2023-09-12T10:22:32,625 Created temporary directory: /tmp/pip-build-tracker-iaiomtc_
2023-09-12T10:22:32,626 Initialized build tracking at /tmp/pip-build-tracker-iaiomtc_
2023-09-12T10:22:32,627 Created build tracker: /tmp/pip-build-tracker-iaiomtc_
2023-09-12T10:22:32,627 Entered build tracker: /tmp/pip-build-tracker-iaiomtc_
2023-09-12T10:22:32,628 Created temporary directory: /tmp/pip-wheel-q_rfth3l
2023-09-12T10:22:32,631 Created temporary directory: /tmp/pip-ephem-wheel-cache-uz075x5v
2023-09-12T10:22:32,662 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-12T10:22:32,666 2 location(s) to search for versions of uta-align:
2023-09-12T10:22:32,666 * https://pypi.org/simple/uta-align/
2023-09-12T10:22:32,666 * https://www.piwheels.org/simple/uta-align/
2023-09-12T10:22:32,667 Fetching project page and analyzing links: https://pypi.org/simple/uta-align/
2023-09-12T10:22:32,667 Getting page https://pypi.org/simple/uta-align/
2023-09-12T10:22:32,669 Found index url https://pypi.org/simple/
2023-09-12T10:22:32,812 Fetched page https://pypi.org/simple/uta-align/ as application/vnd.pypi.simple.v1+json
2023-09-12T10:22:32,818   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
2023-09-12T10:22:32,818   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/)
2023-09-12T10:22:32,819   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
2023-09-12T10:22:32,820   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/)
2023-09-12T10:22:32,820   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
2023-09-12T10:22:32,821   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/)
2023-09-12T10:22:32,822   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/)
2023-09-12T10:22:32,822   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
2023-09-12T10:22:32,823   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/)
2023-09-12T10:22:32,824   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
2023-09-12T10:22:32,824   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/)
2023-09-12T10:22:32,825   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
2023-09-12T10:22:32,826   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/)
2023-09-12T10:22:32,827   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
2023-09-12T10:22:32,827   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/)
2023-09-12T10:22:32,828   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
2023-09-12T10:22:32,828   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/)
2023-09-12T10:22:32,829   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
2023-09-12T10:22:32,829   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/)
2023-09-12T10:22:32,830   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
2023-09-12T10:22:32,830   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/)
2023-09-12T10:22:32,831   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/)
2023-09-12T10:22:32,832   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
2023-09-12T10:22:32,832   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
2023-09-12T10:22:32,833   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
2023-09-12T10:22:32,834   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
2023-09-12T10:22:32,835 Fetching project page and analyzing links: https://www.piwheels.org/simple/uta-align/
2023-09-12T10:22:32,835 Getting page https://www.piwheels.org/simple/uta-align/
2023-09-12T10:22:32,837 Found index url https://www.piwheels.org/simple/
2023-09-12T10:22:34,139 Fetched page https://www.piwheels.org/simple/uta-align/ as text/html
2023-09-12T10:22:34,158   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/)
2023-09-12T10:22:34,159   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/)
2023-09-12T10:22:34,160   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/)
2023-09-12T10:22:34,161   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/)
2023-09-12T10:22:34,162   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/)
2023-09-12T10:22:34,163   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/)
2023-09-12T10:22:34,164   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/)
2023-09-12T10:22:34,165   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/)
2023-09-12T10:22:34,166   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/)
2023-09-12T10:22:34,167   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/)
2023-09-12T10:22:34,167   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/)
2023-09-12T10:22:34,168   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/)
2023-09-12T10:22:34,169   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/)
2023-09-12T10:22:34,170   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/)
2023-09-12T10:22:34,170   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/)
2023-09-12T10:22:34,171   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/)
2023-09-12T10:22:34,172   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/)
2023-09-12T10:22:34,173   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/)
2023-09-12T10:22:34,173   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/)
2023-09-12T10:22:34,174   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/)
2023-09-12T10:22:34,174   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/)
2023-09-12T10:22:34,175   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/)
2023-09-12T10:22:34,176   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/)
2023-09-12T10:22:34,176   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/)
2023-09-12T10:22:34,177   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/)
2023-09-12T10:22:34,178   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/)
2023-09-12T10:22:34,179 Skipping link: not a file: https://www.piwheels.org/simple/uta-align/
2023-09-12T10:22:34,179 Skipping link: not a file: https://pypi.org/simple/uta-align/
2023-09-12T10:22:34,209 Given no hashes to check 1 links for project 'uta-align': discarding no candidates
2023-09-12T10:22:34,235 Collecting uta-align==0.2.0a2
2023-09-12T10:22:34,238   Created temporary directory: /tmp/pip-unpack-kcmhv6b1
2023-09-12T10:22:34,478   Downloading uta-align-0.2.0a2.tar.gz (266 kB)
2023-09-12T10:22:34,718   Added uta-align==0.2.0a2 from https://files.pythonhosted.org/packages/7c/07/3d0483101728198e619f9d45552d2d50dc90fc2937964a899e6fe3908687/uta-align-0.2.0a2.tar.gz to build tracker '/tmp/pip-build-tracker-iaiomtc_'
2023-09-12T10:22:34,727   Created temporary directory: /tmp/pip-build-env-uwgm7p5_
2023-09-12T10:22:34,731   Installing build dependencies: started
2023-09-12T10:22:34,733   Running command pip subprocess to install build dependencies
2023-09-12T10:22:35,897   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-09-12T10:22:36,396   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-12T10:22:38,591   Collecting cython>=0.29
2023-09-12T10:22:38,592     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
2023-09-12T10:22:38,598     Using cached Cython-3.0.2-py2.py3-none-any.whl.metadata (3.1 kB)
2023-09-12T10:22:38,674   Collecting cython-setuptools
2023-09-12T10:22:38,688     Downloading https://www.piwheels.org/simple/cython-setuptools/cython_setuptools-0.2.3-py3-none-any.whl (9.7 kB)
2023-09-12T10:22:38,925   Collecting pysam>=0.15
2023-09-12T10:22:39,065     Downloading pysam-0.21.0.tar.gz (4.1 MB)
2023-09-12T10:22:39,452        ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.1/4.1 MB 10.7 MB/s eta 0:00:00
2023-09-12T10:22:42,095     Installing build dependencies: started
2023-09-12T10:22:42,097     Running command pip subprocess to install build dependencies
2023-09-12T10:22:43,731     Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-12T10:22:45,412     Collecting setuptools>=59.0
2023-09-12T10:22:45,413       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
2023-09-12T10:22:45,420       Using cached setuptools-68.2.1-py3-none-any.whl.metadata (6.3 kB)
2023-09-12T10:22:45,627     Collecting wheel
2023-09-12T10:22:45,643       Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB)
2023-09-12T10:22:47,022     Collecting Cython<3.0,>=0.29.30
2023-09-12T10:22:47,024       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
2023-09-12T10:22:47,030       Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB)
2023-09-12T10:22:47,210     Using cached setuptools-68.2.1-py3-none-any.whl (807 kB)
2023-09-12T10:22:47,245     Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB)
2023-09-12T10:22:49,762     Installing collected packages: wheel, setuptools, Cython
2023-09-12T10:22:54,662     Successfully installed Cython-0.29.36 setuptools-68.2.1 wheel-0.41.2
2023-09-12T10:22:55,278     Installing build dependencies: finished with status 'done'
2023-09-12T10:22:55,281     Getting requirements to build wheel: started
2023-09-12T10:22:55,282     Running command Getting requirements to build wheel
2023-09-12T10:22:55,959     # pysam: cython is available - using cythonize if necessary
2023-09-12T10:22:55,960     # pysam: htslib mode is shared
2023-09-12T10:22:55,961     # pysam: HTSLIB_CONFIGURE_OPTIONS=None
2023-09-12T10:22:55,962     # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc
2023-09-12T10:22:55,962     # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:22:55,963     # pysam: (sysconfig) LDFLAGS=  -g -fwrapv -O2
2023-09-12T10:22:56,278     checking for gcc... arm-linux-gnueabihf-gcc
2023-09-12T10:22:56,554     checking whether the C compiler works... yes
2023-09-12T10:22:56,555     checking for C compiler default output file name... a.out
2023-09-12T10:22:56,727     checking for suffix of executables...
2023-09-12T10:22:56,932     checking whether we are cross compiling... no
2023-09-12T10:22:57,020     checking for suffix of object files... o
2023-09-12T10:22:57,127     checking whether we are using the GNU C compiler... yes
2023-09-12T10:22:57,203     checking whether arm-linux-gnueabihf-gcc accepts -g... yes
2023-09-12T10:22:57,334     checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed
2023-09-12T10:22:57,338     checking for ranlib... ranlib
2023-09-12T10:22:57,348     checking for grep that handles long lines and -e... /usr/bin/grep
2023-09-12T10:22:57,424     checking for C compiler warning flags... -Wall
2023-09-12T10:22:57,434     configure: Default CFLAGS_ARM/X86:  -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:22:57,494     checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no
2023-09-12T10:22:57,545     checking whether C compiler accepts -mavx2... no
2023-09-12T10:22:57,600     checking whether C compiler accepts -mavx512f... no
2023-09-12T10:22:58,058     checking whether C compiler supports ARM Neon... no
2023-09-12T10:22:58,062     checking for pkg-config... /usr/bin/pkg-config
2023-09-12T10:22:58,068     checking pkg-config is at least version 0.9.0... yes
2023-09-12T10:22:58,070     checking for special C compiler options needed for large files... no
2023-09-12T10:22:58,254     checking for _FILE_OFFSET_BITS value needed for large files... 64
2023-09-12T10:22:58,269     checking shared library type for unknown-Linux... plain .so
2023-09-12T10:22:58,378     checking whether the linker supports versioned symbols... no
2023-09-12T10:22:58,553     checking whether the compiler accepts -fvisibility=hidden... yes
2023-09-12T10:22:58,687     checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E
2023-09-12T10:22:58,797     checking for egrep... /usr/bin/grep -E
2023-09-12T10:22:59,262     checking for ANSI C header files... yes
2023-09-12T10:22:59,394     checking for sys/types.h... yes
2023-09-12T10:22:59,580     checking for sys/stat.h... yes
2023-09-12T10:22:59,715     checking for stdlib.h... yes
2023-09-12T10:22:59,857     checking for string.h... yes
2023-09-12T10:22:59,998     checking for memory.h... yes
2023-09-12T10:23:00,139     checking for strings.h... yes
2023-09-12T10:23:00,289     checking for inttypes.h... yes
2023-09-12T10:23:00,484     checking for stdint.h... yes
2023-09-12T10:23:00,639     checking for unistd.h... yes
2023-09-12T10:23:00,663     checking for stdlib.h... (cached) yes
2023-09-12T10:23:00,685     checking for unistd.h... (cached) yes
2023-09-12T10:23:00,866     checking for sys/param.h... yes
2023-09-12T10:23:01,061     checking for getpagesize... yes
2023-09-12T10:23:01,439     checking for working mmap... yes
2023-09-12T10:23:01,635     checking for gmtime_r... yes
2023-09-12T10:23:01,841     checking for fsync... yes
2023-09-12T10:23:02,073     checking for drand48... yes
2023-09-12T10:23:02,297     checking for srand48_deterministic... no
2023-09-12T10:23:02,467     checking whether fdatasync is declared... yes
2023-09-12T10:23:02,653     checking for fdatasync... yes
2023-09-12T10:23:03,082     checking for library containing log... -lm
2023-09-12T10:23:03,188     checking for zlib.h... yes
2023-09-12T10:23:03,371     checking for inflate in -lz... yes
2023-09-12T10:23:03,558     checking for library containing recv... none required
2023-09-12T10:23:03,670     checking for bzlib.h... yes
2023-09-12T10:23:03,862     checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
2023-09-12T10:23:04,115     checking for lzma.h... yes
2023-09-12T10:23:04,302     checking for lzma_easy_buffer_encode in -llzma... yes
2023-09-12T10:23:04,307     checking whether htscodecs files are present... yes
2023-09-12T10:23:04,385     checking for libdeflate.h... yes
2023-09-12T10:23:04,609     checking for libdeflate_deflate_compress in -ldeflate... yes
2023-09-12T10:23:04,770     checking for curl/curl.h... yes
2023-09-12T10:23:05,136     checking for curl_easy_pause in -lcurl... yes
2023-09-12T10:23:05,374     checking for CCHmac... no
2023-09-12T10:23:05,970     checking for library containing HMAC... -lcrypto
2023-09-12T10:23:06,158     checking for library containing regcomp... none required
2023-09-12T10:23:06,295     checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
2023-09-12T10:23:06,376     configure: creating ./config.status
2023-09-12T10:23:06,666     config.status: creating config.mk
2023-09-12T10:23:06,707     config.status: creating htslib.pc.tmp
2023-09-12T10:23:06,760     config.status: creating config.h
2023-09-12T10:23:06,805     config.status: linking htscodecs_bundled.mk to htscodecs.mk
2023-09-12T10:23:07,400     # pysam: htslib configure options: --enable-libcurl
2023-09-12T10:23:07,401     # pysam: htslib_config HTS_CFLAGS_AVX2=
2023-09-12T10:23:07,402     # pysam: htslib_config HTS_CFLAGS_AVX512=
2023-09-12T10:23:07,402     # pysam: htslib_config HTS_CFLAGS_SSE4=
2023-09-12T10:23:07,403     # pysam: htslib_config HTS_HAVE_NEON=
2023-09-12T10:23:07,404     # 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
2023-09-12T10:23:07,405     # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
2023-09-12T10:23:07,406     # pysam: htslib_config PLATFORM=default
2023-09-12T10:23:07,407     # pysam: config_option: ENABLE_GCS=1
2023-09-12T10:23:07,407     # pysam: config_option: ENABLE_PLUGINS=0
2023-09-12T10:23:07,408     # pysam: config_option: ENABLE_S3=1
2023-09-12T10:23:07,409     # pysam: config_option: HAVE_COMMONCRYPTO=0
2023-09-12T10:23:07,410     # pysam: config_option: HAVE_HMAC=1
2023-09-12T10:23:07,410     # pysam: config_option: HAVE_LIBBZ2=1
2023-09-12T10:23:07,411     # pysam: config_option: HAVE_LIBCURL=1
2023-09-12T10:23:07,412     # pysam: config_option: HAVE_LIBDEFLATE=1
2023-09-12T10:23:07,413     # pysam: config_option: HAVE_LIBLZMA=1
2023-09-12T10:23:07,414     # pysam: config_option: HAVE_MMAP=1
2023-09-12T10:23:07,414     running egg_info
2023-09-12T10:23:07,415     writing pysam.egg-info/PKG-INFO
2023-09-12T10:23:07,418     writing dependency_links to pysam.egg-info/dependency_links.txt
2023-09-12T10:23:07,420     writing requirements to pysam.egg-info/requires.txt
2023-09-12T10:23:07,422     writing top-level names to pysam.egg-info/top_level.txt
2023-09-12T10:23:07,460     reading manifest file 'pysam.egg-info/SOURCES.txt'
2023-09-12T10:23:07,490     reading manifest template 'MANIFEST.in'
2023-09-12T10:23:07,492     warning: no files found matching 'KNOWN_BUGS'
2023-09-12T10:23:07,493     warning: no files found matching 'THANKS'
2023-09-12T10:23:07,503     no previously-included directories found matching 'tests/'
2023-09-12T10:23:07,607     adding license file 'COPYING'
2023-09-12T10:23:07,607     adding license file 'AUTHORS'
2023-09-12T10:23:07,631     writing manifest file 'pysam.egg-info/SOURCES.txt'
2023-09-12T10:23:07,753     Getting requirements to build wheel: finished with status 'done'
2023-09-12T10:23:07,764     Preparing metadata (pyproject.toml): started
2023-09-12T10:23:07,765     Running command Preparing metadata (pyproject.toml)
2023-09-12T10:23:08,439     # pysam: cython is available - using cythonize if necessary
2023-09-12T10:23:08,440     # pysam: htslib mode is shared
2023-09-12T10:23:08,441     # pysam: HTSLIB_CONFIGURE_OPTIONS=None
2023-09-12T10:23:08,442     # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc
2023-09-12T10:23:08,444     # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:23:08,445     # pysam: (sysconfig) LDFLAGS=  -g -fwrapv -O2
2023-09-12T10:23:09,101     checking for gcc... arm-linux-gnueabihf-gcc
2023-09-12T10:23:09,462     checking whether the C compiler works... yes
2023-09-12T10:23:09,464     checking for C compiler default output file name... a.out
2023-09-12T10:23:09,666     checking for suffix of executables...
2023-09-12T10:23:10,124     checking whether we are cross compiling... no
2023-09-12T10:23:10,311     checking for suffix of object files... o
2023-09-12T10:23:10,393     checking whether we are using the GNU C compiler... yes
2023-09-12T10:23:10,478     checking whether arm-linux-gnueabihf-gcc accepts -g... yes
2023-09-12T10:23:10,614     checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed
2023-09-12T10:23:10,617     checking for ranlib... ranlib
2023-09-12T10:23:10,625     checking for grep that handles long lines and -e... /usr/bin/grep
2023-09-12T10:23:10,701     checking for C compiler warning flags... -Wall
2023-09-12T10:23:10,712     configure: Default CFLAGS_ARM/X86:  -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:23:10,777     checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no
2023-09-12T10:23:10,830     checking whether C compiler accepts -mavx2... no
2023-09-12T10:23:10,910     checking whether C compiler accepts -mavx512f... no
2023-09-12T10:23:11,418     checking whether C compiler supports ARM Neon... no
2023-09-12T10:23:11,421     checking for pkg-config... /usr/bin/pkg-config
2023-09-12T10:23:11,426     checking pkg-config is at least version 0.9.0... yes
2023-09-12T10:23:11,428     checking for special C compiler options needed for large files... no
2023-09-12T10:23:11,629     checking for _FILE_OFFSET_BITS value needed for large files... 64
2023-09-12T10:23:11,643     checking shared library type for unknown-Linux... plain .so
2023-09-12T10:23:11,760     checking whether the linker supports versioned symbols... no
2023-09-12T10:23:11,935     checking whether the compiler accepts -fvisibility=hidden... yes
2023-09-12T10:23:12,043     checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E
2023-09-12T10:23:12,156     checking for egrep... /usr/bin/grep -E
2023-09-12T10:23:12,649     checking for ANSI C header files... yes
2023-09-12T10:23:12,769     checking for sys/types.h... yes
2023-09-12T10:23:12,901     checking for sys/stat.h... yes
2023-09-12T10:23:13,033     checking for stdlib.h... yes
2023-09-12T10:23:13,172     checking for string.h... yes
2023-09-12T10:23:13,335     checking for memory.h... yes
2023-09-12T10:23:13,527     checking for strings.h... yes
2023-09-12T10:23:13,670     checking for inttypes.h... yes
2023-09-12T10:23:13,813     checking for stdint.h... yes
2023-09-12T10:23:13,968     checking for unistd.h... yes
2023-09-12T10:23:14,031     checking for stdlib.h... (cached) yes
2023-09-12T10:23:14,053     checking for unistd.h... (cached) yes
2023-09-12T10:23:14,225     checking for sys/param.h... yes
2023-09-12T10:23:14,420     checking for getpagesize... yes
2023-09-12T10:23:14,765     checking for working mmap... yes
2023-09-12T10:23:14,971     checking for gmtime_r... yes
2023-09-12T10:23:15,189     checking for fsync... yes
2023-09-12T10:23:15,392     checking for drand48... yes
2023-09-12T10:23:15,612     checking for srand48_deterministic... no
2023-09-12T10:23:15,807     checking whether fdatasync is declared... yes
2023-09-12T10:23:15,995     checking for fdatasync... yes
2023-09-12T10:23:16,492     checking for library containing log... -lm
2023-09-12T10:23:16,619     checking for zlib.h... yes
2023-09-12T10:23:16,806     checking for inflate in -lz... yes
2023-09-12T10:23:16,993     checking for library containing recv... none required
2023-09-12T10:23:17,079     checking for bzlib.h... yes
2023-09-12T10:23:17,259     checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
2023-09-12T10:23:17,472     checking for lzma.h... yes
2023-09-12T10:23:17,658     checking for lzma_easy_buffer_encode in -llzma... yes
2023-09-12T10:23:17,664     checking whether htscodecs files are present... yes
2023-09-12T10:23:17,743     checking for libdeflate.h... yes
2023-09-12T10:23:17,924     checking for libdeflate_deflate_compress in -ldeflate... yes
2023-09-12T10:23:18,073     checking for curl/curl.h... yes
2023-09-12T10:23:18,468     checking for curl_easy_pause in -lcurl... yes
2023-09-12T10:23:18,894     checking for CCHmac... no
2023-09-12T10:23:19,523     checking for library containing HMAC... -lcrypto
2023-09-12T10:23:19,709     checking for library containing regcomp... none required
2023-09-12T10:23:19,851     checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
2023-09-12T10:23:19,923     configure: creating ./config.status
2023-09-12T10:23:20,209     config.status: creating config.mk
2023-09-12T10:23:20,248     config.status: creating htslib.pc.tmp
2023-09-12T10:23:20,292     config.status: creating config.h
2023-09-12T10:23:20,310     config.status: config.h is unchanged
2023-09-12T10:23:20,316     config.status: linking htscodecs_bundled.mk to htscodecs.mk
2023-09-12T10:23:20,792     # pysam: htslib configure options: --enable-libcurl
2023-09-12T10:23:20,793     # pysam: htslib_config HTS_CFLAGS_AVX2=
2023-09-12T10:23:20,794     # pysam: htslib_config HTS_CFLAGS_AVX512=
2023-09-12T10:23:20,795     # pysam: htslib_config HTS_CFLAGS_SSE4=
2023-09-12T10:23:20,796     # pysam: htslib_config HTS_HAVE_NEON=
2023-09-12T10:23:20,797     # 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
2023-09-12T10:23:20,798     # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
2023-09-12T10:23:20,799     # pysam: htslib_config PLATFORM=default
2023-09-12T10:23:20,800     # pysam: config_option: ENABLE_GCS=1
2023-09-12T10:23:20,800     # pysam: config_option: ENABLE_PLUGINS=0
2023-09-12T10:23:20,801     # pysam: config_option: ENABLE_S3=1
2023-09-12T10:23:20,802     # pysam: config_option: HAVE_COMMONCRYPTO=0
2023-09-12T10:23:20,803     # pysam: config_option: HAVE_HMAC=1
2023-09-12T10:23:20,804     # pysam: config_option: HAVE_LIBBZ2=1
2023-09-12T10:23:20,805     # pysam: config_option: HAVE_LIBCURL=1
2023-09-12T10:23:20,807     # pysam: config_option: HAVE_LIBDEFLATE=1
2023-09-12T10:23:20,808     # pysam: config_option: HAVE_LIBLZMA=1
2023-09-12T10:23:20,809     # pysam: config_option: HAVE_MMAP=1
2023-09-12T10:23:20,811     running dist_info
2023-09-12T10:23:20,812     creating /tmp/pip-modern-metadata-09o3204i/pysam.egg-info
2023-09-12T10:23:20,813     writing /tmp/pip-modern-metadata-09o3204i/pysam.egg-info/PKG-INFO
2023-09-12T10:23:20,814     writing dependency_links to /tmp/pip-modern-metadata-09o3204i/pysam.egg-info/dependency_links.txt
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2023-09-12T10:23:20,876     reading manifest template 'MANIFEST.in'
2023-09-12T10:23:20,877     warning: no files found matching 'KNOWN_BUGS'
2023-09-12T10:23:20,878     warning: no files found matching 'THANKS'
2023-09-12T10:23:20,887     no previously-included directories found matching 'tests/'
2023-09-12T10:23:20,993     adding license file 'COPYING'
2023-09-12T10:23:20,994     adding license file 'AUTHORS'
2023-09-12T10:23:21,012     writing manifest file '/tmp/pip-modern-metadata-09o3204i/pysam.egg-info/SOURCES.txt'
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2023-09-12T10:23:21,165     Preparing metadata (pyproject.toml): finished with status 'done'
2023-09-12T10:23:22,820   Collecting setuptools>=45
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2023-09-12T10:23:27,277   Building wheels for collected packages: pysam
2023-09-12T10:23:27,282     Building wheel for pysam (pyproject.toml): started
2023-09-12T10:23:27,283     Running command Building wheel for pysam (pyproject.toml)
2023-09-12T10:23:27,913     # pysam: cython is available - using cythonize if necessary
2023-09-12T10:23:27,914     # pysam: htslib mode is shared
2023-09-12T10:23:27,914     # pysam: HTSLIB_CONFIGURE_OPTIONS=None
2023-09-12T10:23:27,915     # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc
2023-09-12T10:23:27,916     # pysam: (sysconfig) CFLAGS=-Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:23:27,917     # pysam: (sysconfig) LDFLAGS=  -g -fwrapv -O2
2023-09-12T10:23:28,204     checking for gcc... arm-linux-gnueabihf-gcc
2023-09-12T10:23:28,459     checking whether the C compiler works... yes
2023-09-12T10:23:28,460     checking for C compiler default output file name... a.out
2023-09-12T10:23:28,681     checking for suffix of executables...
2023-09-12T10:23:28,883     checking whether we are cross compiling... no
2023-09-12T10:23:28,968     checking for suffix of object files... o
2023-09-12T10:23:29,045     checking whether we are using the GNU C compiler... yes
2023-09-12T10:23:29,117     checking whether arm-linux-gnueabihf-gcc accepts -g... yes
2023-09-12T10:23:29,245     checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed
2023-09-12T10:23:29,247     checking for ranlib... ranlib
2023-09-12T10:23:29,255     checking for grep that handles long lines and -e... /usr/bin/grep
2023-09-12T10:23:29,328     checking for C compiler warning flags... -Wall
2023-09-12T10:23:29,338     configure: Default CFLAGS_ARM/X86:  -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
2023-09-12T10:23:29,394     checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... no
2023-09-12T10:23:29,464     checking whether C compiler accepts -mavx2... no
2023-09-12T10:23:29,541     checking whether C compiler accepts -mavx512f... no
2023-09-12T10:23:30,011     checking whether C compiler supports ARM Neon... no
2023-09-12T10:23:30,014     checking for pkg-config... /usr/bin/pkg-config
2023-09-12T10:23:30,019     checking pkg-config is at least version 0.9.0... yes
2023-09-12T10:23:30,020     checking for special C compiler options needed for large files... no
2023-09-12T10:23:30,205     checking for _FILE_OFFSET_BITS value needed for large files... 64
2023-09-12T10:23:30,220     checking shared library type for unknown-Linux... plain .so
2023-09-12T10:23:30,328     checking whether the linker supports versioned symbols... no
2023-09-12T10:23:30,499     checking whether the compiler accepts -fvisibility=hidden... yes
2023-09-12T10:23:30,605     checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E
2023-09-12T10:23:30,717     checking for egrep... /usr/bin/grep -E
2023-09-12T10:23:31,216     checking for ANSI C header files... yes
2023-09-12T10:23:31,335     checking for sys/types.h... yes
2023-09-12T10:23:31,469     checking for sys/stat.h... yes
2023-09-12T10:23:31,603     checking for stdlib.h... yes
2023-09-12T10:23:31,745     checking for string.h... yes
2023-09-12T10:23:31,914     checking for memory.h... yes
2023-09-12T10:23:32,057     checking for strings.h... yes
2023-09-12T10:23:32,200     checking for inttypes.h... yes
2023-09-12T10:23:32,342     checking for stdint.h... yes
2023-09-12T10:23:32,496     checking for unistd.h... yes
2023-09-12T10:23:32,521     checking for stdlib.h... (cached) yes
2023-09-12T10:23:32,543     checking for unistd.h... (cached) yes
2023-09-12T10:23:32,752     checking for sys/param.h... yes
2023-09-12T10:23:32,945     checking for getpagesize... yes
2023-09-12T10:23:33,286     checking for working mmap... yes
2023-09-12T10:23:33,482     checking for gmtime_r... yes
2023-09-12T10:23:33,685     checking for fsync... yes
2023-09-12T10:23:33,889     checking for drand48... yes
2023-09-12T10:23:34,108     checking for srand48_deterministic... no
2023-09-12T10:23:34,314     checking whether fdatasync is declared... yes
2023-09-12T10:23:34,495     checking for fdatasync... yes
2023-09-12T10:23:34,891     checking for library containing log... -lm
2023-09-12T10:23:35,028     checking for zlib.h... yes
2023-09-12T10:23:35,212     checking for inflate in -lz... yes
2023-09-12T10:23:35,396     checking for library containing recv... none required
2023-09-12T10:23:35,482     checking for bzlib.h... yes
2023-09-12T10:23:35,668     checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
2023-09-12T10:23:36,123     checking for lzma.h... yes
2023-09-12T10:23:36,324     checking for lzma_easy_buffer_encode in -llzma... yes
2023-09-12T10:23:36,329     checking whether htscodecs files are present... yes
2023-09-12T10:23:36,405     checking for libdeflate.h... yes
2023-09-12T10:23:36,586     checking for libdeflate_deflate_compress in -ldeflate... yes
2023-09-12T10:23:36,735     checking for curl/curl.h... yes
2023-09-12T10:23:37,126     checking for curl_easy_pause in -lcurl... yes
2023-09-12T10:23:37,583     checking for CCHmac... no
2023-09-12T10:23:38,249     checking for library containing HMAC... -lcrypto
2023-09-12T10:23:38,439     checking for library containing regcomp... none required
2023-09-12T10:23:38,592     checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
2023-09-12T10:23:38,657     configure: creating ./config.status
2023-09-12T10:23:38,942     config.status: creating config.mk
2023-09-12T10:23:38,982     config.status: creating htslib.pc.tmp
2023-09-12T10:23:39,024     config.status: creating config.h
2023-09-12T10:23:39,043     config.status: config.h is unchanged
2023-09-12T10:23:39,048     config.status: linking htscodecs_bundled.mk to htscodecs.mk
2023-09-12T10:23:39,514     # pysam: htslib configure options: --enable-libcurl
2023-09-12T10:23:39,515     # pysam: htslib_config HTS_CFLAGS_AVX2=
2023-09-12T10:23:39,516     # pysam: htslib_config HTS_CFLAGS_AVX512=
2023-09-12T10:23:39,516     # pysam: htslib_config HTS_CFLAGS_SSE4=
2023-09-12T10:23:39,517     # pysam: htslib_config HTS_HAVE_NEON=
2023-09-12T10:23:39,518     # 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
2023-09-12T10:23:39,519     # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
2023-09-12T10:23:39,520     # pysam: htslib_config PLATFORM=default
2023-09-12T10:23:39,521     # pysam: config_option: ENABLE_GCS=1
2023-09-12T10:23:39,522     # pysam: config_option: ENABLE_PLUGINS=0
2023-09-12T10:23:39,522     # pysam: config_option: ENABLE_S3=1
2023-09-12T10:23:39,523     # pysam: config_option: HAVE_COMMONCRYPTO=0
2023-09-12T10:23:39,524     # pysam: config_option: HAVE_HMAC=1
2023-09-12T10:23:39,525     # pysam: config_option: HAVE_LIBBZ2=1
2023-09-12T10:23:39,525     # pysam: config_option: HAVE_LIBCURL=1
2023-09-12T10:23:39,526     # pysam: config_option: HAVE_LIBDEFLATE=1
2023-09-12T10:23:39,527     # pysam: config_option: HAVE_LIBLZMA=1
2023-09-12T10:23:39,528     # pysam: config_option: HAVE_MMAP=1
2023-09-12T10:23:39,528     running bdist_wheel
2023-09-12T10:23:39,537     running build
2023-09-12T10:23:39,537     running build_py
2023-09-12T10:23:39,543     creating build
2023-09-12T10:23:39,544     creating build/lib.linux-armv7l-cpython-311
2023-09-12T10:23:39,545     creating build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:39,547     copying pysam/config.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:39,549     copying pysam/utils.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:39,551     copying pysam/__init__.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:39,553     copying pysam/version.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:39,555     copying pysam/bcftools.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:39,558     copying pysam/samtools.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:39,560     copying pysam/Pileup.py -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:39,563     creating build/lib.linux-armv7l-cpython-311/pysam/include
2023-09-12T10:23:39,564     copying pysam/include/__init__.py -> build/lib.linux-armv7l-cpython-311/pysam/include
2023-09-12T10:23:39,568     running egg_info
2023-09-12T10:23:39,574     writing pysam.egg-info/PKG-INFO
2023-09-12T10:23:39,577     writing dependency_links to pysam.egg-info/dependency_links.txt
2023-09-12T10:23:39,578     writing requirements to pysam.egg-info/requires.txt
2023-09-12T10:23:39,580     writing top-level names to pysam.egg-info/top_level.txt
2023-09-12T10:23:39,636     reading manifest file 'pysam.egg-info/SOURCES.txt'
2023-09-12T10:23:39,672     reading manifest template 'MANIFEST.in'
2023-09-12T10:23:39,673     warning: no files found matching 'KNOWN_BUGS'
2023-09-12T10:23:39,674     warning: no files found matching 'THANKS'
2023-09-12T10:23:39,682     no previously-included directories found matching 'tests/'
2023-09-12T10:23:39,788     adding license file 'COPYING'
2023-09-12T10:23:39,789     adding license file 'AUTHORS'
2023-09-12T10:23:39,813     writing manifest file 'pysam.egg-info/SOURCES.txt'
2023-09-12T10:23:39,818     /tmp/pip-build-env-rrie22iz/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.
2023-09-12T10:23:39,819     !!

2023-09-12T10:23:39,821             ********************************************************************************
2023-09-12T10:23:39,821             ############################
2023-09-12T10:23:39,822             # Package would be ignored #
2023-09-12T10:23:39,823             ############################
2023-09-12T10:23:39,824             Python recognizes 'pysam.include.htslib.cram' as an importable package[^1],
2023-09-12T10:23:39,825             but it is absent from setuptools' `packages` configuration.

2023-09-12T10:23:39,826             This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-12T10:23:39,827             package, please make sure that 'pysam.include.htslib.cram' is explicitly added
2023-09-12T10:23:39,828             to the `packages` configuration field.

2023-09-12T10:23:39,830             Alternatively, you can also rely on setuptools' discovery methods
2023-09-12T10:23:39,830             (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-12T10:23:39,831             instead of `find_packages(...)`/`find:`).

2023-09-12T10:23:39,833             You can read more about "package discovery" on setuptools documentation page:

2023-09-12T10:23:39,835             - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-12T10:23:39,837             If you don't want 'pysam.include.htslib.cram' to be distributed and are
2023-09-12T10:23:39,838             already explicitly excluding 'pysam.include.htslib.cram' via
2023-09-12T10:23:39,839             `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-12T10:23:39,840             you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-12T10:23:39,841             combination with a more fine grained `package-data` configuration.

2023-09-12T10:23:39,842             You can read more about "package data files" on setuptools documentation page:

2023-09-12T10:23:39,844             - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-12T10:23:39,847             [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-12T10:23:39,847                   even if it does not contain any `.py` files.
2023-09-12T10:23:39,848                   On the other hand, currently there is no concept of package data
2023-09-12T10:23:39,849                   directory, all directories are treated like packages.
2023-09-12T10:23:39,850             ********************************************************************************

2023-09-12T10:23:39,852     !!
2023-09-12T10:23:39,852       check.warn(importable)
2023-09-12T10:23:39,853     /tmp/pip-build-env-rrie22iz/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.
2023-09-12T10:23:39,854     !!

2023-09-12T10:23:39,856             ********************************************************************************
2023-09-12T10:23:39,856             ############################
2023-09-12T10:23:39,857             # Package would be ignored #
2023-09-12T10:23:39,858             ############################
2023-09-12T10:23:39,859             Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package[^1],
2023-09-12T10:23:39,859             but it is absent from setuptools' `packages` configuration.

2023-09-12T10:23:39,861             This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-12T10:23:39,862             package, please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is explicitly added
2023-09-12T10:23:39,863             to the `packages` configuration field.

2023-09-12T10:23:39,864             Alternatively, you can also rely on setuptools' discovery methods
2023-09-12T10:23:39,865             (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-12T10:23:39,866             instead of `find_packages(...)`/`find:`).

2023-09-12T10:23:39,868             You can read more about "package discovery" on setuptools documentation page:

2023-09-12T10:23:39,870             - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-12T10:23:39,872             If you don't want 'pysam.include.htslib.htscodecs.htscodecs' to be distributed and are
2023-09-12T10:23:39,873             already explicitly excluding 'pysam.include.htslib.htscodecs.htscodecs' via
2023-09-12T10:23:39,873             `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-12T10:23:39,874             you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-12T10:23:39,875             combination with a more fine grained `package-data` configuration.

2023-09-12T10:23:39,877             You can read more about "package data files" on setuptools documentation page:

2023-09-12T10:23:39,879             - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-12T10:23:39,882             [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-12T10:23:39,883                   even if it does not contain any `.py` files.
2023-09-12T10:23:39,884                   On the other hand, currently there is no concept of package data
2023-09-12T10:23:39,885                   directory, all directories are treated like packages.
2023-09-12T10:23:39,886             ********************************************************************************

2023-09-12T10:23:39,887     !!
2023-09-12T10:23:39,888       check.warn(importable)
2023-09-12T10:23:39,889     /tmp/pip-build-env-rrie22iz/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.
2023-09-12T10:23:39,890     !!

2023-09-12T10:23:39,893             ********************************************************************************
2023-09-12T10:23:39,893             ############################
2023-09-12T10:23:39,894             # Package would be ignored #
2023-09-12T10:23:39,895             ############################
2023-09-12T10:23:39,897             Python recognizes 'pysam.include.htslib.m4' as an importable package[^1],
2023-09-12T10:23:39,898             but it is absent from setuptools' `packages` configuration.

2023-09-12T10:23:39,900             This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-12T10:23:39,901             package, please make sure that 'pysam.include.htslib.m4' is explicitly added
2023-09-12T10:23:39,902             to the `packages` configuration field.

2023-09-12T10:23:39,903             Alternatively, you can also rely on setuptools' discovery methods
2023-09-12T10:23:39,904             (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-12T10:23:39,905             instead of `find_packages(...)`/`find:`).

2023-09-12T10:23:39,907             You can read more about "package discovery" on setuptools documentation page:

2023-09-12T10:23:39,909             - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-12T10:23:39,910             If you don't want 'pysam.include.htslib.m4' to be distributed and are
2023-09-12T10:23:39,911             already explicitly excluding 'pysam.include.htslib.m4' via
2023-09-12T10:23:39,912             `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-12T10:23:39,918             you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-12T10:23:39,919             combination with a more fine grained `package-data` configuration.

2023-09-12T10:23:39,922             You can read more about "package data files" on setuptools documentation page:

2023-09-12T10:23:39,925             - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-12T10:23:39,929             [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-12T10:23:39,931                   even if it does not contain any `.py` files.
2023-09-12T10:23:39,932                   On the other hand, currently there is no concept of package data
2023-09-12T10:23:39,934                   directory, all directories are treated like packages.
2023-09-12T10:23:39,935             ********************************************************************************

2023-09-12T10:23:39,938     !!
2023-09-12T10:23:39,945       check.warn(importable)
2023-09-12T10:23:39,947     /tmp/pip-build-env-rrie22iz/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.
2023-09-12T10:23:39,949     !!

2023-09-12T10:23:39,951             ********************************************************************************
2023-09-12T10:23:39,953             ############################
2023-09-12T10:23:39,954             # Package would be ignored #
2023-09-12T10:23:39,959             ############################
2023-09-12T10:23:39,960             Python recognizes 'pysam.include.htslib.os' as an importable package[^1],
2023-09-12T10:23:39,962             but it is absent from setuptools' `packages` configuration.

2023-09-12T10:23:39,963             This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-12T10:23:39,964             package, please make sure that 'pysam.include.htslib.os' is explicitly added
2023-09-12T10:23:39,965             to the `packages` configuration field.

2023-09-12T10:23:39,968             Alternatively, you can also rely on setuptools' discovery methods
2023-09-12T10:23:39,969             (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-12T10:23:39,970             instead of `find_packages(...)`/`find:`).

2023-09-12T10:23:39,971             You can read more about "package discovery" on setuptools documentation page:

2023-09-12T10:23:39,973             - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-12T10:23:39,975             If you don't want 'pysam.include.htslib.os' to be distributed and are
2023-09-12T10:23:39,975             already explicitly excluding 'pysam.include.htslib.os' via
2023-09-12T10:23:39,976             `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-12T10:23:39,977             you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-12T10:23:39,978             combination with a more fine grained `package-data` configuration.

2023-09-12T10:23:39,991             You can read more about "package data files" on setuptools documentation page:

2023-09-12T10:23:40,001             - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-12T10:23:40,004             [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-12T10:23:40,004                   even if it does not contain any `.py` files.
2023-09-12T10:23:40,005                   On the other hand, currently there is no concept of package data
2023-09-12T10:23:40,005                   directory, all directories are treated like packages.
2023-09-12T10:23:40,006             ********************************************************************************

2023-09-12T10:23:40,008     !!
2023-09-12T10:23:40,008       check.warn(importable)
2023-09-12T10:23:40,009     /tmp/pip-build-env-rrie22iz/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.
2023-09-12T10:23:40,010     !!

2023-09-12T10:23:40,013             ********************************************************************************
2023-09-12T10:23:40,014             ############################
2023-09-12T10:23:40,015             # Package would be ignored #
2023-09-12T10:23:40,020             ############################
2023-09-12T10:23:40,021             Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1],
2023-09-12T10:23:40,021             but it is absent from setuptools' `packages` configuration.

2023-09-12T10:23:40,023             This leads to an ambiguous overall configuration. If you want to distribute this
2023-09-12T10:23:40,023             package, please make sure that 'pysam.include.samtools.lz4' is explicitly added
2023-09-12T10:23:40,024             to the `packages` configuration field.

2023-09-12T10:23:40,025             Alternatively, you can also rely on setuptools' discovery methods
2023-09-12T10:23:40,026             (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-09-12T10:23:40,027             instead of `find_packages(...)`/`find:`).

2023-09-12T10:23:40,028             You can read more about "package discovery" on setuptools documentation page:

2023-09-12T10:23:40,030             - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-09-12T10:23:40,032             If you don't want 'pysam.include.samtools.lz4' to be distributed and are
2023-09-12T10:23:40,032             already explicitly excluding 'pysam.include.samtools.lz4' via
2023-09-12T10:23:40,033             `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-09-12T10:23:40,033             you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-09-12T10:23:40,034             combination with a more fine grained `package-data` configuration.

2023-09-12T10:23:40,056             You can read more about "package data files" on setuptools documentation page:

2023-09-12T10:23:40,071             - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-09-12T10:23:40,074             [^1]: For Python, any directory (with suitable naming) can be imported,
2023-09-12T10:23:40,074                   even if it does not contain any `.py` files.
2023-09-12T10:23:40,074                   On the other hand, currently there is no concept of package data
2023-09-12T10:23:40,076                   directory, all directories are treated like packages.
2023-09-12T10:23:40,076             ********************************************************************************

2023-09-12T10:23:40,077     !!
2023-09-12T10:23:40,078       check.warn(importable)
2023-09-12T10:23:40,078     copying pysam/cbcftools_util.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,078     copying pysam/csamtools_util.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,079     copying pysam/htslib_util.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,080     copying pysam/htslib_util.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,080     copying pysam/libcalignedsegment.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,081     copying pysam/libcalignedsegment.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,082     copying pysam/libcalignedsegment.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,082     copying pysam/libcalignedsegment.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,083     copying pysam/libcalignmentfile.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,084     copying pysam/libcalignmentfile.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,086     copying pysam/libcalignmentfile.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,087     copying pysam/libcalignmentfile.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,087     copying pysam/libcbcf.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,088     copying pysam/libcbcf.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,088     copying pysam/libcbcf.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,089     copying pysam/libcbcf.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,090     copying pysam/libcbcftools.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,094     copying pysam/libcbcftools.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,096     copying pysam/libcbcftools.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,098     copying pysam/libcbcftools.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,100     copying pysam/libcbgzf.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,108     copying pysam/libcbgzf.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,111     copying pysam/libcbgzf.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,113     copying pysam/libcfaidx.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,128     copying pysam/libcfaidx.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,130     copying pysam/libcfaidx.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,133     copying pysam/libcfaidx.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,136     copying pysam/libchtslib.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,149     copying pysam/libchtslib.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,155     copying pysam/libchtslib.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,157     copying pysam/libchtslib.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,160     copying pysam/libcsamfile.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,166     copying pysam/libcsamfile.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,168     copying pysam/libcsamfile.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,170     copying pysam/libcsamfile.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,172     copying pysam/libcsamtools.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,177     copying pysam/libcsamtools.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,179     copying pysam/libcsamtools.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,182     copying pysam/libcsamtools.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,184     copying pysam/libctabix.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,203     copying pysam/libctabix.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,205     copying pysam/libctabix.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,207     copying pysam/libctabix.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,210     copying pysam/libctabixproxies.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,228     copying pysam/libctabixproxies.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,230     copying pysam/libctabixproxies.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,232     copying pysam/libctabixproxies.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,235     copying pysam/libcutils.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,247     copying pysam/libcutils.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,250     copying pysam/libcutils.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,253     copying pysam/libcutils.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,256     copying pysam/libcvcf.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,294     copying pysam/libcvcf.pxd -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,297     copying pysam/libcvcf.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,300     copying pysam/libcvcf.pyx -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,304     copying pysam/py.typed -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,307     copying pysam/pysam_stream.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,310     copying pysam/pysam_util.c -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,313     copying pysam/pysam_util.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,316     copying pysam/version.h -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,319     copying pysam/version.pyi -> build/lib.linux-armv7l-cpython-311/pysam
2023-09-12T10:23:40,322     creating build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,324     copying samtools/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,327     copying samtools/README -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,331     copying samtools/amplicon_stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,336     copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,340     copying samtools/bam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,344     copying samtools/bam.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,348     copying samtools/bam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,351     copying samtools/bam2depth.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,355     copying samtools/bam2depth.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,359     copying samtools/bam_addrprg.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,363     copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,365     copying samtools/bam_ampliconclip.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,368     copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,371     copying samtools/bam_ampliconclip.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,373     copying samtools/bam_aux.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,375     copying samtools/bam_aux.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,377     copying samtools/bam_cat.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,380     copying samtools/bam_cat.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,384     copying samtools/bam_color.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,387     copying samtools/bam_color.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,390     copying samtools/bam_consensus.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,395     copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,400     copying samtools/bam_fastq.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,403     copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,406     copying samtools/bam_flags.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,408     copying samtools/bam_flags.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,411     copying samtools/bam_import.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,413     copying samtools/bam_import.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,416     copying samtools/bam_index.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,418     copying samtools/bam_index.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,421     copying samtools/bam_lpileup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,424     copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,426     copying samtools/bam_lpileup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,428     copying samtools/bam_markdup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,432     copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,437     copying samtools/bam_mate.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,440     copying samtools/bam_mate.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,443     copying samtools/bam_md.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,446     copying samtools/bam_md.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,448     copying samtools/bam_plbuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,451     copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,453     copying samtools/bam_plbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,456     copying samtools/bam_plcmd.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,458     copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,462     copying samtools/bam_quickcheck.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,464     copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,467     copying samtools/bam_reheader.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,469     copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,472     copying samtools/bam_rmdup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,474     copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,477     copying samtools/bam_rmdupse.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,479     copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,482     copying samtools/bam_samples.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,484     copying samtools/bam_samples.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,486     copying samtools/bam_sort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,491     copying samtools/bam_sort.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,495     copying samtools/bam_split.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,498     copying samtools/bam_split.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,501     copying samtools/bam_stat.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,503     copying samtools/bam_stat.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,506     copying samtools/bamshuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,509     copying samtools/bamshuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,512     copying samtools/bamtk.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,514     copying samtools/bamtk.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,517     copying samtools/bedcov.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,520     copying samtools/bedcov.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,522     copying samtools/bedidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,525     copying samtools/bedidx.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,528     copying samtools/bedidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,530     copying samtools/consensus_pileup.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,533     copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,535     copying samtools/consensus_pileup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,538     copying samtools/coverage.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,541     copying samtools/coverage.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,544     copying samtools/cram_size.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,546     copying samtools/cram_size.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,549     copying samtools/cut_target.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,552     copying samtools/cut_target.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,554     copying samtools/dict.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,556     copying samtools/dict.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,559     copying samtools/faidx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,562     copying samtools/faidx.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,565     copying samtools/padding.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,567     copying samtools/padding.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,570     copying samtools/phase.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,573     copying samtools/phase.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,576     copying samtools/reference.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,579     copying samtools/reference.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,581     copying samtools/reset.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,584     copying samtools/reset.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,587     copying samtools/sam_opts.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,589     copying samtools/sam_opts.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,591     copying samtools/sam_opts.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,594     copying samtools/sam_utils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,596     copying samtools/sam_utils.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,598     copying samtools/sam_utils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,601     copying samtools/sam_view.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,604     copying samtools/sam_view.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,608     copying samtools/sample.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,611     copying samtools/sample.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,614     copying samtools/sample.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,617     copying samtools/samtools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,620     copying samtools/samtools.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,624     copying samtools/samtools.pysam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,627     copying samtools/splaysort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,632     copying samtools/stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,643     copying samtools/stats.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,655     copying samtools/stats_isize.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,657     copying samtools/stats_isize.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,660     copying samtools/stats_isize.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,662     copying samtools/tmp_file.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,664     copying samtools/tmp_file.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,667     copying samtools/tmp_file.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,669     copying samtools/version.sh -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,671     creating build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4
2023-09-12T10:23:40,672     copying samtools/lz4/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4
2023-09-12T10:23:40,674     copying samtools/lz4/lz4.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4
2023-09-12T10:23:40,677     copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4
2023-09-12T10:23:40,681     copying samtools/lz4/lz4.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4
2023-09-12T10:23:40,683     copying samtools/config.h -> build/lib.linux-armv7l-cpython-311/pysam/include/samtools
2023-09-12T10:23:40,685     creating build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,686     copying bcftools/HMM.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,689     copying bcftools/HMM.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,692     copying bcftools/HMM.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,694     copying bcftools/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,697     copying bcftools/README -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,699     copying bcftools/abuf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,702     copying bcftools/abuf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,705     copying bcftools/abuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,707     copying bcftools/bam2bcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,711     copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,714     copying bcftools/bam2bcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,717     copying bcftools/bam2bcf_iaux.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,719     copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,722     copying bcftools/bam2bcf_indel.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,725     copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,728     copying bcftools/bam_sample.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,731     copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,733     copying bcftools/bam_sample.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,736     copying bcftools/bcftools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,738     copying bcftools/bcftools.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,741     copying bcftools/bcftools.pysam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,744     copying bcftools/bin.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,746     copying bcftools/bin.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,749     copying bcftools/bin.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,751     copying bcftools/call.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,754     copying bcftools/ccall.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,757     copying bcftools/ccall.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,759     copying bcftools/cigar_state.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,762     copying bcftools/cols.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,764     copying bcftools/cols.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,766     copying bcftools/cols.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,768     copying bcftools/consensus.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,771     copying bcftools/consensus.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,774     copying bcftools/convert.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,777     copying bcftools/convert.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,781     copying bcftools/convert.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,783     copying bcftools/csq.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,788     copying bcftools/csq.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,793     copying bcftools/dbuf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,796     copying bcftools/dist.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,798     copying bcftools/dist.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,801     copying bcftools/dist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,803     copying bcftools/em.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,806     copying bcftools/em.c.pysam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
2023-09-12T10:23:40,809     copying bcftools/extsort.c -> build/lib.linux-armv7l-cpython-311/pysam/include/bcftools
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2023-09-12T10:23:41,245     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,246     copying htslib/LICENSE -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,248     copying htslib/Makefile -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,251     copying htslib/README -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
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2023-09-12T10:23:41,327     copying htslib/htscodecs_bundled.mk -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
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2023-09-12T10:23:41,365     copying htslib/sam.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,370     copying htslib/sam_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,374     copying htslib/synced_bcf_reader.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,376     copying htslib/tabix.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,380     copying htslib/tbx.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,383     copying htslib/textutils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,386     copying htslib/textutils_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,388     copying htslib/thread_pool.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,392     copying htslib/thread_pool_internal.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,395     copying htslib/vcf.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,402     copying htslib/vcf_sweep.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,404     copying htslib/vcfutils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,408     copying htslib/version.sh -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,411     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,412     copying htslib/cram/cram.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,414     copying htslib/cram/cram_codecs.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,420     copying htslib/cram/cram_codecs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,422     copying htslib/cram/cram_decode.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,428     copying htslib/cram/cram_decode.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,431     copying htslib/cram/cram_encode.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,437     copying htslib/cram/cram_encode.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,440     copying htslib/cram/cram_external.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,444     copying htslib/cram/cram_index.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,447     copying htslib/cram/cram_index.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,450     copying htslib/cram/cram_io.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,457     copying htslib/cram/cram_io.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,460     copying htslib/cram/cram_samtools.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,463     copying htslib/cram/cram_stats.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,465     copying htslib/cram/cram_stats.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,468     copying htslib/cram/cram_structs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,471     copying htslib/cram/mFILE.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,473     copying htslib/cram/mFILE.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,476     copying htslib/cram/misc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,478     copying htslib/cram/open_trace_file.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,481     copying htslib/cram/open_trace_file.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,483     copying htslib/cram/os.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,486     copying htslib/cram/pooled_alloc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,489     copying htslib/cram/pooled_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,491     copying htslib/cram/string_alloc.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,494     copying htslib/cram/string_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram
2023-09-12T10:23:41,496     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs
2023-09-12T10:23:41,498     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,500     copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,502     copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,504     copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,506     copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,509     copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,512     copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,515     copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,518     copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,521     copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,524     copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,528     copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,531     copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,535     copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,537     copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,541     copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,545     copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,548     copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,551     copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,555     copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,559     copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,564     copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,568     copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,572     copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,577     copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,581     copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,585     copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,589     copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,592     copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,595     copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,600     copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,603     copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,606     copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,610     copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,613     copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,617     copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:23:41,620     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4
2023-09-12T10:23:41,621     copying htslib/m4/ax_check_compile_flag.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4
2023-09-12T10:23:41,625     copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4
2023-09-12T10:23:41,628     copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4
2023-09-12T10:23:41,632     copying htslib/m4/pkg.m4 -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4
2023-09-12T10:23:41,636     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os
2023-09-12T10:23:41,637     copying htslib/os/lzma_stub.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os
2023-09-12T10:23:41,641     copying htslib/os/rand.c -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os
2023-09-12T10:23:41,644     copying htslib/config.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib
2023-09-12T10:23:41,647     creating build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,648     copying htslib/htslib/bgzf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,652     copying htslib/htslib/cram.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,655     copying htslib/htslib/faidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,660     copying htslib/htslib/hfile.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,663     copying htslib/htslib/hts.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,668     copying htslib/htslib/hts_defs.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,671     copying htslib/htslib/hts_endian.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,675     copying htslib/htslib/hts_expr.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,678     copying htslib/htslib/hts_log.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,681     copying htslib/htslib/hts_os.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,684     copying htslib/htslib/kbitset.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,687     copying htslib/htslib/kfunc.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,690     copying htslib/htslib/khash.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,693     copying htslib/htslib/khash_str2int.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,697     copying htslib/htslib/klist.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,700     copying htslib/htslib/knetfile.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,703     copying htslib/htslib/kroundup.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,706     copying htslib/htslib/kseq.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,709     copying htslib/htslib/ksort.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,713     copying htslib/htslib/kstring.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,715     copying htslib/htslib/regidx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,718     copying htslib/htslib/sam.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,722     copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,725     copying htslib/htslib/tbx.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,727     copying htslib/htslib/thread_pool.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,730     copying htslib/htslib/vcf.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,734     copying htslib/htslib/vcf_sweep.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,737     copying htslib/htslib/vcfutils.h -> build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib
2023-09-12T10:23:41,744     running build_ext
2023-09-12T10:23:41,816     skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
2023-09-12T10:23:41,817     skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
2023-09-12T10:23:41,818     skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
2023-09-12T10:23:41,819     skipping 'pysam/libcutils.c' Cython extension (up-to-date)
2023-09-12T10:23:41,820     skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
2023-09-12T10:23:41,822     skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
2023-09-12T10:23:41,823     skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
2023-09-12T10:23:41,824     skipping 'pysam/libctabix.c' Cython extension (up-to-date)
2023-09-12T10:23:41,826     skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
2023-09-12T10:23:41,827     skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
2023-09-12T10:23:41,828     skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
2023-09-12T10:23:41,829     skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
2023-09-12T10:23:41,831     skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
2023-09-12T10:23:41,832     creating htslib/config_vars.h for 'pysam.libchtslib' extension
2023-09-12T10:23:41,833     building 'libhts.a'
2023-09-12T10:23:41,880     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
2023-09-12T10:23:42,345     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o kstring.o kstring.c
2023-09-12T10:23:43,201     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
2023-09-12T10:23:45,769     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
2023-09-12T10:23:49,017     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
2023-09-12T10:23:49,688     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
2023-09-12T10:23:51,637     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
2023-09-12T10:23:56,138     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 hfile.o hfile.c
2023-09-12T10:23:57,834     echo '#define HTS_VERSION_TEXT "1.17"' > version.h
2023-09-12T10:23:57,840     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o hts.o hts.c
2023-09-12T10:24:06,396     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
2023-09-12T10:24:08,385     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
2023-09-12T10:24:08,495     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
2023-09-12T10:24:09,139     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
2023-09-12T10:24:09,725     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
2023-09-12T10:24:10,465     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
2023-09-12T10:24:11,393     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 regidx.o regidx.c
2023-09-12T10:24:12,937     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
2023-09-12T10:24:13,612     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
2023-09-12T10:24:27,768     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
2023-09-12T10:24:30,516     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
2023-09-12T10:24:30,866     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
2023-09-12T10:24:31,703     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
2023-09-12T10:24:32,680     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
2023-09-12T10:24:33,595     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
2023-09-12T10:24:48,260     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
2023-09-12T10:24:51,506     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/cram_codecs.o cram/cram_codecs.c
2023-09-12T10:24:57,098     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
2023-09-12T10:25:03,401     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
2023-09-12T10:25:12,000     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
2023-09-12T10:25:13,412     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
2023-09-12T10:25:14,769     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
2023-09-12T10:25:22,499     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
2023-09-12T10:25:23,270     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
2023-09-12T10:25:23,928     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
2023-09-12T10:25:24,456     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
2023-09-12T10:25:24,640     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
2023-09-12T10:25:24,838     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
2023-09-12T10:25:28,597     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
2023-09-12T10:25:32,631     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
2023-09-12T10:25:32,696     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
2023-09-12T10:25:33,491     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
2023-09-12T10:25:38,395     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
2023-09-12T10:25:41,593     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
2023-09-12T10:25:43,733     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
2023-09-12T10:25:44,236     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
2023-09-12T10:25:47,168     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
2023-09-12T10:25:47,448     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
2023-09-12T10:25:47,895     hfile_libcurl.c: In function ‘libcurl_open’:
2023-09-12T10:25:47,897     hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations]
2023-09-12T10:25:47,898      1335 |         if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD,
2023-09-12T10:25:47,899           |         ^~
2023-09-12T10:25:47,900     In file included from hfile_libcurl.c:47:
2023-09-12T10:25:47,901     /usr/include/arm-linux-gnueabihf/curl/curl.h:2858:3: note: declared here
2023-09-12T10:25:47,902      2858 |   CURLINFO_CONTENT_LENGTH_DOWNLOAD
2023-09-12T10:25:47,903           |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:25:49,966     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
2023-09-12T10:25:50,473     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
2023-09-12T10:25:54,459     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
2023-09-12T10:25:55,908     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
2023-09-12T10:25:56,250     ranlib libhts.a
2023-09-12T10:25:56,549     building 'pysam.libchtslib' extension
2023-09-12T10:25:56,550     creating build/temp.linux-armv7l-cpython-311
2023-09-12T10:25:56,551     creating build/temp.linux-armv7l-cpython-311/pysam
2023-09-12T10:25:56,553     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:25:56,862     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:12,153     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:12,752     creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
2023-09-12T10:26:12,753     building 'pysam.libcsamtools' extension
2023-09-12T10:26:12,755     creating build/temp.linux-armv7l-cpython-311/samtools
2023-09-12T10:26:12,757     creating build/temp.linux-armv7l-cpython-311/samtools/lz4
2023-09-12T10:26:12,758     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:13,811     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:17,967     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:18,545     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:21,086     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:21,847     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:23,861     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:24,086     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:24,868     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:25,154     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:28,255     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:29,631     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:29,871     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:30,849     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:31,301     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:31,921     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:36,890     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:38,507     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:40,426     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:40,709     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:43,249     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:43,604     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:44,418     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:46,033     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:47,275     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:48,111     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:57,388     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:58,705     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:26:59,559     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:01,853     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:02,346     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:03,489     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:05,266     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:05,933     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:07,078     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:07,277     samtools/cram_size.c.pysam.c: In function ‘cram_size’:
2023-09-12T10:27:07,289     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=]
2023-09-12T10:27:07,290       563 |     fprintf(outfp, "Total file size       %18"PRId64"\n", end);
2023-09-12T10:27:07,291           |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~            ~~~
2023-09-12T10:27:07,292           |                                                           |
2023-09-12T10:27:07,293           |                                                           off_t {aka long int}
2023-09-12T10:27:07,293     In file included from /tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib/htslib/hts.h:33,
2023-09-12T10:27:07,294                      from /tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib/htslib/sam.h:33,
2023-09-12T10:27:07,295                      from samtools/cram_size.c.pysam.c:39:
2023-09-12T10:27:07,296     /usr/include/inttypes.h:57:41: note: format string is defined here
2023-09-12T10:27:07,296        57 | # define PRId64         __PRI64_PREFIX "d"
2023-09-12T10:27:07,297     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=]
2023-09-12T10:27:07,298       564 |     fprintf(outfp, "Format overhead size  %18"PRId64"\n", end - tot_size);
2023-09-12T10:27:07,299           |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~            ~~~~~~~~~~~~~~
2023-09-12T10:27:07,299           |                                                               |
2023-09-12T10:27:07,300           |                                                               off_t {aka long int}
2023-09-12T10:27:07,300     /usr/include/inttypes.h:57:41: note: format string is defined here
2023-09-12T10:27:07,301        57 | # define PRId64         __PRI64_PREFIX "d"
2023-09-12T10:27:08,158     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:08,821     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:09,864     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:10,697     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:16,904     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:18,241     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:21,424     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:22,391     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:23,448     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:23,761     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:24,276     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:27,376     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:28,181     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:28,384     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:33,588     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:34,239     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:34,709     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:35,103     building 'pysam.libcbcftools' extension
2023-09-12T10:27:35,105     creating build/temp.linux-armv7l-cpython-311/bcftools
2023-09-12T10:27:35,108     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:36,131     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:38,930     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:41,464     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:43,139     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:45,642     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:47,571     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:47,772     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:48,091     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:48,849     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:49,079     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:51,543     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:27:57,847     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:07,046     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:07,312     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:07,906     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:08,441     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:22,514     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:23,113     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:23,744     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:24,179     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:24,511     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:28,430     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:31,088     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:32,154     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:33,763     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:35,643     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:37,049     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:40,237     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:40,731     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:41,169     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:41,541     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:41,921     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:51,483     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:52,854     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:55,542     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:28:57,661     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:00,349     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:03,986     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:05,572     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:08,640     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:08,994     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:09,637     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:11,398     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:13,838     bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’:
2023-09-12T10:29:13,839     bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
2023-09-12T10:29:13,840       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
2023-09-12T10:29:13,841           |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:29:13,842     In file included from /tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib/htslib/kstring.h:30,
2023-09-12T10:29:13,843                      from /tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib/htslib/hts.h:37,
2023-09-12T10:29:13,844                      from /tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib/htslib/vcf.h:39,
2023-09-12T10:29:13,846                      from bcftools/vcfmerge.c.pysam.c:35:
2023-09-12T10:29:13,847     /usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’ declared here
2023-09-12T10:29:13,848       556 | extern void *calloc (size_t __nmemb, size_t __size)
2023-09-12T10:29:13,849           |              ^~~~~~
2023-09-12T10:29:22,789     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:31,400     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:31,675     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:33,400     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:36,048     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:37,444     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:38,333     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:42,820     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:44,826     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:45,267     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:45,606     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:46,763     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:47,439     building 'pysam.libcutils' extension
2023-09-12T10:29:47,440     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:59,437     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:59,583     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:29:59,763     building 'pysam.libcalignmentfile' extension
2023-09-12T10:29:59,765     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:30:04,593     pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
2023-09-12T10:30:04,716     pysam/libcalignmentfile.c:28658:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:30:04,788     28658 |         (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
2023-09-12T10:30:04,797           |               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:30:04,827     pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
2023-09-12T10:30:04,910     pysam/libcalignmentfile.c:14341:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:30:04,962     14341 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
2023-09-12T10:30:04,962           |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:30:45,893     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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,$ORIGIN
2023-09-12T10:30:46,122     building 'pysam.libcsamfile' extension
2023-09-12T10:30:46,124     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-armv7l-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2023-09-12T10:30:48,484     arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libcsamfile.o -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2023-09-12T10:30:48,635     building 'pysam.libcalignedsegment' extension
2023-09-12T10:30:48,636     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:30:57,302     pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
2023-09-12T10:30:57,317     pysam/libcalignedsegment.c:14415:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:30:57,317     14415 |   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
2023-09-12T10:30:57,319           |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:31:50,845     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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,$ORIGIN
2023-09-12T10:31:51,130     building 'pysam.libctabix' extension
2023-09-12T10:31:51,131     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-armv7l-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2023-09-12T10:32:14,928     arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pysam/libctabix.o -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -Lbuild/lib.linux-armv7l-cpython-311/pysam -L/usr/lib/arm-linux-gnueabihf -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2023-09-12T10:32:15,121     building 'pysam.libcfaidx' extension
2023-09-12T10:32:15,123     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:32:29,711     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:32:29,887     building 'pysam.libcbcf' extension
2023-09-12T10:32:29,887     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:32:40,393     pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’:
2023-09-12T10:32:40,458     pysam/libcbcf.c:67371:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:32:40,459     67371 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
2023-09-12T10:32:40,460           |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:32:40,473     pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’:
2023-09-12T10:32:40,538     pysam/libcbcf.c:67096:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:32:40,539     67096 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
2023-09-12T10:32:40,540           |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:32:40,545     pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’:
2023-09-12T10:32:40,609     pysam/libcbcf.c:72230:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:32:40,610     72230 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
2023-09-12T10:32:40,611           |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:32:41,415     pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’:
2023-09-12T10:32:41,451     pysam/libcbcf.c:35394:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:32:41,452     35394 |           bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
2023-09-12T10:32:41,453           |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:32:41,484     pysam/libcbcf.c:35420:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
2023-09-12T10:32:41,484     35420 |           bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
2023-09-12T10:32:41,485           |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:33:56,107     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:33:56,442     building 'pysam.libcbgzf' extension
2023-09-12T10:33:56,443     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:34:02,078     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:34:02,245     building 'pysam.libctabixproxies' extension
2023-09-12T10:34:02,246     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:34:22,820     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:34:23,062     building 'pysam.libcvcf' extension
2023-09-12T10:34:23,063     arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/htslib -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/samtools/lz4 -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/bcftools -I/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:35:02,801     pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’:
2023-09-12T10:35:02,828     pysam/libcvcf.c:25833:15: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized]
2023-09-12T10:35:02,828     25833 |   __pyx_t_8 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 873, __pyx_L1_error)
2023-09-12T10:35:02,829           |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2023-09-12T10:35:02,848     pysam/libcvcf.c:20265:10: note: ‘__pyx_v_qual’ was declared here
2023-09-12T10:35:02,849     20265 |   double __pyx_v_qual;
2023-09-12T10:35:02,850           |          ^~~~~~~~~~~~
2023-09-12T10:35:30,208     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-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3/pysam -L/tmp/pip-install-u8y1wpp7/pysam_5d4ee3062c0f4587b45e5e2ec04b31f3 -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
2023-09-12T10:35:31,447     installing to build/bdist.linux-armv7l/wheel
2023-09-12T10:35:31,448     running install
2023-09-12T10:35:31,482     running install_lib
2023-09-12T10:35:31,487     creating build/bdist.linux-armv7l
2023-09-12T10:35:31,488     creating build/bdist.linux-armv7l/wheel
2023-09-12T10:35:31,491     creating build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,492     copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,513     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,515     copying build/lib.linux-armv7l-cpython-311/pysam/version.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,517     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,519     copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,522     copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,542     copying build/lib.linux-armv7l-cpython-311/pysam/config.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:31,544     creating build/bdist.linux-armv7l/wheel/pysam/include
2023-09-12T10:35:31,547     creating build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,548     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,551     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,554     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,556     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfisec.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,559     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsort.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,562     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/main.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,564     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,566     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,568     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfisec.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,571     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,574     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,575     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,578     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,580     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfplugin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,583     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfindex.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,585     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,588     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,590     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,592     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,595     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,597     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,599     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,601     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,603     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cigar_state.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,605     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,607     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,609     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfview.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,612     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,615     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcffilter.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,618     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,621     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,623     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfnorm.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,628     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/README -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,630     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,634     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,637     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,640     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,643     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,646     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mcall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,649     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,652     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcmp.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,654     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,657     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,659     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,662     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,664     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,666     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,669     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ccall.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,671     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcnv.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,675     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,677     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconvert.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,681     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,683     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/rbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,687     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,689     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfstats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,692     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,695     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/utlist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,698     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/cols.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,700     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsom.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,702     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcnv.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,706     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tabix.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,708     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/str_finder.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,710     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconcat.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,714     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/reheader.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,717     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hex.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,719     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,722     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,724     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/hclust.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,727     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfquery.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,729     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,732     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfquery.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,734     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,737     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,742     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/csq.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,748     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcffilter.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,751     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfhead.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,753     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/call.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,755     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,757     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,759     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ccall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,762     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mpileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,765     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,768     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconvert.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,773     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,776     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,779     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfstats.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,783     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,786     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,791     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/variantkey.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,794     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf_indel.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,798     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,801     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfmerge.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,805     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/csq.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,810     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/main.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,813     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,815     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfindex.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,818     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kheap.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,821     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/prob1.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,823     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tsv2vcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,825     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,827     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/em.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,830     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfannotate.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,836     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,838     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/ploidy.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,840     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/khash_str2str.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,842     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
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2023-09-12T10:35:31,847     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/smpl_ilist.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,849     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,851     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/abuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,853     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mw.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,856     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,858     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/convert.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,860     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bcftools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,862     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mpileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,866     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/gvcf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,868     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfhead.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,870     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/reheader.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,873     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,875     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfview.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,877     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/em.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,879     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,882     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfcall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,885     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/mcall.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,888     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/dist.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,890     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfroh.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,894     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam_sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,896     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,899     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/regidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,902     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bam2bcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,904     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/tabix.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,906     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/read_consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,909     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfnorm.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,913     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfplugin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,916     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/extsort.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,919     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfroh.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,921     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfannotate.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,927     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfgtcheck.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,931     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfconcat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,935     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/bin.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,938     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/filter.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,943     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfsom.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,947     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/kmin.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,950     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/vcfmerge.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,956     copying build/lib.linux-armv7l-cpython-311/pysam/include/bcftools/HMM.c -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2023-09-12T10:35:31,959     copying build/lib.linux-armv7l-cpython-311/pysam/include/__init__.py -> build/bdist.linux-armv7l/wheel/pysam/include
2023-09-12T10:35:31,963     creating build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,965     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_view.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,970     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam2depth.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,973     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,975     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/padding.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,977     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/phase.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,980     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reset.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,983     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,985     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reference.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,987     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,990     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_split.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,992     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cut_target.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,995     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_quickcheck.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:31,997     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamshuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,000     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,002     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,004     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,006     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,009     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_sort.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,012     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_stat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,015     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,017     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_split.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,020     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,023     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/faidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,025     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,030     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_index.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,032     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/amplicon_stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,036     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_addrprg.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,038     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/README -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,041     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/faidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,044     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,046     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,048     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,050     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,052     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_aux.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,055     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cram_size.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,057     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,059     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,062     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,065     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plcmd.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,068     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_fastq.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,071     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,073     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_markdup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,077     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedcov.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,079     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_consensus.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,083     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_color.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,086     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/splaysort.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,088     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reset.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,091     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,093     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_import.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,095     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,098     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedcov.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,100     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_aux.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,102     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/dict.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,104     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_stat.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,107     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,109     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamtk.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,111     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,113     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/amplicon_stats.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,117     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_mate.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,119     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,122     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_cat.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,124     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_md.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,127     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,131     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,133     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,136     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdupse.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,138     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cut_target.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,140     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_lpileup.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,142     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_flags.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,145     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,147     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,149     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,150     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_color.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,153     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/samtools.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,155     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_mate.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,157     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/tmp_file.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,160     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamshuf.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,162     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_md.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,164     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/coverage.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,167     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_opts.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,169     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_markdup.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,173     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/consensus_pileup.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,176     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bamtk.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,178     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_view.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,181     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_samples.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,184     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,186     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,189     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_fastq.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,192     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_rmdupse.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,195     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_samples.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,198     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_addrprg.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,201     creating build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4
2023-09-12T10:35:32,203     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4
2023-09-12T10:35:32,207     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4
2023-09-12T10:35:32,211     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/lz4.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4
2023-09-12T10:35:32,215     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/lz4/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/samtools/lz4
2023-09-12T10:35:32,218     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_plcmd.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,223     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_cat.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,226     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_quickcheck.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,229     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_consensus.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,236     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_import.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,239     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,242     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_reheader.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,246     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/coverage.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,249     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/dict.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,252     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,255     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_sort.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,262     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/phase.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,266     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam2depth.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,271     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/stats_isize.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,274     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sam_utils.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,277     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_flags.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,280     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/padding.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,284     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/reference.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,287     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bedidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,290     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,292     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_reheader.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,295     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_index.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,298     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/cram_size.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,301     copying build/lib.linux-armv7l-cpython-311/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2023-09-12T10:35:32,304     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,305     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/Makefile -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,308     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs_bundled.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,312     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,312     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/string_alloc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,316     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_structs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,319     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_stats.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,321     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,323     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/pooled_alloc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,325     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/open_trace_file.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,327     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_encode.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,329     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_encode.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,334     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_io.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,336     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/mFILE.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,339     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_samtools.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,341     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_stats.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,344     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/pooled_alloc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,346     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_external.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,349     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/misc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,351     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/open_trace_file.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,354     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_decode.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,359     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_io.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,366     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_decode.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,368     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_codecs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,374     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_codecs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,376     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/os.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,379     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_index.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,381     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/mFILE.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,383     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/cram_index.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,385     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/cram/string_alloc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/cram
2023-09-12T10:35:32,387     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htsfile.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,389     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_gcs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,391     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib_vars.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,393     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs
2023-09-12T10:35:32,395     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,396     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/version.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,398     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
2023-09-12T10:35:32,400     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,403     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,405     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/permute.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,407     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
2023-09-12T10:35:32,409     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
2023-09-12T10:35:32,411     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
2023-09-12T10:35:32,415     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
2023-09-12T10:35:32,417     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
2023-09-12T10:35:32,419     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
2023-09-12T10:35:32,422     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rle.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,424     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
2023-09-12T10:35:32,426     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
2023-09-12T10:35:32,430     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/utils.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,432     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/varint.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,434     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
2023-09-12T10:35:32,438     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/utils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,440     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
2023-09-12T10:35:32,443     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
2023-09-12T10:35:32,445     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
2023-09-12T10:35:32,449     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
2023-09-12T10:35:32,453     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
2023-09-12T10:35:32,455     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
2023-09-12T10:35:32,458     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
2023-09-12T10:35:32,460     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
2023-09-12T10:35:32,463     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
2023-09-12T10:35:32,468     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pack.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,470     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,472     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
2023-09-12T10:35:32,478     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
2023-09-12T10:35:32,482     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/rle.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,484     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs/htscodecs/pack.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htscodecs/htscodecs
2023-09-12T10:35:32,486     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
2023-09-12T10:35:32,491     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
2023-09-12T10:35:32,494     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,496     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/faidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,499     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/errmod.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,502     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/README -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,504     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/plugin.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,507     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/header.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,509     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bgzf.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,513     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4
2023-09-12T10:35:32,514     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
2023-09-12T10:35:32,518     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/m4/pkg.m4 -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/m4
2023-09-12T10:35:32,520     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
2023-09-12T10:35:32,522     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
2023-09-12T10:35:32,524     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.h.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,527     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/md5.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,529     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcf.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,534     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/kstring.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,537     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/os
2023-09-12T10:35:32,538     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os/lzma_stub.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/os
2023-09-12T10:35:32,541     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/os/rand.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/os
2023-09-12T10:35:32,544     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcfutils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,546     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htscodecs_external.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,549     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/sam.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,554     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_time_funcs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,557     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/probaln.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,559     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_libcurl.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,562     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/vcf_sweep.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,565     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,567     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/version.sh -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,570     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/config.mk.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,572     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/tbx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,574     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_os.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,576     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/thread_pool.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,580     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/sam_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,582     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/multipart.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,584     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bgzip.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,587     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/builddir_vars.mk.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,589     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/thread_pool_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,591     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bcf_sr_sort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,594     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/header.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,598     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_expr.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,600     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/regidx.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,603     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_s3_write.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,605     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/configure.ac -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,608     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/textutils_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,610     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/configure -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,616     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/realn.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,619     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_s3.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,622     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib.pc.in -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,624     creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,625     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kseq.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,628     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_os.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,630     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/khash_str2int.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,632     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_expr.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,634     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/khash.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,637     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kroundup.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,640     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/sam.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,644     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/cram.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,647     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_log.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,649     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_endian.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,651     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kfunc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,653     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/knetfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,655     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts_defs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,657     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hts.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,660     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/hfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,663     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kstring.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,665     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/bgzf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,668     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/tbx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,670     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,672     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/klist.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,675     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/thread_pool.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,677     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/synced_bcf_reader.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,680     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcfutils.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,682     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/kbitset.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,684     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/faidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,687     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,691     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/ksort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,693     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib/vcf_sweep.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2023-09-12T10:35:32,695     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/bcf_sr_sort.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,698     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/textutils.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,700     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/region.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,703     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/htslib.mk -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,705     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,711     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/synced_bcf_reader.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,715     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/LICENSE -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,717     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hts_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,719     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/tabix.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,722     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/hfile_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,725     copying build/lib.linux-armv7l-cpython-311/pysam/include/htslib/kfunc.c -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2023-09-12T10:35:32,727     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,732     copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,743     copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,764     copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,775     copying build/lib.linux-armv7l-cpython-311/pysam/py.typed -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,777     copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,779     copying build/lib.linux-armv7l-cpython-311/pysam/utils.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,781     copying build/lib.linux-armv7l-cpython-311/pysam/__init__.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,783     copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,801     copying build/lib.linux-armv7l-cpython-311/pysam/pysam_util.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,802     copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,804     copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,806     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,810     copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,812     copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,815     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,819     copying build/lib.linux-armv7l-cpython-311/pysam/version.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,821     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,825     copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,827     copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,912     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,915     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,981     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,983     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,985     copying build/lib.linux-armv7l-cpython-311/pysam/cbcftools_util.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,986     copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,989     copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:32,997     copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,000     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,002     copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,004     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,010     copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,020     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,022     copying build/lib.linux-armv7l-cpython-311/pysam/htslib_util.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,024     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcf.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,086     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,088     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,090     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,125     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,127     copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,130     copying build/lib.linux-armv7l-cpython-311/pysam/csamtools_util.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,132     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,177     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,179     copying build/lib.linux-armv7l-cpython-311/pysam/htslib_util.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,181     copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,202     copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,204     copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,220     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,276     copying build/lib.linux-armv7l-cpython-311/pysam/version.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,278     copying build/lib.linux-armv7l-cpython-311/pysam/libchtslib.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,283     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,330     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamfile.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,333     copying build/lib.linux-armv7l-cpython-311/pysam/libcfaidx.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,335     copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,338     copying build/lib.linux-armv7l-cpython-311/pysam/bcftools.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,340     copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,371     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignmentfile.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,402     copying build/lib.linux-armv7l-cpython-311/pysam/samtools.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,404     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,409     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,414     copying build/lib.linux-armv7l-cpython-311/pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,421     copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,424     copying build/lib.linux-armv7l-cpython-311/pysam/libctabix.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,427     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.pyi -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,429     copying build/lib.linux-armv7l-cpython-311/pysam/libcutils.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,432     copying build/lib.linux-armv7l-cpython-311/pysam/libcsamtools.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,434     copying build/lib.linux-armv7l-cpython-311/pysam/Pileup.py -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,436     copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pxd -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,438     copying build/lib.linux-armv7l-cpython-311/pysam/libctabixproxies.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,441     copying build/lib.linux-armv7l-cpython-311/pysam/pysam_stream.h -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,443     copying build/lib.linux-armv7l-cpython-311/pysam/libcbcftools.pyx -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,445     copying build/lib.linux-armv7l-cpython-311/pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,496     copying build/lib.linux-armv7l-cpython-311/pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,544     copying build/lib.linux-armv7l-cpython-311/pysam/pysam_util.c -> build/bdist.linux-armv7l/wheel/pysam
2023-09-12T10:35:33,546     running install_egg_info
2023-09-12T10:35:33,551     Copying pysam.egg-info to build/bdist.linux-armv7l/wheel/pysam-0.21.0-py3.11.egg-info
2023-09-12T10:35:33,564     running install_scripts
2023-09-12T10:35:33,616     creating build/bdist.linux-armv7l/wheel/pysam-0.21.0.dist-info/WHEEL
2023-09-12T10:35:33,619     creating '/tmp/pip-wheel-l48gxo5e/.tmp-fbfb297j/pysam-0.21.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-09-12T10:35:33,624     adding 'pysam/Pileup.py'
2023-09-12T10:35:33,626     adding 'pysam/__init__.py'
2023-09-12T10:35:33,628     adding 'pysam/bcftools.py'
2023-09-12T10:35:33,630     adding 'pysam/cbcftools_util.h'
2023-09-12T10:35:33,631     adding 'pysam/config.py'
2023-09-12T10:35:33,633     adding 'pysam/csamtools_util.h'
2023-09-12T10:35:33,635     adding 'pysam/htslib_util.c'
2023-09-12T10:35:33,637     adding 'pysam/htslib_util.h'
2023-09-12T10:35:33,823     adding 'pysam/libcalignedsegment.c'
2023-09-12T10:35:34,452     adding 'pysam/libcalignedsegment.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:34,479     adding 'pysam/libcalignedsegment.pxd'
2023-09-12T10:35:34,481     adding 'pysam/libcalignedsegment.pyi'
2023-09-12T10:35:34,494     adding 'pysam/libcalignedsegment.pyx'
2023-09-12T10:35:34,627     adding 'pysam/libcalignmentfile.c'
2023-09-12T10:35:35,102     adding 'pysam/libcalignmentfile.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:35,122     adding 'pysam/libcalignmentfile.pxd'
2023-09-12T10:35:35,124     adding 'pysam/libcalignmentfile.pyi'
2023-09-12T10:35:35,136     adding 'pysam/libcalignmentfile.pyx'
2023-09-12T10:35:35,368     adding 'pysam/libcbcf.c'
2023-09-12T10:35:36,170     adding 'pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:36,206     adding 'pysam/libcbcf.pxd'
2023-09-12T10:35:36,209     adding 'pysam/libcbcf.pyi'
2023-09-12T10:35:36,223     adding 'pysam/libcbcf.pyx'
2023-09-12T10:35:36,235     adding 'pysam/libcbcftools.c'
2023-09-12T10:35:37,045     adding 'pysam/libcbcftools.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:37,075     adding 'pysam/libcbcftools.pxd'
2023-09-12T10:35:37,077     adding 'pysam/libcbcftools.pyi'
2023-09-12T10:35:37,079     adding 'pysam/libcbcftools.pyx'
2023-09-12T10:35:37,109     adding 'pysam/libcbgzf.c'
2023-09-12T10:35:37,181     adding 'pysam/libcbgzf.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:37,185     adding 'pysam/libcbgzf.pyi'
2023-09-12T10:35:37,187     adding 'pysam/libcbgzf.pyx'
2023-09-12T10:35:37,238     adding 'pysam/libcfaidx.c'
2023-09-12T10:35:37,410     adding 'pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:37,417     adding 'pysam/libcfaidx.pxd'
2023-09-12T10:35:37,419     adding 'pysam/libcfaidx.pyi'
2023-09-12T10:35:37,422     adding 'pysam/libcfaidx.pyx'
2023-09-12T10:35:37,477     adding 'pysam/libchtslib.c'
2023-09-12T10:35:38,547     adding 'pysam/libchtslib.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:38,599     adding 'pysam/libchtslib.pxd'
2023-09-12T10:35:38,601     adding 'pysam/libchtslib.pyi'
2023-09-12T10:35:38,604     adding 'pysam/libchtslib.pyx'
2023-09-12T10:35:38,625     adding 'pysam/libcsamfile.c'
2023-09-12T10:35:38,651     adding 'pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:38,654     adding 'pysam/libcsamfile.pxd'
2023-09-12T10:35:38,655     adding 'pysam/libcsamfile.pyi'
2023-09-12T10:35:38,656     adding 'pysam/libcsamfile.pyx'
2023-09-12T10:35:38,667     adding 'pysam/libcsamtools.c'
2023-09-12T10:35:39,228     adding 'pysam/libcsamtools.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:39,248     adding 'pysam/libcsamtools.pxd'
2023-09-12T10:35:39,250     adding 'pysam/libcsamtools.pyi'
2023-09-12T10:35:39,251     adding 'pysam/libcsamtools.pyx'
2023-09-12T10:35:39,323     adding 'pysam/libctabix.c'
2023-09-12T10:35:39,573     adding 'pysam/libctabix.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:39,585     adding 'pysam/libctabix.pxd'
2023-09-12T10:35:39,586     adding 'pysam/libctabix.pyi'
2023-09-12T10:35:39,591     adding 'pysam/libctabix.pyx'
2023-09-12T10:35:39,665     adding 'pysam/libctabixproxies.c'
2023-09-12T10:35:39,914     adding 'pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:39,924     adding 'pysam/libctabixproxies.pxd'
2023-09-12T10:35:39,926     adding 'pysam/libctabixproxies.pyi'
2023-09-12T10:35:39,929     adding 'pysam/libctabixproxies.pyx'
2023-09-12T10:35:39,971     adding 'pysam/libcutils.c'
2023-09-12T10:35:40,107     adding 'pysam/libcutils.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:40,113     adding 'pysam/libcutils.pxd'
2023-09-12T10:35:40,114     adding 'pysam/libcutils.pyi'
2023-09-12T10:35:40,117     adding 'pysam/libcutils.pyx'
2023-09-12T10:35:40,245     adding 'pysam/libcvcf.c'
2023-09-12T10:35:40,803     adding 'pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so'
2023-09-12T10:35:40,825     adding 'pysam/libcvcf.pxd'
2023-09-12T10:35:40,826     adding 'pysam/libcvcf.pyi'
2023-09-12T10:35:40,832     adding 'pysam/libcvcf.pyx'
2023-09-12T10:35:40,834     adding 'pysam/py.typed'
2023-09-12T10:35:40,835     adding 'pysam/pysam_stream.h'
2023-09-12T10:35:40,836     adding 'pysam/pysam_util.c'
2023-09-12T10:35:40,838     adding 'pysam/pysam_util.h'
2023-09-12T10:35:40,839     adding 'pysam/samtools.py'
2023-09-12T10:35:40,841     adding 'pysam/utils.py'
2023-09-12T10:35:40,842     adding 'pysam/version.h'
2023-09-12T10:35:40,844     adding 'pysam/version.py'
2023-09-12T10:35:40,845     adding 'pysam/version.pyi'
2023-09-12T10:35:40,847     adding 'pysam/include/__init__.py'
2023-09-12T10:35:40,851     adding 'pysam/include/bcftools/HMM.c'
2023-09-12T10:35:40,854     adding 'pysam/include/bcftools/HMM.c.pysam.c'
2023-09-12T10:35:40,855     adding 'pysam/include/bcftools/HMM.h'
2023-09-12T10:35:40,862     adding 'pysam/include/bcftools/LICENSE'
2023-09-12T10:35:40,864     adding 'pysam/include/bcftools/README'
2023-09-12T10:35:40,867     adding 'pysam/include/bcftools/abuf.c'
2023-09-12T10:35:40,871     adding 'pysam/include/bcftools/abuf.c.pysam.c'
2023-09-12T10:35:40,873     adding 'pysam/include/bcftools/abuf.h'
2023-09-12T10:35:40,879     adding 'pysam/include/bcftools/bam2bcf.c'
2023-09-12T10:35:40,885     adding 'pysam/include/bcftools/bam2bcf.c.pysam.c'
2023-09-12T10:35:40,887     adding 'pysam/include/bcftools/bam2bcf.h'
2023-09-12T10:35:40,891     adding 'pysam/include/bcftools/bam2bcf_iaux.c'
2023-09-12T10:35:40,895     adding 'pysam/include/bcftools/bam2bcf_iaux.c.pysam.c'
2023-09-12T10:35:40,900     adding 'pysam/include/bcftools/bam2bcf_indel.c'
2023-09-12T10:35:40,905     adding 'pysam/include/bcftools/bam2bcf_indel.c.pysam.c'
2023-09-12T10:35:40,907     adding 'pysam/include/bcftools/bam_sample.c'
2023-09-12T10:35:40,909     adding 'pysam/include/bcftools/bam_sample.c.pysam.c'
2023-09-12T10:35:40,911     adding 'pysam/include/bcftools/bam_sample.h'
2023-09-12T10:35:40,912     adding 'pysam/include/bcftools/bcftools.h'
2023-09-12T10:35:40,914     adding 'pysam/include/bcftools/bcftools.pysam.c'
2023-09-12T10:35:40,915     adding 'pysam/include/bcftools/bcftools.pysam.h'
2023-09-12T10:35:40,917     adding 'pysam/include/bcftools/bin.c'
2023-09-12T10:35:40,918     adding 'pysam/include/bcftools/bin.c.pysam.c'
2023-09-12T10:35:40,919     adding 'pysam/include/bcftools/bin.h'
2023-09-12T10:35:40,921     adding 'pysam/include/bcftools/call.h'
2023-09-12T10:35:40,923     adding 'pysam/include/bcftools/ccall.c'
2023-09-12T10:35:40,925     adding 'pysam/include/bcftools/ccall.c.pysam.c'
2023-09-12T10:35:40,927     adding 'pysam/include/bcftools/cigar_state.h'
2023-09-12T10:35:40,928     adding 'pysam/include/bcftools/cols.c'
2023-09-12T10:35:40,930     adding 'pysam/include/bcftools/cols.c.pysam.c'
2023-09-12T10:35:40,931     adding 'pysam/include/bcftools/cols.h'
2023-09-12T10:35:40,933     adding 'pysam/include/bcftools/config.h'
2023-09-12T10:35:40,938     adding 'pysam/include/bcftools/consensus.c'
2023-09-12T10:35:40,944     adding 'pysam/include/bcftools/consensus.c.pysam.c'
2023-09-12T10:35:40,950     adding 'pysam/include/bcftools/convert.c'
2023-09-12T10:35:40,957     adding 'pysam/include/bcftools/convert.c.pysam.c'
2023-09-12T10:35:40,959     adding 'pysam/include/bcftools/convert.h'
2023-09-12T10:35:40,978     adding 'pysam/include/bcftools/csq.c'
2023-09-12T10:35:40,999     adding 'pysam/include/bcftools/csq.c.pysam.c'
2023-09-12T10:35:41,002     adding 'pysam/include/bcftools/dbuf.h'
2023-09-12T10:35:41,003     adding 'pysam/include/bcftools/dist.c'
2023-09-12T10:35:41,005     adding 'pysam/include/bcftools/dist.c.pysam.c'
2023-09-12T10:35:41,006     adding 'pysam/include/bcftools/dist.h'
2023-09-12T10:35:41,008     adding 'pysam/include/bcftools/em.c'
2023-09-12T10:35:41,009     adding 'pysam/include/bcftools/em.c.pysam.c'
2023-09-12T10:35:41,011     adding 'pysam/include/bcftools/extsort.c'
2023-09-12T10:35:41,013     adding 'pysam/include/bcftools/extsort.c.pysam.c'
2023-09-12T10:35:41,014     adding 'pysam/include/bcftools/extsort.h'
2023-09-12T10:35:41,028     adding 'pysam/include/bcftools/filter.c'
2023-09-12T10:35:41,042     adding 'pysam/include/bcftools/filter.c.pysam.c'
2023-09-12T10:35:41,045     adding 'pysam/include/bcftools/filter.h'
2023-09-12T10:35:41,046     adding 'pysam/include/bcftools/gvcf.c'
2023-09-12T10:35:41,048     adding 'pysam/include/bcftools/gvcf.c.pysam.c'
2023-09-12T10:35:41,049     adding 'pysam/include/bcftools/gvcf.h'
2023-09-12T10:35:41,051     adding 'pysam/include/bcftools/hclust.c'
2023-09-12T10:35:41,054     adding 'pysam/include/bcftools/hclust.c.pysam.c'
2023-09-12T10:35:41,055     adding 'pysam/include/bcftools/hclust.h'
2023-09-12T10:35:41,056     adding 'pysam/include/bcftools/hex.h'
2023-09-12T10:35:41,058     adding 'pysam/include/bcftools/khash_str2str.h'
2023-09-12T10:35:41,059     adding 'pysam/include/bcftools/kheap.h'
2023-09-12T10:35:41,061     adding 'pysam/include/bcftools/kmin.c'
2023-09-12T10:35:41,063     adding 'pysam/include/bcftools/kmin.c.pysam.c'
2023-09-12T10:35:41,065     adding 'pysam/include/bcftools/kmin.h'
2023-09-12T10:35:41,066     adding 'pysam/include/bcftools/main.c'
2023-09-12T10:35:41,068     adding 'pysam/include/bcftools/main.c.pysam.c'
2023-09-12T10:35:41,076     adding 'pysam/include/bcftools/mcall.c'
2023-09-12T10:35:41,083     adding 'pysam/include/bcftools/mcall.c.pysam.c'
2023-09-12T10:35:41,092     adding 'pysam/include/bcftools/mpileup.c'
2023-09-12T10:35:41,101     adding 'pysam/include/bcftools/mpileup.c.pysam.c'
2023-09-12T10:35:41,104     adding 'pysam/include/bcftools/mw.h'
2023-09-12T10:35:41,106     adding 'pysam/include/bcftools/ploidy.c'
2023-09-12T10:35:41,108     adding 'pysam/include/bcftools/ploidy.c.pysam.c'
2023-09-12T10:35:41,110     adding 'pysam/include/bcftools/ploidy.h'
2023-09-12T10:35:41,112     adding 'pysam/include/bcftools/prob1.c'
2023-09-12T10:35:41,115     adding 'pysam/include/bcftools/prob1.c.pysam.c'
2023-09-12T10:35:41,117     adding 'pysam/include/bcftools/prob1.h'
2023-09-12T10:35:41,119     adding 'pysam/include/bcftools/rbuf.h'
2023-09-12T10:35:41,122     adding 'pysam/include/bcftools/read_consensus.c'
2023-09-12T10:35:41,126     adding 'pysam/include/bcftools/read_consensus.c.pysam.c'
2023-09-12T10:35:41,128     adding 'pysam/include/bcftools/read_consensus.h'
2023-09-12T10:35:41,130     adding 'pysam/include/bcftools/regidx.c'
2023-09-12T10:35:41,133     adding 'pysam/include/bcftools/regidx.c.pysam.c'
2023-09-12T10:35:41,135     adding 'pysam/include/bcftools/regidx.h'
2023-09-12T10:35:41,138     adding 'pysam/include/bcftools/reheader.c'
2023-09-12T10:35:41,141     adding 'pysam/include/bcftools/reheader.c.pysam.c'
2023-09-12T10:35:41,143     adding 'pysam/include/bcftools/smpl_ilist.c'
2023-09-12T10:35:41,145     adding 'pysam/include/bcftools/smpl_ilist.c.pysam.c'
2023-09-12T10:35:41,146     adding 'pysam/include/bcftools/smpl_ilist.h'
2023-09-12T10:35:41,148     adding 'pysam/include/bcftools/str_finder.c'
2023-09-12T10:35:41,149     adding 'pysam/include/bcftools/str_finder.c.pysam.c'
2023-09-12T10:35:41,151     adding 'pysam/include/bcftools/str_finder.h'
2023-09-12T10:35:41,152     adding 'pysam/include/bcftools/tabix.c'
2023-09-12T10:35:41,154     adding 'pysam/include/bcftools/tabix.c.pysam.c'
2023-09-12T10:35:41,155     adding 'pysam/include/bcftools/tsv2vcf.c'
2023-09-12T10:35:41,157     adding 'pysam/include/bcftools/tsv2vcf.c.pysam.c'
2023-09-12T10:35:41,158     adding 'pysam/include/bcftools/tsv2vcf.h'
2023-09-12T10:35:41,161     adding 'pysam/include/bcftools/utlist.h'
2023-09-12T10:35:41,165     adding 'pysam/include/bcftools/variantkey.h'
2023-09-12T10:35:41,179     adding 'pysam/include/bcftools/vcfannotate.c'
2023-09-12T10:35:41,195     adding 'pysam/include/bcftools/vcfannotate.c.pysam.c'
2023-09-12T10:35:41,198     adding 'pysam/include/bcftools/vcfbuf.c'
2023-09-12T10:35:41,201     adding 'pysam/include/bcftools/vcfbuf.c.pysam.c'
2023-09-12T10:35:41,203     adding 'pysam/include/bcftools/vcfbuf.h'
2023-09-12T10:35:41,208     adding 'pysam/include/bcftools/vcfcall.c'
2023-09-12T10:35:41,214     adding 'pysam/include/bcftools/vcfcall.c.pysam.c'
2023-09-12T10:35:41,220     adding 'pysam/include/bcftools/vcfcnv.c'
2023-09-12T10:35:41,226     adding 'pysam/include/bcftools/vcfcnv.c.pysam.c'
2023-09-12T10:35:41,232     adding 'pysam/include/bcftools/vcfconcat.c'
2023-09-12T10:35:41,238     adding 'pysam/include/bcftools/vcfconcat.c.pysam.c'
2023-09-12T10:35:41,245     adding 'pysam/include/bcftools/vcfconvert.c'
2023-09-12T10:35:41,252     adding 'pysam/include/bcftools/vcfconvert.c.pysam.c'
2023-09-12T10:35:41,256     adding 'pysam/include/bcftools/vcffilter.c'
2023-09-12T10:35:41,260     adding 'pysam/include/bcftools/vcffilter.c.pysam.c'
2023-09-12T10:35:41,266     adding 'pysam/include/bcftools/vcfgtcheck.c'
2023-09-12T10:35:41,272     adding 'pysam/include/bcftools/vcfgtcheck.c.pysam.c'
2023-09-12T10:35:41,274     adding 'pysam/include/bcftools/vcfhead.c'
2023-09-12T10:35:41,275     adding 'pysam/include/bcftools/vcfhead.c.pysam.c'
2023-09-12T10:35:41,277     adding 'pysam/include/bcftools/vcfindex.c'
2023-09-12T10:35:41,279     adding 'pysam/include/bcftools/vcfindex.c.pysam.c'
2023-09-12T10:35:41,283     adding 'pysam/include/bcftools/vcfisec.c'
2023-09-12T10:35:41,286     adding 'pysam/include/bcftools/vcfisec.c.pysam.c'
2023-09-12T10:35:41,300     adding 'pysam/include/bcftools/vcfmerge.c'
2023-09-12T10:35:41,315     adding 'pysam/include/bcftools/vcfmerge.c.pysam.c'
2023-09-12T10:35:41,325     adding 'pysam/include/bcftools/vcfnorm.c'
2023-09-12T10:35:41,335     adding 'pysam/include/bcftools/vcfnorm.c.pysam.c'
2023-09-12T10:35:41,340     adding 'pysam/include/bcftools/vcfplugin.c'
2023-09-12T10:35:41,343     adding 'pysam/include/bcftools/vcfplugin.c.pysam.c'
2023-09-12T10:35:41,346     adding 'pysam/include/bcftools/vcfquery.c'
2023-09-12T10:35:41,348     adding 'pysam/include/bcftools/vcfquery.c.pysam.c'
2023-09-12T10:35:41,354     adding 'pysam/include/bcftools/vcfroh.c'
2023-09-12T10:35:41,360     adding 'pysam/include/bcftools/vcfroh.c.pysam.c'
2023-09-12T10:35:41,363     adding 'pysam/include/bcftools/vcfsom.c'
2023-09-12T10:35:41,366     adding 'pysam/include/bcftools/vcfsom.c.pysam.c'
2023-09-12T10:35:41,369     adding 'pysam/include/bcftools/vcfsort.c'
2023-09-12T10:35:41,371     adding 'pysam/include/bcftools/vcfsort.c.pysam.c'
2023-09-12T10:35:41,379     adding 'pysam/include/bcftools/vcfstats.c'
2023-09-12T10:35:41,388     adding 'pysam/include/bcftools/vcfstats.c.pysam.c'
2023-09-12T10:35:41,393     adding 'pysam/include/bcftools/vcfview.c'
2023-09-12T10:35:41,398     adding 'pysam/include/bcftools/vcfview.c.pysam.c'
2023-09-12T10:35:41,400     adding 'pysam/include/bcftools/vcmp.c'
2023-09-12T10:35:41,401     adding 'pysam/include/bcftools/vcmp.c.pysam.c'
2023-09-12T10:35:41,402     adding 'pysam/include/bcftools/vcmp.h'
2023-09-12T10:35:41,404     adding 'pysam/include/bcftools/version.c'
2023-09-12T10:35:41,405     adding 'pysam/include/bcftools/version.c.pysam.c'
2023-09-12T10:35:41,407     adding 'pysam/include/bcftools/version.sh'
2023-09-12T10:35:41,410     adding 'pysam/include/htslib/LICENSE'
2023-09-12T10:35:41,414     adding 'pysam/include/htslib/Makefile'
2023-09-12T10:35:41,416     adding 'pysam/include/htslib/README'
2023-09-12T10:35:41,419     adding 'pysam/include/htslib/bcf_sr_sort.c'
2023-09-12T10:35:41,421     adding 'pysam/include/htslib/bcf_sr_sort.h'
2023-09-12T10:35:41,430     adding 'pysam/include/htslib/bgzf.c'
2023-09-12T10:35:41,433     adding 'pysam/include/htslib/bgzip.c'
2023-09-12T10:35:41,435     adding 'pysam/include/htslib/builddir_vars.mk.in'
2023-09-12T10:35:41,436     adding 'pysam/include/htslib/config.h'
2023-09-12T10:35:41,437     adding 'pysam/include/htslib/config.h.in'
2023-09-12T10:35:41,439     adding 'pysam/include/htslib/config.mk.in'
2023-09-12T10:35:41,460     adding 'pysam/include/htslib/configure'
2023-09-12T10:35:41,465     adding 'pysam/include/htslib/configure.ac'
2023-09-12T10:35:41,467     adding 'pysam/include/htslib/errmod.c'
2023-09-12T10:35:41,470     adding 'pysam/include/htslib/faidx.c'
2023-09-12T10:35:41,480     adding 'pysam/include/htslib/header.c'
2023-09-12T10:35:41,482     adding 'pysam/include/htslib/header.h'
2023-09-12T10:35:41,487     adding 'pysam/include/htslib/hfile.c'
2023-09-12T10:35:41,489     adding 'pysam/include/htslib/hfile_gcs.c'
2023-09-12T10:35:41,491     adding 'pysam/include/htslib/hfile_internal.h'
2023-09-12T10:35:41,497     adding 'pysam/include/htslib/hfile_libcurl.c'
2023-09-12T10:35:41,502     adding 'pysam/include/htslib/hfile_s3.c'
2023-09-12T10:35:41,505     adding 'pysam/include/htslib/hfile_s3_write.c'
2023-09-12T10:35:41,523     adding 'pysam/include/htslib/hts.c'
2023-09-12T10:35:41,527     adding 'pysam/include/htslib/hts_expr.c'
2023-09-12T10:35:41,529     adding 'pysam/include/htslib/hts_internal.h'
2023-09-12T10:35:41,530     adding 'pysam/include/htslib/hts_os.c'
2023-09-12T10:35:41,532     adding 'pysam/include/htslib/hts_time_funcs.h'
2023-09-12T10:35:41,533     adding 'pysam/include/htslib/htscodecs_bundled.mk'
2023-09-12T10:35:41,535     adding 'pysam/include/htslib/htscodecs_external.mk'
2023-09-12T10:35:41,537     adding 'pysam/include/htslib/htsfile.c'
2023-09-12T10:35:41,538     adding 'pysam/include/htslib/htslib.mk'
2023-09-12T10:35:41,539     adding 'pysam/include/htslib/htslib.pc.in'
2023-09-12T10:35:41,541     adding 'pysam/include/htslib/htslib_vars.mk'
2023-09-12T10:35:41,543     adding 'pysam/include/htslib/kfunc.c'
2023-09-12T10:35:41,545     adding 'pysam/include/htslib/kstring.c'
2023-09-12T10:35:41,547     adding 'pysam/include/htslib/md5.c'
2023-09-12T10:35:41,549     adding 'pysam/include/htslib/multipart.c'
2023-09-12T10:35:41,550     adding 'pysam/include/htslib/plugin.c'
2023-09-12T10:35:41,553     adding 'pysam/include/htslib/probaln.c'
2023-09-12T10:35:41,555     adding 'pysam/include/htslib/realn.c'
2023-09-12T10:35:41,559     adding 'pysam/include/htslib/regidx.c'
2023-09-12T10:35:41,560     adding 'pysam/include/htslib/region.c'
2023-09-12T10:35:41,585     adding 'pysam/include/htslib/sam.c'
2023-09-12T10:35:41,588     adding 'pysam/include/htslib/sam_internal.h'
2023-09-12T10:35:41,594     adding 'pysam/include/htslib/synced_bcf_reader.c'
2023-09-12T10:35:41,597     adding 'pysam/include/htslib/tabix.c'
2023-09-12T10:35:41,600     adding 'pysam/include/htslib/tbx.c'
2023-09-12T10:35:41,602     adding 'pysam/include/htslib/textutils.c'
2023-09-12T10:35:41,604     adding 'pysam/include/htslib/textutils_internal.h'
2023-09-12T10:35:41,610     adding 'pysam/include/htslib/thread_pool.c'
2023-09-12T10:35:41,612     adding 'pysam/include/htslib/thread_pool_internal.h'
2023-09-12T10:35:41,632     adding 'pysam/include/htslib/vcf.c'
2023-09-12T10:35:41,635     adding 'pysam/include/htslib/vcf_sweep.c'
2023-09-12T10:35:41,638     adding 'pysam/include/htslib/vcfutils.c'
2023-09-12T10:35:41,640     adding 'pysam/include/htslib/version.sh'
2023-09-12T10:35:41,642     adding 'pysam/include/htslib/cram/cram.h'
2023-09-12T10:35:41,654     adding 'pysam/include/htslib/cram/cram_codecs.c'
2023-09-12T10:35:41,656     adding 'pysam/include/htslib/cram/cram_codecs.h'
2023-09-12T10:35:41,668     adding 'pysam/include/htslib/cram/cram_decode.c'
2023-09-12T10:35:41,671     adding 'pysam/include/htslib/cram/cram_decode.h'
2023-09-12T10:35:41,685     adding 'pysam/include/htslib/cram/cram_encode.c'
2023-09-12T10:35:41,688     adding 'pysam/include/htslib/cram/cram_encode.h'
2023-09-12T10:35:41,691     adding 'pysam/include/htslib/cram/cram_external.c'
2023-09-12T10:35:41,694     adding 'pysam/include/htslib/cram/cram_index.c'
2023-09-12T10:35:41,696     adding 'pysam/include/htslib/cram/cram_index.h'
2023-09-12T10:35:41,715     adding 'pysam/include/htslib/cram/cram_io.c'
2023-09-12T10:35:41,719     adding 'pysam/include/htslib/cram/cram_io.h'
2023-09-12T10:35:41,720     adding 'pysam/include/htslib/cram/cram_samtools.h'
2023-09-12T10:35:41,722     adding 'pysam/include/htslib/cram/cram_stats.c'
2023-09-12T10:35:41,723     adding 'pysam/include/htslib/cram/cram_stats.h'
2023-09-12T10:35:41,727     adding 'pysam/include/htslib/cram/cram_structs.h'
2023-09-12T10:35:41,730     adding 'pysam/include/htslib/cram/mFILE.c'
2023-09-12T10:35:41,731     adding 'pysam/include/htslib/cram/mFILE.h'
2023-09-12T10:35:41,733     adding 'pysam/include/htslib/cram/misc.h'
2023-09-12T10:35:41,735     adding 'pysam/include/htslib/cram/open_trace_file.c'
2023-09-12T10:35:41,737     adding 'pysam/include/htslib/cram/open_trace_file.h'
2023-09-12T10:35:41,738     adding 'pysam/include/htslib/cram/os.h'
2023-09-12T10:35:41,740     adding 'pysam/include/htslib/cram/pooled_alloc.c'
2023-09-12T10:35:41,741     adding 'pysam/include/htslib/cram/pooled_alloc.h'
2023-09-12T10:35:41,743     adding 'pysam/include/htslib/cram/string_alloc.c'
2023-09-12T10:35:41,744     adding 'pysam/include/htslib/cram/string_alloc.h'
2023-09-12T10:35:41,749     adding 'pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c'
2023-09-12T10:35:41,751     adding 'pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h'
2023-09-12T10:35:41,752     adding 'pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h'
2023-09-12T10:35:41,754     adding 'pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h'
2023-09-12T10:35:41,759     adding 'pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c'
2023-09-12T10:35:41,761     adding 'pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h'
2023-09-12T10:35:41,763     adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs.c'
2023-09-12T10:35:41,764     adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs.h'
2023-09-12T10:35:41,765     adding 'pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h'
2023-09-12T10:35:41,767     adding 'pysam/include/htslib/htscodecs/htscodecs/pack.c'
2023-09-12T10:35:41,769     adding 'pysam/include/htslib/htscodecs/htscodecs/pack.h'
2023-09-12T10:35:41,771     adding 'pysam/include/htslib/htscodecs/htscodecs/permute.h'
2023-09-12T10:35:41,773     adding 'pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h'
2023-09-12T10:35:41,775     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h'
2023-09-12T10:35:41,778     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static.c'
2023-09-12T10:35:41,780     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static.h'
2023-09-12T10:35:41,782     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h'
2023-09-12T10:35:41,785     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c'
2023-09-12T10:35:41,787     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h'
2023-09-12T10:35:41,792     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c'
2023-09-12T10:35:41,797     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c'
2023-09-12T10:35:41,804     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c'
2023-09-12T10:35:41,810     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c'
2023-09-12T10:35:41,812     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h'
2023-09-12T10:35:41,817     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c'
2023-09-12T10:35:41,820     adding 'pysam/include/htslib/htscodecs/htscodecs/rANS_word.h'
2023-09-12T10:35:41,822     adding 'pysam/include/htslib/htscodecs/htscodecs/rle.c'
2023-09-12T10:35:41,824     adding 'pysam/include/htslib/htscodecs/htscodecs/rle.h'
2023-09-12T10:35:41,830     adding 'pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c'
2023-09-12T10:35:41,832     adding 'pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h'
2023-09-12T10:35:41,834     adding 'pysam/include/htslib/htscodecs/htscodecs/utils.c'
2023-09-12T10:35:41,835     adding 'pysam/include/htslib/htscodecs/htscodecs/utils.h'
2023-09-12T10:35:41,837     adding 'pysam/include/htslib/htscodecs/htscodecs/varint.h'
2023-09-12T10:35:41,839     adding 'pysam/include/htslib/htscodecs/htscodecs/varint2.h'
2023-09-12T10:35:41,841     adding 'pysam/include/htslib/htscodecs/htscodecs/version.h'
2023-09-12T10:35:41,844     adding 'pysam/include/htslib/htslib/bgzf.h'
2023-09-12T10:35:41,847     adding 'pysam/include/htslib/htslib/cram.h'
2023-09-12T10:35:41,849     adding 'pysam/include/htslib/htslib/faidx.h'
2023-09-12T10:35:41,851     adding 'pysam/include/htslib/htslib/hfile.h'
2023-09-12T10:35:41,859     adding 'pysam/include/htslib/htslib/hts.h'
2023-09-12T10:35:41,861     adding 'pysam/include/htslib/htslib/hts_defs.h'
2023-09-12T10:35:41,863     adding 'pysam/include/htslib/htslib/hts_endian.h'
2023-09-12T10:35:41,865     adding 'pysam/include/htslib/htslib/hts_expr.h'
2023-09-12T10:35:41,866     adding 'pysam/include/htslib/htslib/hts_log.h'
2023-09-12T10:35:41,868     adding 'pysam/include/htslib/htslib/hts_os.h'
2023-09-12T10:35:41,869     adding 'pysam/include/htslib/htslib/kbitset.h'
2023-09-12T10:35:41,871     adding 'pysam/include/htslib/htslib/kfunc.h'
2023-09-12T10:35:41,873     adding 'pysam/include/htslib/htslib/khash.h'
2023-09-12T10:35:41,875     adding 'pysam/include/htslib/htslib/khash_str2int.h'
2023-09-12T10:35:41,877     adding 'pysam/include/htslib/htslib/klist.h'
2023-09-12T10:35:41,878     adding 'pysam/include/htslib/htslib/knetfile.h'
2023-09-12T10:35:41,880     adding 'pysam/include/htslib/htslib/kroundup.h'
2023-09-12T10:35:41,881     adding 'pysam/include/htslib/htslib/kseq.h'
2023-09-12T10:35:41,884     adding 'pysam/include/htslib/htslib/ksort.h'
2023-09-12T10:35:41,886     adding 'pysam/include/htslib/htslib/kstring.h'
2023-09-12T10:35:41,888     adding 'pysam/include/htslib/htslib/regidx.h'
2023-09-12T10:35:41,899     adding 'pysam/include/htslib/htslib/sam.h'
2023-09-12T10:35:41,902     adding 'pysam/include/htslib/htslib/synced_bcf_reader.h'
2023-09-12T10:35:41,904     adding 'pysam/include/htslib/htslib/tbx.h'
2023-09-12T10:35:41,906     adding 'pysam/include/htslib/htslib/thread_pool.h'
2023-09-12T10:35:41,914     adding 'pysam/include/htslib/htslib/vcf.h'
2023-09-12T10:35:41,916     adding 'pysam/include/htslib/htslib/vcf_sweep.h'
2023-09-12T10:35:41,918     adding 'pysam/include/htslib/htslib/vcfutils.h'
2023-09-12T10:35:41,920     adding 'pysam/include/htslib/m4/ax_check_compile_flag.m4'
2023-09-12T10:35:41,921     adding 'pysam/include/htslib/m4/hts_hide_dynamic_syms.m4'
2023-09-12T10:35:41,923     adding 'pysam/include/htslib/m4/hts_prog_cc_warnings.m4'
2023-09-12T10:35:41,925     adding 'pysam/include/htslib/m4/pkg.m4'
2023-09-12T10:35:41,927     adding 'pysam/include/htslib/os/lzma_stub.h'
2023-09-12T10:35:41,928     adding 'pysam/include/htslib/os/rand.c'
2023-09-12T10:35:41,932     adding 'pysam/include/samtools/LICENSE'
2023-09-12T10:35:41,933     adding 'pysam/include/samtools/README'
2023-09-12T10:35:41,940     adding 'pysam/include/samtools/amplicon_stats.c'
2023-09-12T10:35:41,948     adding 'pysam/include/samtools/amplicon_stats.c.pysam.c'
2023-09-12T10:35:41,951     adding 'pysam/include/samtools/bam.c'
2023-09-12T10:35:41,953     adding 'pysam/include/samtools/bam.c.pysam.c'
2023-09-12T10:35:41,954     adding 'pysam/include/samtools/bam.h'
2023-09-12T10:35:41,958     adding 'pysam/include/samtools/bam2depth.c'
2023-09-12T10:35:41,962     adding 'pysam/include/samtools/bam2depth.c.pysam.c'
2023-09-12T10:35:41,965     adding 'pysam/include/samtools/bam_addrprg.c'
2023-09-12T10:35:41,967     adding 'pysam/include/samtools/bam_addrprg.c.pysam.c'
2023-09-12T10:35:41,971     adding 'pysam/include/samtools/bam_ampliconclip.c'
2023-09-12T10:35:41,975     adding 'pysam/include/samtools/bam_ampliconclip.c.pysam.c'
2023-09-12T10:35:41,977     adding 'pysam/include/samtools/bam_ampliconclip.h'
2023-09-12T10:35:41,978     adding 'pysam/include/samtools/bam_aux.c'
2023-09-12T10:35:41,979     adding 'pysam/include/samtools/bam_aux.c.pysam.c'
2023-09-12T10:35:41,982     adding 'pysam/include/samtools/bam_cat.c'
2023-09-12T10:35:41,985     adding 'pysam/include/samtools/bam_cat.c.pysam.c'
2023-09-12T10:35:41,986     adding 'pysam/include/samtools/bam_color.c'
2023-09-12T10:35:41,988     adding 'pysam/include/samtools/bam_color.c.pysam.c'
2023-09-12T10:35:41,999     adding 'pysam/include/samtools/bam_consensus.c'
2023-09-12T10:35:42,012     adding 'pysam/include/samtools/bam_consensus.c.pysam.c'
2023-09-12T10:35:42,016     adding 'pysam/include/samtools/bam_fastq.c'
2023-09-12T10:35:42,020     adding 'pysam/include/samtools/bam_fastq.c.pysam.c'
2023-09-12T10:35:42,022     adding 'pysam/include/samtools/bam_flags.c'
2023-09-12T10:35:42,023     adding 'pysam/include/samtools/bam_flags.c.pysam.c'
2023-09-12T10:35:42,026     adding 'pysam/include/samtools/bam_import.c'
2023-09-12T10:35:42,028     adding 'pysam/include/samtools/bam_import.c.pysam.c'
2023-09-12T10:35:42,030     adding 'pysam/include/samtools/bam_index.c'
2023-09-12T10:35:42,032     adding 'pysam/include/samtools/bam_index.c.pysam.c'
2023-09-12T10:35:42,034     adding 'pysam/include/samtools/bam_lpileup.c'
2023-09-12T10:35:42,036     adding 'pysam/include/samtools/bam_lpileup.c.pysam.c'
2023-09-12T10:35:42,037     adding 'pysam/include/samtools/bam_lpileup.h'
2023-09-12T10:35:42,045     adding 'pysam/include/samtools/bam_markdup.c'
2023-09-12T10:35:42,055     adding 'pysam/include/samtools/bam_markdup.c.pysam.c'
2023-09-12T10:35:42,059     adding 'pysam/include/samtools/bam_mate.c'
2023-09-12T10:35:42,062     adding 'pysam/include/samtools/bam_mate.c.pysam.c'
2023-09-12T10:35:42,065     adding 'pysam/include/samtools/bam_md.c'
2023-09-12T10:35:42,068     adding 'pysam/include/samtools/bam_md.c.pysam.c'
2023-09-12T10:35:42,069     adding 'pysam/include/samtools/bam_plbuf.c'
2023-09-12T10:35:42,070     adding 'pysam/include/samtools/bam_plbuf.c.pysam.c'
2023-09-12T10:35:42,072     adding 'pysam/include/samtools/bam_plbuf.h'
2023-09-12T10:35:42,077     adding 'pysam/include/samtools/bam_plcmd.c'
2023-09-12T10:35:42,082     adding 'pysam/include/samtools/bam_plcmd.c.pysam.c'
2023-09-12T10:35:42,084     adding 'pysam/include/samtools/bam_quickcheck.c'
2023-09-12T10:35:42,086     adding 'pysam/include/samtools/bam_quickcheck.c.pysam.c'
2023-09-12T10:35:42,089     adding 'pysam/include/samtools/bam_reheader.c'
2023-09-12T10:35:42,091     adding 'pysam/include/samtools/bam_reheader.c.pysam.c'
2023-09-12T10:35:42,093     adding 'pysam/include/samtools/bam_rmdup.c'
2023-09-12T10:35:42,095     adding 'pysam/include/samtools/bam_rmdup.c.pysam.c'
2023-09-12T10:35:42,097     adding 'pysam/include/samtools/bam_rmdupse.c'
2023-09-12T10:35:42,099     adding 'pysam/include/samtools/bam_rmdupse.c.pysam.c'
2023-09-12T10:35:42,101     adding 'pysam/include/samtools/bam_samples.c'
2023-09-12T10:35:42,104     adding 'pysam/include/samtools/bam_samples.c.pysam.c'
2023-09-12T10:35:42,117     adding 'pysam/include/samtools/bam_sort.c'
2023-09-12T10:35:42,132     adding 'pysam/include/samtools/bam_sort.c.pysam.c'
2023-09-12T10:35:42,136     adding 'pysam/include/samtools/bam_split.c'
2023-09-12T10:35:42,139     adding 'pysam/include/samtools/bam_split.c.pysam.c'
2023-09-12T10:35:42,141     adding 'pysam/include/samtools/bam_stat.c'
2023-09-12T10:35:42,143     adding 'pysam/include/samtools/bam_stat.c.pysam.c'
2023-09-12T10:35:42,146     adding 'pysam/include/samtools/bamshuf.c'
2023-09-12T10:35:42,148     adding 'pysam/include/samtools/bamshuf.c.pysam.c'
2023-09-12T10:35:42,151     adding 'pysam/include/samtools/bamtk.c'
2023-09-12T10:35:42,153     adding 'pysam/include/samtools/bamtk.c.pysam.c'
2023-09-12T10:35:42,155     adding 'pysam/include/samtools/bedcov.c'
2023-09-12T10:35:42,157     adding 'pysam/include/samtools/bedcov.c.pysam.c'
2023-09-12T10:35:42,160     adding 'pysam/include/samtools/bedidx.c'
2023-09-12T10:35:42,163     adding 'pysam/include/samtools/bedidx.c.pysam.c'
2023-09-12T10:35:42,164     adding 'pysam/include/samtools/bedidx.h'
2023-09-12T10:35:42,165     adding 'pysam/include/samtools/config.h'
2023-09-12T10:35:42,168     adding 'pysam/include/samtools/consensus_pileup.c'
2023-09-12T10:35:42,170     adding 'pysam/include/samtools/consensus_pileup.c.pysam.c'
2023-09-12T10:35:42,172     adding 'pysam/include/samtools/consensus_pileup.h'
2023-09-12T10:35:42,175     adding 'pysam/include/samtools/coverage.c'
2023-09-12T10:35:42,179     adding 'pysam/include/samtools/coverage.c.pysam.c'
2023-09-12T10:35:42,182     adding 'pysam/include/samtools/cram_size.c'
2023-09-12T10:35:42,185     adding 'pysam/include/samtools/cram_size.c.pysam.c'
2023-09-12T10:35:42,187     adding 'pysam/include/samtools/cut_target.c'
2023-09-12T10:35:42,188     adding 'pysam/include/samtools/cut_target.c.pysam.c'
2023-09-12T10:35:42,190     adding 'pysam/include/samtools/dict.c'
2023-09-12T10:35:42,192     adding 'pysam/include/samtools/dict.c.pysam.c'
2023-09-12T10:35:42,194     adding 'pysam/include/samtools/faidx.c'
2023-09-12T10:35:42,197     adding 'pysam/include/samtools/faidx.c.pysam.c'
2023-09-12T10:35:42,200     adding 'pysam/include/samtools/padding.c'
2023-09-12T10:35:42,203     adding 'pysam/include/samtools/padding.c.pysam.c'
2023-09-12T10:35:42,207     adding 'pysam/include/samtools/phase.c'
2023-09-12T10:35:42,212     adding 'pysam/include/samtools/phase.c.pysam.c'
2023-09-12T10:35:42,214     adding 'pysam/include/samtools/reference.c'
2023-09-12T10:35:42,217     adding 'pysam/include/samtools/reference.c.pysam.c'
2023-09-12T10:35:42,220     adding 'pysam/include/samtools/reset.c'
2023-09-12T10:35:42,223     adding 'pysam/include/samtools/reset.c.pysam.c'
2023-09-12T10:35:42,224     adding 'pysam/include/samtools/sam_opts.c'
2023-09-12T10:35:42,226     adding 'pysam/include/samtools/sam_opts.c.pysam.c'
2023-09-12T10:35:42,227     adding 'pysam/include/samtools/sam_opts.h'
2023-09-12T10:35:42,229     adding 'pysam/include/samtools/sam_utils.c'
2023-09-12T10:35:42,231     adding 'pysam/include/samtools/sam_utils.c.pysam.c'
2023-09-12T10:35:42,232     adding 'pysam/include/samtools/sam_utils.h'
2023-09-12T10:35:42,239     adding 'pysam/include/samtools/sam_view.c'
2023-09-12T10:35:42,246     adding 'pysam/include/samtools/sam_view.c.pysam.c'
2023-09-12T10:35:42,248     adding 'pysam/include/samtools/sample.c'
2023-09-12T10:35:42,249     adding 'pysam/include/samtools/sample.c.pysam.c'
2023-09-12T10:35:42,251     adding 'pysam/include/samtools/sample.h'
2023-09-12T10:35:42,252     adding 'pysam/include/samtools/samtools.h'
2023-09-12T10:35:42,253     adding 'pysam/include/samtools/samtools.pysam.c'
2023-09-12T10:35:42,255     adding 'pysam/include/samtools/samtools.pysam.h'
2023-09-12T10:35:42,257     adding 'pysam/include/samtools/splaysort.h'
2023-09-12T10:35:42,268     adding 'pysam/include/samtools/stats.c'
2023-09-12T10:35:42,280     adding 'pysam/include/samtools/stats.c.pysam.c'
2023-09-12T10:35:42,283     adding 'pysam/include/samtools/stats_isize.c'
2023-09-12T10:35:42,285     adding 'pysam/include/samtools/stats_isize.c.pysam.c'
2023-09-12T10:35:42,286     adding 'pysam/include/samtools/stats_isize.h'
2023-09-12T10:35:42,288     adding 'pysam/include/samtools/tmp_file.c'
2023-09-12T10:35:42,291     adding 'pysam/include/samtools/tmp_file.c.pysam.c'
2023-09-12T10:35:42,293     adding 'pysam/include/samtools/tmp_file.h'
2023-09-12T10:35:42,294     adding 'pysam/include/samtools/version.sh'
2023-09-12T10:35:42,296     adding 'pysam/include/samtools/lz4/LICENSE'
2023-09-12T10:35:42,302     adding 'pysam/include/samtools/lz4/lz4.c'
2023-09-12T10:35:42,308     adding 'pysam/include/samtools/lz4/lz4.c.pysam.c'
2023-09-12T10:35:42,312     adding 'pysam/include/samtools/lz4/lz4.h'
2023-09-12T10:35:42,314     adding 'pysam-0.21.0.dist-info/AUTHORS'
2023-09-12T10:35:42,316     adding 'pysam-0.21.0.dist-info/COPYING'
2023-09-12T10:35:42,317     adding 'pysam-0.21.0.dist-info/METADATA'
2023-09-12T10:35:42,318     adding 'pysam-0.21.0.dist-info/WHEEL'
2023-09-12T10:35:42,319     adding 'pysam-0.21.0.dist-info/top_level.txt'
2023-09-12T10:35:42,326     adding 'pysam-0.21.0.dist-info/RECORD'
2023-09-12T10:35:42,505     removing build/bdist.linux-armv7l/wheel
2023-09-12T10:35:43,000     Building wheel for pysam (pyproject.toml): finished with status 'done'
2023-09-12T10:35:43,932     Created wheel for pysam: filename=pysam-0.21.0-cp311-cp311-linux_armv7l.whl size=16179600 sha256=ccf6de8085b5863b1fe15609e46ee7c075317c36d63227b788f9d8ecde845f1a
2023-09-12T10:35:43,933     Stored in directory: /home/piwheels/.cache/pip/wheels/52/2d/ed/b1e5c4ad36c535940dc1b1da900d05f571f88ff26f7be95f4c
2023-09-12T10:35:43,950   Successfully built pysam
2023-09-12T10:35:46,696   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
2023-09-12T10:35:47,225     Creating /tmp/pip-build-env-uwgm7p5_/overlay/local/bin
2023-09-12T10:35:47,227     changing mode of /tmp/pip-build-env-uwgm7p5_/overlay/local/bin/wheel to 755
2023-09-12T10:35:52,622     changing mode of /tmp/pip-build-env-uwgm7p5_/overlay/local/bin/cygdb to 755
2023-09-12T10:35:52,624     changing mode of /tmp/pip-build-env-uwgm7p5_/overlay/local/bin/cython to 755
2023-09-12T10:35:52,626     changing mode of /tmp/pip-build-env-uwgm7p5_/overlay/local/bin/cythonize to 755
2023-09-12T10:35:53,724     changing mode of /tmp/pip-build-env-uwgm7p5_/overlay/local/bin/chardetect to 755
2023-09-12T10:35:54,444     changing mode of /tmp/pip-build-env-uwgm7p5_/overlay/local/bin/virtualenv to 755
2023-09-12T10:35:57,067     changing mode of /tmp/pip-build-env-uwgm7p5_/overlay/local/bin/cython-setuptools to 755
2023-09-12T10:35:57,824     changing mode of /tmp/pip-build-env-uwgm7p5_/overlay/local/bin/tox to 755
2023-09-12T10:35:58,111   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
2023-09-12T10:35:59,377   Installing build dependencies: finished with status 'done'
2023-09-12T10:35:59,380   Getting requirements to build wheel: started
2023-09-12T10:35:59,381   Running command Getting requirements to build wheel
2023-09-12T10:36:10,306   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
2023-09-12T10:36:10,306   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

2023-09-12T10:36:10,602   Error compiling Cython file:
2023-09-12T10:36:10,602   ------------------------------------------------------------
2023-09-12T10:36:10,603   ...
2023-09-12T10:36:10,604   INSERTION.inverse     = DELETION
2023-09-12T10:36:10,604   DELETION.inverse      = INSERTION
2023-09-12T10:36:10,605   SEQ_MATCH.inverse     = SEQ_MATCH
2023-09-12T10:36:10,606   SEQ_MISMATCH.inverse  = SEQ_MISMATCH

2023-09-12T10:36:10,607   cpdef tuple BAM_OPS = (MATCH, INSERTION, DELETION, SKIPPED, SOFT_CLIP, HARD_CLIP, PADDING, SEQ_MATCH, SEQ_MISMATCH)
2023-09-12T10:36:10,608         ^
2023-09-12T10:36:10,608   ------------------------------------------------------------

2023-09-12T10:36:10,610   uta_align/align/cigar_utils.pyx:62:6: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.

2023-09-12T10:36:10,612   Error compiling Cython file:
2023-09-12T10:36:10,612   ------------------------------------------------------------
2023-09-12T10:36:10,613   ...
2023-09-12T10:36:10,613   # Create mapping from ord(char_op) to op
2023-09-12T10:36:10,613   _temp_map = [None]*256
2023-09-12T10:36:10,614   for _op in BAM_OPS:
2023-09-12T10:36:10,614       _temp_map[_op.code] = _op

2023-09-12T10:36:10,615   cpdef tuple BAM_OP_CHAR_MAP = tuple(_temp_map)
2023-09-12T10:36:10,616         ^
2023-09-12T10:36:10,616   ------------------------------------------------------------

2023-09-12T10:36:10,617   uta_align/align/cigar_utils.pyx:69:6: Variables cannot be declared with 'cpdef'. Use 'cdef' instead.
2023-09-12T10:36:11,137   Compiling uta_align/align/algorithms.pyx because it changed.
2023-09-12T10:36:11,138   Compiling uta_align/align/cigar_utils.pyx because it changed.
2023-09-12T10:36:11,139   [1/2] Cythonizing uta_align/align/algorithms.pyx
2023-09-12T10:36:11,139   [2/2] Cythonizing uta_align/align/cigar_utils.pyx
2023-09-12T10:36:11,140   Traceback (most recent call last):
2023-09-12T10:36:11,140     File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
2023-09-12T10:36:11,141       main()
2023-09-12T10:36:11,141     File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
2023-09-12T10:36:11,142       json_out['return_val'] = hook(**hook_input['kwargs'])
2023-09-12T10:36:11,142                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,143     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
2023-09-12T10:36:11,143       return hook(config_settings)
2023-09-12T10:36:11,144              ^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,145     File "/tmp/pip-build-env-uwgm7p5_/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 355, in get_requires_for_build_wheel
2023-09-12T10:36:11,146       return self._get_build_requires(config_settings, requirements=['wheel'])
2023-09-12T10:36:11,147              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,148     File "/tmp/pip-build-env-uwgm7p5_/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 325, in _get_build_requires
2023-09-12T10:36:11,149       self.run_setup()
2023-09-12T10:36:11,150     File "/tmp/pip-build-env-uwgm7p5_/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 341, in run_setup
2023-09-12T10:36:11,151       exec(code, locals())
2023-09-12T10:36:11,152     File "<string>", line 52, in <module>
2023-09-12T10:36:11,153     File "/tmp/pip-build-env-uwgm7p5_/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
2023-09-12T10:36:11,154       cythonize_one(*args)
2023-09-12T10:36:11,155     File "/tmp/pip-build-env-uwgm7p5_/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
2023-09-12T10:36:11,156       raise CompileError(None, pyx_file)
2023-09-12T10:36:11,157   Cython.Compiler.Errors.CompileError: uta_align/align/cigar_utils.pyx
2023-09-12T10:36:11,557   ERROR: [present-rich] Getting requirements to build wheel exited with 1
2023-09-12T10:36:11,570   [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/tmpt0z6314r[/]
2023-09-12T10:36:11,571   [bold magenta]cwd[/]: /tmp/pip-wheel-q_rfth3l/uta-align_43720bf8306a4f058f39c7738d72273a
2023-09-12T10:36:11,571   Getting requirements to build wheel: finished with status 'error'
2023-09-12T10:36:11,574 ERROR: [present-rich] Getting requirements to build wheel exited with 1
2023-09-12T10:36:11,579 Exception information:
2023-09-12T10:36:11,579 Traceback (most recent call last):
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
2023-09-12T10:36:11,579     status = run_func(*args)
2023-09-12T10:36:11,579              ^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper
2023-09-12T10:36:11,579     return func(self, options, args)
2023-09-12T10:36:11,579            ^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 147, in run
2023-09-12T10:36:11,579     requirement_set = resolver.resolve(reqs, check_supported_wheels=True)
2023-09-12T10:36:11,579                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 92, in resolve
2023-09-12T10:36:11,579     result = self._result = resolver.resolve(
2023-09-12T10:36:11,579                             ^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve
2023-09-12T10:36:11,579     state = resolution.resolve(requirements, max_rounds=max_rounds)
2023-09-12T10:36:11,579             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 397, in resolve
2023-09-12T10:36:11,579     self._add_to_criteria(self.state.criteria, r, parent=None)
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria
2023-09-12T10:36:11,579     if not criterion.candidates:
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/structs.py", line 156, in __bool__
2023-09-12T10:36:11,579     return bool(self._sequence)
2023-09-12T10:36:11,579            ^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in __bool__
2023-09-12T10:36:11,579     return any(self)
2023-09-12T10:36:11,579            ^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in <genexpr>
2023-09-12T10:36:11,579     return (c for c in iterator if id(c) not in self._incompatible_ids)
2023-09-12T10:36:11,579            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built
2023-09-12T10:36:11,579     candidate = func()
2023-09-12T10:36:11,579                 ^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link
2023-09-12T10:36:11,579     self._link_candidate_cache[link] = LinkCandidate(
2023-09-12T10:36:11,579                                        ^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__
2023-09-12T10:36:11,579     super().__init__(
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__
2023-09-12T10:36:11,579     self.dist = self._prepare()
2023-09-12T10:36:11,579                 ^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare
2023-09-12T10:36:11,579     dist = self._prepare_distribution()
2023-09-12T10:36:11,579            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution
2023-09-12T10:36:11,579     return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
2023-09-12T10:36:11,579            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 538, in prepare_linked_requirement
2023-09-12T10:36:11,579     return self._prepare_linked_requirement(req, parallel_builds)
2023-09-12T10:36:11,579            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 653, in _prepare_linked_requirement
2023-09-12T10:36:11,579     dist = _get_prepared_distribution(
2023-09-12T10:36:11,579            ^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution
2023-09-12T10:36:11,579     abstract_dist.prepare_distribution_metadata(
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 48, in prepare_distribution_metadata
2023-09-12T10:36:11,579     self._install_build_reqs(finder)
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 118, in _install_build_reqs
2023-09-12T10:36:11,579     build_reqs = self._get_build_requires_wheel()
2023-09-12T10:36:11,579                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 95, in _get_build_requires_wheel
2023-09-12T10:36:11,579     return backend.get_requires_for_build_wheel()
2023-09-12T10:36:11,579            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/misc.py", line 697, in get_requires_for_build_wheel
2023-09-12T10:36:11,579     return super().get_requires_for_build_wheel(config_settings=cs)
2023-09-12T10:36:11,579            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_impl.py", line 166, in get_requires_for_build_wheel
2023-09-12T10:36:11,579     return self._call_hook('get_requires_for_build_wheel', {
2023-09-12T10:36:11,579            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook
2023-09-12T10:36:11,579     self._subprocess_runner(
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/subprocess.py", line 252, in runner
2023-09-12T10:36:11,579     call_subprocess(
2023-09-12T10:36:11,579   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess
2023-09-12T10:36:11,579     raise error
2023-09-12T10:36:11,579 pip._internal.exceptions.InstallationSubprocessError: Getting requirements to build wheel exited with 1
2023-09-12T10:36:11,596 Removed uta-align==0.2.0a2 from https://files.pythonhosted.org/packages/7c/07/3d0483101728198e619f9d45552d2d50dc90fc2937964a899e6fe3908687/uta-align-0.2.0a2.tar.gz from build tracker '/tmp/pip-build-tracker-iaiomtc_'
2023-09-12T10:36:11,597 Removed build tracker: '/tmp/pip-build-tracker-iaiomtc_'