2026-08-17T08:36:14,178 Created temporary directory: /tmp/pip-ephem-wheel-cache-vn2kp1gz 2026-08-17T08:36:14,180 Created temporary directory: /tmp/pip-build-tracker-ex9xvhf5 2026-08-17T08:36:14,180 Initialized build tracking at /tmp/pip-build-tracker-ex9xvhf5 2026-08-17T08:36:14,181 Created build tracker: /tmp/pip-build-tracker-ex9xvhf5 2026-08-17T08:36:14,181 Entered build tracker: /tmp/pip-build-tracker-ex9xvhf5 2026-08-17T08:36:14,182 Created temporary directory: /tmp/pip-wheel-ozhykbd0 2026-08-17T08:36:14,185 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-08-17T08:36:14,187 Created temporary directory: /tmp/pip-ephem-wheel-cache-s4ceadnc 2026-08-17T08:36:14,208 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-17T08:36:14,212 2 location(s) to search for versions of cgat: 2026-08-17T08:36:14,212 * https://pypi.org/simple/cgat/ 2026-08-17T08:36:14,212 * https://www.piwheels.org/simple/cgat/ 2026-08-17T08:36:14,213 Fetching project page and analyzing links: https://pypi.org/simple/cgat/ 2026-08-17T08:36:14,213 Getting page https://pypi.org/simple/cgat/ 2026-08-17T08:36:14,215 Found index url https://pypi.org/simple 2026-08-17T08:36:14,441 Fetched page https://pypi.org/simple/cgat/ as application/vnd.pypi.simple.v1+json 2026-08-17T08:36:14,449 Found link https://files.pythonhosted.org/packages/82/a0/23011460a9548932524dd5b17d18b02e1803b5b638b78503f2b9319837a7/CGAT-0.1.tar.gz (from https://pypi.org/simple/cgat/), version: 0.1 2026-08-17T08:36:14,450 Found link https://files.pythonhosted.org/packages/90/20/9ecc442d1b6d352d72480376b3713a29875b9dbaf0d72bb820e4bfc9bf28/CGAT-0.1.1.tar.gz (from https://pypi.org/simple/cgat/), version: 0.1.1 2026-08-17T08:36:14,451 Found link https://files.pythonhosted.org/packages/e4/fe/5858c1d7f331982f24326b8220a0c54564c069435cce5bde568ceb9b4373/CGAT-0.1.3.tar.gz (from https://pypi.org/simple/cgat/), version: 0.1.3 2026-08-17T08:36:14,451 Found link https://files.pythonhosted.org/packages/96/85/e31f136aab7e0803f82c62e1a9f0dd5d17d873ea3892ec1e4dfc759f7f51/CGAT-0.1.4.tar.gz (from https://pypi.org/simple/cgat/), version: 0.1.4 2026-08-17T08:36:14,452 Found link https://files.pythonhosted.org/packages/ba/e8/1ef67c7be3f57254b74c41b89e6b79112ed7360226d891d15fcc95b95cfd/CGAT-0.1.5.tar.gz (from https://pypi.org/simple/cgat/), version: 0.1.5 2026-08-17T08:36:14,453 Found link https://files.pythonhosted.org/packages/13/ca/99f09c68029bc1cd011c8c946a74fd9b970a40a26bc54eb279bd0f0045c2/CGAT-0.1.6.tar.gz (from https://pypi.org/simple/cgat/), version: 0.1.6 2026-08-17T08:36:14,454 Found link https://files.pythonhosted.org/packages/94/b0/2d158572aa0ec70826ac5805d5fd5a42631dcb8f2ea0d6150dfc41794212/CGAT-0.1.7.tar.gz (from https://pypi.org/simple/cgat/), version: 0.1.7 2026-08-17T08:36:14,455 Found link https://files.pythonhosted.org/packages/c9/96/19787a37483d45b902ce2378bce0ee6ca1c538b253fb0eb28b5b23b7d7a5/CGAT-0.1.8.tar.gz (from https://pypi.org/simple/cgat/), version: 0.1.8 2026-08-17T08:36:14,455 Found link https://files.pythonhosted.org/packages/f2/d1/ca23c8156b4ae13b7b82e02b56055a9cf7a6d3eb38f28c39898da8a5784c/CGAT-0.1.9.tar.gz (from https://pypi.org/simple/cgat/), version: 0.1.9 2026-08-17T08:36:14,456 Found link https://files.pythonhosted.org/packages/c5/97/065fec28bcca210fadaa3be6f1b149922d69bff46ed56debf746355b2372/CGAT-0.2.0.tar.gz (from https://pypi.org/simple/cgat/), version: 0.2.0 2026-08-17T08:36:14,457 Found link https://files.pythonhosted.org/packages/2e/e8/3fe3d5cfb0348a9e13f87f253265a6906f4d41391137506f46c0019af93c/CGAT-0.2.1.tar.gz (from https://pypi.org/simple/cgat/), version: 0.2.1 2026-08-17T08:36:14,458 Found link https://files.pythonhosted.org/packages/d7/dd/870a8ff2404e9786faa3dd3ca8d6ae65d58dc7a6e4470cbd6d08c1646d84/CGAT-0.2.2.tar.gz (from https://pypi.org/simple/cgat/), version: 0.2.2 2026-08-17T08:36:14,458 Found link https://files.pythonhosted.org/packages/f2/f3/b80f5dad0f604ca68840639f5ac64147768b044b8f0797d7bc1fb8d69ba7/CGAT-0.2.3.tar.gz (from https://pypi.org/simple/cgat/), version: 0.2.3 2026-08-17T08:36:14,459 Found link https://files.pythonhosted.org/packages/05/d5/d8deed8eebc26c37a4e463345a137ab5e0d4fa0ac9dc92617bc12f495f43/CGAT-0.2.4.tar.gz (from https://pypi.org/simple/cgat/), version: 0.2.4 2026-08-17T08:36:14,460 Found link https://files.pythonhosted.org/packages/89/75/6a2b039d71228269b1aa918bc640646cb55ad6d047a497c55dc11778ae42/CGAT-0.2.5.tar.gz (from https://pypi.org/simple/cgat/), version: 0.2.5 2026-08-17T08:36:14,460 Found link https://files.pythonhosted.org/packages/fe/86/be2a14843dc272abe33dd0de754e8ba142fc07c3cfe11410be7230d27078/CGAT-0.2.6.tar.gz (from https://pypi.org/simple/cgat/), version: 0.2.6 2026-08-17T08:36:14,461 Found link https://files.pythonhosted.org/packages/a3/ff/e5f2175450e1a362b941d96afd139a4c66ad884765cfe7d7bb7d9a735a95/CGAT-0.2.7.tar.gz (from https://pypi.org/simple/cgat/), version: 0.2.7 2026-08-17T08:36:14,461 Found link https://files.pythonhosted.org/packages/ba/39/a13ca9d92ef0caf2852617fff6ebdb8e83697bb1a2e61fb9dc4608f5e4f9/CGAT-0.3.0.tar.gz (from https://pypi.org/simple/cgat/), version: 0.3.0 2026-08-17T08:36:14,462 Found link https://files.pythonhosted.org/packages/4a/4e/775ffc1bf3c9a7e13ffd22ce69cb9d61826c69855f0523225977f9884bdc/CGAT-0.3.1.tar.gz (from https://pypi.org/simple/cgat/), version: 0.3.1 2026-08-17T08:36:14,463 Found link https://files.pythonhosted.org/packages/88/19/c19e9e16c3b8e19f05381c780f3583eae2982c91c163ee8e2aa3311eec7e/CGAT-0.3.2.tar.gz (from https://pypi.org/simple/cgat/), version: 0.3.2 2026-08-17T08:36:14,463 Found link https://files.pythonhosted.org/packages/af/31/d29170e58d6fc06571753b9b54f6aad686a376d310e87b0810099e8bbbac/CGAT-0.3.3.tar.gz (from https://pypi.org/simple/cgat/), version: 0.3.3 2026-08-17T08:36:14,464 Found link https://files.pythonhosted.org/packages/46/9f/4131b77f952d136662feba4cdc9562115f3eddf2dddf6cbc2bb7c0f3299c/cgat-0.5.1.tar.gz (from https://pypi.org/simple/cgat/), version: 0.5.1 2026-08-17T08:36:14,465 Found link https://files.pythonhosted.org/packages/9e/8e/83ff5d238ac6bc75be300a50bcfbb64ebe77d90b053ef094db1af962abda/cgat-0.5.2.tar.gz (from https://pypi.org/simple/cgat/), version: 0.5.2 2026-08-17T08:36:14,465 Found link https://files.pythonhosted.org/packages/d7/05/6518cd6bf64bc0d15f474ea707979b8a47d502b2ee7c043d3a5e33f602c9/cgat-0.5.3.tar.gz (from https://pypi.org/simple/cgat/), version: 0.5.3 2026-08-17T08:36:14,466 Found link https://files.pythonhosted.org/packages/b6/58/4a88bde62300df47727a502c91b91a1e5d3399c4f72715c3a802bcd19faa/cgat-0.5.4.tar.gz (from https://pypi.org/simple/cgat/), version: 0.5.4 2026-08-17T08:36:14,467 Found link https://files.pythonhosted.org/packages/dc/54/bce4257afde6befa7728b1911c1b2499b8a6edbc51e5ab6bca7d7c5dd70a/cgat-0.5.5.tar.gz (from https://pypi.org/simple/cgat/), version: 0.5.5 2026-08-17T08:36:14,468 Found link https://files.pythonhosted.org/packages/c6/30/6c6b3d2820998a407c14b540e0b656de4177d36cb427ffe1ac8bb90c2e82/cgat-0.5.6.tar.gz (from https://pypi.org/simple/cgat/), version: 0.5.6 2026-08-17T08:36:14,468 Found link https://files.pythonhosted.org/packages/0e/10/ebbb6959f3d636e59a3572e3f864dacf9f89246406bf962baf17e041da8b/cgat-0.6.0.tar.gz (from https://pypi.org/simple/cgat/), version: 0.6.0 2026-08-17T08:36:14,469 Found link https://files.pythonhosted.org/packages/c9/4c/0883d231913824036e12e6285f27632973b3a37e6f1e2131df843a66fe67/cgat-0.6.2.tar.gz (from https://pypi.org/simple/cgat/), version: 0.6.2 2026-08-17T08:36:14,470 Found link https://files.pythonhosted.org/packages/8f/54/f60bc2a2fafe1f80e95537255d184abf7ddf10e3ea32ec825d9dbd856c68/cgat-0.6.3.tar.gz (from https://pypi.org/simple/cgat/), version: 0.6.3 2026-08-17T08:36:14,470 Found link https://files.pythonhosted.org/packages/97/88/3c7b98b4c6db4d539d8807416c0aad0fed4e2967ef02adef5e9422073581/cgat-0.6.4.tar.gz (from https://pypi.org/simple/cgat/), version: 0.6.4 2026-08-17T08:36:14,471 Found link https://files.pythonhosted.org/packages/3f/a8/9a48c094a91bc3ce135636a8680246d017acb366fe7ee50acdbec071ad53/cgat-0.6.5.tar.gz (from https://pypi.org/simple/cgat/), version: 0.6.5 2026-08-17T08:36:14,472 Found link https://files.pythonhosted.org/packages/48/d6/a2b30b119fa7e1ee3132a8b327e6295f7672e0fa596560a89f4eabf35404/cgat-0.7.0.tar.gz (from https://pypi.org/simple/cgat/), version: 0.7.0 2026-08-17T08:36:14,473 Found link https://files.pythonhosted.org/packages/ce/63/2b08a8083cba0480c3d71bd00ff295c56295fdb9f7e9be091eab02890586/cgat-0.7.1.tar.gz (from https://pypi.org/simple/cgat/), version: 0.7.1 2026-08-17T08:36:14,473 Found link https://files.pythonhosted.org/packages/ef/c4/51ff925472539041ad23edf0ebf3b5f3fa496c716f13f22f85f88254c7ee/cgat-0.7.2.tar.gz (from https://pypi.org/simple/cgat/), version: 0.7.2 2026-08-17T08:36:14,474 Found link https://files.pythonhosted.org/packages/97/0e/3c1cf0cc4518880ce3a5615bca98ce43d8dbe515f1bdfa56b91097fe165b/cgat-0.7.3.tar.gz (from https://pypi.org/simple/cgat/), version: 0.7.3 2026-08-17T08:36:14,475 Found link https://files.pythonhosted.org/packages/75/38/43dceda856be627a037d26ab5f5aec93149bf8bfc276564b6d03e35b6035/cgat-0.7.9.tar.gz (from https://pypi.org/simple/cgat/) (requires-python:>=3.10), version: 0.7.9 2026-08-17T08:36:14,476 Found link https://files.pythonhosted.org/packages/94/89/d6d25b52fc4bd5f0291f0caa1aa607c4f54fce250e411ed0de06ac2f1221/cgat-0.7.10.tar.gz (from https://pypi.org/simple/cgat/) (requires-python:>=3.10), version: 0.7.10 2026-08-17T08:36:14,476 Found link https://files.pythonhosted.org/packages/83/60/e6e8f4c2708430dcfea4357ab5ebeb204044af5ac37426d5b50282f4baee/cgat-0.7.11.tar.gz (from https://pypi.org/simple/cgat/) (requires-python:>=3.10), version: 0.7.11 2026-08-17T08:36:14,477 Fetching project page and analyzing links: https://www.piwheels.org/simple/cgat/ 2026-08-17T08:36:14,478 Getting page https://www.piwheels.org/simple/cgat/ 2026-08-17T08:36:14,479 Found index url https://www.piwheels.org/simple 2026-08-17T08:36:14,664 Fetched page https://www.piwheels.org/simple/cgat/ as text/html 2026-08-17T08:36:14,665 Skipping link: not a file: https://www.piwheels.org/simple/cgat/ 2026-08-17T08:36:14,666 Skipping link: not a file: https://pypi.org/simple/cgat/ 2026-08-17T08:36:14,691 Given no hashes to check 1 links for project 'cgat': discarding no candidates 2026-08-17T08:36:14,711 Collecting cgat==0.7.11 2026-08-17T08:36:14,713 Created temporary directory: /tmp/pip-unpack-6izquol8 2026-08-17T08:36:14,938 Downloading cgat-0.7.11.tar.gz (424 kB) 2026-08-17T08:36:15,658 Added cgat==0.7.11 from https://files.pythonhosted.org/packages/83/60/e6e8f4c2708430dcfea4357ab5ebeb204044af5ac37426d5b50282f4baee/cgat-0.7.11.tar.gz to build tracker '/tmp/pip-build-tracker-ex9xvhf5' 2026-08-17T08:36:15,666 Created temporary directory: /tmp/pip-build-env-n3uthlnq 2026-08-17T08:36:15,670 Installing build dependencies: started 2026-08-17T08:36:15,671 Running command pip subprocess to install build dependencies 2026-08-17T08:36:16,836 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-08-17T08:36:17,709 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-08-17T08:36:17,732 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-17T08:36:19,512 Collecting setuptools>=64.0 2026-08-17T08:36:19,513 Obtaining dependency information for setuptools>=64.0 from https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata 2026-08-17T08:36:19,528 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-08-17T08:36:19,767 Collecting wheel 2026-08-17T08:36:19,768 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl.metadata 2026-08-17T08:36:19,781 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl.metadata (2.3 kB) 2026-08-17T08:36:21,933 Collecting Cython>=0.29.35 2026-08-17T08:36:21,934 Obtaining dependency information for Cython>=0.29.35 from https://www.piwheels.org/simple/cython/cython-3.2.9-cp311-cp311-linux_armv7l.whl.metadata 2026-08-17T08:36:21,948 Using cached https://www.piwheels.org/simple/cython/cython-3.2.9-cp311-cp311-linux_armv7l.whl.metadata (4.6 kB) 2026-08-17T08:36:23,082 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-08-17T08:36:23,089 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-08-17T08:36:23,096 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-08-17T08:36:23,102 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-08-17T08:36:23,109 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-08-17T08:36:23,552 Link requires a different Python (3.11.2 not in: '>=3.12'): https://files.pythonhosted.org/packages/d3/e1/f2fe8f6113a657a1da83b358b16755e528a602c6976a43724a88f42b482a/numpy-2.5.0rc1.tar.gz (from https://pypi.org/simple/numpy/) (requires-python:>=3.12) 2026-08-17T08:36:23,561 Link requires a different Python (3.11.2 not in: '>=3.12'): https://files.pythonhosted.org/packages/e7/05/3d27272d30698dc0ecb7fdfaa41ad70303b444f81722bb99bce1d818638a/numpy-2.5.0.tar.gz (from https://pypi.org/simple/numpy/) (requires-python:>=3.12) 2026-08-17T08:36:23,570 Link requires a different Python (3.11.2 not in: '>=3.12'): https://files.pythonhosted.org/packages/22/fd/89965aa4ac08c74998539fcbf24fa3540f3e15237fbeb6bcf9c908f4aade/numpy-2.5.1.tar.gz (from https://pypi.org/simple/numpy/) (requires-python:>=3.12) 2026-08-17T08:36:23,583 Link requires a different Python (3.11.2 not in: '>=3.12'): https://files.pythonhosted.org/packages/9a/80/db0b4559e57ec36362bedbb05530a87fafbcb6067708c946967a41d449e7/numpy-2.5.2.tar.gz (from https://pypi.org/simple/numpy/) (requires-python:>=3.12) 2026-08-17T08:36:23,898 Collecting numpy 2026-08-17T08:36:23,899 Obtaining dependency information for numpy from https://www.piwheels.org/simple/numpy/numpy-2.4.6-cp311-cp311-linux_armv7l.whl.metadata 2026-08-17T08:36:23,912 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.6-cp311-cp311-linux_armv7l.whl.metadata (6.6 kB) 2026-08-17T08:36:24,262 Collecting pysam 2026-08-17T08:36:24,263 Obtaining dependency information for pysam from https://archive1.piwheels.org/simple/pysam/pysam-0.24.0-cp311-cp311-linux_armv7l.whl.metadata 2026-08-17T08:36:24,513 Downloading https://archive1.piwheels.org/simple/pysam/pysam-0.24.0-cp311-cp311-linux_armv7l.whl.metadata (1.6 kB) 2026-08-17T08:36:24,701 Collecting packaging>=24.0 2026-08-17T08:36:24,702 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl.metadata 2026-08-17T08:36:24,715 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl.metadata (3.6 kB) 2026-08-17T08:36:24,917 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl (33 kB) 2026-08-17T08:36:25,712 Using cached https://www.piwheels.org/simple/cython/cython-3.2.9-cp311-cp311-linux_armv7l.whl (11.2 MB) 2026-08-17T08:36:26,356 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.6-cp311-cp311-linux_armv7l.whl (6.3 MB) 2026-08-17T08:36:26,502 Downloading https://archive1.piwheels.org/simple/pysam/pysam-0.24.0-cp311-cp311-linux_armv7l.whl (17.8 MB) 2026-08-17T08:36:27,720 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.8/17.8 MB 11.6 MB/s eta 0:00:00 2026-08-17T08:36:27,935 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl (129 kB) 2026-08-17T08:36:27,998 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-17T08:36:28,027 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl (33 kB) 2026-08-17T08:36:28,813 Using cached https://www.piwheels.org/simple/cython/cython-3.2.9-cp311-cp311-linux_armv7l.whl (11.2 MB) 2026-08-17T08:36:29,558 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.6-cp311-cp311-linux_armv7l.whl (6.3 MB) 2026-08-17T08:36:31,148 Using cached https://archive1.piwheels.org/simple/pysam/pysam-0.24.0-cp311-cp311-linux_armv7l.whl (17.8 MB) 2026-08-17T08:36:31,808 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl (129 kB) 2026-08-17T08:36:31,886 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-17T08:36:34,779 Installing collected packages: setuptools, pysam, packaging, numpy, Cython, wheel 2026-08-17T08:36:48,858 Creating /tmp/pip-build-env-n3uthlnq/overlay/local/bin 2026-08-17T08:36:48,860 changing mode of /tmp/pip-build-env-n3uthlnq/overlay/local/bin/f2py to 755 2026-08-17T08:36:48,862 changing mode of /tmp/pip-build-env-n3uthlnq/overlay/local/bin/numpy-config to 755 2026-08-17T08:36:52,599 changing mode of /tmp/pip-build-env-n3uthlnq/overlay/local/bin/cygdb to 755 2026-08-17T08:36:52,601 changing mode of /tmp/pip-build-env-n3uthlnq/overlay/local/bin/cython to 755 2026-08-17T08:36:52,603 changing mode of /tmp/pip-build-env-n3uthlnq/overlay/local/bin/cythonize to 755 2026-08-17T08:36:52,742 changing mode of /tmp/pip-build-env-n3uthlnq/overlay/local/bin/wheel to 755 2026-08-17T08:36:52,786 Successfully installed Cython-3.2.9 numpy-2.4.6 packaging-26.3 pysam-0.24.0 setuptools-84.0.0 wheel-0.48.0 2026-08-17T08:36:53,315 Installing build dependencies: finished with status 'done' 2026-08-17T08:36:53,322 Getting requirements to build wheel: started 2026-08-17T08:36:53,323 Running command Getting requirements to build wheel 2026-08-17T08:36:54,225 :42: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2026-08-17T08:36:54,332 /tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-08-17T08:36:54,333 !! 2026-08-17T08:36:54,334 ******************************************************************************** 2026-08-17T08:36:54,335 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-08-17T08:36:54,336 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-08-17T08:36:54,337 or your builds will no longer be supported. 2026-08-17T08:36:54,338 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-17T08:36:54,338 ******************************************************************************** 2026-08-17T08:36:54,340 !! 2026-08-17T08:36:54,340 corresp(dist, value, root_dir) 2026-08-17T08:36:54,577 /tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-17T08:36:54,578 !! 2026-08-17T08:36:54,579 ******************************************************************************** 2026-08-17T08:36:54,579 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-17T08:36:54,580 License :: OSI Approved 2026-08-17T08:36:54,581 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-17T08:36:54,581 ******************************************************************************** 2026-08-17T08:36:54,582 !! 2026-08-17T08:36:54,583 dist._finalize_license_expression() 2026-08-17T08:36:54,583 /tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-17T08:36:54,584 !! 2026-08-17T08:36:54,585 ******************************************************************************** 2026-08-17T08:36:54,585 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-17T08:36:54,586 License :: OSI Approved 2026-08-17T08:36:54,587 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-17T08:36:54,588 ******************************************************************************** 2026-08-17T08:36:54,589 !! 2026-08-17T08:36:54,589 self._finalize_license_expression() 2026-08-17T08:36:54,594 WARNING: Dependency check for wigToBigWig failed: not found in PATH 2026-08-17T08:36:54,594 WARNING: Dependency check for bedtools failed: not found in PATH 2026-08-17T08:36:54,595 Discovered packages: ['cgat', 'cgat.NCL', 'cgat.tools'] 2026-08-17T08:36:54,596 running egg_info 2026-08-17T08:36:54,602 writing cgat.egg-info/PKG-INFO 2026-08-17T08:36:54,605 writing dependency_links to cgat.egg-info/dependency_links.txt 2026-08-17T08:36:54,608 writing entry points to cgat.egg-info/entry_points.txt 2026-08-17T08:36:54,609 writing requirements to cgat.egg-info/requires.txt 2026-08-17T08:36:54,611 writing top-level names to cgat.egg-info/top_level.txt 2026-08-17T08:36:54,647 reading manifest file 'cgat.egg-info/SOURCES.txt' 2026-08-17T08:36:54,657 reading manifest template 'MANIFEST.in' 2026-08-17T08:36:54,663 warning: no previously-included files matching '*' found under directory 'tests' 2026-08-17T08:36:54,663 adding license file 'LICENSE' 2026-08-17T08:36:54,672 writing manifest file 'cgat.egg-info/SOURCES.txt' 2026-08-17T08:36:54,822 Getting requirements to build wheel: finished with status 'done' 2026-08-17T08:36:54,825 Created temporary directory: /tmp/pip-modern-metadata-7fz_uvvh 2026-08-17T08:36:54,828 Preparing metadata (pyproject.toml): started 2026-08-17T08:36:54,829 Running command Preparing metadata (pyproject.toml) 2026-08-17T08:36:55,653 :42: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2026-08-17T08:36:55,728 /tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-08-17T08:36:55,728 !! 2026-08-17T08:36:55,729 ******************************************************************************** 2026-08-17T08:36:55,730 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-08-17T08:36:55,732 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-08-17T08:36:55,732 or your builds will no longer be supported. 2026-08-17T08:36:55,733 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-17T08:36:55,734 ******************************************************************************** 2026-08-17T08:36:55,734 !! 2026-08-17T08:36:55,735 corresp(dist, value, root_dir) 2026-08-17T08:36:55,964 /tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-17T08:36:55,965 !! 2026-08-17T08:36:55,966 ******************************************************************************** 2026-08-17T08:36:55,966 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-17T08:36:55,967 License :: OSI Approved 2026-08-17T08:36:55,968 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-17T08:36:55,969 ******************************************************************************** 2026-08-17T08:36:55,969 !! 2026-08-17T08:36:55,970 dist._finalize_license_expression() 2026-08-17T08:36:55,970 /tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-17T08:36:55,971 !! 2026-08-17T08:36:55,973 ******************************************************************************** 2026-08-17T08:36:55,973 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-17T08:36:55,974 License :: OSI Approved 2026-08-17T08:36:55,975 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-17T08:36:55,976 ******************************************************************************** 2026-08-17T08:36:55,977 !! 2026-08-17T08:36:55,978 self._finalize_license_expression() 2026-08-17T08:36:55,979 WARNING: Dependency check for wigToBigWig failed: not found in PATH 2026-08-17T08:36:55,980 WARNING: Dependency check for bedtools failed: not found in PATH 2026-08-17T08:36:55,981 Discovered packages: ['cgat', 'cgat.NCL', 'cgat.tools'] 2026-08-17T08:36:55,982 running dist_info 2026-08-17T08:36:55,993 creating /tmp/pip-modern-metadata-7fz_uvvh/cgat.egg-info 2026-08-17T08:36:55,994 writing /tmp/pip-modern-metadata-7fz_uvvh/cgat.egg-info/PKG-INFO 2026-08-17T08:36:55,998 writing dependency_links to /tmp/pip-modern-metadata-7fz_uvvh/cgat.egg-info/dependency_links.txt 2026-08-17T08:36:56,000 writing entry points to /tmp/pip-modern-metadata-7fz_uvvh/cgat.egg-info/entry_points.txt 2026-08-17T08:36:56,001 writing requirements to /tmp/pip-modern-metadata-7fz_uvvh/cgat.egg-info/requires.txt 2026-08-17T08:36:56,002 writing top-level names to /tmp/pip-modern-metadata-7fz_uvvh/cgat.egg-info/top_level.txt 2026-08-17T08:36:56,004 writing manifest file '/tmp/pip-modern-metadata-7fz_uvvh/cgat.egg-info/SOURCES.txt' 2026-08-17T08:36:56,037 reading manifest file '/tmp/pip-modern-metadata-7fz_uvvh/cgat.egg-info/SOURCES.txt' 2026-08-17T08:36:56,039 reading manifest template 'MANIFEST.in' 2026-08-17T08:36:56,044 warning: no previously-included files matching '*' found under directory 'tests' 2026-08-17T08:36:56,044 adding license file 'LICENSE' 2026-08-17T08:36:56,051 writing manifest file '/tmp/pip-modern-metadata-7fz_uvvh/cgat.egg-info/SOURCES.txt' 2026-08-17T08:36:56,052 creating '/tmp/pip-modern-metadata-7fz_uvvh/cgat-0.7.11.dist-info' 2026-08-17T08:36:56,234 Preparing metadata (pyproject.toml): finished with status 'done' 2026-08-17T08:36:56,239 Source in /tmp/pip-wheel-ozhykbd0/cgat_201e4fc7df9641c3ad750e6c43611023 has version 0.7.11, which satisfies requirement cgat==0.7.11 from https://files.pythonhosted.org/packages/83/60/e6e8f4c2708430dcfea4357ab5ebeb204044af5ac37426d5b50282f4baee/cgat-0.7.11.tar.gz 2026-08-17T08:36:56,240 Removed cgat==0.7.11 from https://files.pythonhosted.org/packages/83/60/e6e8f4c2708430dcfea4357ab5ebeb204044af5ac37426d5b50282f4baee/cgat-0.7.11.tar.gz from build tracker '/tmp/pip-build-tracker-ex9xvhf5' 2026-08-17T08:36:56,245 Created temporary directory: /tmp/pip-unpack-0semgrpy 2026-08-17T08:36:56,246 Building wheels for collected packages: cgat 2026-08-17T08:36:56,250 Created temporary directory: /tmp/pip-wheel-blitm_r4 2026-08-17T08:36:56,251 Destination directory: /tmp/pip-wheel-blitm_r4 2026-08-17T08:36:56,253 Building wheel for cgat (pyproject.toml): started 2026-08-17T08:36:56,254 Running command Building wheel for cgat (pyproject.toml) 2026-08-17T08:36:57,061 :42: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2026-08-17T08:36:57,134 /tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-08-17T08:36:57,135 !! 2026-08-17T08:36:57,136 ******************************************************************************** 2026-08-17T08:36:57,136 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-08-17T08:36:57,137 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-08-17T08:36:57,138 or your builds will no longer be supported. 2026-08-17T08:36:57,138 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-17T08:36:57,139 ******************************************************************************** 2026-08-17T08:36:57,140 !! 2026-08-17T08:36:57,141 corresp(dist, value, root_dir) 2026-08-17T08:36:57,396 /tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-17T08:36:57,396 !! 2026-08-17T08:36:57,398 ******************************************************************************** 2026-08-17T08:36:57,398 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-17T08:36:57,399 License :: OSI Approved 2026-08-17T08:36:57,400 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-17T08:36:57,401 ******************************************************************************** 2026-08-17T08:36:57,402 !! 2026-08-17T08:36:57,403 dist._finalize_license_expression() 2026-08-17T08:36:57,404 /tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-17T08:36:57,404 !! 2026-08-17T08:36:57,405 ******************************************************************************** 2026-08-17T08:36:57,406 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-17T08:36:57,407 License :: OSI Approved 2026-08-17T08:36:57,408 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-17T08:36:57,409 ******************************************************************************** 2026-08-17T08:36:57,410 !! 2026-08-17T08:36:57,411 self._finalize_license_expression() 2026-08-17T08:36:57,411 WARNING: Dependency check for wigToBigWig failed: not found in PATH 2026-08-17T08:36:57,412 WARNING: Dependency check for bedtools failed: not found in PATH 2026-08-17T08:36:57,412 Discovered packages: ['cgat', 'cgat.NCL', 'cgat.tools'] 2026-08-17T08:36:57,413 running bdist_wheel 2026-08-17T08:36:57,423 running build 2026-08-17T08:36:57,423 running build_py 2026-08-17T08:36:57,425 creating build/lib.linux-armv7l-cpython-311/doc 2026-08-17T08:36:57,427 copying doc/collect.py -> build/lib.linux-armv7l-cpython-311/doc 2026-08-17T08:36:57,429 copying doc/conf.py -> build/lib.linux-armv7l-cpython-311/doc 2026-08-17T08:36:57,431 creating build/lib.linux-armv7l-cpython-311/scripts 2026-08-17T08:36:57,432 copying scripts/cgat_check_deps.py -> build/lib.linux-armv7l-cpython-311/scripts 2026-08-17T08:36:57,435 copying scripts/conda.py -> build/lib.linux-armv7l-cpython-311/scripts 2026-08-17T08:36:57,439 creating build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,440 copying cgat/FastaIterator.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,442 copying cgat/AGP.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,444 copying cgat/Variants.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,447 copying cgat/__init__.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,449 copying cgat/Genomics.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,452 copying cgat/GFF3.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,454 copying cgat/Histogram2D.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,455 copying cgat/MatrixTools.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,458 copying cgat/Stats.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,460 copying cgat/SequenceProperties.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,463 copying cgat/RateEstimation.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,465 copying cgat/Histogram.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,468 copying cgat/AString.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,470 copying cgat/Iterators.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,471 copying cgat/AlignmentCoordinates.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,474 copying cgat/TreeTools.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,476 copying cgat/SetTools.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,479 copying cgat/cgat.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,481 copying cgat/makeGeneset.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,483 copying cgat/Blat.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,486 copying cgat/Sra.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,488 copying cgat/Glam2Scan.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,490 copying cgat/Intervals.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,492 copying cgat/RLE.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,494 copying cgat/dictzip.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,496 copying cgat/GTF.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,499 copying cgat/VCF.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,501 copying cgat/Bed.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,504 copying cgat/version.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,505 copying cgat/Fastq.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,508 copying cgat/IndexedGenome.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,510 copying cgat/Tree.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,513 copying cgat/Masker.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,515 copying cgat/Motifs.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,516 copying cgat/IndexedFasta.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,519 copying cgat/Glam2.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,521 copying cgat/MEME.py -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:57,524 creating build/lib.linux-armv7l-cpython-311/doc/python 2026-08-17T08:36:57,525 copying doc/python/Trackers.py -> build/lib.linux-armv7l-cpython-311/doc/python 2026-08-17T08:36:57,528 creating build/lib.linux-armv7l-cpython-311/cgat/NCL 2026-08-17T08:36:57,529 copying cgat/NCL/__init__.py -> build/lib.linux-armv7l-cpython-311/cgat/NCL 2026-08-17T08:36:57,535 creating build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,536 copying cgat/tools/bam2stats.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,539 copying cgat/tools/bam2bam.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,541 copying cgat/tools/bed2gff.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,543 copying cgat/tools/gff2coverage.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,545 copying cgat/tools/bam2fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,548 copying cgat/tools/fastq2table.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,550 copying cgat/tools/fastq2tpm.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,552 copying cgat/tools/__init__.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,553 copying cgat/tools/vcf_vs_vcf.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,555 copying cgat/tools/gff32gtf.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,557 copying cgat/tools/gtf2gff.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,560 copying cgat/tools/bcl2fastq.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,562 copying cgat/tools/fastq2tsv.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,564 copying cgat/tools/fasta2bed.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,566 copying cgat/tools/fastq2fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,568 copying cgat/tools/diff_bed.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,570 copying cgat/tools/bams2bam.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,572 copying cgat/tools/vcf2vcf.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,575 copying cgat/tools/fastq2fastq.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,577 copying cgat/tools/bam2bam_split_reads.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,579 copying cgat/tools/data2histogram.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,581 copying cgat/tools/bam2geneprofile.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,584 copying cgat/tools/fasta2stats.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,585 copying cgat/tools/csvs2csv.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,587 copying cgat/tools/bam2wiggle.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,590 copying cgat/tools/cgat_rebuild_extensions.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,592 copying cgat/tools/gff2fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,594 copying cgat/tools/fasta2table.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,596 copying cgat/tools/gtf2tsv.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,599 copying cgat/tools/fastq2summary.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,601 copying cgat/tools/beds2beds.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,603 copying cgat/tools/cgat_get_options.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,605 copying cgat/tools/gtfs2tsv.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,608 copying cgat/tools/gff2psl.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,610 copying cgat/tools/bed_vs_bed.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,612 copying cgat/tools/fastqs2fastqs.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,614 copying cgat/tools/gff2histogram.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,616 copying cgat/tools/gtf2table.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,619 copying cgat/tools/extract_stats.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,621 copying cgat/tools/bed2graph.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,623 copying cgat/tools/diff_bam.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,625 copying cgat/tools/fasta2fastq.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,628 copying cgat/tools/bed2stats.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,630 copying cgat/tools/diff_chains.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,633 copying cgat/tools/table2stats.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,636 copying cgat/tools/bam_compare_alignments.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,638 copying cgat/tools/bam2window_stats.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,640 copying cgat/tools/bed2bed.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,644 copying cgat/tools/split_file.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,647 copying cgat/tools/tables2table.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,868 copying cgat/tools/fastas2fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,870 copying cgat/tools/split_fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,873 copying cgat/tools/index_fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,875 copying cgat/tools/bam_vs_bed.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,878 copying cgat/tools/vcf_stats.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,881 copying cgat/tools/gtf2fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,883 copying cgat/tools/fasta2fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,886 copying cgat/tools/fastqs2fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,889 copying cgat/tools/bam_pileup2tsv.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,892 copying cgat/tools/gff2stats.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,894 copying cgat/tools/bam2bed.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,897 copying cgat/tools/genome_bed.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,899 copying cgat/tools/beds2counts.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,901 copying cgat/tools/gff2bed.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,903 copying cgat/tools/bed2table.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,906 copying cgat/tools/bam_vs_gtf.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,908 copying cgat/tools/diff_gtf.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,910 copying cgat/tools/vcf_compare_phase.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,913 copying cgat/tools/fasta2kmercontent.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,915 copying cgat/tools/fastqs2fastq.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,917 copying cgat/tools/bam2fastq.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,919 copying cgat/tools/bed2fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,921 copying cgat/tools/split_gff.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,923 copying cgat/tools/fasta2variants.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,925 copying cgat/tools/vcf2tsv.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,927 copying cgat/tools/bam2depth.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,929 copying cgat/tools/table2table.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,931 copying cgat/tools/bam_vs_bam.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,932 copying cgat/tools/vcfstats2db.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,934 copying cgat/tools/wig2bed.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,937 copying cgat/tools/csv2csv.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,938 copying cgat/tools/gff2table.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,940 copying cgat/tools/index2bed.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,943 copying cgat/tools/fasta2vcf.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,944 copying cgat/tools/gff2gff.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,947 copying cgat/tools/diff_fasta.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,949 copying cgat/tools/gtf2gtf.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,952 copying cgat/tools/cgat_script_template.py -> build/lib.linux-armv7l-cpython-311/cgat/tools 2026-08-17T08:36:57,954 running egg_info 2026-08-17T08:36:57,966 writing cgat.egg-info/PKG-INFO 2026-08-17T08:36:57,968 writing dependency_links to cgat.egg-info/dependency_links.txt 2026-08-17T08:36:57,969 writing entry points to cgat.egg-info/entry_points.txt 2026-08-17T08:36:57,971 writing requirements to cgat.egg-info/requires.txt 2026-08-17T08:36:57,972 writing top-level names to cgat.egg-info/top_level.txt 2026-08-17T08:36:57,997 reading manifest file 'cgat.egg-info/SOURCES.txt' 2026-08-17T08:36:58,006 reading manifest template 'MANIFEST.in' 2026-08-17T08:36:58,010 warning: no previously-included files matching '*' found under directory 'tests' 2026-08-17T08:36:58,011 adding license file 'LICENSE' 2026-08-17T08:36:58,019 writing manifest file 'cgat.egg-info/SOURCES.txt' 2026-08-17T08:36:58,028 copying cgat/GeneModelAnalysis.pyx -> build/lib.linux-armv7l-cpython-311/cgat 2026-08-17T08:36:58,034 creating build/lib.linux-armv7l-cpython-311/cgat/BamTools 2026-08-17T08:36:58,035 copying cgat/BamTools/bamtools.pyx -> build/lib.linux-armv7l-cpython-311/cgat/BamTools 2026-08-17T08:36:58,039 copying cgat/BamTools/geneprofile.pyx -> build/lib.linux-armv7l-cpython-311/cgat/BamTools 2026-08-17T08:36:58,043 copying cgat/BamTools/peakshape.pyx -> build/lib.linux-armv7l-cpython-311/cgat/BamTools 2026-08-17T08:36:58,046 creating build/lib.linux-armv7l-cpython-311/cgat/VCFTools 2026-08-17T08:36:58,047 copying cgat/VCFTools/vcftools.pyx -> build/lib.linux-armv7l-cpython-311/cgat/VCFTools 2026-08-17T08:36:58,050 copying cgat/NCL/_cnestedlist.pxd -> build/lib.linux-armv7l-cpython-311/cgat/NCL 2026-08-17T08:36:58,052 copying cgat/NCL/cnestedlist.pyx -> build/lib.linux-armv7l-cpython-311/cgat/NCL 2026-08-17T08:36:58,055 copying cgat/NCL/default.h -> build/lib.linux-armv7l-cpython-311/cgat/NCL 2026-08-17T08:36:58,057 copying cgat/NCL/intervaldb.c -> build/lib.linux-armv7l-cpython-311/cgat/NCL 2026-08-17T08:36:58,060 copying cgat/NCL/intervaldb.h -> build/lib.linux-armv7l-cpython-311/cgat/NCL 2026-08-17T08:36:58,062 creating build/lib.linux-armv7l-cpython-311/cgat/Components 2026-08-17T08:36:58,063 copying cgat/Components/Components.pyx -> build/lib.linux-armv7l-cpython-311/cgat/Components 2026-08-17T08:36:58,066 copying cgat/Components/connected_components.cpp -> build/lib.linux-armv7l-cpython-311/cgat/Components 2026-08-17T08:36:58,068 copying cgat/Components/connected_components.h -> build/lib.linux-armv7l-cpython-311/cgat/Components 2026-08-17T08:36:58,070 creating build/lib.linux-armv7l-cpython-311/cgat/FastqTools 2026-08-17T08:36:58,071 copying cgat/FastqTools/fastqtools.pyx -> build/lib.linux-armv7l-cpython-311/cgat/FastqTools 2026-08-17T08:36:58,082 running build_ext 2026-08-17T08:37:00,004 Compiling cgat/Components/Components.pyx because it changed. 2026-08-17T08:37:00,004 [1/1] Cythonizing cgat/Components/Components.pyx 2026-08-17T08:37:00,005 building 'cgat.Components' extension 2026-08-17T08:37:00,007 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Icgat/Components -I/usr/include -I/usr/include/python3.11 -c cgat/Components/Components.cpp -o build/temp.linux-armv7l-cpython-311/cgat/Components/Components.o 2026-08-17T08:37:07,867 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Icgat/Components -I/usr/include -I/usr/include/python3.11 -c cgat/Components/connected_components.cpp -o build/temp.linux-armv7l-cpython-311/cgat/Components/connected_components.o 2026-08-17T08:37:13,113 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/cgat/Components/Components.o build/temp.linux-armv7l-cpython-311/cgat/Components/connected_components.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/cgat/Components.cpython-311-arm-linux-gnueabihf.so 2026-08-17T08:37:13,542 warning: cgat/NCL/cnestedlist.pyx:106:24: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-08-17T08:37:13,543 warning: cgat/NCL/cnestedlist.pyx:106:28: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-08-17T08:37:13,548 warning: cgat/NCL/cnestedlist.pyx:389:24: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-08-17T08:37:13,549 warning: cgat/NCL/cnestedlist.pyx:389:28: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-08-17T08:37:13,563 warning: cgat/NCL/cnestedlist.pyx:265:26: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-08-17T08:37:13,564 warning: cgat/NCL/cnestedlist.pyx:265:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-08-17T08:37:13,570 warning: cgat/NCL/cnestedlist.pyx:353:26: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-08-17T08:37:13,570 warning: cgat/NCL/cnestedlist.pyx:353:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2026-08-17T08:37:14,029 Compiling cgat/NCL/cnestedlist.pyx because it changed. 2026-08-17T08:37:14,031 [1/1] Cythonizing cgat/NCL/cnestedlist.pyx 2026-08-17T08:37:14,032 building 'cgat.NCL.cnestedlist' extension 2026-08-17T08:37:14,032 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Icgat/NCL -I/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c cgat/NCL/cnestedlist.c -o build/temp.linux-armv7l-cpython-311/cgat/NCL/cnestedlist.o 2026-08-17T08:37:23,540 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Icgat/NCL -I/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c cgat/NCL/intervaldb.c -o build/temp.linux-armv7l-cpython-311/cgat/NCL/intervaldb.o 2026-08-17T08:37:24,924 cgat/NCL/intervaldb.c: In function ‘write_binary_files’: 2026-08-17T08:37:24,925 cgat/NCL/intervaldb.c:762:42: warning: ‘%s’ directive writing up to 2047 bytes into a region of size 1004 [-Wformat-overflow=] 2026-08-17T08:37:24,926 762 | sprintf(err_msg,"unable to open file %s for writing",path); 2026-08-17T08:37:24,926 | ^~ ~~~~ 2026-08-17T08:37:24,927 cgat/NCL/intervaldb.c:762:5: note: ‘sprintf’ output between 33 and 2080 bytes into a destination of size 1024 2026-08-17T08:37:24,927 762 | sprintf(err_msg,"unable to open file %s for writing",path); 2026-08-17T08:37:24,928 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:37:25,177 cgat/NCL/intervaldb.c: In function ‘text_file_to_binaries’: 2026-08-17T08:37:25,178 cgat/NCL/intervaldb.c:1015:19: warning: ‘.size’ directive writing 5 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2026-08-17T08:37:25,178 1015 | sprintf(path,"%s.size",filestem); /* SAVE BASIC SIZE INFO*/ 2026-08-17T08:37:25,179 | ^~~~~ 2026-08-17T08:37:25,180 cgat/NCL/intervaldb.c:1015:3: note: ‘sprintf’ output between 6 and 2053 bytes into a destination of size 2048 2026-08-17T08:37:25,181 1015 | sprintf(path,"%s.size",filestem); /* SAVE BASIC SIZE INFO*/ 2026-08-17T08:37:25,181 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:37:25,182 cgat/NCL/intervaldb.c:1029:21: warning: ‘.index’ directive writing 6 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2026-08-17T08:37:25,182 1029 | sprintf(path,"%s.index",filestem); /* SAVE INDEX INFO*/ 2026-08-17T08:37:25,183 | ^~~~~~ 2026-08-17T08:37:25,184 cgat/NCL/intervaldb.c:1029:5: note: ‘sprintf’ output between 7 and 2054 bytes into a destination of size 2048 2026-08-17T08:37:25,184 1029 | sprintf(path,"%s.index",filestem); /* SAVE INDEX INFO*/ 2026-08-17T08:37:25,185 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:37:25,186 cgat/NCL/intervaldb.c:1045:21: warning: ‘.subhead’ directive writing 8 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2026-08-17T08:37:25,187 1045 | sprintf(path,"%s.subhead",filestem); /* SAVE THE SUBHEADER LIST */ 2026-08-17T08:37:25,187 | ^~~~~~~~ 2026-08-17T08:37:25,188 cgat/NCL/intervaldb.c:1045:5: note: ‘sprintf’ output between 9 and 2056 bytes into a destination of size 2048 2026-08-17T08:37:25,189 1045 | sprintf(path,"%s.subhead",filestem); /* SAVE THE SUBHEADER LIST */ 2026-08-17T08:37:25,189 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:37:25,190 cgat/NCL/intervaldb.c:1061:19: warning: ‘.idb’ directive writing 4 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2026-08-17T08:37:25,191 1061 | sprintf(path,"%s.idb",filestem); /* SAVE THE ACTUAL INTERVAL DB*/ 2026-08-17T08:37:25,191 | ^~~~ 2026-08-17T08:37:25,192 cgat/NCL/intervaldb.c:1061:3: note: ‘sprintf’ output between 5 and 2052 bytes into a destination of size 2048 2026-08-17T08:37:25,193 1061 | sprintf(path,"%s.idb",filestem); /* SAVE THE ACTUAL INTERVAL DB*/ 2026-08-17T08:37:25,193 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:37:25,346 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/cgat/NCL/cnestedlist.o build/temp.linux-armv7l-cpython-311/cgat/NCL/intervaldb.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/cgat/NCL/cnestedlist.cpython-311-arm-linux-gnueabihf.so 2026-08-17T08:37:33,864 Compiling cgat/GeneModelAnalysis.pyx because it changed. 2026-08-17T08:37:33,865 [1/1] Cythonizing cgat/GeneModelAnalysis.pyx 2026-08-17T08:37:33,867 building 'cgat.GeneModelAnalysis' extension 2026-08-17T08:37:33,867 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include -I/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c cgat/GeneModelAnalysis.c -o build/temp.linux-armv7l-cpython-311/cgat/GeneModelAnalysis.o 2026-08-17T08:37:53,833 cgat/GeneModelAnalysis.c:16966:18: warning: ‘__pyx_f_4cgat_17GeneModelAnalysis___add’ defined but not used [-Wunused-function] 2026-08-17T08:37:53,834 16966 | static PyObject *__pyx_f_4cgat_17GeneModelAnalysis___add(PyArrayObject *__pyx_v_counts, PyObject *__pyx_v_positions, int __pyx_v_offset, int __pyx_v_length) { 2026-08-17T08:37:53,834 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:40:49,341 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/cgat/GeneModelAnalysis.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/cgat/GeneModelAnalysis.cpython-311-arm-linux-gnueabihf.so 2026-08-17T08:40:53,288 warning: cgat/BamTools/bamtools.pyx:812:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:53,290 warning: cgat/BamTools/bamtools.pyx:813:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:53,290 warning: cgat/BamTools/bamtools.pyx:814:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:53,291 warning: cgat/BamTools/bamtools.pyx:815:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:53,292 warning: cgat/BamTools/bamtools.pyx:816:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:53,293 warning: cgat/BamTools/bamtools.pyx:817:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:53,294 warning: cgat/BamTools/bamtools.pyx:818:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:53,295 warning: cgat/BamTools/bamtools.pyx:819:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:53,296 warning: cgat/BamTools/bamtools.pyx:820:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:53,296 warning: cgat/BamTools/bamtools.pyx:821:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:53,297 warning: cgat/BamTools/bamtools.pyx:822:31: local variable 'alignment_details_view' referenced before assignment 2026-08-17T08:40:55,928 Compiling cgat/BamTools/bamtools.pyx because it changed. 2026-08-17T08:40:55,928 [1/1] Cythonizing cgat/BamTools/bamtools.pyx 2026-08-17T08:40:55,929 building 'cgat.BamTools.bamtools' extension 2026-08-17T08:40:55,930 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include -I/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c cgat/BamTools/bamtools.c -o build/temp.linux-armv7l-cpython-311/cgat/BamTools/bamtools.o 2026-08-17T08:40:56,817 cgat/BamTools/bamtools.c: In function ‘__pyx_f_4cgat_8BamTools_8bamtools_get_cigar_stats’: 2026-08-17T08:40:56,836 cgat/BamTools/bamtools.c:21830:33: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-08-17T08:40:56,837 21830 | for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_6; __pyx_v_k++) { 2026-08-17T08:40:56,837 | ^ 2026-08-17T08:40:57,494 cgat/BamTools/bamtools.c: In function ‘__pyx_pf_4cgat_8BamTools_8bamtools_2bam2stats_count’: 2026-08-17T08:40:57,521 cgat/BamTools/bamtools.c:30429:27: warning: too many arguments for format [-Wformat-extra-args] 2026-08-17T08:40:57,522 30429 | (void)(printf(__pyx_k_i_i_i_i_i_i_i_i_i_i, (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_25 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_45 * __pyx_v_alignment_details_view.strides[1]) ))), (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_46 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_47 * __pyx_v_alignment_details_view.strides[1]) ))), (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_48 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_49 * __pyx_v_alignment_details_view.strides[1]) ))), (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_50 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_51 * __pyx_v_alignment_details_view.strides[1]) ))), (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_52 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_53 * __pyx_v_alignment_details_view.strides[1]) ))), (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_54 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_55 * __pyx_v_alignment_details_view.strides[1]) ))), (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_56 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_57 * __pyx_v_alignment_details_view.strides[1]) ))), (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_58 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_59 * __pyx_v_alignment_details_view.strides[1]) ))), (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_60 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_61 * __pyx_v_alignment_details_view.strides[1]) ))), (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_62 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_63 * __pyx_v_alignment_details_view.strides[1]) ))), (*((uint16_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_alignment_details_view.data + __pyx_t_64 * __pyx_v_alignment_details_view.strides[0]) ) + __pyx_t_65 * __pyx_v_alignment_details_view.strides[1]) ))))); 2026-08-17T08:40:57,522 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:40:58,083 cgat/BamTools/bamtools.c: In function ‘__pyx_f_4cgat_8BamTools_8bamtools_count_md_tag_mismatches’: 2026-08-17T08:40:58,118 cgat/BamTools/bamtools.c:39208:37: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-08-17T08:40:58,119 39208 | for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_11; __pyx_v_x++) { 2026-08-17T08:40:58,119 | ^ 2026-08-17T08:40:58,178 cgat/BamTools/bamtools.c:39416:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-08-17T08:40:58,179 39416 | for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_11; __pyx_v_x++) { 2026-08-17T08:40:58,179 | ^ 2026-08-17T08:40:58,259 cgat/BamTools/bamtools.c: In function ‘__pyx_pf_4cgat_8BamTools_8bamtools_8bam2stats_window_count’: 2026-08-17T08:40:58,294 cgat/BamTools/bamtools.c:40087:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-08-17T08:40:58,295 40087 | for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_4; __pyx_v_x++) { 2026-08-17T08:40:58,296 | ^ 2026-08-17T08:40:58,485 cgat/BamTools/bamtools.c:41719:58: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2026-08-17T08:40:58,486 41719 | for (__pyx_v_idx = __pyx_v_window_start; __pyx_v_idx <= __pyx_t_23; __pyx_v_idx++) { 2026-08-17T08:40:58,486 | ^~ 2026-08-17T08:40:58,528 cgat/BamTools/bamtools.c:41757:37: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-08-17T08:40:58,528 41757 | for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_4; __pyx_v_x++) { 2026-08-17T08:40:58,529 | ^ 2026-08-17T08:40:58,973 cgat/BamTools/bamtools.c: In function ‘__pyx_pf_4cgat_8BamTools_8bamtools_22merge_pairs’: 2026-08-17T08:40:59,016 cgat/BamTools/bamtools.c:48016:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-08-17T08:40:59,017 48016 | __pyx_t_4 = (__pyx_v_end > (__pyx_v_contig_sizes[__pyx_t_14])); 2026-08-17T08:40:59,017 | ^ 2026-08-17T08:41:33,854 cgat/BamTools/bamtools.c: In function ‘__pyx_pw_4cgat_8BamTools_8bamtools_7bam2bam_filter_bam’: 2026-08-17T08:41:33,890 cgat/BamTools/bamtools.c:36059:8: warning: ‘__pyx_v_remove_contig_tids’ may be used uninitialized [-Wmaybe-uninitialized] 2026-08-17T08:41:33,891 36059 | int *__pyx_v_remove_contig_tids; 2026-08-17T08:41:33,891 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:41:41,485 cgat/BamTools/bamtools.c: In function ‘__pyx_pf_4cgat_8BamTools_8bamtools_24bams2bam_filter.constprop’: 2026-08-17T08:41:41,530 cgat/BamTools/bamtools.c:49186:8: warning: ‘__pyx_v_remove_contig_tids’ may be used uninitialized [-Wmaybe-uninitialized] 2026-08-17T08:41:41,531 49186 | int *__pyx_v_remove_contig_tids; 2026-08-17T08:41:41,531 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:41:41,577 cgat/BamTools/bamtools.c:52147:63: warning: ‘__pyx_v_map_tid2tid’ may be used uninitialized [-Wmaybe-uninitialized] 2026-08-17T08:41:41,577 52147 | __pyx_t_5 = __Pyx_PyLong_From_int((__pyx_v_map_tid2tid[__pyx_t_14])); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 2381, __pyx_L1_error) 2026-08-17T08:41:41,578 | ^ 2026-08-17T08:41:41,625 cgat/BamTools/bamtools.c:49198:8: note: ‘__pyx_v_map_tid2tid’ was declared here 2026-08-17T08:41:41,626 49198 | int *__pyx_v_map_tid2tid; 2026-08-17T08:41:41,626 | ^~~~~~~~~~~~~~~~~~~ 2026-08-17T08:41:54,340 In function ‘__Pyx_PyLong_From_int64_t’, 2026-08-17T08:41:54,340 inlined from ‘__pyx_pf_4cgat_8BamTools_8bamtools_2bam2stats_count.constprop’ at cgat/BamTools/bamtools.c:28453:18: 2026-08-17T08:41:54,401 cgat/BamTools/bamtools.c:65682:22: warning: ‘__pyx_v_fastq_nreads’ may be used uninitialized [-Wmaybe-uninitialized] 2026-08-17T08:41:54,401 65682 | return PyLong_FromLongLong((PY_LONG_LONG) value); 2026-08-17T08:41:54,402 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:41:54,403 cgat/BamTools/bamtools.c: In function ‘__pyx_pf_4cgat_8BamTools_8bamtools_2bam2stats_count.constprop’: 2026-08-17T08:41:54,421 cgat/BamTools/bamtools.c:22334:11: note: ‘__pyx_v_fastq_nreads’ was declared here 2026-08-17T08:41:54,422 22334 | int64_t __pyx_v_fastq_nreads; 2026-08-17T08:41:54,423 | ^~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:41:54,447 cgat/BamTools/bamtools.c:28710:31: warning: ‘__pyx_v_fastq_counts’ may be used uninitialized [-Wmaybe-uninitialized] 2026-08-17T08:41:54,447 28710 | __pyx_v_fastq_count = (&(__pyx_v_fastq_counts[__pyx_v_read_index])); 2026-08-17T08:41:54,448 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:41:54,468 cgat/BamTools/bamtools.c:22335:56: note: ‘__pyx_v_fastq_counts’ was declared here 2026-08-17T08:41:54,469 22335 | struct __pyx_t_4cgat_8BamTools_8bamtools_CountsType *__pyx_v_fastq_counts; 2026-08-17T08:41:54,469 | ^~~~~~~~~~~~~~~~~~~~ 2026-08-17T08:42:15,302 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/cgat/BamTools/bamtools.o -L/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/pysam -L/usr/lib -L/usr/lib/arm-linux-gnueabihf -lhts -lctabixproxies.cpython-311-arm-linux-gnueabihf -lcfaidx.cpython-311-arm-linux-gnueabihf -lcsamfile.cpython-311-arm-linux-gnueabihf -lcvcf.cpython-311-arm-linux-gnueabihf -lcbcf.cpython-311-arm-linux-gnueabihf -lctabix.cpython-311-arm-linux-gnueabihf -lchtslib.cpython-311-arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/cgat/BamTools/bamtools.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/pysam -Wl,-rpath,/usr/lib -Wl,-rpath,/usr/lib 2026-08-17T08:42:15,339 /usr/bin/ld: cannot find -lhts: No such file or directory 2026-08-17T08:42:15,364 collect2: error: ld returned 1 exit status 2026-08-17T08:42:15,368 error: Command '['arm-linux-gnueabihf-gcc', '-shared', '-Wl,-O1', '-Wl,-Bsymbolic-functions', '-g', '-fwrapv', '-O2', 'build/temp.linux-armv7l-cpython-311/cgat/BamTools/bamtools.o', '-L/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/pysam', '-L/usr/lib', '-L/usr/lib/arm-linux-gnueabihf', '-lhts', '-lctabixproxies.cpython-311-arm-linux-gnueabihf', '-lcfaidx.cpython-311-arm-linux-gnueabihf', '-lcsamfile.cpython-311-arm-linux-gnueabihf', '-lcvcf.cpython-311-arm-linux-gnueabihf', '-lcbcf.cpython-311-arm-linux-gnueabihf', '-lctabix.cpython-311-arm-linux-gnueabihf', '-lchtslib.cpython-311-arm-linux-gnueabihf', '-o', 'build/lib.linux-armv7l-cpython-311/cgat/BamTools/bamtools.cpython-311-arm-linux-gnueabihf.so', '-Wl,-rpath,/tmp/pip-build-env-n3uthlnq/overlay/local/lib/python3.11/dist-packages/pysam', '-Wl,-rpath,/usr/lib', '-Wl,-rpath,/usr/lib']' returned non-zero exit status 1. 2026-08-17T08:42:16,557 ERROR: [present-rich] Building wheel for cgat (pyproject.toml) exited with 1 2026-08-17T08:42:16,570 [bold magenta]full command[/]: [blue]/usr/bin/python3 /usr/lib/python3/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmp4vivw_kk[/] 2026-08-17T08:42:16,571 [bold magenta]cwd[/]: /tmp/pip-wheel-ozhykbd0/cgat_201e4fc7df9641c3ad750e6c43611023 2026-08-17T08:42:16,571 Building wheel for cgat (pyproject.toml): finished with status 'error' 2026-08-17T08:42:16,575 ERROR: Failed building wheel for cgat 2026-08-17T08:42:16,577 Failed to build cgat 2026-08-17T08:42:16,578 ERROR: Failed to build one or more wheels 2026-08-17T08:42:16,580 Exception information: 2026-08-17T08:42:16,580 Traceback (most recent call last): 2026-08-17T08:42:16,580 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 160, in exc_logging_wrapper 2026-08-17T08:42:16,580 status = run_func(*args) 2026-08-17T08:42:16,580 ^^^^^^^^^^^^^^^ 2026-08-17T08:42:16,580 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 247, in wrapper 2026-08-17T08:42:16,580 return func(self, options, args) 2026-08-17T08:42:16,580 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2026-08-17T08:42:16,580 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 201, in run 2026-08-17T08:42:16,580 raise CommandError("Failed to build one or more wheels") 2026-08-17T08:42:16,580 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2026-08-17T08:42:16,584 Removed build tracker: '/tmp/pip-build-tracker-ex9xvhf5'