2024-03-04T07:52:48,301 Created temporary directory: /tmp/pip-build-tracker-d_9svb51
2024-03-04T07:52:48,303 Initialized build tracking at /tmp/pip-build-tracker-d_9svb51
2024-03-04T07:52:48,303 Created build tracker: /tmp/pip-build-tracker-d_9svb51
2024-03-04T07:52:48,303 Entered build tracker: /tmp/pip-build-tracker-d_9svb51
2024-03-04T07:52:48,304 Created temporary directory: /tmp/pip-wheel-h03auc_5
2024-03-04T07:52:48,308 Created temporary directory: /tmp/pip-ephem-wheel-cache-7ytk5pqg
2024-03-04T07:52:48,331 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-03-04T07:52:48,335 2 location(s) to search for versions of uta-align:
2024-03-04T07:52:48,335 * https://pypi.org/simple/uta-align/
2024-03-04T07:52:48,335 * https://www.piwheels.org/simple/uta-align/
2024-03-04T07:52:48,336 Fetching project page and analyzing links: https://pypi.org/simple/uta-align/
2024-03-04T07:52:48,336 Getting page https://pypi.org/simple/uta-align/
2024-03-04T07:52:48,338 Found index url https://pypi.org/simple/
2024-03-04T07:52:48,388 Fetched page https://pypi.org/simple/uta-align/ as application/vnd.pypi.simple.v1+json
2024-03-04T07:52:48,394   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
2024-03-04T07:52:48,394   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/)
2024-03-04T07:52:48,394   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
2024-03-04T07:52:48,395   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/)
2024-03-04T07:52:48,395   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
2024-03-04T07:52:48,395   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/)
2024-03-04T07:52:48,395   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/)
2024-03-04T07:52:48,396   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
2024-03-04T07:52:48,396   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/)
2024-03-04T07:52:48,396   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
2024-03-04T07:52:48,396   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/)
2024-03-04T07:52:48,397   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
2024-03-04T07:52:48,397   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/)
2024-03-04T07:52:48,397   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
2024-03-04T07:52:48,397   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/)
2024-03-04T07:52:48,398   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
2024-03-04T07:52:48,398   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/)
2024-03-04T07:52:48,398   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
2024-03-04T07:52:48,398   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/)
2024-03-04T07:52:48,399   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
2024-03-04T07:52:48,399   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/)
2024-03-04T07:52:48,399   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/)
2024-03-04T07:52:48,399   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
2024-03-04T07:52:48,400   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
2024-03-04T07:52:48,400   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
2024-03-04T07:52:48,400   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
2024-03-04T07:52:48,400   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
2024-03-04T07:52:48,401 Fetching project page and analyzing links: https://www.piwheels.org/simple/uta-align/
2024-03-04T07:52:48,401 Getting page https://www.piwheels.org/simple/uta-align/
2024-03-04T07:52:48,402 Found index url https://www.piwheels.org/simple/
2024-03-04T07:52:48,588 Fetched page https://www.piwheels.org/simple/uta-align/ as text/html
2024-03-04T07:52:48,597   Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.3.0a0-cp311-cp311-linux_armv6l.whl#sha256=fc65db985e03837e737b03c0a36b910e0cec18b21b731f3a33e84a74149707db (from https://www.piwheels.org/simple/uta-align/)
2024-03-04T07:52:48,597   Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.3.0a0-cp311-cp311-linux_armv7l.whl#sha256=fc65db985e03837e737b03c0a36b910e0cec18b21b731f3a33e84a74149707db (from https://www.piwheels.org/simple/uta-align/)
2024-03-04T07:52:48,598   Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.3.0a0-cp37-cp37m-linux_armv6l.whl#sha256=364a1ba4e603e17e767fccc392bfb7aef78095000a7b7ab28227147010441d34 (from https://www.piwheels.org/simple/uta-align/)
2024-03-04T07:52:48,598   Skipping link: No binaries permitted for uta-align: https://www.piwheels.org/simple/uta-align/uta_align-0.3.0a0-cp37-cp37m-linux_armv7l.whl#sha256=364a1ba4e603e17e767fccc392bfb7aef78095000a7b7ab28227147010441d34 (from https://www.piwheels.org/simple/uta-align/)
2024-03-04T07:52:48,598   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/)
2024-03-04T07:52:48,598   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/)
2024-03-04T07:52:48,598   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/)
2024-03-04T07:52:48,599   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/)
2024-03-04T07:52:48,599   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/)
2024-03-04T07:52:48,599   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/)
2024-03-04T07:52:48,599   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/)
2024-03-04T07:52:48,599   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/)
2024-03-04T07:52:48,599   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/)
2024-03-04T07:52:48,600   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/)
2024-03-04T07:52:48,600   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/)
2024-03-04T07:52:48,600   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/)
2024-03-04T07:52:48,600   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/)
2024-03-04T07:52:48,601   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/)
2024-03-04T07:52:48,601   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/)
2024-03-04T07:52:48,601   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/)
2024-03-04T07:52:48,601   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/)
2024-03-04T07:52:48,601   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/)
2024-03-04T07:52:48,602   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/)
2024-03-04T07:52:48,602   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/)
2024-03-04T07:52:48,602   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/)
2024-03-04T07:52:48,602   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/)
2024-03-04T07:52:48,602   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/)
2024-03-04T07:52:48,602   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/)
2024-03-04T07:52:48,603   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/)
2024-03-04T07:52:48,603   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/)
2024-03-04T07:52:48,603 Skipping link: not a file: https://www.piwheels.org/simple/uta-align/
2024-03-04T07:52:48,603 Skipping link: not a file: https://pypi.org/simple/uta-align/
2024-03-04T07:52:48,623 Given no hashes to check 1 links for project 'uta-align': discarding no candidates
2024-03-04T07:52:48,639 Collecting uta-align==0.3.0a0
2024-03-04T07:52:48,641   Created temporary directory: /tmp/pip-unpack-fpzxdyay
2024-03-04T07:52:48,692   Downloading uta-align-0.3.0a0.tar.gz (335 kB)
2024-03-04T07:52:48,963   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-d_9svb51'
2024-03-04T07:52:48,972   Created temporary directory: /tmp/pip-build-env-xm0e3hgj
2024-03-04T07:52:48,982   Installing build dependencies: started
2024-03-04T07:52:48,983   Running command pip subprocess to install build dependencies
2024-03-04T07:52:50,159   Using pip 23.3.1 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9)
2024-03-04T07:52:50,711   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-03-04T07:52:52,284   Collecting cython>=0.29
2024-03-04T07:52:52,286     Obtaining dependency information for cython>=0.29 from https://files.pythonhosted.org/packages/e3/7f/f584f5d15323feb897d42ef0e9d910649e2150d7a30cf7e7a8cc1d236e6f/Cython-3.0.8-py2.py3-none-any.whl.metadata
2024-03-04T07:52:52,299     Using cached Cython-3.0.8-py2.py3-none-any.whl.metadata (3.2 kB)
2024-03-04T07:52:52,375   Collecting cython-setuptools
2024-03-04T07:52:52,389     Downloading https://www.piwheels.org/simple/cython-setuptools/cython_setuptools-0.2.3-py3-none-any.whl (9.7 kB)
2024-03-04T07:52:52,680   Collecting pysam>=0.15
2024-03-04T07:52:52,727     Downloading https://www.piwheels.org/simple/pysam/pysam-0.22.0-cp39-cp39-linux_armv7l.whl (17.5 MB)
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2024-03-04T07:53:11,562   Collecting setuptools>=45
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2024-03-04T07:53:12,000   Collecting setuptools_scm
2024-03-04T07:53:12,018     Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-8.0.4-py3-none-any.whl (42 kB)
2024-03-04T07:53:12,685   Collecting tox
2024-03-04T07:53:12,727     Using cached https://www.piwheels.org/simple/tox/tox-4.13.0-py3-none-any.whl (155 kB)
2024-03-04T07:53:12,968   Collecting wheel
2024-03-04T07:53:12,995     Using cached https://www.piwheels.org/simple/wheel/wheel-0.42.0-py3-none-any.whl (65 kB)
2024-03-04T07:53:13,204   Collecting click (from cython-setuptools)
2024-03-04T07:53:13,248     Using cached https://www.piwheels.org/simple/click/click-8.1.7-py3-none-any.whl (97 kB)
2024-03-04T07:53:13,648   Collecting packaging>=20 (from setuptools_scm)
2024-03-04T07:53:13,665     Using cached https://www.piwheels.org/simple/packaging/packaging-23.2-py3-none-any.whl (53 kB)
2024-03-04T07:53:13,798   Collecting typing-extensions (from setuptools_scm)
2024-03-04T07:53:13,833     Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.10.0-py3-none-any.whl (33 kB)
2024-03-04T07:53:14,072   Collecting tomli>=1 (from setuptools_scm)
2024-03-04T07:53:14,129     Using cached https://www.piwheels.org/simple/tomli/tomli-2.0.1-py3-none-any.whl (12 kB)
2024-03-04T07:53:14,509   Collecting cachetools>=5.3.2 (from tox)
2024-03-04T07:53:14,523     Downloading https://www.piwheels.org/simple/cachetools/cachetools-5.3.3-py3-none-any.whl (9.3 kB)
2024-03-04T07:53:14,670   Collecting chardet>=5.2 (from tox)
2024-03-04T07:53:14,690     Using cached https://www.piwheels.org/simple/chardet/chardet-5.2.0-py3-none-any.whl (199 kB)
2024-03-04T07:53:14,859   Collecting colorama>=0.4.6 (from tox)
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2024-03-04T07:53:15,082   Collecting filelock>=3.13.1 (from tox)
2024-03-04T07:53:15,112     Using cached https://www.piwheels.org/simple/filelock/filelock-3.13.1-py3-none-any.whl (11 kB)
2024-03-04T07:53:15,322   Collecting platformdirs>=4.1 (from tox)
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2024-03-04T07:53:15,506   Collecting pluggy>=1.3 (from tox)
2024-03-04T07:53:15,534     Using cached https://www.piwheels.org/simple/pluggy/pluggy-1.4.0-py3-none-any.whl (20 kB)
2024-03-04T07:53:15,655   Collecting pyproject-api>=1.6.1 (from tox)
2024-03-04T07:53:15,677     Using cached https://www.piwheels.org/simple/pyproject-api/pyproject_api-1.6.1-py3-none-any.whl (12 kB)
2024-03-04T07:53:16,383   Collecting virtualenv>=20.25 (from tox)
2024-03-04T07:53:16,412     Using cached https://www.piwheels.org/simple/virtualenv/virtualenv-20.25.1-py3-none-any.whl (3.8 MB)
2024-03-04T07:53:17,269   Collecting distlib<1,>=0.3.7 (from virtualenv>=20.25->tox)
2024-03-04T07:53:17,287     Using cached https://www.piwheels.org/simple/distlib/distlib-0.3.8-py2.py3-none-any.whl (468 kB)
2024-03-04T07:53:17,439   Using cached Cython-3.0.8-py2.py3-none-any.whl (1.2 MB)
2024-03-04T07:53:19,533   Installing collected packages: distlib, wheel, typing-extensions, tomli, setuptools, pysam, pluggy, platformdirs, packaging, filelock, cython, colorama, click, chardet, cachetools, virtualenv, setuptools_scm, pyproject-api, cython-setuptools, tox
2024-03-04T07:53:20,121     Creating /tmp/pip-build-env-xm0e3hgj/overlay/bin
2024-03-04T07:53:20,124     changing mode of /tmp/pip-build-env-xm0e3hgj/overlay/bin/wheel to 755
2024-03-04T07:53:30,073     changing mode of /tmp/pip-build-env-xm0e3hgj/overlay/bin/cygdb to 755
2024-03-04T07:53:30,076     changing mode of /tmp/pip-build-env-xm0e3hgj/overlay/bin/cython to 755
2024-03-04T07:53:30,078     changing mode of /tmp/pip-build-env-xm0e3hgj/overlay/bin/cythonize to 755
2024-03-04T07:53:31,179     changing mode of /tmp/pip-build-env-xm0e3hgj/overlay/bin/chardetect to 755
2024-03-04T07:53:32,114     changing mode of /tmp/pip-build-env-xm0e3hgj/overlay/bin/virtualenv to 755
2024-03-04T07:53:32,566     changing mode of /tmp/pip-build-env-xm0e3hgj/overlay/bin/cython-setuptools to 755
2024-03-04T07:53:33,313     changing mode of /tmp/pip-build-env-xm0e3hgj/overlay/bin/tox to 755
2024-03-04T07:53:33,357   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 tomli-2.0.1 tox-4.13.0 typing-extensions-4.10.0 virtualenv-20.25.1 wheel-0.42.0

2024-03-04T07:53:33,552   [notice] A new release of pip is available: 23.3.1 -> 24.0
2024-03-04T07:53:33,552   [notice] To update, run: python3 -m pip install --upgrade pip
2024-03-04T07:53:34,060   Installing build dependencies: finished with status 'done'
2024-03-04T07:53:34,064   Getting requirements to build wheel: started
2024-03-04T07:53:34,065   Running command Getting requirements to build wheel
2024-03-04T07:53:50,361   Compiling uta_align/align/algorithms.pyx because it depends on /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/Cython/Includes/posix/types.pxd.
2024-03-04T07:53:50,362   Compiling uta_align/align/cigar_utils.pyx because it depends on /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/Cython/Includes/posix/types.pxd.
2024-03-04T07:53:50,362   [1/2] Cythonizing uta_align/align/algorithms.pyx
2024-03-04T07:53:50,362   [2/2] Cythonizing uta_align/align/cigar_utils.pyx
2024-03-04T07:53:51,015   Getting requirements to build wheel: finished with status 'done'
2024-03-04T07:53:51,083   Created temporary directory: /tmp/pip-modern-metadata-2000vesf
2024-03-04T07:53:51,086   Preparing metadata (pyproject.toml): started
2024-03-04T07:53:51,087   Running command Preparing metadata (pyproject.toml)
2024-03-04T07:53:53,269   WARNING setuptools_scm._integration.setuptools pyproject.toml does not contain a tool.setuptools_scm section
2024-03-04T07:53:53,281   WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
2024-03-04T07:53:53,392   running dist_info
2024-03-04T07:53:53,425   creating /tmp/pip-modern-metadata-2000vesf/uta_align.egg-info
2024-03-04T07:53:53,435   writing /tmp/pip-modern-metadata-2000vesf/uta_align.egg-info/PKG-INFO
2024-03-04T07:53:53,442   writing dependency_links to /tmp/pip-modern-metadata-2000vesf/uta_align.egg-info/dependency_links.txt
2024-03-04T07:53:53,447   writing requirements to /tmp/pip-modern-metadata-2000vesf/uta_align.egg-info/requires.txt
2024-03-04T07:53:53,448   writing top-level names to /tmp/pip-modern-metadata-2000vesf/uta_align.egg-info/top_level.txt
2024-03-04T07:53:53,450   writing manifest file '/tmp/pip-modern-metadata-2000vesf/uta_align.egg-info/SOURCES.txt'
2024-03-04T07:53:53,486   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/htslib_util.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,487   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/bgzf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,487   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/cram.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,487   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/faidx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,487   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/hfile.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,487   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/hts.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,488   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kstring.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,488   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/sam.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,488   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/tbx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,488   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,488   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcfutils.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,488   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,488   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/htslib_util.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,488   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/bgzf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,489   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/cram.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,489   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/faidx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,489   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/hfile.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,489   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/hts.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,489   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kstring.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,489   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/sam.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,489   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/tbx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,490   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,490   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcfutils.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,490   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:53:53,535   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2024-03-04T07:53:53,547   reading manifest file '/tmp/pip-modern-metadata-2000vesf/uta_align.egg-info/SOURCES.txt'
2024-03-04T07:53:53,550   adding license file 'LICENSE.txt'
2024-03-04T07:53:53,552   writing manifest file '/tmp/pip-modern-metadata-2000vesf/uta_align.egg-info/SOURCES.txt'
2024-03-04T07:53:53,553   creating '/tmp/pip-modern-metadata-2000vesf/uta_align-0.3.0a0.dist-info'
2024-03-04T07:53:53,781   Preparing metadata (pyproject.toml): finished with status 'done'
2024-03-04T07:53:53,787   Source in /tmp/pip-wheel-h03auc_5/uta-align_51c324d0e90e468c920735fda25f23d3 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
2024-03-04T07:53:53,788   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-d_9svb51'
2024-03-04T07:53:53,792 Created temporary directory: /tmp/pip-unpack-mdp0bw4k
2024-03-04T07:53:53,793 Created temporary directory: /tmp/pip-unpack-2lbyo87b
2024-03-04T07:53:53,823 Building wheels for collected packages: uta-align
2024-03-04T07:53:53,827   Created temporary directory: /tmp/pip-wheel-44jyhqnx
2024-03-04T07:53:53,827   Destination directory: /tmp/pip-wheel-44jyhqnx
2024-03-04T07:53:53,829   Building wheel for uta-align (pyproject.toml): started
2024-03-04T07:53:53,830   Running command Building wheel for uta-align (pyproject.toml)
2024-03-04T07:53:55,860   WARNING setuptools_scm._integration.setuptools pyproject.toml does not contain a tool.setuptools_scm section
2024-03-04T07:53:55,872   WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
2024-03-04T07:53:56,017   running bdist_wheel
2024-03-04T07:53:56,086   running build
2024-03-04T07:53:56,086   running build_ext
2024-03-04T07:53:56,093   building 'uta_align.align.algorithms' extension
2024-03-04T07:53:56,093   creating build
2024-03-04T07:53:56,094   creating build/temp.linux-armv7l-cpython-39
2024-03-04T07:53:56,094   creating build/temp.linux-armv7l-cpython-39/uta_align
2024-03-04T07:53:56,095   creating build/temp.linux-armv7l-cpython-39/uta_align/align
2024-03-04T07:53:56,096   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam -I/tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib -I/tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/samtools -I/usr/include/python3.9 -c uta_align/align/algorithms.c -o build/temp.linux-armv7l-cpython-39/uta_align/align/algorithms.o
2024-03-04T07:53:56,674   uta_align/align/algorithms.c: In function ‘__pyx_pf_9uta_align_5align_10algorithms_8needleman_wunsch_altshul_erikson’:
2024-03-04T07:53:56,681   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]
2024-03-04T07:53:56,681   15310 |   for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
2024-03-04T07:53:56,682         |                                 ^
2024-03-04T07:53:56,689   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]
2024-03-04T07:53:56,689   15347 |     __pyx_t_6 = (__pyx_v_j < __pyx_v_m);
2024-03-04T07:53:56,689         |                            ^
2024-03-04T07:53:56,696   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]
2024-03-04T07:53:56,697   15379 |   for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
2024-03-04T07:53:56,697         |                                 ^
2024-03-04T07:53:56,704   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]
2024-03-04T07:53:56,704   15462 |     __pyx_t_6 = (__pyx_v_i < __pyx_v_n);
2024-03-04T07:53:56,704         |                            ^
2024-03-04T07:53:56,712   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]
2024-03-04T07:53:56,712   15493 |     for (__pyx_t_7 = 1; __pyx_t_7 < __pyx_t_9; __pyx_t_7+=1) {
2024-03-04T07:53:56,712         |                                   ^
2024-03-04T07:53:57,606   In file included from /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h:4,
2024-03-04T07:53:57,606                    from uta_align/align/algorithms.c:1264:
2024-03-04T07:53:57,606   At top level:
2024-03-04T07:53:57,607   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:190:12: warning: ‘kseq_read’ defined but not used [-Wunused-function]
2024-03-04T07:53:57,607     190 |  SCOPE int kseq_read(kseq_t *seq) \
2024-03-04T07:53:57,607         |            ^~~~~~~~~
2024-03-04T07:53:57,607   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:244:2: note: in expansion of macro ‘__KSEQ_READ’
2024-03-04T07:53:57,607     244 |  __KSEQ_READ(SCOPE)
2024-03-04T07:53:57,607         |  ^~~~~~~~~~~
2024-03-04T07:53:57,608   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T07:53:57,608     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T07:53:57,608         |                                   ^~~~~~~~~~
2024-03-04T07:53:57,608   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T07:53:57,608       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T07:53:57,608         | ^~~~~~~~~
2024-03-04T07:53:57,609   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:174:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
2024-03-04T07:53:57,609     174 |  SCOPE void kseq_destroy(kseq_t *ks)         \
2024-03-04T07:53:57,609         |             ^~~~~~~~~~~~
2024-03-04T07:53:57,609   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:243:2: note: in expansion of macro ‘__KSEQ_BASIC’
2024-03-04T07:53:57,609     243 |  __KSEQ_BASIC(SCOPE, type_t)     \
2024-03-04T07:53:57,609         |  ^~~~~~~~~~~~
2024-03-04T07:53:57,609   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T07:53:57,610     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T07:53:57,610         |                                   ^~~~~~~~~~
2024-03-04T07:53:57,610   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T07:53:57,610       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T07:53:57,610         | ^~~~~~~~~
2024-03-04T07:53:57,610   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:168:16: warning: ‘kseq_init’ defined but not used [-Wunused-function]
2024-03-04T07:53:57,610     168 |  SCOPE kseq_t *kseq_init(type_t fd)         \
2024-03-04T07:53:57,611         |                ^~~~~~~~~
2024-03-04T07:53:57,611   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:243:2: note: in expansion of macro ‘__KSEQ_BASIC’
2024-03-04T07:53:57,611     243 |  __KSEQ_BASIC(SCOPE, type_t)     \
2024-03-04T07:53:57,611         |  ^~~~~~~~~~~~
2024-03-04T07:53:57,611   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T07:53:57,611     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T07:53:57,611         |                                   ^~~~~~~~~~
2024-03-04T07:53:57,612   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T07:53:57,612       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T07:53:57,612         | ^~~~~~~~~
2024-03-04T07:54:17,187   creating build/lib.linux-armv7l-cpython-39
2024-03-04T07:54:17,187   creating build/lib.linux-armv7l-cpython-39/uta_align
2024-03-04T07:54:17,188   creating build/lib.linux-armv7l-cpython-39/uta_align/align
2024-03-04T07:54:17,188   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/uta_align/align/algorithms.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/uta_align/align/algorithms.cpython-39-arm-linux-gnueabihf.so
2024-03-04T07:54:17,351   building 'uta_align.align.cigar_utils' extension
2024-03-04T07:54:17,352   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam -I/tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib -I/tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/samtools -I/usr/include/python3.9 -c uta_align/align/cigar_utils.c -o build/temp.linux-armv7l-cpython-39/uta_align/align/cigar_utils.o
2024-03-04T07:54:17,811   In file included from /usr/include/python3.9/Python.h:120,
2024-03-04T07:54:17,811                    from uta_align/align/cigar_utils.c:47:
2024-03-04T07:54:17,811   uta_align/align/cigar_utils.c: In function ‘__pyx_f_9uta_align_5align_11cigar_utils_13CigarSequence__extend_from_cigar_slice’:
2024-03-04T07:54:17,814   uta_align/align/cigar_utils.c:8829:37: warning: passing argument 1 of ‘PySlice_Unpack’ from incompatible pointer type [-Wincompatible-pointer-types]
2024-03-04T07:54:17,814    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)
2024-03-04T07:54:17,814   /usr/include/python3.9/sliceobject.h:51:21: note: in definition of macro ‘PySlice_GetIndicesEx’
2024-03-04T07:54:17,814      51 |     PySlice_Unpack((slice), (start), (stop), (step)) < 0 ?                  \
2024-03-04T07:54:17,814         |                     ^~~~~
2024-03-04T07:54:17,814   /usr/include/python3.9/sliceobject.h:55:42: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘PySliceObject *’
2024-03-04T07:54:17,815      55 | PyAPI_FUNC(int) PySlice_Unpack(PyObject *slice,
2024-03-04T07:54:17,815         |                                ~~~~~~~~~~^~~~~
2024-03-04T07:54:17,824   uta_align/align/cigar_utils.c: In function ‘__pyx_f_9uta_align_5align_11cigar_utils_13CigarSequence__alloc_buf’:
2024-03-04T07:54:17,829   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]
2024-03-04T07:54:17,829    9760 |   __pyx_t_1 = (__pyx_v_self->cigar_buf_len < __pyx_v_n);
2024-03-04T07:54:17,829         |                                            ^
2024-03-04T07:54:17,832   uta_align/align/cigar_utils.c: In function ‘__pyx_pf_9uta_align_5align_11cigar_utils_13CigarSequence_6__contains__’:
2024-03-04T07:54:17,838   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]
2024-03-04T07:54:17,838   10227 |     __pyx_t_6 = (((__pyx_v_self->cigar_buf[__pyx_v_i]) & 15) == __pyx_v_op);
2024-03-04T07:54:17,838         |                                                              ^~
2024-03-04T07:54:17,843   uta_align/align/cigar_utils.c: In function ‘__pyx_f_9uta_align_5align_11cigar_utils_13CigarSequence_count’:
2024-03-04T07:54:17,848   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]
2024-03-04T07:54:17,848   10399 |     __pyx_t_9 = (((__pyx_v_self->cigar_buf[__pyx_v_i]) & 15) == __pyx_v_op);
2024-03-04T07:54:17,849         |                                                              ^~
2024-03-04T07:54:17,866   uta_align/align/cigar_utils.c: In function ‘__pyx_f_9uta_align_5align_11cigar_utils_13CigarSequence_ref_len’:
2024-03-04T07:54:17,872   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]
2024-03-04T07:54:17,872   11121 |       __pyx_t_9 = ((__pyx_v_query + __pyx_v_n) >= __pyx_v_query_bases);
2024-03-04T07:54:17,872         |                                                ^~
2024-03-04T07:54:17,881   uta_align/align/cigar_utils.c: In function ‘__pyx_f_9uta_align_5align_11cigar_utils_13CigarSequence_query_len’:
2024-03-04T07:54:17,887   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]
2024-03-04T07:54:17,887   11614 |       __pyx_t_10 = ((__pyx_v_ref + __pyx_v_n) >= __pyx_v_ref_bases);
2024-03-04T07:54:17,887         |                                               ^~
2024-03-04T07:54:17,973   uta_align/align/cigar_utils.c: In function ‘__pyx_pf_9uta_align_5align_11cigar_utils_13CigarSequence_38to_string’:
2024-03-04T07:54:17,981   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]
2024-03-04T07:54:17,981   14774 |   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
2024-03-04T07:54:17,981         |                                 ^
2024-03-04T07:54:17,990   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]
2024-03-04T07:54:17,990   14823 |   for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
2024-03-04T07:54:17,990         |                                 ^
2024-03-04T07:54:18,953   In file included from /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h:4,
2024-03-04T07:54:18,954                    from uta_align/align/cigar_utils.c:1263:
2024-03-04T07:54:18,954   At top level:
2024-03-04T07:54:18,955   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:190:12: warning: ‘kseq_read’ defined but not used [-Wunused-function]
2024-03-04T07:54:18,955     190 |  SCOPE int kseq_read(kseq_t *seq) \
2024-03-04T07:54:18,955         |            ^~~~~~~~~
2024-03-04T07:54:18,955   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:244:2: note: in expansion of macro ‘__KSEQ_READ’
2024-03-04T07:54:18,955     244 |  __KSEQ_READ(SCOPE)
2024-03-04T07:54:18,955         |  ^~~~~~~~~~~
2024-03-04T07:54:18,956   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T07:54:18,956     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T07:54:18,956         |                                   ^~~~~~~~~~
2024-03-04T07:54:18,956   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T07:54:18,956       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T07:54:18,956         | ^~~~~~~~~
2024-03-04T07:54:18,956   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:174:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function]
2024-03-04T07:54:18,957     174 |  SCOPE void kseq_destroy(kseq_t *ks)         \
2024-03-04T07:54:18,957         |             ^~~~~~~~~~~~
2024-03-04T07:54:18,957   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:243:2: note: in expansion of macro ‘__KSEQ_BASIC’
2024-03-04T07:54:18,957     243 |  __KSEQ_BASIC(SCOPE, type_t)     \
2024-03-04T07:54:18,957         |  ^~~~~~~~~~~~
2024-03-04T07:54:18,957   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T07:54:18,957     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T07:54:18,957         |                                   ^~~~~~~~~~
2024-03-04T07:54:18,958   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T07:54:18,958       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T07:54:18,958         | ^~~~~~~~~
2024-03-04T07:54:18,958   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:168:16: warning: ‘kseq_init’ defined but not used [-Wunused-function]
2024-03-04T07:54:18,958     168 |  SCOPE kseq_t *kseq_init(type_t fd)         \
2024-03-04T07:54:18,958         |                ^~~~~~~~~
2024-03-04T07:54:18,958   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:243:2: note: in expansion of macro ‘__KSEQ_BASIC’
2024-03-04T07:54:18,959     243 |  __KSEQ_BASIC(SCOPE, type_t)     \
2024-03-04T07:54:18,959         |  ^~~~~~~~~~~~
2024-03-04T07:54:18,959   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h:246:35: note: in expansion of macro ‘KSEQ_INIT2’
2024-03-04T07:54:18,959     246 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
2024-03-04T07:54:18,959         |                                   ^~~~~~~~~~
2024-03-04T07:54:18,959   /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h:9:1: note: in expansion of macro ‘KSEQ_INIT’
2024-03-04T07:54:18,959       9 | KSEQ_INIT(BGZF *, bgzf_read)
2024-03-04T07:54:18,959         | ^~~~~~~~~
2024-03-04T07:54:38,516   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/uta_align/align/cigar_utils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/uta_align/align/cigar_utils.cpython-39-arm-linux-gnueabihf.so
2024-03-04T07:54:38,694   installing to build/bdist.linux-armv7l/wheel
2024-03-04T07:54:38,695   running install
2024-03-04T07:54:38,720   running install_lib
2024-03-04T07:54:38,733   creating build/bdist.linux-armv7l
2024-03-04T07:54:38,733   creating build/bdist.linux-armv7l/wheel
2024-03-04T07:54:38,735   creating build/bdist.linux-armv7l/wheel/uta_align
2024-03-04T07:54:38,736   creating build/bdist.linux-armv7l/wheel/uta_align/align
2024-03-04T07:54:38,737   copying build/lib.linux-armv7l-cpython-39/uta_align/align/cigar_utils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/uta_align/align
2024-03-04T07:54:38,760   copying build/lib.linux-armv7l-cpython-39/uta_align/align/algorithms.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/uta_align/align
2024-03-04T07:54:38,786   running install_egg_info
2024-03-04T07:54:38,802   running egg_info
2024-03-04T07:54:38,812   writing uta_align.egg-info/PKG-INFO
2024-03-04T07:54:38,819   writing dependency_links to uta_align.egg-info/dependency_links.txt
2024-03-04T07:54:38,823   writing requirements to uta_align.egg-info/requires.txt
2024-03-04T07:54:38,825   writing top-level names to uta_align.egg-info/top_level.txt
2024-03-04T07:54:38,830   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/htslib_util.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,830   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/bgzf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,831   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/cram.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,831   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/faidx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,832   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/hfile.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,832   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/hts.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,832   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kstring.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,833   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/sam.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,833   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/tbx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,833   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,834   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcfutils.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,834   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,834   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/htslib_util.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,835   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/bgzf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,835   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/cram.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,835   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/faidx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,836   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/hfile.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,836   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/hts.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,836   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/kstring.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,837   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/sam.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,837   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/tbx.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,837   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcf.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,838   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcfutils.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,838   dependency /tmp/pip-build-env-xm0e3hgj/overlay/lib/python3.9/site-packages/pysam/pysam_stream.h won't be automatically included in the manifest: the path must be relative
2024-03-04T07:54:38,879   ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
2024-03-04T07:54:38,891   reading manifest file 'uta_align.egg-info/SOURCES.txt'
2024-03-04T07:54:38,897   adding license file 'LICENSE.txt'
2024-03-04T07:54:38,901   writing manifest file 'uta_align.egg-info/SOURCES.txt'
2024-03-04T07:54:38,903   Copying uta_align.egg-info to build/bdist.linux-armv7l/wheel/uta_align-0.3.0a0-py3.9.egg-info
2024-03-04T07:54:38,912   running install_scripts
2024-03-04T07:54:38,958   creating build/bdist.linux-armv7l/wheel/uta_align-0.3.0a0.dist-info/WHEEL
2024-03-04T07:54:38,962   creating '/tmp/pip-wheel-44jyhqnx/.tmp-p6c60yw2/uta_align-0.3.0a0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-03-04T07:54:39,142   adding 'uta_align/align/algorithms.cpython-39-arm-linux-gnueabihf.so'
2024-03-04T07:54:39,329   adding 'uta_align/align/cigar_utils.cpython-39-arm-linux-gnueabihf.so'
2024-03-04T07:54:39,338   adding 'uta_align-0.3.0a0.dist-info/LICENSE.txt'
2024-03-04T07:54:39,340   adding 'uta_align-0.3.0a0.dist-info/METADATA'
2024-03-04T07:54:39,341   adding 'uta_align-0.3.0a0.dist-info/WHEEL'
2024-03-04T07:54:39,343   adding 'uta_align-0.3.0a0.dist-info/top_level.txt'
2024-03-04T07:54:39,344   adding 'uta_align-0.3.0a0.dist-info/RECORD'
2024-03-04T07:54:39,364   removing build/bdist.linux-armv7l/wheel
2024-03-04T07:54:39,515   Building wheel for uta-align (pyproject.toml): finished with status 'done'
2024-03-04T07:54:39,539   Created wheel for uta-align: filename=uta_align-0.3.0a0-cp39-cp39-linux_armv7l.whl size=670014 sha256=ea88b398d93f9315873ae8e5829936a4ea7757178fe88808b4994bd4f0a84082
2024-03-04T07:54:39,540   Stored in directory: /tmp/pip-ephem-wheel-cache-7ytk5pqg/wheels/f8/1a/94/c3f6eb9efc0936ac51ee0f26f866fb929419111c1a1b1f2498
2024-03-04T07:54:39,553 Successfully built uta-align
2024-03-04T07:54:39,587 Removed build tracker: '/tmp/pip-build-tracker-d_9svb51'