2024-03-04T05:45:00,464 Created temporary directory: /tmp/pip-build-tracker-prrqt6fj
2024-03-04T05:45:00,465 Initialized build tracking at /tmp/pip-build-tracker-prrqt6fj
2024-03-04T05:45:00,466 Created build tracker: /tmp/pip-build-tracker-prrqt6fj
2024-03-04T05:45:00,466 Entered build tracker: /tmp/pip-build-tracker-prrqt6fj
2024-03-04T05:45:00,467 Created temporary directory: /tmp/pip-wheel-4bgekayg
2024-03-04T05:45:00,470 Created temporary directory: /tmp/pip-ephem-wheel-cache-ofm9xo93
2024-03-04T05:45:00,492 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-03-04T05:45:00,495 2 location(s) to search for versions of uta-align:
2024-03-04T05:45:00,495 * https://pypi.org/simple/uta-align/
2024-03-04T05:45:00,495 * https://www.piwheels.org/simple/uta-align/
2024-03-04T05:45:00,496 Fetching project page and analyzing links: https://pypi.org/simple/uta-align/
2024-03-04T05:45:00,497 Getting page https://pypi.org/simple/uta-align/
2024-03-04T05:45:00,499 Found index url https://pypi.org/simple/
2024-03-04T05:45:00,728 Fetched page https://pypi.org/simple/uta-align/ as application/vnd.pypi.simple.v1+json
2024-03-04T05:45:00,734   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
2024-03-04T05:45:00,734   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/)
2024-03-04T05:45:00,735   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
2024-03-04T05:45:00,736   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/)
2024-03-04T05:45:00,736   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
2024-03-04T05:45:00,737   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/)
2024-03-04T05:45:00,737   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/)
2024-03-04T05:45:00,738   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
2024-03-04T05:45:00,739   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/)
2024-03-04T05:45:00,740   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
2024-03-04T05:45:00,740   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/)
2024-03-04T05:45:00,741   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
2024-03-04T05:45:00,742   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/)
2024-03-04T05:45:00,742   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
2024-03-04T05:45:00,743   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/)
2024-03-04T05:45:00,743   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
2024-03-04T05:45:00,744   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/)
2024-03-04T05:45:00,745   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
2024-03-04T05:45:00,745   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/)
2024-03-04T05:45:00,746   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
2024-03-04T05:45:00,746   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/)
2024-03-04T05:45:00,747   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/)
2024-03-04T05:45:00,748   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
2024-03-04T05:45:00,748   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
2024-03-04T05:45:00,749   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
2024-03-04T05:45:00,750   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
2024-03-04T05:45:00,751   Found link https://files.pythonhosted.org/packages/95/c5/883aa80e54870d4646838c083bfc48f892f0b17999c6ae59f3dd364efa90/uta-align-0.3.0a0.tar.gz (from https://pypi.org/simple/uta-align/), version: 0.3.0a0
2024-03-04T05:45:00,751 Fetching project page and analyzing links: https://www.piwheels.org/simple/uta-align/
2024-03-04T05:45:00,752 Getting page https://www.piwheels.org/simple/uta-align/
2024-03-04T05:45:00,754 Found index url https://www.piwheels.org/simple/
2024-03-04T05:45:00,930 Fetched page https://www.piwheels.org/simple/uta-align/ as text/html
2024-03-04T05:45:00,937   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/)
2024-03-04T05:45:00,938   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/)
2024-03-04T05:45:00,939   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/)
2024-03-04T05:45:00,939   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/)
2024-03-04T05:45:00,940   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/)
2024-03-04T05:45:00,940   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/)
2024-03-04T05:45:00,941   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/)
2024-03-04T05:45:00,941   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/)
2024-03-04T05:45:00,942   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/)
2024-03-04T05:45:00,942   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/)
2024-03-04T05:45:00,943   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/)
2024-03-04T05:45:00,943   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/)
2024-03-04T05:45:00,944   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/)
2024-03-04T05:45:00,945   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/)
2024-03-04T05:45:00,945   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/)
2024-03-04T05:45:00,946   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/)
2024-03-04T05:45:00,947   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/)
2024-03-04T05:45:00,947   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/)
2024-03-04T05:45:00,948   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/)
2024-03-04T05:45:00,948   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/)
2024-03-04T05:45:00,948   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/)
2024-03-04T05:45:00,949   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/)
2024-03-04T05:45:00,949   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/)
2024-03-04T05:45:00,950   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/)
2024-03-04T05:45:00,951   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/)
2024-03-04T05:45:00,951   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/)
2024-03-04T05:45:00,952 Skipping link: not a file: https://www.piwheels.org/simple/uta-align/
2024-03-04T05:45:00,953 Skipping link: not a file: https://pypi.org/simple/uta-align/
2024-03-04T05:45:00,975 Given no hashes to check 1 links for project 'uta-align': discarding no candidates
2024-03-04T05:45:00,994 Collecting uta-align==0.3.0a0
2024-03-04T05:45:00,997   Created temporary directory: /tmp/pip-unpack-ej1qxmac
2024-03-04T05:45:01,233   Downloading uta-align-0.3.0a0.tar.gz (335 kB)
2024-03-04T05:45:01,507   Added uta-align==0.3.0a0 from https://files.pythonhosted.org/packages/95/c5/883aa80e54870d4646838c083bfc48f892f0b17999c6ae59f3dd364efa90/uta-align-0.3.0a0.tar.gz to build tracker '/tmp/pip-build-tracker-prrqt6fj'
2024-03-04T05:45:01,516   Created temporary directory: /tmp/pip-build-env-h239wsj9
2024-03-04T05:45:01,520   Installing build dependencies: started
2024-03-04T05:45:01,522   Running command pip subprocess to install build dependencies
2024-03-04T05:45:03,819   Using pip 23.3.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2024-03-04T05:45:05,050   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-03-04T05:45:07,162   Collecting cython>=0.29
2024-03-04T05:45:07,188     Using cached https://www.piwheels.org/simple/cython/Cython-3.0.8-cp311-cp311-linux_armv7l.whl (11.7 MB)
2024-03-04T05:45:07,790   Collecting cython-setuptools
2024-03-04T05:45:07,805     Downloading https://www.piwheels.org/simple/cython-setuptools/cython_setuptools-0.2.3-py3-none-any.whl (9.7 kB)
2024-03-04T05:45:12,538   Collecting pysam>=0.15
2024-03-04T05:45:13,035     Using cached https://www.piwheels.org/simple/pysam/pysam-0.22.0-cp311-cp311-linux_armv7l.whl (17.8 MB)
2024-03-04T05:45:19,693   Collecting setuptools>=45
2024-03-04T05:45:19,715     Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.1.1-py3-none-any.whl (819 kB)
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2024-03-04T05:46:04,904   Installing collected packages: distlib, wheel, typing-extensions, setuptools, pysam, pluggy, platformdirs, packaging, filelock, cython, colorama, click, chardet, cachetools, virtualenv, setuptools_scm, pyproject-api, cython-setuptools, tox
2024-03-04T05:46:05,528     Creating /tmp/pip-build-env-h239wsj9/overlay/local/bin
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2024-03-04T05:46:17,759     changing mode of /tmp/pip-build-env-h239wsj9/overlay/local/bin/tox to 755
2024-03-04T05:46:18,018   Successfully installed cachetools-5.3.3 chardet-5.2.0 click-8.1.7 colorama-0.4.6 cython-3.0.8 cython-setuptools-0.2.3 distlib-0.3.8 filelock-3.13.1 packaging-23.2 platformdirs-4.2.0 pluggy-1.4.0 pyproject-api-1.6.1 pysam-0.22.0 setuptools-69.1.1 setuptools_scm-8.0.4 tox-4.13.0 typing-extensions-4.10.0 virtualenv-20.25.1 wheel-0.42.0

2024-03-04T05:46:18,510   [notice] A new release of pip is available: 23.3.1 -> 24.0
2024-03-04T05:46:18,510   [notice] To update, run: python3 -m pip install --upgrade pip
2024-03-04T05:46:18,988   Installing build dependencies: finished with status 'done'
2024-03-04T05:46:18,992   Getting requirements to build wheel: started
2024-03-04T05:46:18,993   Running command Getting requirements to build wheel
2024-03-04T05:46:27,211   Compiling uta_align/align/algorithms.pyx because it depends on /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/Cython/Includes/posix/types.pxd.
2024-03-04T05:46:27,212   Compiling uta_align/align/cigar_utils.pyx because it depends on /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/Cython/Includes/posix/types.pxd.
2024-03-04T05:46:27,212   [1/2] Cythonizing uta_align/align/algorithms.pyx
2024-03-04T05:46:27,213   [2/2] Cythonizing uta_align/align/cigar_utils.pyx
2024-03-04T05:46:27,781   Getting requirements to build wheel: finished with status 'done'
2024-03-04T05:46:27,825   Created temporary directory: /tmp/pip-modern-metadata-xg57v9i1
2024-03-04T05:46:27,827   Preparing metadata (pyproject.toml): started
2024-03-04T05:46:27,828   Running command Preparing metadata (pyproject.toml)
2024-03-04T05:46:29,774   WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
2024-03-04T05:46:29,870   running dist_info
2024-03-04T05:46:29,893   creating /tmp/pip-modern-metadata-xg57v9i1/uta_align.egg-info
2024-03-04T05:46:29,902   writing /tmp/pip-modern-metadata-xg57v9i1/uta_align.egg-info/PKG-INFO
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2024-03-04T05:46:29,941   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/htslib_util.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,941   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/bgzf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,942   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/cram.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,942   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/faidx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,943   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/hfile.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,944   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/hts.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,944   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kstring.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,945   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/sam.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,945   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/tbx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,946   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/vcf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,946   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/vcfutils.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,947   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,947   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/htslib_util.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,948   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/bgzf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,948   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/cram.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,949   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/faidx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,949   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/hfile.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,950   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/hts.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,951   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kstring.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,951   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/sam.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,952   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/tbx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,952   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/vcf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,953   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/vcfutils.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,954   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:46:29,982   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2024-03-04T05:46:29,986   reading manifest file '/tmp/pip-modern-metadata-xg57v9i1/uta_align.egg-info/SOURCES.txt'
2024-03-04T05:46:29,988   adding license file 'LICENSE.txt'
2024-03-04T05:46:29,990   writing manifest file '/tmp/pip-modern-metadata-xg57v9i1/uta_align.egg-info/SOURCES.txt'
2024-03-04T05:46:29,991   creating '/tmp/pip-modern-metadata-xg57v9i1/uta_align-0.3.0a0.dist-info'
2024-03-04T05:46:30,222   Preparing metadata (pyproject.toml): finished with status 'done'
2024-03-04T05:46:30,227   Source in /tmp/pip-wheel-4bgekayg/uta-align_f0215ccb2e7b47f1b2b8ceab93bb2f26 has version 0.3.0a0, which satisfies requirement uta-align==0.3.0a0 from https://files.pythonhosted.org/packages/95/c5/883aa80e54870d4646838c083bfc48f892f0b17999c6ae59f3dd364efa90/uta-align-0.3.0a0.tar.gz
2024-03-04T05:46:30,228   Removed uta-align==0.3.0a0 from https://files.pythonhosted.org/packages/95/c5/883aa80e54870d4646838c083bfc48f892f0b17999c6ae59f3dd364efa90/uta-align-0.3.0a0.tar.gz from build tracker '/tmp/pip-build-tracker-prrqt6fj'
2024-03-04T05:46:30,232 Created temporary directory: /tmp/pip-unpack-mjnlj934
2024-03-04T05:46:30,233 Created temporary directory: /tmp/pip-unpack-4w28br7k
2024-03-04T05:46:30,260 Building wheels for collected packages: uta-align
2024-03-04T05:46:30,264   Created temporary directory: /tmp/pip-wheel-bo4s24f0
2024-03-04T05:46:30,264   Destination directory: /tmp/pip-wheel-bo4s24f0
2024-03-04T05:46:30,266   Building wheel for uta-align (pyproject.toml): started
2024-03-04T05:46:30,268   Running command Building wheel for uta-align (pyproject.toml)
2024-03-04T05:46:32,162   WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
2024-03-04T05:46:32,290   running bdist_wheel
2024-03-04T05:46:32,356   running build
2024-03-04T05:46:32,357   running build_ext
2024-03-04T05:46:32,362   building 'uta_align.align.algorithms' extension
2024-03-04T05:46:32,363   creating build
2024-03-04T05:46:32,363   creating build/temp.linux-armv7l-cpython-311
2024-03-04T05:46:32,364   creating build/temp.linux-armv7l-cpython-311/uta_align
2024-03-04T05:46:32,365   creating build/temp.linux-armv7l-cpython-311/uta_align/align
2024-03-04T05:46:32,366   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c uta_align/align/algorithms.c -o build/temp.linux-armv7l-cpython-311/uta_align/align/algorithms.o
2024-03-04T05:46:33,161   uta_align/align/algorithms.c: In function ‘__pyx_pf_9uta_align_5align_10algorithms_8needleman_wunsch_altshul_erikson’:
2024-03-04T05:46:33,175   uta_align/align/algorithms.c:15310:33: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2024-03-04T05:46:33,175   15310 |   for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
2024-03-04T05:46:33,176         |                                 ^
2024-03-04T05:46:33,189   uta_align/align/algorithms.c:15347:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2024-03-04T05:46:33,190   15347 |     __pyx_t_6 = (__pyx_v_j < __pyx_v_m);
2024-03-04T05:46:33,190         |                            ^
2024-03-04T05:46:33,204   uta_align/align/algorithms.c:15379:33: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2024-03-04T05:46:33,204   15379 |   for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
2024-03-04T05:46:33,205         |                                 ^
2024-03-04T05:46:33,219   uta_align/align/algorithms.c:15462:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2024-03-04T05:46:33,219   15462 |     __pyx_t_6 = (__pyx_v_i < __pyx_v_n);
2024-03-04T05:46:33,220         |                            ^
2024-03-04T05:46:33,233   uta_align/align/algorithms.c:15493:35: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2024-03-04T05:46:33,234   15493 |     for (__pyx_t_7 = 1; __pyx_t_7 < __pyx_t_9; __pyx_t_7+=1) {
2024-03-04T05:46:33,235         |                                   ^
2024-03-04T05:46:34,729   In file included from /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:4,
2024-03-04T05:46:34,730                    from uta_align/align/algorithms.c:1264:
2024-03-04T05:46:34,730   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h: At top level:
2024-03-04T05:46:34,730   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:190:19: warning: ‘kseq_read’ defined but not used [-Wunused-function]
2024-03-04T05:46:34,731     190 |         SCOPE int kseq_read(kseq_t *seq) \
2024-03-04T05:46:34,732         |                   ^~~~~~~~~
2024-03-04T05:46:34,732   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:244:9: note: in expansion of macro ‘__KSEQ_READ’
2024-03-04T05:46:34,733     244 |         __KSEQ_READ(SCOPE)
2024-03-04T05:46:34,733         |         ^~~~~~~~~~~
2024-03-04T05:46:34,734   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T05:46:34,735     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T05:46:34,735         |                                   ^~~~~~~~~~
2024-03-04T05:46:34,736   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T05:46:34,736       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T05:46:34,737         | ^~~~~~~~~
2024-03-04T05:46:34,738   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:174:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
2024-03-04T05:46:34,738     174 |         SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
2024-03-04T05:46:34,739         |                    ^~~~~~~~~~~~
2024-03-04T05:46:34,739   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:243:9: note: in expansion of macro ‘__KSEQ_BASIC’
2024-03-04T05:46:34,740     243 |         __KSEQ_BASIC(SCOPE, type_t)                                     \
2024-03-04T05:46:34,740         |         ^~~~~~~~~~~~
2024-03-04T05:46:34,741   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T05:46:34,742     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T05:46:34,742         |                                   ^~~~~~~~~~
2024-03-04T05:46:34,743   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T05:46:34,744       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T05:46:34,744         | ^~~~~~~~~
2024-03-04T05:46:34,745   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:168:23: warning: ‘kseq_init’ defined but not used [-Wunused-function]
2024-03-04T05:46:34,745     168 |         SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
2024-03-04T05:46:34,746         |                       ^~~~~~~~~
2024-03-04T05:46:34,746   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:243:9: note: in expansion of macro ‘__KSEQ_BASIC’
2024-03-04T05:46:34,746     243 |         __KSEQ_BASIC(SCOPE, type_t)                                     \
2024-03-04T05:46:34,747         |         ^~~~~~~~~~~~
2024-03-04T05:46:34,747   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T05:46:34,748     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T05:46:34,748         |                                   ^~~~~~~~~~
2024-03-04T05:46:34,749   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T05:46:34,749       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T05:46:34,750         | ^~~~~~~~~
2024-03-04T05:46:56,665   creating build/lib.linux-armv7l-cpython-311
2024-03-04T05:46:56,666   creating build/lib.linux-armv7l-cpython-311/uta_align
2024-03-04T05:46:56,666   creating build/lib.linux-armv7l-cpython-311/uta_align/align
2024-03-04T05:46:56,667   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/uta_align/align/algorithms.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/uta_align/align/algorithms.cpython-311-arm-linux-gnueabihf.so
2024-03-04T05:46:56,801   building 'uta_align.align.cigar_utils' extension
2024-03-04T05:46:56,802   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c uta_align/align/cigar_utils.c -o build/temp.linux-armv7l-cpython-311/uta_align/align/cigar_utils.o
2024-03-04T05:46:57,362   In file included from /usr/include/python3.11/Python.h:74,
2024-03-04T05:46:57,362                    from uta_align/align/cigar_utils.c:47:
2024-03-04T05:46:57,363   uta_align/align/cigar_utils.c: In function ‘__pyx_f_9uta_align_5align_11cigar_utils_13CigarSequence__extend_from_cigar_slice’:
2024-03-04T05:46:57,365   uta_align/align/cigar_utils.c:8829:37: warning: passing argument 1 of ‘PySlice_Unpack’ from incompatible pointer type [-Wincompatible-pointer-types]
2024-03-04T05:46:57,366    8829 |   __pyx_t_1 = PySlice_GetIndicesEx(((PySliceObject *)__pyx_v_sliceobj), __pyx_v_other->cigar_len, (&__pyx_v_start), (&__pyx_v_stop), (&__pyx_v_step), (&__pyx_v_slicelen)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 222, __pyx_L1_error)
2024-03-04T05:46:57,367   /usr/include/python3.11/sliceobject.h:51:21: note: in definition of macro ‘PySlice_GetIndicesEx’
2024-03-04T05:46:57,367      51 |     PySlice_Unpack((slice), (start), (stop), (step)) < 0 ?                  \
2024-03-04T05:46:57,368         |                     ^~~~~
2024-03-04T05:46:57,369   /usr/include/python3.11/sliceobject.h:55:42: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘PySliceObject *’
2024-03-04T05:46:57,370      55 | PyAPI_FUNC(int) PySlice_Unpack(PyObject *slice,
2024-03-04T05:46:57,371         |                                ~~~~~~~~~~^~~~~
2024-03-04T05:46:57,382   uta_align/align/cigar_utils.c: In function ‘__pyx_f_9uta_align_5align_11cigar_utils_13CigarSequence__alloc_buf’:
2024-03-04T05:46:57,390   uta_align/align/cigar_utils.c:9760:44: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2024-03-04T05:46:57,391    9760 |   __pyx_t_1 = (__pyx_v_self->cigar_buf_len < __pyx_v_n);
2024-03-04T05:46:57,392         |                                            ^
2024-03-04T05:46:57,395   uta_align/align/cigar_utils.c: In function ‘__pyx_pf_9uta_align_5align_11cigar_utils_13CigarSequence_6__contains__’:
2024-03-04T05:46:57,404   uta_align/align/cigar_utils.c:10227:62: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2024-03-04T05:46:57,405   10227 |     __pyx_t_6 = (((__pyx_v_self->cigar_buf[__pyx_v_i]) & 15) == __pyx_v_op);
2024-03-04T05:46:57,405         |                                                              ^~
2024-03-04T05:46:57,410   uta_align/align/cigar_utils.c: In function ‘__pyx_f_9uta_align_5align_11cigar_utils_13CigarSequence_count’:
2024-03-04T05:46:57,418   uta_align/align/cigar_utils.c:10399:62: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2024-03-04T05:46:57,419   10399 |     __pyx_t_9 = (((__pyx_v_self->cigar_buf[__pyx_v_i]) & 15) == __pyx_v_op);
2024-03-04T05:46:57,420         |                                                              ^~
2024-03-04T05:46:57,439   uta_align/align/cigar_utils.c: In function ‘__pyx_f_9uta_align_5align_11cigar_utils_13CigarSequence_ref_len’:
2024-03-04T05:46:57,449   uta_align/align/cigar_utils.c:11121:48: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2024-03-04T05:46:57,449   11121 |       __pyx_t_9 = ((__pyx_v_query + __pyx_v_n) >= __pyx_v_query_bases);
2024-03-04T05:46:57,450         |                                                ^~
2024-03-04T05:46:57,459   uta_align/align/cigar_utils.c: In function ‘__pyx_f_9uta_align_5align_11cigar_utils_13CigarSequence_query_len’:
2024-03-04T05:46:57,469   uta_align/align/cigar_utils.c:11614:47: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2024-03-04T05:46:57,470   11614 |       __pyx_t_10 = ((__pyx_v_ref + __pyx_v_n) >= __pyx_v_ref_bases);
2024-03-04T05:46:57,471         |                                               ^~
2024-03-04T05:46:57,586   uta_align/align/cigar_utils.c: In function ‘__pyx_pf_9uta_align_5align_11cigar_utils_13CigarSequence_38to_string’:
2024-03-04T05:46:57,599   uta_align/align/cigar_utils.c:14774:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare]
2024-03-04T05:46:57,599   14774 |   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
2024-03-04T05:46:57,600         |                                 ^
2024-03-04T05:46:57,613   uta_align/align/cigar_utils.c:14823:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare]
2024-03-04T05:46:57,613   14823 |   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
2024-03-04T05:46:57,614         |                                 ^
2024-03-04T05:46:59,033   In file included from /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:4,
2024-03-04T05:46:59,034                    from uta_align/align/cigar_utils.c:1263:
2024-03-04T05:46:59,034   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h: At top level:
2024-03-04T05:46:59,035   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:190:19: warning: ‘kseq_read’ defined but not used [-Wunused-function]
2024-03-04T05:46:59,036     190 |         SCOPE int kseq_read(kseq_t *seq) \
2024-03-04T05:46:59,036         |                   ^~~~~~~~~
2024-03-04T05:46:59,037   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:244:9: note: in expansion of macro ‘__KSEQ_READ’
2024-03-04T05:46:59,037     244 |         __KSEQ_READ(SCOPE)
2024-03-04T05:46:59,038         |         ^~~~~~~~~~~
2024-03-04T05:46:59,038   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T05:46:59,039     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T05:46:59,039         |                                   ^~~~~~~~~~
2024-03-04T05:46:59,040   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T05:46:59,040       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T05:46:59,041         | ^~~~~~~~~
2024-03-04T05:46:59,041   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:174:20: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
2024-03-04T05:46:59,042     174 |         SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
2024-03-04T05:46:59,042         |                    ^~~~~~~~~~~~
2024-03-04T05:46:59,043   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:243:9: note: in expansion of macro ‘__KSEQ_BASIC’
2024-03-04T05:46:59,044     243 |         __KSEQ_BASIC(SCOPE, type_t)                                     \
2024-03-04T05:46:59,045         |         ^~~~~~~~~~~~
2024-03-04T05:46:59,045   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T05:46:59,046     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T05:46:59,047         |                                   ^~~~~~~~~~
2024-03-04T05:46:59,048   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T05:46:59,049       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T05:46:59,050         | ^~~~~~~~~
2024-03-04T05:46:59,051   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:168:23: warning: ‘kseq_init’ defined but not used [-Wunused-function]
2024-03-04T05:46:59,052     168 |         SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
2024-03-04T05:46:59,053         |                       ^~~~~~~~~
2024-03-04T05:46:59,053   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:243:9: note: in expansion of macro ‘__KSEQ_BASIC’
2024-03-04T05:46:59,054     243 |         __KSEQ_BASIC(SCOPE, type_t)                                     \
2024-03-04T05:46:59,055         |         ^~~~~~~~~~~~
2024-03-04T05:46:59,055   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T05:46:59,056     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T05:46:59,057         |                                   ^~~~~~~~~~
2024-03-04T05:46:59,058   /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T05:46:59,058       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T05:46:59,059         | ^~~~~~~~~
2024-03-04T05:47:20,467   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/uta_align/align/cigar_utils.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/uta_align/align/cigar_utils.cpython-311-arm-linux-gnueabihf.so
2024-03-04T05:47:20,618   installing to build/bdist.linux-armv7l/wheel
2024-03-04T05:47:20,618   running install
2024-03-04T05:47:20,642   running install_lib
2024-03-04T05:47:20,654   creating build/bdist.linux-armv7l
2024-03-04T05:47:20,654   creating build/bdist.linux-armv7l/wheel
2024-03-04T05:47:20,656   creating build/bdist.linux-armv7l/wheel/uta_align
2024-03-04T05:47:20,657   creating build/bdist.linux-armv7l/wheel/uta_align/align
2024-03-04T05:47:20,658   copying build/lib.linux-armv7l-cpython-311/uta_align/align/algorithms.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/uta_align/align
2024-03-04T05:47:20,673   copying build/lib.linux-armv7l-cpython-311/uta_align/align/cigar_utils.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/uta_align/align
2024-03-04T05:47:20,690   running install_egg_info
2024-03-04T05:47:20,705   running egg_info
2024-03-04T05:47:20,714   writing uta_align.egg-info/PKG-INFO
2024-03-04T05:47:20,719   writing dependency_links to uta_align.egg-info/dependency_links.txt
2024-03-04T05:47:20,722   writing requirements to uta_align.egg-info/requires.txt
2024-03-04T05:47:20,723   writing top-level names to uta_align.egg-info/top_level.txt
2024-03-04T05:47:20,728   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/htslib_util.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,728   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/bgzf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,729   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/cram.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,729   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/faidx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,730   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/hfile.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,730   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/hts.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,731   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kstring.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,731   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/sam.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,732   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/tbx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,732   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/vcf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,733   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/vcfutils.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,734   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,735   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/htslib_util.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,735   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/bgzf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,735   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/cram.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,736   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/faidx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,736   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/hfile.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,737   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/hts.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,737   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/kstring.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,738   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/sam.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,738   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/tbx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,739   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/vcf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,740   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib/htslib/vcfutils.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,740   dependency /tmp/pip-build-env-h239wsj9/overlay/local/lib/python3.11/dist-packages/pysam/pysam_stream.h won't be automatically included in the manifest: the path must be relative
2024-03-04T05:47:20,766   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2024-03-04T05:47:20,770   reading manifest file 'uta_align.egg-info/SOURCES.txt'
2024-03-04T05:47:20,775   adding license file 'LICENSE.txt'
2024-03-04T05:47:20,777   writing manifest file 'uta_align.egg-info/SOURCES.txt'
2024-03-04T05:47:20,779   Copying uta_align.egg-info to build/bdist.linux-armv7l/wheel/uta_align-0.3.0a0-py3.11.egg-info
2024-03-04T05:47:20,788   running install_scripts
2024-03-04T05:47:20,833   creating build/bdist.linux-armv7l/wheel/uta_align-0.3.0a0.dist-info/WHEEL
2024-03-04T05:47:20,836   creating '/tmp/pip-wheel-bo4s24f0/.tmp-z27xzq12/uta_align-0.3.0a0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-03-04T05:47:21,012   adding 'uta_align/align/algorithms.cpython-311-arm-linux-gnueabihf.so'
2024-03-04T05:47:21,190   adding 'uta_align/align/cigar_utils.cpython-311-arm-linux-gnueabihf.so'
2024-03-04T05:47:21,199   adding 'uta_align-0.3.0a0.dist-info/LICENSE.txt'
2024-03-04T05:47:21,200   adding 'uta_align-0.3.0a0.dist-info/METADATA'
2024-03-04T05:47:21,201   adding 'uta_align-0.3.0a0.dist-info/WHEEL'
2024-03-04T05:47:21,202   adding 'uta_align-0.3.0a0.dist-info/top_level.txt'
2024-03-04T05:47:21,203   adding 'uta_align-0.3.0a0.dist-info/RECORD'
2024-03-04T05:47:21,216   removing build/bdist.linux-armv7l/wheel
2024-03-04T05:47:21,373   Building wheel for uta-align (pyproject.toml): finished with status 'done'
2024-03-04T05:47:21,391   Created wheel for uta-align: filename=uta_align-0.3.0a0-cp311-cp311-linux_armv7l.whl size=704034 sha256=fc65db985e03837e737b03c0a36b910e0cec18b21b731f3a33e84a74149707db
2024-03-04T05:47:21,392   Stored in directory: /tmp/pip-ephem-wheel-cache-ofm9xo93/wheels/55/33/6c/405e2b71c997645c87bcc7aea0eadaf68473c737c3656bd0eb
2024-03-04T05:47:21,402 Successfully built uta-align
2024-03-04T05:47:21,421 Removed build tracker: '/tmp/pip-build-tracker-prrqt6fj'