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,133     copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,136     copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,139     copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,144     copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,147     copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,149     copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,153     copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,155     copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,158     copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,160     copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,164     copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,166     copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,168     copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,171     copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,173     copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,176     copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:39,178     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4
2023-09-12T10:23:39,179     copying htslib/m4/ax_check_compile_flag.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4
2023-09-12T10:23:39,181     copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4
2023-09-12T10:23:39,184     copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4
2023-09-12T10:23:39,186     copying htslib/m4/pkg.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4
2023-09-12T10:23:39,189     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os
2023-09-12T10:23:39,190     copying htslib/os/lzma_stub.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os
2023-09-12T10:23:39,193     copying htslib/os/rand.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os
2023-09-12T10:23:39,195     copying htslib/config.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:39,197     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,198     copying htslib/htslib/bgzf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,201     copying htslib/htslib/cram.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,204     copying htslib/htslib/faidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,207     copying htslib/htslib/hfile.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,210     copying htslib/htslib/hts.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,213     copying htslib/htslib/hts_defs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,215     copying htslib/htslib/hts_endian.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,218     copying htslib/htslib/hts_expr.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,220     copying htslib/htslib/hts_log.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,223     copying htslib/htslib/hts_os.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,225     copying htslib/htslib/kbitset.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,227     copying htslib/htslib/kfunc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,230     copying htslib/htslib/khash.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,232     copying htslib/htslib/khash_str2int.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,235     copying htslib/htslib/klist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,237     copying htslib/htslib/knetfile.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,240     copying htslib/htslib/kroundup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,242     copying htslib/htslib/kseq.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,245     copying htslib/htslib/ksort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,248     copying htslib/htslib/kstring.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,250     copying htslib/htslib/regidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,253     copying htslib/htslib/sam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,257     copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,259     copying htslib/htslib/tbx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,261     copying htslib/htslib/thread_pool.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,264     copying htslib/htslib/vcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,268     copying htslib/htslib/vcf_sweep.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,270     copying htslib/htslib/vcfutils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:39,276     running build_ext
2023-09-12T10:23:39,346     skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
2023-09-12T10:23:39,347     skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
2023-09-12T10:23:39,348     skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
2023-09-12T10:23:39,349     skipping 'pysam/libcutils.c' Cython extension (up-to-date)
2023-09-12T10:23:39,351     skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
2023-09-12T10:23:39,352     skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
2023-09-12T10:23:39,353     skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
2023-09-12T10:23:39,354     skipping 'pysam/libctabix.c' Cython extension (up-to-date)
2023-09-12T10:23:39,356     skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
2023-09-12T10:23:39,357     skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
2023-09-12T10:23:39,358     skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
2023-09-12T10:23:39,359     skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
2023-09-12T10:23:39,361     skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
2023-09-12T10:23:39,362     creating htslib/config_vars.h for 'pysam.libchtslib' extension
2023-09-12T10:23:39,363     building 'libhts.a'
2023-09-12T10:23:39,408     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
2023-09-12T10:23:39,900     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
2023-09-12T10:23:40,816     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o bcf_sr_sort.o bcf_sr_sort.c
2023-09-12T10:23:43,371     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
2023-09-12T10:23:46,643     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
2023-09-12T10:23:47,318     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
2023-09-12T10:23:49,269     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
2023-09-12T10:23:53,803     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
2023-09-12T10:23:55,494     echo '#define HTS_VERSION_TEXT "1.17"' > version.h
2023-09-12T10:23:55,501     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
2023-09-12T10:24:04,045     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
2023-09-12T10:24:05,995     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o hts_os.o hts_os.c
2023-09-12T10:24:06,106     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
2023-09-12T10:24:06,751     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
2023-09-12T10:24:07,307     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o probaln.o probaln.c
2023-09-12T10:24:08,048     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
2023-09-12T10:24:08,974     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
2023-09-12T10:24:10,521     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 region.o region.c
2023-09-12T10:24:11,164     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
2023-09-12T10:24:25,346     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
2023-09-12T10:24:28,108     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
2023-09-12T10:24:28,460     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
2023-09-12T10:24:29,330     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
2023-09-12T10:24:30,300     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
2023-09-12T10:24:31,259     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
2023-09-12T10:24:45,876     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
2023-09-12T10:24:49,141     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
2023-09-12T10:24:54,722     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
2023-09-12T10:25:00,982     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
2023-09-12T10:25:09,097     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
2023-09-12T10:25:10,257     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
2023-09-12T10:25:11,723     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
2023-09-12T10:25:19,458     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
2023-09-12T10:25:20,196     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 cram/mFILE.o cram/mFILE.c
2023-09-12T10:25:20,857     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
2023-09-12T10:25:21,387     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
2023-09-12T10:25:21,569     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
2023-09-12T10:25:21,766     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 htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
2023-09-12T10:25:25,571     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
2023-09-12T10:25:29,609     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
2023-09-12T10:25:29,676     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
2023-09-12T10:25:30,513     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
2023-09-12T10:25:35,377     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
2023-09-12T10:25:38,613     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
2023-09-12T10:25:40,722     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
2023-09-12T10:25:41,193     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
2023-09-12T10:25:44,138     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
2023-09-12T10:25:44,419     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
2023-09-12T10:25:44,865     hfile_libcurl.c: In function ‘libcurl_open’:
2023-09-12T10:25:44,867     hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations]
2023-09-12T10:25:44,868      1335 |         if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD,
2023-09-12T10:25:44,868           |         ^~
2023-09-12T10:25:44,869     In file included from hfile_libcurl.c:47:
2023-09-12T10:25:44,870     /usr/include/arm-linux-gnueabihf/curl/curl.h:2858:3: note: declared here
2023-09-12T10:25:44,871      2858 |   CURLINFO_CONTENT_LENGTH_DOWNLOAD
2023-09-12T10:25:44,872           |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:25:46,929     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
2023-09-12T10:25:47,417     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
2023-09-12T10:25:50,393     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
2023-09-12T10:25:52,733     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
2023-09-12T10:25:54,267     ranlib libhts.a
2023-09-12T10:25:55,731     building 'pysam.libchtslib' extension
2023-09-12T10:25:55,732     creating build/temp.linux-armv7l-cpython-311
2023-09-12T10:25:55,733     creating build/temp.linux-armv7l-cpython-311/pysam
2023-09-12T10:25:55,735     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:25:56,077     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:11,314     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:11,920     creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
2023-09-12T10:26:11,923     building 'pysam.libcsamtools' extension
2023-09-12T10:26:11,924     creating build/temp.linux-armv7l-cpython-311/samtools
2023-09-12T10:26:11,927     creating build/temp.linux-armv7l-cpython-311/samtools/lz4
2023-09-12T10:26:11,929     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:12,983     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:17,138     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:17,719     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:20,248     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:20,979     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:22,965     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:23,191     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:24,009     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:24,299     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:27,408     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:28,813     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:29,052     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:30,061     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:30,515     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:31,140     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:36,123     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:37,750     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:38,830     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:39,039     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:42,679     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:43,032     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:43,813     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:45,293     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:46,806     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:47,641     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:56,886     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:58,199     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:26:59,009     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:01,286     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:01,777     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:02,889     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:04,679     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:05,316     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:06,453     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:06,653     samtools/cram_size.c.pysam.c: In function ‘cram_size’:
2023-09-12T10:27:06,655     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=]
2023-09-12T10:27:06,656       563 |     fprintf(outfp, "Total file size       %18"PRId64"\n", end);
2023-09-12T10:27:06,656           |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~            ~~~
2023-09-12T10:27:06,657           |                                                           |
2023-09-12T10:27:06,658           |                                                           off_t {aka long int}
2023-09-12T10:27:06,659     In file included from /tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib/htslib/hts.h:33,
2023-09-12T10:27:06,659                      from /tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib/htslib/sam.h:33,
2023-09-12T10:27:06,660                      from samtools/cram_size.c.pysam.c:39:
2023-09-12T10:27:06,661     /usr/include/inttypes.h:57:41: note: format string is defined here
2023-09-12T10:27:06,662        57 | # define PRId64         __PRI64_PREFIX "d"
2023-09-12T10:27:06,664     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=]
2023-09-12T10:27:06,666       564 |     fprintf(outfp, "Format overhead size  %18"PRId64"\n", end - tot_size);
2023-09-12T10:27:06,667           |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~            ~~~~~~~~~~~~~~
2023-09-12T10:27:06,669           |                                                               |
2023-09-12T10:27:06,671           |                                                               off_t {aka long int}
2023-09-12T10:27:06,672     /usr/include/inttypes.h:57:41: note: format string is defined here
2023-09-12T10:27:06,673        57 | # define PRId64         __PRI64_PREFIX "d"
2023-09-12T10:27:07,527     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:08,188     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:09,235     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:09,885     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:16,080     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:17,426     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:20,591     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:21,559     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:22,619     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:22,929     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:23,471     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:26,561     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:27,584     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:27,788     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:32,949     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:33,641     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:34,116     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:34,507     building 'pysam.libcbcftools' extension
2023-09-12T10:27:34,508     creating build/temp.linux-armv7l-cpython-311/bcftools
2023-09-12T10:27:34,511     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:35,531     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:38,331     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:40,856     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:42,562     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:45,058     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:46,992     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:47,191     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:47,506     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:48,234     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:48,469     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:50,948     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:27:57,161     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:06,365     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:06,630     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:07,198     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:07,750     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:21,790     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:22,389     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:23,029     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:23,464     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:23,808     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:27,709     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:30,401     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:31,470     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:33,078     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:34,963     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:36,379     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:39,563     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:40,027     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:40,460     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:40,824     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:41,230     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:50,759     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:52,142     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:54,833     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:56,961     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:28:59,652     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:03,270     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:04,837     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:07,948     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:08,317     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:08,958     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:10,724     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:13,164     bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’:
2023-09-12T10:29:13,166     bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
2023-09-12T10:29:13,172       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
2023-09-12T10:29:13,172           |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:29:13,173     In file included from /tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib/htslib/kstring.h:30,
2023-09-12T10:29:13,174                      from /tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib/htslib/hts.h:37,
2023-09-12T10:29:13,174                      from /tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib/htslib/vcf.h:39,
2023-09-12T10:29:13,175                      from bcftools/vcfmerge.c.pysam.c:35:
2023-09-12T10:29:13,176     /usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’ declared here
2023-09-12T10:29:13,177       556 | extern void *calloc (size_t __nmemb, size_t __size)
2023-09-12T10:29:13,177           |              ^~~~~~
2023-09-12T10:29:22,104     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:30,687     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:30,985     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:32,289     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:34,922     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:36,512     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:37,320     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:41,807     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:43,800     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:44,241     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:44,582     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:45,652     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:46,111     building 'pysam.libcutils' extension
2023-09-12T10:29:46,112     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:58,048     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:58,197     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:29:58,378     building 'pysam.libcalignmentfile' extension
2023-09-12T10:29:58,379     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:30:03,218     pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
2023-09-12T10:30:03,297     pysam/libcalignmentfile.c:28658:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:30:03,340     28658 |         (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
2023-09-12T10:30:03,372           |               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:30:03,452     pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
2023-09-12T10:30:03,475     pysam/libcalignmentfile.c:14341:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:30:03,482     14341 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
2023-09-12T10:30:03,530           |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:30:44,530     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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,$ORIGIN
2023-09-12T10:30:44,760     building 'pysam.libcsamfile' extension
2023-09-12T10:30:44,761     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-armv7l-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2023-09-12T10:30:47,108     arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcsamfile.o -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2023-09-12T10:30:47,264     building 'pysam.libcalignedsegment' extension
2023-09-12T10:30:47,265     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:30:55,957     pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
2023-09-12T10:30:55,972     pysam/libcalignedsegment.c:14415:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:30:55,973     14415 |   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
2023-09-12T10:30:55,975           |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:31:49,580     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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,$ORIGIN
2023-09-12T10:31:49,864     building 'pysam.libctabix' extension
2023-09-12T10:31:49,865     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-armv7l-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2023-09-12T10:32:13,580     arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libctabix.o -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2023-09-12T10:32:13,771     building 'pysam.libcfaidx' extension
2023-09-12T10:32:13,772     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:32:28,389     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:32:28,566     building 'pysam.libcbcf' extension
2023-09-12T10:32:28,567     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:32:39,017     pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’:
2023-09-12T10:32:39,083     pysam/libcbcf.c:67371:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:32:39,085     67371 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
2023-09-12T10:32:39,085           |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:32:39,098     pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’:
2023-09-12T10:32:39,165     pysam/libcbcf.c:67096:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:32:39,166     67096 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
2023-09-12T10:32:39,166           |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:32:39,172     pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’:
2023-09-12T10:32:39,239     pysam/libcbcf.c:72230:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:32:39,240     72230 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
2023-09-12T10:32:39,241           |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:32:40,048     pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’:
2023-09-12T10:32:40,084     pysam/libcbcf.c:35394:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:32:40,085     35394 |           bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
2023-09-12T10:32:40,086           |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:32:40,118     pysam/libcbcf.c:35420:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:32:40,119     35420 |           bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
2023-09-12T10:32:40,120           |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:33:54,702     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:33:55,035     building 'pysam.libcbgzf' extension
2023-09-12T10:33:55,036     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:34:00,656     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:34:00,823     building 'pysam.libctabixproxies' extension
2023-09-12T10:34:00,824     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:34:21,397     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:34:21,589     building 'pysam.libcvcf' extension
2023-09-12T10:34:21,590     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/htslib -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/samtools/lz4 -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/bcftools -I/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:35:01,067     pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’:
2023-09-12T10:35:01,094     pysam/libcvcf.c:25833:15: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized]
2023-09-12T10:35:01,094     25833 |   __pyx_t_8 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 873, __pyx_L1_error)
2023-09-12T10:35:01,095           |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:35:01,116     pysam/libcvcf.c:20265:10: note: ‘__pyx_v_qual’ was declared here
2023-09-12T10:35:01,116     20265 |   double __pyx_v_qual;
2023-09-12T10:35:01,117           |          ^~~~~~~~~~~~
2023-09-12T10:35:28,439     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-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67/pysam -L/tmp/pip-install-31yeq0ch/pysam_72f18c1093e84b21a44796c2cdfdfb67 -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
2023-09-12T10:35:29,648     installing to build/bdist.linux-armv7l/wheel
2023-09-12T10:35:29,650     running install
2023-09-12T10:35:29,675     running install_lib
2023-09-12T10:35:29,681     creating build/bdist.linux-armv7l
2023-09-12T10:35:29,682     creating build/bdist.linux-armv7l/wheel
2023-09-12T10:35:29,687     creating build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:29,689     copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:29,761     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:29,764     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:29,766     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:29,768     creating build/bdist.linux-armv7l/wheel/pysam/include
2023-09-12T10:35:29,772     creating build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,773     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plcmd.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,778     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_view.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,783     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,787     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,790     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,796     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_flags.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,799     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,802     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_stat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,805     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/phase.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,810     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,813     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_reheader.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,816     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamtk.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,819     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_color.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,822     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,825     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,828     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,830     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_md.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,834     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_markdup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,839     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/amplicon_stats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,843     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,846     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,849     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,855     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/amplicon_stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,859     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cut_target.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,863     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,866     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamshuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,869     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam2depth.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,873     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_markdup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,877     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plcmd.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,881     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_addrprg.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,884     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,887     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,890     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdupse.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,894     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,897     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_fastq.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,901     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_aux.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,903     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cut_target.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,906     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/coverage.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,910     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,912     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,915     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_mate.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,919     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedcov.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,922     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,924     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/padding.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,929     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,932     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_mate.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,936     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,939     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,942     creating build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4
2023-09-12T10:35:29,944     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4
2023-09-12T10:35:29,950     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4
2023-09-12T10:35:29,953     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4
2023-09-12T10:35:29,957     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4
2023-09-12T10:35:29,961     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_sort.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,968     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reference.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,972     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_quickcheck.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,975     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_flags.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,978     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,981     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,985     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,990     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reset.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,994     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_reheader.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:29,998     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamshuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,002     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,005     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,008     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,011     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_quickcheck.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,015     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/padding.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,018     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,021     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,025     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,028     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_aux.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,031     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/faidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,035     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_addrprg.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,038     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_samples.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,042     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,046     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_split.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,050     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdupse.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,054     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/faidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,057     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cram_size.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,059     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reset.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,062     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_import.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,064     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_fastq.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,067     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_index.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,069     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,071     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_sort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,076     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,078     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedcov.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,080     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,082     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_index.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,085     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/README -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,087     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_md.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,089     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,091     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/splaysort.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,094     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_stat.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,096     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamtk.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,098     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/dict.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,101     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/phase.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,103     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,106     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,108     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reference.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,111     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_import.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,113     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,116     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,118     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,120     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_cat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,123     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_samples.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,125     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,129     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_split.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,132     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,135     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/dict.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,137     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_cat.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,140     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,143     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/coverage.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,145     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam2depth.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,149     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,151     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,153     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_view.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,156     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cram_size.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,159     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_color.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:30,161     copying build/lib.linux-armv7l-cpython-311/pysam/include/__init__.py -> build/bdist.linux-armv7l/wheel/pysam/include
2023-09-12T10:35:30,165     creating build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,167     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,170     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mpileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,173     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/call.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,175     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,178     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,180     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,182     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,185     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,187     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,189     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,192     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,194     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,196     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mpileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,201     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfstats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,204     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcnv.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,207     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,211     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,213     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,215     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsom.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,218     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,220     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/em.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,222     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcnv.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,226     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/reheader.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,228     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfroh.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,232     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,234     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,236     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfroh.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,240     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/main.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,242     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,244     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfhead.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,247     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfplugin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,251     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cigar_state.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,254     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/main.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,257     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mw.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,262     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,267     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,270     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsom.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,274     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,277     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfview.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,281     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/csq.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,288     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,292     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/reheader.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,295     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,298     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,301     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mcall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,305     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,308     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,310     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_indel.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,312     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,315     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfnorm.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,319     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,321     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,322     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hex.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,324     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconvert.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,327     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,331     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,333     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,335     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,337     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,339     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,341     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsort.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,344     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,346     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,348     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,350     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,353     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,358     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfgtcheck.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,361     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfplugin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,364     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfhead.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,366     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfindex.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,368     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,370     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,374     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,376     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconvert.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,379     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,382     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,385     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfquery.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,388     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcffilter.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,392     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/variantkey.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,396     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/csq.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,404     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,409     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,413     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,418     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tabix.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,422     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,426     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,430     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,433     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfview.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,438     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfmerge.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,447     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,457     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,460     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfindex.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,463     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcffilter.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,467     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,470     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ccall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,473     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfmerge.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,479     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,481     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,483     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,486     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,488     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,490     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfisec.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,492     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,494     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,497     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,499     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,501     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,504     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,506     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,508     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ccall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,511     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/README -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,513     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/rbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,515     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,518     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfannotate.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,522     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,524     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,527     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,529     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,531     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kheap.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,534     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,536     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,538     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconcat.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,541     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,543     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,546     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconcat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,549     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/utlist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,553     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfstats.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,556     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,558     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfisec.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,561     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,564     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,566     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,568     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,570     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tabix.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,572     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,575     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfquery.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,577     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfannotate.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,583     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,586     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,588     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/khash_str2str.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,590     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfnorm.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,594     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,597     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/em.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,599     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,602     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mcall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:30,606     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,607     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bcf_sr_sort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,609     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/realn.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,612     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,617     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.h.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,619     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/regidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,622     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,625     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,627     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_encode.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,629     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_codecs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,633     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/string_alloc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,635     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/misc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,637     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_index.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,640     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/os.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,642     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,645     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/open_trace_file.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,647     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/mFILE.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,649     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_io.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,652     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_external.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,654     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_codecs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,656     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/pooled_alloc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,658     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_samtools.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,660     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/string_alloc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,663     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,665     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/pooled_alloc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,667     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_io.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,674     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_decode.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,682     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_index.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,684     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/mFILE.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,688     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_decode.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,690     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/open_trace_file.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,694     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_structs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,698     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_stats.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,700     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_encode.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:30,709     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/kstring.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,713     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4
2023-09-12T10:35:30,714     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
2023-09-12T10:35:30,717     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4/pkg.m4 -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4
2023-09-12T10:35:30,720     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
2023-09-12T10:35:30,722     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
2023-09-12T10:35:30,725     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/md5.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,728     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/sam_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,731     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/probaln.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,734     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/sam.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,747     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.mk.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,750     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/tbx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,755     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_s3.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,759     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/header.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,762     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/configure -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,771     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcf_sweep.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,774     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/kfunc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,776     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/builddir_vars.mk.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,778     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/thread_pool.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,782     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,784     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/thread_pool_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,786     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/errmod.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,788     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htsfile.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,791     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_os.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,793     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_expr.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,796     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,799     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bcf_sr_sort.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,801     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_libcurl.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,805     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib.pc.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,806     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bgzf.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,811     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs_bundled.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,813     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/Makefile -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,816     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_gcs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,818     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib_vars.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,820     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,823     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/configure.ac -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,826     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/faidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,829     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/textutils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,831     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,836     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/os
2023-09-12T10:35:30,837     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os/rand.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/os
2023-09-12T10:35:30,840     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os/lzma_stub.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/os
2023-09-12T10:35:30,842     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/multipart.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,845     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bgzip.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,848     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/README -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,850     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/textutils_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,852     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,854     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs_external.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,856     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,859     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcfutils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,861     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_time_funcs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,864     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/region.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,866     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/plugin.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,868     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,871     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/tabix.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,875     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs
2023-09-12T10:35:30,877     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,878     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
2023-09-12T10:35:30,881     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
2023-09-12T10:35:30,884     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/utils.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,887     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
2023-09-12T10:35:30,889     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
2023-09-12T10:35:30,893     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
2023-09-12T10:35:30,896     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/version.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,897     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
2023-09-12T10:35:30,899     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
2023-09-12T10:35:30,902     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
2023-09-12T10:35:30,904     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
2023-09-12T10:35:30,908     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
2023-09-12T10:35:30,910     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
2023-09-12T10:35:30,913     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
2023-09-12T10:35:30,916     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
2023-09-12T10:35:30,918     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
2023-09-12T10:35:30,922     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
2023-09-12T10:35:30,925     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
2023-09-12T10:35:30,927     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,929     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/utils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,932     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
2023-09-12T10:35:30,934     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
2023-09-12T10:35:30,938     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
2023-09-12T10:35:30,941     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
2023-09-12T10:35:30,944     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pack.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,947     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,949     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
2023-09-12T10:35:30,951     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/varint.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,954     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rle.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,956     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/permute.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,958     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
2023-09-12T10:35:30,961     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pack.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,963     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,965     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
2023-09-12T10:35:30,968     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rle.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:30,970     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/header.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:30,974     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:30,975     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/klist.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:30,978     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:30,981     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kseq.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:30,983     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/sam.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:30,987     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kfunc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:30,989     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcfutils.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:30,991     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_os.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:30,993     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_log.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:30,995     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/khash.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:30,998     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/cram.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,000     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_expr.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,002     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/tbx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,004     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kroundup.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,007     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_defs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,009     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/thread_pool.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,011     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kstring.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,013     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/synced_bcf_reader.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,016     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,019     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,022     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kbitset.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,024     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/faidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,026     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/khash_str2int.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,028     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcf_sweep.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,030     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,032     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_endian.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,035     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/bgzf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,037     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/ksort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,040     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/knetfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:31,042     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/synced_bcf_reader.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:31,045     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_s3_write.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:31,047     copying build/lib.linux-armv7l-cpython-311/pysam/config.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,049     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,050     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,052     copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,055     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,057     copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,059     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,105     copying build/lib.linux-armv7l-cpython-311/pysam/pysam_util.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,107     copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,109     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,113     copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,126     copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,135     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,137     copying build/lib.linux-armv7l-cpython-311/pysam/pysam_util.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,139     copying build/lib.linux-armv7l-cpython-311/pysam/csamtools_util.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,141     copying build/lib.linux-armv7l-cpython-311/pysam/version.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,143     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,145     copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,146     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,151     copying build/lib.linux-armv7l-cpython-311/pysam/bcftools.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,153     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,157     copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,160     copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,162     copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,181     copying build/lib.linux-armv7l-cpython-311/pysam/Pileup.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,184     copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,187     copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,294     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,299     copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,301     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,337     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,343     copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,346     copying build/lib.linux-armv7l-cpython-311/pysam/samtools.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,348     copying build/lib.linux-armv7l-cpython-311/pysam/utils.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,350     copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,371     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,373     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,376     copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,395     copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,398     copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,405     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,408     copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,411     copying build/lib.linux-armv7l-cpython-311/pysam/htslib_util.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,413     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,414     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,477     copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,481     copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,495     copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,516     copying build/lib.linux-armv7l-cpython-311/pysam/version.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,520     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,527     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,601     copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,603     copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,605     copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,616     copying build/lib.linux-armv7l-cpython-311/pysam/cbcftools_util.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,618     copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,620     copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,623     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,656     copying build/lib.linux-armv7l-cpython-311/pysam/htslib_util.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,658     copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,686     copying build/lib.linux-armv7l-cpython-311/pysam/py.typed -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,688     copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,708     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,711     copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,713     copying build/lib.linux-armv7l-cpython-311/pysam/pysam_stream.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,715     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,719     copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,721     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,754     copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,756     copying build/lib.linux-armv7l-cpython-311/pysam/version.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,758     copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,776     copying build/lib.linux-armv7l-cpython-311/pysam/__init__.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,779     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,781     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,827     copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,829     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,893     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,895     running install_egg_info
2023-09-12T10:35:31,900     Copying pysam.egg-info to build/bdist.linux-armv7l/wheel/pysam-0.21.0-py3.11.egg-info
2023-09-12T10:35:31,912     running install_scripts
2023-09-12T10:35:31,964     creating build/bdist.linux-armv7l/wheel/pysam-0.21.0.dist-info/WHEEL
2023-09-12T10:35:31,967     creating '/tmp/pip-wheel-ebpnsq80/.tmp-7gz6grer/pysam-0.21.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-09-12T10:35:31,971     adding 'pysam/Pileup.py'
2023-09-12T10:35:31,972     adding 'pysam/__init__.py'
2023-09-12T10:35:31,974     adding 'pysam/bcftools.py'
2023-09-12T10:35:31,975     adding 'pysam/cbcftools_util.h'
2023-09-12T10:35:31,976     adding 'pysam/config.py'
2023-09-12T10:35:31,977     adding 'pysam/csamtools_util.h'
2023-09-12T10:35:31,979     adding 'pysam/htslib_util.c'
2023-09-12T10:35:31,980     adding 'pysam/htslib_util.h'
2023-09-12T10:35:32,165     adding 'pysam/libcalignedsegment.c'
2023-09-12T10:35:32,794     adding 'pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:32,820     adding 'pysam/libcalignedsegment.pxd'
2023-09-12T10:35:32,822     adding 'pysam/libcalignedsegment.pyi'
2023-09-12T10:35:32,834     adding 'pysam/libcalignedsegment.pyx'
2023-09-12T10:35:32,967     adding 'pysam/libcalignmentfile.c'
2023-09-12T10:35:33,443     adding 'pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:33,462     adding 'pysam/libcalignmentfile.pxd'
2023-09-12T10:35:33,464     adding 'pysam/libcalignmentfile.pyi'
2023-09-12T10:35:33,476     adding 'pysam/libcalignmentfile.pyx'
2023-09-12T10:35:33,707     adding 'pysam/libcbcf.c'
2023-09-12T10:35:34,510     adding 'pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:34,545     adding 'pysam/libcbcf.pxd'
2023-09-12T10:35:34,547     adding 'pysam/libcbcf.pyi'
2023-09-12T10:35:34,562     adding 'pysam/libcbcf.pyx'
2023-09-12T10:35:34,573     adding 'pysam/libcbcftools.c'
2023-09-12T10:35:35,385     adding 'pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:35,415     adding 'pysam/libcbcftools.pxd'
2023-09-12T10:35:35,417     adding 'pysam/libcbcftools.pyi'
2023-09-12T10:35:35,418     adding 'pysam/libcbcftools.pyx'
2023-09-12T10:35:35,448     adding 'pysam/libcbgzf.c'
2023-09-12T10:35:35,520     adding 'pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:35,524     adding 'pysam/libcbgzf.pyi'
2023-09-12T10:35:35,526     adding 'pysam/libcbgzf.pyx'
2023-09-12T10:35:35,578     adding 'pysam/libcfaidx.c'
2023-09-12T10:35:35,749     adding 'pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:35,757     adding 'pysam/libcfaidx.pxd'
2023-09-12T10:35:35,759     adding 'pysam/libcfaidx.pyi'
2023-09-12T10:35:35,761     adding 'pysam/libcfaidx.pyx'
2023-09-12T10:35:35,817     adding 'pysam/libchtslib.c'
2023-09-12T10:35:36,892     adding 'pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:36,944     adding 'pysam/libchtslib.pxd'
2023-09-12T10:35:36,947     adding 'pysam/libchtslib.pyi'
2023-09-12T10:35:36,950     adding 'pysam/libchtslib.pyx'
2023-09-12T10:35:36,972     adding 'pysam/libcsamfile.c'
2023-09-12T10:35:36,997     adding 'pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:37,000     adding 'pysam/libcsamfile.pxd'
2023-09-12T10:35:37,001     adding 'pysam/libcsamfile.pyi'
2023-09-12T10:35:37,003     adding 'pysam/libcsamfile.pyx'
2023-09-12T10:35:37,013     adding 'pysam/libcsamtools.c'
2023-09-12T10:35:37,577     adding 'pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:37,598     adding 'pysam/libcsamtools.pxd'
2023-09-12T10:35:37,599     adding 'pysam/libcsamtools.pyi'
2023-09-12T10:35:37,600     adding 'pysam/libcsamtools.pyx'
2023-09-12T10:35:37,673     adding 'pysam/libctabix.c'
2023-09-12T10:35:37,924     adding 'pysam/libctabix.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:37,938     adding 'pysam/libctabix.pxd'
2023-09-12T10:35:37,940     adding 'pysam/libctabix.pyi'
2023-09-12T10:35:37,945     adding 'pysam/libctabix.pyx'
2023-09-12T10:35:38,019     adding 'pysam/libctabixproxies.c'
2023-09-12T10:35:38,269     adding 'pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:38,279     adding 'pysam/libctabixproxies.pxd'
2023-09-12T10:35:38,281     adding 'pysam/libctabixproxies.pyi'
2023-09-12T10:35:38,284     adding 'pysam/libctabixproxies.pyx'
2023-09-12T10:35:38,326     adding 'pysam/libcutils.c'
2023-09-12T10:35:38,462     adding 'pysam/libcutils.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:38,468     adding 'pysam/libcutils.pxd'
2023-09-12T10:35:38,470     adding 'pysam/libcutils.pyi'
2023-09-12T10:35:38,472     adding 'pysam/libcutils.pyx'
2023-09-12T10:35:38,601     adding 'pysam/libcvcf.c'
2023-09-12T10:35:39,162     adding 'pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:39,185     adding 'pysam/libcvcf.pxd'
2023-09-12T10:35:39,186     adding 'pysam/libcvcf.pyi'
2023-09-12T10:35:39,191     adding 'pysam/libcvcf.pyx'
2023-09-12T10:35:39,193     adding 'pysam/py.typed'
2023-09-12T10:35:39,195     adding 'pysam/pysam_stream.h'
2023-09-12T10:35:39,196     adding 'pysam/pysam_util.c'
2023-09-12T10:35:39,198     adding 'pysam/pysam_util.h'
2023-09-12T10:35:39,200     adding 'pysam/samtools.py'
2023-09-12T10:35:39,201     adding 'pysam/utils.py'
2023-09-12T10:35:39,203     adding 'pysam/version.h'
2023-09-12T10:35:39,204     adding 'pysam/version.py'
2023-09-12T10:35:39,206     adding 'pysam/version.pyi'
2023-09-12T10:35:39,207     adding 'pysam/include/__init__.py'
2023-09-12T10:35:39,212     adding 'pysam/include/bcftools/HMM.c'
2023-09-12T10:35:39,215     adding 'pysam/include/bcftools/HMM.c.pysam.c'
2023-09-12T10:35:39,217     adding 'pysam/include/bcftools/HMM.h'
2023-09-12T10:35:39,223     adding 'pysam/include/bcftools/LICENSE'
2023-09-12T10:35:39,225     adding 'pysam/include/bcftools/README'
2023-09-12T10:35:39,229     adding 'pysam/include/bcftools/abuf.c'
2023-09-12T10:35:39,233     adding 'pysam/include/bcftools/abuf.c.pysam.c'
2023-09-12T10:35:39,235     adding 'pysam/include/bcftools/abuf.h'
2023-09-12T10:35:39,241     adding 'pysam/include/bcftools/bam2bcf.c'
2023-09-12T10:35:39,247     adding 'pysam/include/bcftools/bam2bcf.c.pysam.c'
2023-09-12T10:35:39,249     adding 'pysam/include/bcftools/bam2bcf.h'
2023-09-12T10:35:39,253     adding 'pysam/include/bcftools/bam2bcf_iaux.c'
2023-09-12T10:35:39,257     adding 'pysam/include/bcftools/bam2bcf_iaux.c.pysam.c'
2023-09-12T10:35:39,262     adding 'pysam/include/bcftools/bam2bcf_indel.c'
2023-09-12T10:35:39,267     adding 'pysam/include/bcftools/bam2bcf_indel.c.pysam.c'
2023-09-12T10:35:39,269     adding 'pysam/include/bcftools/bam_sample.c'
2023-09-12T10:35:39,272     adding 'pysam/include/bcftools/bam_sample.c.pysam.c'
2023-09-12T10:35:39,273     adding 'pysam/include/bcftools/bam_sample.h'
2023-09-12T10:35:39,275     adding 'pysam/include/bcftools/bcftools.h'
2023-09-12T10:35:39,276     adding 'pysam/include/bcftools/bcftools.pysam.c'
2023-09-12T10:35:39,278     adding 'pysam/include/bcftools/bcftools.pysam.h'
2023-09-12T10:35:39,279     adding 'pysam/include/bcftools/bin.c'
2023-09-12T10:35:39,280     adding 'pysam/include/bcftools/bin.c.pysam.c'
2023-09-12T10:35:39,282     adding 'pysam/include/bcftools/bin.h'
2023-09-12T10:35:39,284     adding 'pysam/include/bcftools/call.h'
2023-09-12T10:35:39,286     adding 'pysam/include/bcftools/ccall.c'
2023-09-12T10:35:39,288     adding 'pysam/include/bcftools/ccall.c.pysam.c'
2023-09-12T10:35:39,290     adding 'pysam/include/bcftools/cigar_state.h'
2023-09-12T10:35:39,291     adding 'pysam/include/bcftools/cols.c'
2023-09-12T10:35:39,293     adding 'pysam/include/bcftools/cols.c.pysam.c'
2023-09-12T10:35:39,294     adding 'pysam/include/bcftools/cols.h'
2023-09-12T10:35:39,295     adding 'pysam/include/bcftools/config.h'
2023-09-12T10:35:39,301     adding 'pysam/include/bcftools/consensus.c'
2023-09-12T10:35:39,307     adding 'pysam/include/bcftools/consensus.c.pysam.c'
2023-09-12T10:35:39,313     adding 'pysam/include/bcftools/convert.c'
2023-09-12T10:35:39,320     adding 'pysam/include/bcftools/convert.c.pysam.c'
2023-09-12T10:35:39,322     adding 'pysam/include/bcftools/convert.h'
2023-09-12T10:35:39,341     adding 'pysam/include/bcftools/csq.c'
2023-09-12T10:35:39,361     adding 'pysam/include/bcftools/csq.c.pysam.c'
2023-09-12T10:35:39,364     adding 'pysam/include/bcftools/dbuf.h'
2023-09-12T10:35:39,366     adding 'pysam/include/bcftools/dist.c'
2023-09-12T10:35:39,367     adding 'pysam/include/bcftools/dist.c.pysam.c'
2023-09-12T10:35:39,369     adding 'pysam/include/bcftools/dist.h'
2023-09-12T10:35:39,371     adding 'pysam/include/bcftools/em.c'
2023-09-12T10:35:39,373     adding 'pysam/include/bcftools/em.c.pysam.c'
2023-09-12T10:35:39,375     adding 'pysam/include/bcftools/extsort.c'
2023-09-12T10:35:39,377     adding 'pysam/include/bcftools/extsort.c.pysam.c'
2023-09-12T10:35:39,378     adding 'pysam/include/bcftools/extsort.h'
2023-09-12T10:35:39,391     adding 'pysam/include/bcftools/filter.c'
2023-09-12T10:35:39,405     adding 'pysam/include/bcftools/filter.c.pysam.c'
2023-09-12T10:35:39,408     adding 'pysam/include/bcftools/filter.h'
2023-09-12T10:35:39,410     adding 'pysam/include/bcftools/gvcf.c'
2023-09-12T10:35:39,411     adding 'pysam/include/bcftools/gvcf.c.pysam.c'
2023-09-12T10:35:39,413     adding 'pysam/include/bcftools/gvcf.h'
2023-09-12T10:35:39,415     adding 'pysam/include/bcftools/hclust.c'
2023-09-12T10:35:39,417     adding 'pysam/include/bcftools/hclust.c.pysam.c'
2023-09-12T10:35:39,418     adding 'pysam/include/bcftools/hclust.h'
2023-09-12T10:35:39,420     adding 'pysam/include/bcftools/hex.h'
2023-09-12T10:35:39,421     adding 'pysam/include/bcftools/khash_str2str.h'
2023-09-12T10:35:39,423     adding 'pysam/include/bcftools/kheap.h'
2023-09-12T10:35:39,425     adding 'pysam/include/bcftools/kmin.c'
2023-09-12T10:35:39,427     adding 'pysam/include/bcftools/kmin.c.pysam.c'
2023-09-12T10:35:39,428     adding 'pysam/include/bcftools/kmin.h'
2023-09-12T10:35:39,430     adding 'pysam/include/bcftools/main.c'
2023-09-12T10:35:39,432     adding 'pysam/include/bcftools/main.c.pysam.c'
2023-09-12T10:35:39,439     adding 'pysam/include/bcftools/mcall.c'
2023-09-12T10:35:39,447     adding 'pysam/include/bcftools/mcall.c.pysam.c'
2023-09-12T10:35:39,455     adding 'pysam/include/bcftools/mpileup.c'
2023-09-12T10:35:39,464     adding 'pysam/include/bcftools/mpileup.c.pysam.c'
2023-09-12T10:35:39,467     adding 'pysam/include/bcftools/mw.h'
2023-09-12T10:35:39,470     adding 'pysam/include/bcftools/ploidy.c'
2023-09-12T10:35:39,471     adding 'pysam/include/bcftools/ploidy.c.pysam.c'
2023-09-12T10:35:39,473     adding 'pysam/include/bcftools/ploidy.h'
2023-09-12T10:35:39,476     adding 'pysam/include/bcftools/prob1.c'
2023-09-12T10:35:39,479     adding 'pysam/include/bcftools/prob1.c.pysam.c'
2023-09-12T10:35:39,480     adding 'pysam/include/bcftools/prob1.h'
2023-09-12T10:35:39,482     adding 'pysam/include/bcftools/rbuf.h'
2023-09-12T10:35:39,486     adding 'pysam/include/bcftools/read_consensus.c'
2023-09-12T10:35:39,492     adding 'pysam/include/bcftools/read_consensus.c.pysam.c'
2023-09-12T10:35:39,494     adding 'pysam/include/bcftools/read_consensus.h'
2023-09-12T10:35:39,496     adding 'pysam/include/bcftools/regidx.c'
2023-09-12T10:35:39,499     adding 'pysam/include/bcftools/regidx.c.pysam.c'
2023-09-12T10:35:39,501     adding 'pysam/include/bcftools/regidx.h'
2023-09-12T10:35:39,505     adding 'pysam/include/bcftools/reheader.c'
2023-09-12T10:35:39,508     adding 'pysam/include/bcftools/reheader.c.pysam.c'
2023-09-12T10:35:39,510     adding 'pysam/include/bcftools/smpl_ilist.c'
2023-09-12T10:35:39,512     adding 'pysam/include/bcftools/smpl_ilist.c.pysam.c'
2023-09-12T10:35:39,513     adding 'pysam/include/bcftools/smpl_ilist.h'
2023-09-12T10:35:39,515     adding 'pysam/include/bcftools/str_finder.c'
2023-09-12T10:35:39,517     adding 'pysam/include/bcftools/str_finder.c.pysam.c'
2023-09-12T10:35:39,519     adding 'pysam/include/bcftools/str_finder.h'
2023-09-12T10:35:39,520     adding 'pysam/include/bcftools/tabix.c'
2023-09-12T10:35:39,522     adding 'pysam/include/bcftools/tabix.c.pysam.c'
2023-09-12T10:35:39,524     adding 'pysam/include/bcftools/tsv2vcf.c'
2023-09-12T10:35:39,525     adding 'pysam/include/bcftools/tsv2vcf.c.pysam.c'
2023-09-12T10:35:39,527     adding 'pysam/include/bcftools/tsv2vcf.h'
2023-09-12T10:35:39,530     adding 'pysam/include/bcftools/utlist.h'
2023-09-12T10:35:39,534     adding 'pysam/include/bcftools/variantkey.h'
2023-09-12T10:35:39,548     adding 'pysam/include/bcftools/vcfannotate.c'
2023-09-12T10:35:39,564     adding 'pysam/include/bcftools/vcfannotate.c.pysam.c'
2023-09-12T10:35:39,568     adding 'pysam/include/bcftools/vcfbuf.c'
2023-09-12T10:35:39,571     adding 'pysam/include/bcftools/vcfbuf.c.pysam.c'
2023-09-12T10:35:39,572     adding 'pysam/include/bcftools/vcfbuf.h'
2023-09-12T10:35:39,578     adding 'pysam/include/bcftools/vcfcall.c'
2023-09-12T10:35:39,584     adding 'pysam/include/bcftools/vcfcall.c.pysam.c'
2023-09-12T10:35:39,590     adding 'pysam/include/bcftools/vcfcnv.c'
2023-09-12T10:35:39,596     adding 'pysam/include/bcftools/vcfcnv.c.pysam.c'
2023-09-12T10:35:39,602     adding 'pysam/include/bcftools/vcfconcat.c'
2023-09-12T10:35:39,608     adding 'pysam/include/bcftools/vcfconcat.c.pysam.c'
2023-09-12T10:35:39,615     adding 'pysam/include/bcftools/vcfconvert.c'
2023-09-12T10:35:39,622     adding 'pysam/include/bcftools/vcfconvert.c.pysam.c'
2023-09-12T10:35:39,627     adding 'pysam/include/bcftools/vcffilter.c'
2023-09-12T10:35:39,631     adding 'pysam/include/bcftools/vcffilter.c.pysam.c'
2023-09-12T10:35:39,636     adding 'pysam/include/bcftools/vcfgtcheck.c'
2023-09-12T10:35:39,642     adding 'pysam/include/bcftools/vcfgtcheck.c.pysam.c'
2023-09-12T10:35:39,644     adding 'pysam/include/bcftools/vcfhead.c'
2023-09-12T10:35:39,645     adding 'pysam/include/bcftools/vcfhead.c.pysam.c'
2023-09-12T10:35:39,647     adding 'pysam/include/bcftools/vcfindex.c'
2023-09-12T10:35:39,649     adding 'pysam/include/bcftools/vcfindex.c.pysam.c'
2023-09-12T10:35:39,653     adding 'pysam/include/bcftools/vcfisec.c'
2023-09-12T10:35:39,656     adding 'pysam/include/bcftools/vcfisec.c.pysam.c'
2023-09-12T10:35:39,670     adding 'pysam/include/bcftools/vcfmerge.c'
2023-09-12T10:35:39,686     adding 'pysam/include/bcftools/vcfmerge.c.pysam.c'
2023-09-12T10:35:39,696     adding 'pysam/include/bcftools/vcfnorm.c'
2023-09-12T10:35:39,706     adding 'pysam/include/bcftools/vcfnorm.c.pysam.c'
2023-09-12T10:35:39,710     adding 'pysam/include/bcftools/vcfplugin.c'
2023-09-12T10:35:39,713     adding 'pysam/include/bcftools/vcfplugin.c.pysam.c'
2023-09-12T10:35:39,716     adding 'pysam/include/bcftools/vcfquery.c'
2023-09-12T10:35:39,718     adding 'pysam/include/bcftools/vcfquery.c.pysam.c'
2023-09-12T10:35:39,724     adding 'pysam/include/bcftools/vcfroh.c'
2023-09-12T10:35:39,730     adding 'pysam/include/bcftools/vcfroh.c.pysam.c'
2023-09-12T10:35:39,733     adding 'pysam/include/bcftools/vcfsom.c'
2023-09-12T10:35:39,736     adding 'pysam/include/bcftools/vcfsom.c.pysam.c'
2023-09-12T10:35:39,739     adding 'pysam/include/bcftools/vcfsort.c'
2023-09-12T10:35:39,741     adding 'pysam/include/bcftools/vcfsort.c.pysam.c'
2023-09-12T10:35:39,749     adding 'pysam/include/bcftools/vcfstats.c'
2023-09-12T10:35:39,758     adding 'pysam/include/bcftools/vcfstats.c.pysam.c'
2023-09-12T10:35:39,763     adding 'pysam/include/bcftools/vcfview.c'
2023-09-12T10:35:39,767     adding 'pysam/include/bcftools/vcfview.c.pysam.c'
2023-09-12T10:35:39,769     adding 'pysam/include/bcftools/vcmp.c'
2023-09-12T10:35:39,770     adding 'pysam/include/bcftools/vcmp.c.pysam.c'
2023-09-12T10:35:39,772     adding 'pysam/include/bcftools/vcmp.h'
2023-09-12T10:35:39,773     adding 'pysam/include/bcftools/version.c'
2023-09-12T10:35:39,775     adding 'pysam/include/bcftools/version.c.pysam.c'
2023-09-12T10:35:39,776     adding 'pysam/include/bcftools/version.sh'
2023-09-12T10:35:39,779     adding 'pysam/include/htslib/LICENSE'
2023-09-12T10:35:39,784     adding 'pysam/include/htslib/Makefile'
2023-09-12T10:35:39,785     adding 'pysam/include/htslib/README'
2023-09-12T10:35:39,788     adding 'pysam/include/htslib/bcf_sr_sort.c'
2023-09-12T10:35:39,790     adding 'pysam/include/htslib/bcf_sr_sort.h'
2023-09-12T10:35:39,799     adding 'pysam/include/htslib/bgzf.c'
2023-09-12T10:35:39,803     adding 'pysam/include/htslib/bgzip.c'
2023-09-12T10:35:39,804     adding 'pysam/include/htslib/builddir_vars.mk.in'
2023-09-12T10:35:39,806     adding 'pysam/include/htslib/config.h'
2023-09-12T10:35:39,807     adding 'pysam/include/htslib/config.h.in'
2023-09-12T10:35:39,808     adding 'pysam/include/htslib/config.mk.in'
2023-09-12T10:35:39,830     adding 'pysam/include/htslib/configure'
2023-09-12T10:35:39,835     adding 'pysam/include/htslib/configure.ac'
2023-09-12T10:35:39,836     adding 'pysam/include/htslib/errmod.c'
2023-09-12T10:35:39,840     adding 'pysam/include/htslib/faidx.c'
2023-09-12T10:35:39,848     adding 'pysam/include/htslib/header.c'
2023-09-12T10:35:39,851     adding 'pysam/include/htslib/header.h'
2023-09-12T10:35:39,856     adding 'pysam/include/htslib/hfile.c'
2023-09-12T10:35:39,858     adding 'pysam/include/htslib/hfile_gcs.c'
2023-09-12T10:35:39,860     adding 'pysam/include/htslib/hfile_internal.h'
2023-09-12T10:35:39,866     adding 'pysam/include/htslib/hfile_libcurl.c'
2023-09-12T10:35:39,871     adding 'pysam/include/htslib/hfile_s3.c'
2023-09-12T10:35:39,874     adding 'pysam/include/htslib/hfile_s3_write.c'
2023-09-12T10:35:39,892     adding 'pysam/include/htslib/hts.c'
2023-09-12T10:35:39,896     adding 'pysam/include/htslib/hts_expr.c'
2023-09-12T10:35:39,898     adding 'pysam/include/htslib/hts_internal.h'
2023-09-12T10:35:39,899     adding 'pysam/include/htslib/hts_os.c'
2023-09-12T10:35:39,901     adding 'pysam/include/htslib/hts_time_funcs.h'
2023-09-12T10:35:39,902     adding 'pysam/include/htslib/htscodecs_bundled.mk'
2023-09-12T10:35:39,904     adding 'pysam/include/htslib/htscodecs_external.mk'
2023-09-12T10:35:39,906     adding 'pysam/include/htslib/htsfile.c'
2023-09-12T10:35:39,907     adding 'pysam/include/htslib/htslib.mk'
2023-09-12T10:35:39,909     adding 'pysam/include/htslib/htslib.pc.in'
2023-09-12T10:35:39,910     adding 'pysam/include/htslib/htslib_vars.mk'
2023-09-12T10:35:39,912     adding 'pysam/include/htslib/kfunc.c'
2023-09-12T10:35:39,914     adding 'pysam/include/htslib/kstring.c'
2023-09-12T10:35:39,916     adding 'pysam/include/htslib/md5.c'
2023-09-12T10:35:39,918     adding 'pysam/include/htslib/multipart.c'
2023-09-12T10:35:39,919     adding 'pysam/include/htslib/plugin.c'
2023-09-12T10:35:39,922     adding 'pysam/include/htslib/probaln.c'
2023-09-12T10:35:39,924     adding 'pysam/include/htslib/realn.c'
2023-09-12T10:35:39,927     adding 'pysam/include/htslib/regidx.c'
2023-09-12T10:35:39,929     adding 'pysam/include/htslib/region.c'
2023-09-12T10:35:39,953     adding 'pysam/include/htslib/sam.c'
2023-09-12T10:35:39,956     adding 'pysam/include/htslib/sam_internal.h'
2023-09-12T10:35:39,962     adding 'pysam/include/htslib/synced_bcf_reader.c'
2023-09-12T10:35:39,965     adding 'pysam/include/htslib/tabix.c'
2023-09-12T10:35:39,968     adding 'pysam/include/htslib/tbx.c'
2023-09-12T10:35:39,970     adding 'pysam/include/htslib/textutils.c'
2023-09-12T10:35:39,972     adding 'pysam/include/htslib/textutils_internal.h'
2023-09-12T10:35:39,978     adding 'pysam/include/htslib/thread_pool.c'
2023-09-12T10:35:39,980     adding 'pysam/include/htslib/thread_pool_internal.h'
2023-09-12T10:35:40,000     adding 'pysam/include/htslib/vcf.c'
2023-09-12T10:35:40,003     adding 'pysam/include/htslib/vcf_sweep.c'
2023-09-12T10:35:40,006     adding 'pysam/include/htslib/vcfutils.c'
2023-09-12T10:35:40,008     adding 'pysam/include/htslib/version.sh'
2023-09-12T10:35:40,011     adding 'pysam/include/htslib/cram/cram.h'
2023-09-12T10:35:40,022     adding 'pysam/include/htslib/cram/cram_codecs.c'
2023-09-12T10:35:40,025     adding 'pysam/include/htslib/cram/cram_codecs.h'
2023-09-12T10:35:40,037     adding 'pysam/include/htslib/cram/cram_decode.c'
2023-09-12T10:35:40,040     adding 'pysam/include/htslib/cram/cram_decode.h'
2023-09-12T10:35:40,054     adding 'pysam/include/htslib/cram/cram_encode.c'
2023-09-12T10:35:40,056     adding 'pysam/include/htslib/cram/cram_encode.h'
2023-09-12T10:35:40,060     adding 'pysam/include/htslib/cram/cram_external.c'
2023-09-12T10:35:40,063     adding 'pysam/include/htslib/cram/cram_index.c'
2023-09-12T10:35:40,065     adding 'pysam/include/htslib/cram/cram_index.h'
2023-09-12T10:35:40,083     adding 'pysam/include/htslib/cram/cram_io.c'
2023-09-12T10:35:40,087     adding 'pysam/include/htslib/cram/cram_io.h'
2023-09-12T10:35:40,089     adding 'pysam/include/htslib/cram/cram_samtools.h'
2023-09-12T10:35:40,091     adding 'pysam/include/htslib/cram/cram_stats.c'
2023-09-12T10:35:40,092     adding 'pysam/include/htslib/cram/cram_stats.h'
2023-09-12T10:35:40,096     adding 'pysam/include/htslib/cram/cram_structs.h'
2023-09-12T10:35:40,099     adding 'pysam/include/htslib/cram/mFILE.c'
2023-09-12T10:35:40,100     adding 'pysam/include/htslib/cram/mFILE.h'
2023-09-12T10:35:40,102     adding 'pysam/include/htslib/cram/misc.h'
2023-09-12T10:35:40,104     adding 'pysam/include/htslib/cram/open_trace_file.c'
2023-09-12T10:35:40,106     adding 'pysam/include/htslib/cram/open_trace_file.h'
2023-09-12T10:35:40,107     adding 'pysam/include/htslib/cram/os.h'
2023-09-12T10:35:40,109     adding 'pysam/include/htslib/cram/pooled_alloc.c'
2023-09-12T10:35:40,110     adding 'pysam/include/htslib/cram/pooled_alloc.h'
2023-09-12T10:35:40,112     adding 'pysam/include/htslib/cram/string_alloc.c'
2023-09-12T10:35:40,113     adding 'pysam/include/htslib/cram/string_alloc.h'
2023-09-12T10:35:40,118     adding 'pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c'
2023-09-12T10:35:40,120     adding 'pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h'
2023-09-12T10:35:40,121     adding 'pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h'
2023-09-12T10:35:40,123     adding 'pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h'
2023-09-12T10:35:40,128     adding 'pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c'
2023-09-12T10:35:40,131     adding 'pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h'
2023-09-12T10:35:40,132     adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs.c'
2023-09-12T10:35:40,133     adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs.h'
2023-09-12T10:35:40,135     adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h'
2023-09-12T10:35:40,137     adding 'pysam/include/htslib/htscodecs/htscodecs/pack.c'
2023-09-12T10:35:40,138     adding 'pysam/include/htslib/htscodecs/htscodecs/pack.h'
2023-09-12T10:35:40,141     adding 'pysam/include/htslib/htscodecs/htscodecs/permute.h'
2023-09-12T10:35:40,142     adding 'pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h'
2023-09-12T10:35:40,145     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h'
2023-09-12T10:35:40,148     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static.c'
2023-09-12T10:35:40,150     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static.h'
2023-09-12T10:35:40,152     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h'
2023-09-12T10:35:40,155     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c'
2023-09-12T10:35:40,157     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h'
2023-09-12T10:35:40,162     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c'
2023-09-12T10:35:40,166     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c'
2023-09-12T10:35:40,173     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c'
2023-09-12T10:35:40,179     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c'
2023-09-12T10:35:40,181     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h'
2023-09-12T10:35:40,187     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c'
2023-09-12T10:35:40,190     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_word.h'
2023-09-12T10:35:40,192     adding 'pysam/include/htslib/htscodecs/htscodecs/rle.c'
2023-09-12T10:35:40,193     adding 'pysam/include/htslib/htscodecs/htscodecs/rle.h'
2023-09-12T10:35:40,199     adding 'pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c'
2023-09-12T10:35:40,201     adding 'pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h'
2023-09-12T10:35:40,203     adding 'pysam/include/htslib/htscodecs/htscodecs/utils.c'
2023-09-12T10:35:40,205     adding 'pysam/include/htslib/htscodecs/htscodecs/utils.h'
2023-09-12T10:35:40,207     adding 'pysam/include/htslib/htscodecs/htscodecs/varint.h'
2023-09-12T10:35:40,209     adding 'pysam/include/htslib/htscodecs/htscodecs/varint2.h'
2023-09-12T10:35:40,210     adding 'pysam/include/htslib/htscodecs/htscodecs/version.h'
2023-09-12T10:35:40,213     adding 'pysam/include/htslib/htslib/bgzf.h'
2023-09-12T10:35:40,216     adding 'pysam/include/htslib/htslib/cram.h'
2023-09-12T10:35:40,218     adding 'pysam/include/htslib/htslib/faidx.h'
2023-09-12T10:35:40,221     adding 'pysam/include/htslib/htslib/hfile.h'
2023-09-12T10:35:40,228     adding 'pysam/include/htslib/htslib/hts.h'
2023-09-12T10:35:40,230     adding 'pysam/include/htslib/htslib/hts_defs.h'
2023-09-12T10:35:40,232     adding 'pysam/include/htslib/htslib/hts_endian.h'
2023-09-12T10:35:40,234     adding 'pysam/include/htslib/htslib/hts_expr.h'
2023-09-12T10:35:40,236     adding 'pysam/include/htslib/htslib/hts_log.h'
2023-09-12T10:35:40,237     adding 'pysam/include/htslib/htslib/hts_os.h'
2023-09-12T10:35:40,239     adding 'pysam/include/htslib/htslib/kbitset.h'
2023-09-12T10:35:40,240     adding 'pysam/include/htslib/htslib/kfunc.h'
2023-09-12T10:35:40,243     adding 'pysam/include/htslib/htslib/khash.h'
2023-09-12T10:35:40,244     adding 'pysam/include/htslib/htslib/khash_str2int.h'
2023-09-12T10:35:40,246     adding 'pysam/include/htslib/htslib/klist.h'
2023-09-12T10:35:40,247     adding 'pysam/include/htslib/htslib/knetfile.h'
2023-09-12T10:35:40,249     adding 'pysam/include/htslib/htslib/kroundup.h'
2023-09-12T10:35:40,250     adding 'pysam/include/htslib/htslib/kseq.h'
2023-09-12T10:35:40,252     adding 'pysam/include/htslib/htslib/ksort.h'
2023-09-12T10:35:40,255     adding 'pysam/include/htslib/htslib/kstring.h'
2023-09-12T10:35:40,257     adding 'pysam/include/htslib/htslib/regidx.h'
2023-09-12T10:35:40,268     adding 'pysam/include/htslib/htslib/sam.h'
2023-09-12T10:35:40,271     adding 'pysam/include/htslib/htslib/synced_bcf_reader.h'
2023-09-12T10:35:40,273     adding 'pysam/include/htslib/htslib/tbx.h'
2023-09-12T10:35:40,276     adding 'pysam/include/htslib/htslib/thread_pool.h'
2023-09-12T10:35:40,284     adding 'pysam/include/htslib/htslib/vcf.h'
2023-09-12T10:35:40,298     adding 'pysam/include/htslib/htslib/vcf_sweep.h'
2023-09-12T10:35:40,300     adding 'pysam/include/htslib/htslib/vcfutils.h'
2023-09-12T10:35:40,302     adding 'pysam/include/htslib/m4/ax_check_compile_flag.m4'
2023-09-12T10:35:40,303     adding 'pysam/include/htslib/m4/hts_hide_dynamic_syms.m4'
2023-09-12T10:35:40,305     adding 'pysam/include/htslib/m4/hts_prog_cc_warnings.m4'
2023-09-12T10:35:40,307     adding 'pysam/include/htslib/m4/pkg.m4'
2023-09-12T10:35:40,309     adding 'pysam/include/htslib/os/lzma_stub.h'
2023-09-12T10:35:40,310     adding 'pysam/include/htslib/os/rand.c'
2023-09-12T10:35:40,314     adding 'pysam/include/samtools/LICENSE'
2023-09-12T10:35:40,315     adding 'pysam/include/samtools/README'
2023-09-12T10:35:40,322     adding 'pysam/include/samtools/amplicon_stats.c'
2023-09-12T10:35:40,330     adding 'pysam/include/samtools/amplicon_stats.c.pysam.c'
2023-09-12T10:35:40,332     adding 'pysam/include/samtools/bam.c'
2023-09-12T10:35:40,334     adding 'pysam/include/samtools/bam.c.pysam.c'
2023-09-12T10:35:40,336     adding 'pysam/include/samtools/bam.h'
2023-09-12T10:35:40,339     adding 'pysam/include/samtools/bam2depth.c'
2023-09-12T10:35:40,343     adding 'pysam/include/samtools/bam2depth.c.pysam.c'
2023-09-12T10:35:40,346     adding 'pysam/include/samtools/bam_addrprg.c'
2023-09-12T10:35:40,348     adding 'pysam/include/samtools/bam_addrprg.c.pysam.c'
2023-09-12T10:35:40,352     adding 'pysam/include/samtools/bam_ampliconclip.c'
2023-09-12T10:35:40,356     adding 'pysam/include/samtools/bam_ampliconclip.c.pysam.c'
2023-09-12T10:35:40,358     adding 'pysam/include/samtools/bam_ampliconclip.h'
2023-09-12T10:35:40,359     adding 'pysam/include/samtools/bam_aux.c'
2023-09-12T10:35:40,360     adding 'pysam/include/samtools/bam_aux.c.pysam.c'
2023-09-12T10:35:40,363     adding 'pysam/include/samtools/bam_cat.c'
2023-09-12T10:35:40,366     adding 'pysam/include/samtools/bam_cat.c.pysam.c'
2023-09-12T10:35:40,367     adding 'pysam/include/samtools/bam_color.c'
2023-09-12T10:35:40,369     adding 'pysam/include/samtools/bam_color.c.pysam.c'
2023-09-12T10:35:40,380     adding 'pysam/include/samtools/bam_consensus.c'
2023-09-12T10:35:40,392     adding 'pysam/include/samtools/bam_consensus.c.pysam.c'
2023-09-12T10:35:40,397     adding 'pysam/include/samtools/bam_fastq.c'
2023-09-12T10:35:40,401     adding 'pysam/include/samtools/bam_fastq.c.pysam.c'
2023-09-12T10:35:40,403     adding 'pysam/include/samtools/bam_flags.c'
2023-09-12T10:35:40,404     adding 'pysam/include/samtools/bam_flags.c.pysam.c'
2023-09-12T10:35:40,406     adding 'pysam/include/samtools/bam_import.c'
2023-09-12T10:35:40,409     adding 'pysam/include/samtools/bam_import.c.pysam.c'
2023-09-12T10:35:40,411     adding 'pysam/include/samtools/bam_index.c'
2023-09-12T10:35:40,413     adding 'pysam/include/samtools/bam_index.c.pysam.c'
2023-09-12T10:35:40,414     adding 'pysam/include/samtools/bam_lpileup.c'
2023-09-12T10:35:40,416     adding 'pysam/include/samtools/bam_lpileup.c.pysam.c'
2023-09-12T10:35:40,417     adding 'pysam/include/samtools/bam_lpileup.h'
2023-09-12T10:35:40,426     adding 'pysam/include/samtools/bam_markdup.c'
2023-09-12T10:35:40,435     adding 'pysam/include/samtools/bam_markdup.c.pysam.c'
2023-09-12T10:35:40,439     adding 'pysam/include/samtools/bam_mate.c'
2023-09-12T10:35:40,443     adding 'pysam/include/samtools/bam_mate.c.pysam.c'
2023-09-12T10:35:40,445     adding 'pysam/include/samtools/bam_md.c'
2023-09-12T10:35:40,448     adding 'pysam/include/samtools/bam_md.c.pysam.c'
2023-09-12T10:35:40,449     adding 'pysam/include/samtools/bam_plbuf.c'
2023-09-12T10:35:40,451     adding 'pysam/include/samtools/bam_plbuf.c.pysam.c'
2023-09-12T10:35:40,452     adding 'pysam/include/samtools/bam_plbuf.h'
2023-09-12T10:35:40,457     adding 'pysam/include/samtools/bam_plcmd.c'
2023-09-12T10:35:40,462     adding 'pysam/include/samtools/bam_plcmd.c.pysam.c'
2023-09-12T10:35:40,465     adding 'pysam/include/samtools/bam_quickcheck.c'
2023-09-12T10:35:40,467     adding 'pysam/include/samtools/bam_quickcheck.c.pysam.c'
2023-09-12T10:35:40,469     adding 'pysam/include/samtools/bam_reheader.c'
2023-09-12T10:35:40,472     adding 'pysam/include/samtools/bam_reheader.c.pysam.c'
2023-09-12T10:35:40,474     adding 'pysam/include/samtools/bam_rmdup.c'
2023-09-12T10:35:40,476     adding 'pysam/include/samtools/bam_rmdup.c.pysam.c'
2023-09-12T10:35:40,478     adding 'pysam/include/samtools/bam_rmdupse.c'
2023-09-12T10:35:40,480     adding 'pysam/include/samtools/bam_rmdupse.c.pysam.c'
2023-09-12T10:35:40,482     adding 'pysam/include/samtools/bam_samples.c'
2023-09-12T10:35:40,485     adding 'pysam/include/samtools/bam_samples.c.pysam.c'
2023-09-12T10:35:40,498     adding 'pysam/include/samtools/bam_sort.c'
2023-09-12T10:35:40,513     adding 'pysam/include/samtools/bam_sort.c.pysam.c'
2023-09-12T10:35:40,517     adding 'pysam/include/samtools/bam_split.c'
2023-09-12T10:35:40,520     adding 'pysam/include/samtools/bam_split.c.pysam.c'
2023-09-12T10:35:40,522     adding 'pysam/include/samtools/bam_stat.c'
2023-09-12T10:35:40,524     adding 'pysam/include/samtools/bam_stat.c.pysam.c'
2023-09-12T10:35:40,527     adding 'pysam/include/samtools/bamshuf.c'
2023-09-12T10:35:40,530     adding 'pysam/include/samtools/bamshuf.c.pysam.c'
2023-09-12T10:35:40,532     adding 'pysam/include/samtools/bamtk.c'
2023-09-12T10:35:40,534     adding 'pysam/include/samtools/bamtk.c.pysam.c'
2023-09-12T10:35:40,536     adding 'pysam/include/samtools/bedcov.c'
2023-09-12T10:35:40,538     adding 'pysam/include/samtools/bedcov.c.pysam.c'
2023-09-12T10:35:40,541     adding 'pysam/include/samtools/bedidx.c'
2023-09-12T10:35:40,544     adding 'pysam/include/samtools/bedidx.c.pysam.c'
2023-09-12T10:35:40,545     adding 'pysam/include/samtools/bedidx.h'
2023-09-12T10:35:40,546     adding 'pysam/include/samtools/config.h'
2023-09-12T10:35:40,549     adding 'pysam/include/samtools/consensus_pileup.c'
2023-09-12T10:35:40,551     adding 'pysam/include/samtools/consensus_pileup.c.pysam.c'
2023-09-12T10:35:40,553     adding 'pysam/include/samtools/consensus_pileup.h'
2023-09-12T10:35:40,556     adding 'pysam/include/samtools/coverage.c'
2023-09-12T10:35:40,560     adding 'pysam/include/samtools/coverage.c.pysam.c'
2023-09-12T10:35:40,563     adding 'pysam/include/samtools/cram_size.c'
2023-09-12T10:35:40,566     adding 'pysam/include/samtools/cram_size.c.pysam.c'
2023-09-12T10:35:40,568     adding 'pysam/include/samtools/cut_target.c'
2023-09-12T10:35:40,570     adding 'pysam/include/samtools/cut_target.c.pysam.c'
2023-09-12T10:35:40,571     adding 'pysam/include/samtools/dict.c'
2023-09-12T10:35:40,573     adding 'pysam/include/samtools/dict.c.pysam.c'
2023-09-12T10:35:40,575     adding 'pysam/include/samtools/faidx.c'
2023-09-12T10:35:40,578     adding 'pysam/include/samtools/faidx.c.pysam.c'
2023-09-12T10:35:40,581     adding 'pysam/include/samtools/padding.c'
2023-09-12T10:35:40,584     adding 'pysam/include/samtools/padding.c.pysam.c'
2023-09-12T10:35:40,588     adding 'pysam/include/samtools/phase.c'
2023-09-12T10:35:40,592     adding 'pysam/include/samtools/phase.c.pysam.c'
2023-09-12T10:35:40,595     adding 'pysam/include/samtools/reference.c'
2023-09-12T10:35:40,598     adding 'pysam/include/samtools/reference.c.pysam.c'
2023-09-12T10:35:40,600     adding 'pysam/include/samtools/reset.c'
2023-09-12T10:35:40,603     adding 'pysam/include/samtools/reset.c.pysam.c'
2023-09-12T10:35:40,605     adding 'pysam/include/samtools/sam_opts.c'
2023-09-12T10:35:40,607     adding 'pysam/include/samtools/sam_opts.c.pysam.c'
2023-09-12T10:35:40,608     adding 'pysam/include/samtools/sam_opts.h'
2023-09-12T10:35:40,610     adding 'pysam/include/samtools/sam_utils.c'
2023-09-12T10:35:40,611     adding 'pysam/include/samtools/sam_utils.c.pysam.c'
2023-09-12T10:35:40,613     adding 'pysam/include/samtools/sam_utils.h'
2023-09-12T10:35:40,619     adding 'pysam/include/samtools/sam_view.c'
2023-09-12T10:35:40,626     adding 'pysam/include/samtools/sam_view.c.pysam.c'
2023-09-12T10:35:40,628     adding 'pysam/include/samtools/sample.c'
2023-09-12T10:35:40,630     adding 'pysam/include/samtools/sample.c.pysam.c'
2023-09-12T10:35:40,631     adding 'pysam/include/samtools/sample.h'
2023-09-12T10:35:40,633     adding 'pysam/include/samtools/samtools.h'
2023-09-12T10:35:40,634     adding 'pysam/include/samtools/samtools.pysam.c'
2023-09-12T10:35:40,635     adding 'pysam/include/samtools/samtools.pysam.h'
2023-09-12T10:35:40,637     adding 'pysam/include/samtools/splaysort.h'
2023-09-12T10:35:40,648     adding 'pysam/include/samtools/stats.c'
2023-09-12T10:35:40,661     adding 'pysam/include/samtools/stats.c.pysam.c'
2023-09-12T10:35:40,664     adding 'pysam/include/samtools/stats_isize.c'
2023-09-12T10:35:40,665     adding 'pysam/include/samtools/stats_isize.c.pysam.c'
2023-09-12T10:35:40,667     adding 'pysam/include/samtools/stats_isize.h'
2023-09-12T10:35:40,669     adding 'pysam/include/samtools/tmp_file.c'
2023-09-12T10:35:40,671     adding 'pysam/include/samtools/tmp_file.c.pysam.c'
2023-09-12T10:35:40,673     adding 'pysam/include/samtools/tmp_file.h'
2023-09-12T10:35:40,674     adding 'pysam/include/samtools/version.sh'
2023-09-12T10:35:40,676     adding 'pysam/include/samtools/lz4/LICENSE'
2023-09-12T10:35:40,682     adding 'pysam/include/samtools/lz4/lz4.c'
2023-09-12T10:35:40,688     adding 'pysam/include/samtools/lz4/lz4.c.pysam.c'
2023-09-12T10:35:40,692     adding 'pysam/include/samtools/lz4/lz4.h'
2023-09-12T10:35:40,695     adding 'pysam-0.21.0.dist-info/AUTHORS'
2023-09-12T10:35:40,696     adding 'pysam-0.21.0.dist-info/COPYING'
2023-09-12T10:35:40,697     adding 'pysam-0.21.0.dist-info/METADATA'
2023-09-12T10:35:40,698     adding 'pysam-0.21.0.dist-info/WHEEL'
2023-09-12T10:35:40,700     adding 'pysam-0.21.0.dist-info/top_level.txt'
2023-09-12T10:35:40,707     adding 'pysam-0.21.0.dist-info/RECORD'
2023-09-12T10:35:40,876     removing build/bdist.linux-armv7l/wheel
2023-09-12T10:35:41,132     Building wheel for pysam (pyproject.toml): finished with status 'done'
2023-09-12T10:35:41,740     Created wheel for pysam: filename=pysam-0.21.0-cp311-cp311-linux_armv7l.whl size=16179621 sha256=4aaf42e7aabfbdf9d65fe5eafc7aae5e11fefe0df40c60248373f3a96fe06bec
2023-09-12T10:35:41,741     Stored in directory: /home/piwheels/.cache/pip/wheels/52/2d/ed/b1e5c4ad36c535940dc1b1da900d05f571f88ff26f7be95f4c
2023-09-12T10:35:41,758   Successfully built pysam
2023-09-12T10:35:44,493   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
2023-09-12T10:35:45,028     Creating /tmp/pip-build-env-i12qz61r/overlay/local/bin
2023-09-12T10:35:45,030     changing mode of /tmp/pip-build-env-i12qz61r/overlay/local/bin/wheel to 755
2023-09-12T10:35:51,324     changing mode of /tmp/pip-build-env-i12qz61r/overlay/local/bin/cygdb to 755
2023-09-12T10:35:51,326     changing mode of /tmp/pip-build-env-i12qz61r/overlay/local/bin/cython to 755
2023-09-12T10:35:51,329     changing mode of /tmp/pip-build-env-i12qz61r/overlay/local/bin/cythonize to 755
2023-09-12T10:35:52,464     changing mode of /tmp/pip-build-env-i12qz61r/overlay/local/bin/chardetect to 755
2023-09-12T10:35:53,502     changing mode of /tmp/pip-build-env-i12qz61r/overlay/local/bin/virtualenv to 755
2023-09-12T10:35:56,138     changing mode of /tmp/pip-build-env-i12qz61r/overlay/local/bin/cython-setuptools to 755
2023-09-12T10:35:57,358     changing mode of /tmp/pip-build-env-i12qz61r/overlay/local/bin/tox to 755
2023-09-12T10:35:57,653   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
2023-09-12T10:35:59,701   Installing build dependencies: finished with status 'done'
2023-09-12T10:35:59,704   Getting requirements to build wheel: started
2023-09-12T10:35:59,706   Running command Getting requirements to build wheel
2023-09-12T10:36:10,369   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
2023-09-12T10:36:10,369   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

2023-09-12T10:36:10,662   Error compiling Cython file:
2023-09-12T10:36:10,663   ------------------------------------------------------------
2023-09-12T10:36:10,664   ...
2023-09-12T10:36:10,664   INSERTION.inverse     = DELETION
2023-09-12T10:36:10,665   DELETION.inverse      = INSERTION
2023-09-12T10:36:10,665   SEQ_MATCH.inverse     = SEQ_MATCH
2023-09-12T10:36:10,666   SEQ_MISMATCH.inverse  = SEQ_MISMATCH

2023-09-12T10:36:10,667   cpdef tuple BAM_OPS = (MATCH, INSERTION, DELETION, SKIPPED, SOFT_CLIP, HARD_CLIP, PADDING, SEQ_MATCH, SEQ_MISMATCH)
2023-09-12T10:36:10,668         ^
2023-09-12T10:36:10,668   ------------------------------------------------------------

2023-09-12T10:36:10,670   uta_align/align/cigar_utils.pyx:62:6: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.

2023-09-12T10:36:10,671   Error compiling Cython file:
2023-09-12T10:36:10,672   ------------------------------------------------------------
2023-09-12T10:36:10,672   ...
2023-09-12T10:36:10,674   # Create mapping from ord(char_op) to op
2023-09-12T10:36:10,674   _temp_map = [None]*256
2023-09-12T10:36:10,674   for _op in BAM_OPS:
2023-09-12T10:36:10,675       _temp_map[_op.code] = _op

2023-09-12T10:36:10,676   cpdef tuple BAM_OP_CHAR_MAP = tuple(_temp_map)
2023-09-12T10:36:10,676         ^
2023-09-12T10:36:10,677   ------------------------------------------------------------

2023-09-12T10:36:10,677   uta_align/align/cigar_utils.pyx:69:6: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
2023-09-12T10:36:11,201   Compiling uta_align/align/algorithms.pyx because it changed.
2023-09-12T10:36:11,202   Compiling uta_align/align/cigar_utils.pyx because it changed.
2023-09-12T10:36:11,202   [1/2] Cythonizing uta_align/align/algorithms.pyx
2023-09-12T10:36:11,203   [2/2] Cythonizing uta_align/align/cigar_utils.pyx
2023-09-12T10:36:11,203   Traceback (most recent call last):
2023-09-12T10:36:11,204     File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
2023-09-12T10:36:11,204       main()
2023-09-12T10:36:11,205     File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
2023-09-12T10:36:11,205       json_out['return_val'] = hook(**hook_input['kwargs'])
2023-09-12T10:36:11,206                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,206     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
2023-09-12T10:36:11,207       return hook(config_settings)
2023-09-12T10:36:11,207              ^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,208     File "/tmp/pip-build-env-i12qz61r/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 355, in get_requires_for_build_wheel
2023-09-12T10:36:11,209       return self._get_build_requires(config_settings, requirements=['wheel'])
2023-09-12T10:36:11,210              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,211     File "/tmp/pip-build-env-i12qz61r/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 325, in _get_build_requires
2023-09-12T10:36:11,212       self.run_setup()
2023-09-12T10:36:11,213     File "/tmp/pip-build-env-i12qz61r/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 341, in run_setup
2023-09-12T10:36:11,214       exec(code, locals())
2023-09-12T10:36:11,215     File "<string>", line 52, in <module>
2023-09-12T10:36:11,216     File "/tmp/pip-build-env-i12qz61r/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
2023-09-12T10:36:11,217       cythonize_one(*args)
2023-09-12T10:36:11,218     File "/tmp/pip-build-env-i12qz61r/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
2023-09-12T10:36:11,219       raise CompileError(None, pyx_file)
2023-09-12T10:36:11,220   Cython.Compiler.Errors.CompileError: uta_align/align/cigar_utils.pyx
2023-09-12T10:36:11,618   ERROR: [present-rich] Getting requirements to build wheel exited with 1
2023-09-12T10:36:11,631   [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/tmpnwq3u9g7[/]
2023-09-12T10:36:11,632   [bold magenta]cwd[/]: /tmp/pip-wheel-1vk64f1r/uta-align_376ec37222844ccb8c09fc565b068795
2023-09-12T10:36:11,632   Getting requirements to build wheel: finished with status 'error'
2023-09-12T10:36:11,635 ERROR: [present-rich] Getting requirements to build wheel exited with 1
2023-09-12T10:36:11,641 Exception information:
2023-09-12T10:36:11,641 Traceback (most recent call last):
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
2023-09-12T10:36:11,641     status = run_func(*args)
2023-09-12T10:36:11,641              ^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper
2023-09-12T10:36:11,641     return func(self, options, args)
2023-09-12T10:36:11,641            ^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 147, in run
2023-09-12T10:36:11,641     requirement_set = resolver.resolve(reqs, check_supported_wheels=True)
2023-09-12T10:36:11,641                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 92, in resolve
2023-09-12T10:36:11,641     result = self._result = resolver.resolve(
2023-09-12T10:36:11,641                             ^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve
2023-09-12T10:36:11,641     state = resolution.resolve(requirements, max_rounds=max_rounds)
2023-09-12T10:36:11,641             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 397, in resolve
2023-09-12T10:36:11,641     self._add_to_criteria(self.state.criteria, r, parent=None)
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria
2023-09-12T10:36:11,641     if not criterion.candidates:
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/structs.py", line 156, in __bool__
2023-09-12T10:36:11,641     return bool(self._sequence)
2023-09-12T10:36:11,641            ^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in __bool__
2023-09-12T10:36:11,641     return any(self)
2023-09-12T10:36:11,641            ^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in <genexpr>
2023-09-12T10:36:11,641     return (c for c in iterator if id(c) not in self._incompatible_ids)
2023-09-12T10:36:11,641            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built
2023-09-12T10:36:11,641     candidate = func()
2023-09-12T10:36:11,641                 ^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link
2023-09-12T10:36:11,641     self._link_candidate_cache[link] = LinkCandidate(
2023-09-12T10:36:11,641                                        ^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__
2023-09-12T10:36:11,641     super().__init__(
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__
2023-09-12T10:36:11,641     self.dist = self._prepare()
2023-09-12T10:36:11,641                 ^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare
2023-09-12T10:36:11,641     dist = self._prepare_distribution()
2023-09-12T10:36:11,641            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution
2023-09-12T10:36:11,641     return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
2023-09-12T10:36:11,641            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 538, in prepare_linked_requirement
2023-09-12T10:36:11,641     return self._prepare_linked_requirement(req, parallel_builds)
2023-09-12T10:36:11,641            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 653, in _prepare_linked_requirement
2023-09-12T10:36:11,641     dist = _get_prepared_distribution(
2023-09-12T10:36:11,641            ^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution
2023-09-12T10:36:11,641     abstract_dist.prepare_distribution_metadata(
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 48, in prepare_distribution_metadata
2023-09-12T10:36:11,641     self._install_build_reqs(finder)
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 118, in _install_build_reqs
2023-09-12T10:36:11,641     build_reqs = self._get_build_requires_wheel()
2023-09-12T10:36:11,641                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 95, in _get_build_requires_wheel
2023-09-12T10:36:11,641     return backend.get_requires_for_build_wheel()
2023-09-12T10:36:11,641            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/misc.py", line 697, in get_requires_for_build_wheel
2023-09-12T10:36:11,641     return super().get_requires_for_build_wheel(config_settings=cs)
2023-09-12T10:36:11,641            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_impl.py", line 166, in get_requires_for_build_wheel
2023-09-12T10:36:11,641     return self._call_hook('get_requires_for_build_wheel', {
2023-09-12T10:36:11,641            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook
2023-09-12T10:36:11,641     self._subprocess_runner(
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/subprocess.py", line 252, in runner
2023-09-12T10:36:11,641     call_subprocess(
2023-09-12T10:36:11,641   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess
2023-09-12T10:36:11,641     raise error
2023-09-12T10:36:11,641 pip._internal.exceptions.InstallationSubprocessError: Getting requirements to build wheel exited with 1
2023-09-12T10:36:11,664 Removed uta-align==0.2.0 from https://files.pythonhosted.org/packages/64/bc/5306c731e7d4d304e9d1f7fee2a8fa1d79640626ccaac9f9df660078893c/uta-align-0.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-ugq70naj'
2023-09-12T10:36:11,666 Removed build tracker: '/tmp/pip-build-tracker-ugq70naj'