2021-07-13T11:03:31,690 Created temporary directory: /tmp/pip-ephem-wheel-cache-8qwq46g8
2021-07-13T11:03:31,693 Created temporary directory: /tmp/pip-req-tracker-8wlln_k6
2021-07-13T11:03:31,693 Initialized build tracking at /tmp/pip-req-tracker-8wlln_k6
2021-07-13T11:03:31,693 Created build tracker: /tmp/pip-req-tracker-8wlln_k6
2021-07-13T11:03:31,693 Entered build tracker: /tmp/pip-req-tracker-8wlln_k6
2021-07-13T11:03:31,694 Created temporary directory: /tmp/pip-wheel-79xzglx3
2021-07-13T11:03:31,724 1 location(s) to search for versions of cyvcf2:
2021-07-13T11:03:31,724 * https://pypi.org/simple/cyvcf2/
2021-07-13T11:03:31,724 Fetching project page and analyzing links: https://pypi.org/simple/cyvcf2/
2021-07-13T11:03:31,725 Getting page https://pypi.org/simple/cyvcf2/
2021-07-13T11:03:31,726 Found index url https://pypi.org/simple
2021-07-13T11:03:31,855   Found link https://files.pythonhosted.org/packages/d1/07/b59d41fc3aa2d21f8db3d31d9bac643534bbe0cdefca8da88aced413ad68/cyvcf2-0.1.0.tar.gz#sha256=39f01726d1efabb31beaef4e5137040d62740b0532f40edd3478ceec0a89b248 (from https://pypi.org/simple/cyvcf2/), version: 0.1.0
2021-07-13T11:03:31,856   Found link https://files.pythonhosted.org/packages/57/6f/3d1ca274114e9540e76455c07e86fbfeccda10fe2dd37f6e3c6a220dcba0/cyvcf2-0.1.1.tar.gz#sha256=058bce2988daf45ea504e01c8ddb3aaf7da374dd4468e106f2adf5279ef27e1b (from https://pypi.org/simple/cyvcf2/), version: 0.1.1
2021-07-13T11:03:31,856   Found link https://files.pythonhosted.org/packages/bc/6b/ca8177b9effc1ec07cd99dde61e4e38c5c9d61606d4cfe9e83859ac414ec/cyvcf2-0.1.2.tar.gz#sha256=d194e632770c301ba9386535f8948f7e9ffa534858af8f7b4b3b6a1c3648bef8 (from https://pypi.org/simple/cyvcf2/), version: 0.1.2
2021-07-13T11:03:31,856   Found link https://files.pythonhosted.org/packages/8e/c8/accc184a5363cc7a06d1839275aede48950c9a2d798bba0f8306742f4c3e/cyvcf2-0.1.3.tar.gz#sha256=c78b7edfa7fb529f8527c919730f394e166ee94a78a578af144314a3a9f25970 (from https://pypi.org/simple/cyvcf2/), version: 0.1.3
2021-07-13T11:03:31,857   Found link https://files.pythonhosted.org/packages/40/65/c1ca5e2fd8be5d973825df310f5709ef52174151ad5987fd4ba0d137bb8d/cyvcf2-0.1.4.tar.gz#sha256=e41b06d411b8ca2978fb0e4b42c4e9214b8f7c63c02bd6847b4fbe96e33c9e55 (from https://pypi.org/simple/cyvcf2/), version: 0.1.4
2021-07-13T11:03:31,857   Found link https://files.pythonhosted.org/packages/c4/4f/921d799e89e2b7cf75707eed4df46c5063911c9801d11b58a68c91425b72/cyvcf2-0.1.5.tar.gz#sha256=ea875c78a705b95f5611c2847c1ea9b7afda081a720a3e74207d9ecbf9feb012 (from https://pypi.org/simple/cyvcf2/), version: 0.1.5
2021-07-13T11:03:31,857   Found link https://files.pythonhosted.org/packages/e5/0f/859f772e646c5536fd3a71ee6144200cb4c490eb5326321699507b6c91ef/cyvcf2-0.1.6.tar.gz#sha256=e14d06e7821c55b2da9dd9ccd7dc6f97e57d8bda070a8e4621d9b0fd883bcdcb (from https://pypi.org/simple/cyvcf2/), version: 0.1.6
2021-07-13T11:03:31,858   Found link https://files.pythonhosted.org/packages/6c/97/e86516e60c558df1b54c2e27cf0a2f955816ff185200c79590e6015f6ab1/cyvcf2-0.1.7.tar.gz#sha256=a4b13b57aec0a31ff4c40e4956ecdbae5ada05b32b95fafba3d84021c70caf5b (from https://pypi.org/simple/cyvcf2/), version: 0.1.7
2021-07-13T11:03:31,858   Found link https://files.pythonhosted.org/packages/79/22/0e1470adc46976c0afdc63d220d03cc127e1a79f94d92b75e5ea55763cea/cyvcf2-0.1.8.tar.gz#sha256=840ba9ab5105eb2286d164c965ee2c2d288ebcf72ad0d1306cda5b1f6f2ab29c (from https://pypi.org/simple/cyvcf2/), version: 0.1.8
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2021-07-13T11:03:31,858   Found link https://files.pythonhosted.org/packages/26/e6/da2bd392f09586057131c5d41257f41a563f599b558b6521b9696ce65958/cyvcf2-0.2.0.tar.gz#sha256=2227d53ac75d6c0f0e7dafda33b79c9af17dad85acec20c96efe07d21d4c2fd7 (from https://pypi.org/simple/cyvcf2/), version: 0.2.0
2021-07-13T11:03:31,859   Found link https://files.pythonhosted.org/packages/12/f7/3f8109acdec97cf6bc783bbe3748e88af49ba759cd23f7bbe7ec9db3b6bd/cyvcf2-0.2.1.tar.gz#sha256=095da551679aea1647c827980a9e55caf1f75416d2b5063c4c3a738937c12609 (from https://pypi.org/simple/cyvcf2/), version: 0.2.1
2021-07-13T11:03:31,859   Found link https://files.pythonhosted.org/packages/ff/5e/91139637a81d6b31df9a306b8f2d83c07fe92dc8aaf55e5fd77d26257539/cyvcf2-0.2.2.tar.gz#sha256=76fb1f17d8e4d91a2cba462b69f999f2c59f34a54df25a9be48f4d0942bc534a (from https://pypi.org/simple/cyvcf2/), version: 0.2.2
2021-07-13T11:03:31,859   Found link https://files.pythonhosted.org/packages/e4/4b/e61200a26181d76e53be4b8eb7e67daa9ccbd64b79c2accb61e964ebef47/cyvcf2-0.2.3.tar.gz#sha256=a5d113ec1a89ce5d488640f096a8bbf8dff1d4f400b3de67cc76a198eb9e8856 (from https://pypi.org/simple/cyvcf2/), version: 0.2.3
2021-07-13T11:03:31,860   Found link https://files.pythonhosted.org/packages/3a/7c/70298b7ccb4801d91998d3c590521946b6d40d44db71c33af9d02584a0f8/cyvcf2-0.2.4.tar.gz#sha256=48f1a85f837f8e993a1538b933fd8fa37625038b6f7c45f38e9c2873e79bbff6 (from https://pypi.org/simple/cyvcf2/), version: 0.2.4
2021-07-13T11:03:31,860   Found link https://files.pythonhosted.org/packages/0c/77/ab52a01f24afaffa97e3b1d6c774d5c6923e0eaadee8562636ffa2931b32/cyvcf2-0.2.5.tar.gz#sha256=9f44b95d7995242c30b6606dee1203b53b893cc19c3ab77af36e147d61796f3e (from https://pypi.org/simple/cyvcf2/), version: 0.2.5
2021-07-13T11:03:31,860   Found link https://files.pythonhosted.org/packages/f5/33/e056c1bf8bab395ff0058bc0cd51c534b429d2a89152ecc32e9624fe12e3/cyvcf2-0.2.6.tar.gz#sha256=c62c95582698e8c5e98cfa655b9b802b402baacee9966faa8aa300dac5d3dfd3 (from https://pypi.org/simple/cyvcf2/), version: 0.2.6
2021-07-13T11:03:31,861   Found link https://files.pythonhosted.org/packages/18/12/bd09382d770f6a290981bd18d62db75e18540ed5a30a0dadee5c2ca9ac7d/cyvcf2-0.2.7.tar.gz#sha256=53f8e1d4cd3cccf363b0a6756d3e2fa455f5780edf189bc594c4f5792c9cb8ed (from https://pypi.org/simple/cyvcf2/), version: 0.2.7
2021-07-13T11:03:31,861   Found link https://files.pythonhosted.org/packages/b0/85/38adbe84e488dc3ebdcdf86e5f272f800c434779db3fcb9de4c346229165/cyvcf2-0.2.8.tar.gz#sha256=023be6aae116e494a8c04fce91fcf00014e1cd11663d667d693e93f94842f182 (from https://pypi.org/simple/cyvcf2/), version: 0.2.8
2021-07-13T11:03:31,861   Found link https://files.pythonhosted.org/packages/ed/9a/fc22c3b1fe701e12e5fceb45b242c181d3c1cd912b704bd3ef342f0cc7b4/cyvcf2-0.3.0.tar.gz#sha256=4e4cd7c82eb95b9e7f682f640ca8f58a77f9302cfb927c94c51f406cbe1a20d1 (from https://pypi.org/simple/cyvcf2/), version: 0.3.0
2021-07-13T11:03:31,861   Found link https://files.pythonhosted.org/packages/81/fc/4fd2e10fb8080cffc70903b1455627c493c5a3aa6250fd44bd391de722e7/cyvcf2-0.3.2.tar.gz#sha256=37e324fb6fedc0c4338822ea4cd57dcc3287eb1b67fb78ea25a20a4b70745538 (from https://pypi.org/simple/cyvcf2/), version: 0.3.2
2021-07-13T11:03:31,862   Found link https://files.pythonhosted.org/packages/e5/d3/4d84212662ceffbd7af3a3a145ee066c93ac388f02ff6c38bb55d1c718de/cyvcf2-0.4.0.tar.gz#sha256=e65723c1250b2f5ce51337e3b84e53e5a7adf392f06653690bf6267160aafcc2 (from https://pypi.org/simple/cyvcf2/), version: 0.4.0
2021-07-13T11:03:31,862   Found link https://files.pythonhosted.org/packages/be/8a/91ba05cf12be401fa448775976774bd97e21ea958082914b774ea52dca8d/cyvcf2-0.4.1.tar.gz#sha256=0a70098db9d94be2be49e0c0bd059e8ada97990aa9e5ddfb4e0f934231c72070 (from https://pypi.org/simple/cyvcf2/), version: 0.4.1
2021-07-13T11:03:31,862   Found link https://files.pythonhosted.org/packages/f7/37/1cd2786c8531516d87386ab13a786f3b9a06ef505d911b98f09ae7b09fe9/cyvcf2-0.4.2.tar.gz#sha256=088ac2a964a0a4f501678064e8113793aff5200b07b9734a79b0430d6815ba3e (from https://pypi.org/simple/cyvcf2/), version: 0.4.2
2021-07-13T11:03:31,862   Found link https://files.pythonhosted.org/packages/ee/44/b828f8e650ddc658e07c215b22a0611b350581560c936be4c1513dde5e24/cyvcf2-0.5.0.tar.gz#sha256=199f361ad1c9446a401833358aaa3c9b1cb588b650649c29c1572a919166dd21 (from https://pypi.org/simple/cyvcf2/), version: 0.5.0
2021-07-13T11:03:31,863   Found link https://files.pythonhosted.org/packages/17/d8/4161752c57e6be524969fe7bfd8773a860593cb1d81828c399fc9c611152/cyvcf2-0.5.1.tar.gz#sha256=346a88d1cd28695022dc80ff39f2f753e3588265e58627d1cb2228bab2650bca (from https://pypi.org/simple/cyvcf2/), version: 0.5.1
2021-07-13T11:03:31,863   Found link https://files.pythonhosted.org/packages/f8/9c/05215397eb6076718b0349cc0c47859e32a9f51b251577241aeb4a3a396f/cyvcf2-0.5.2.tar.gz#sha256=5e1c181044dab11f20ba61c70730d3741aec7b53f4425ed707baf50c4eec5d68 (from https://pypi.org/simple/cyvcf2/), version: 0.5.2
2021-07-13T11:03:31,863   Found link https://files.pythonhosted.org/packages/d8/eb/ace70f60162207c7ee83f48e49b46054e3332042e0d04411ccfc9d35731c/cyvcf2-0.5.3.tar.gz#sha256=ab041aaaf0e3ba0f597b75f83019f4b15793f65df45799e100550049e99ca8c0 (from https://pypi.org/simple/cyvcf2/), version: 0.5.3
2021-07-13T11:03:31,864   Found link https://files.pythonhosted.org/packages/dd/12/433768e01c285407d1c294c8d3dd367ff44774b23620aa22b627ea799cc2/cyvcf2-0.5.5.tar.gz#sha256=79d75b115616bf4782cf452352e7e1d494c7ca38c452e65a80263996ced91594 (from https://pypi.org/simple/cyvcf2/), version: 0.5.5
2021-07-13T11:03:31,867   Found link https://files.pythonhosted.org/packages/fd/cb/9c261f27fe3231f02d58afd43bed010e6c211afe9b37328076fa3134eade/cyvcf2-0.6.1.tar.gz#sha256=047b0695aeb1f4f52dc4697154990e66fdad7632c9c696b937c414925a847567 (from https://pypi.org/simple/cyvcf2/), version: 0.6.1
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2021-07-13T11:03:31,868   Found link https://files.pythonhosted.org/packages/32/f5/93d6562835de2efe426e0170e1077737468d3e428cfac7bdc875a2da3dc4/cyvcf2-0.6.5.tar.gz#sha256=84dfbce005efa3a88c0fd321b01d403addab9ac81aba128b9ea5ec1da7ed2791 (from https://pypi.org/simple/cyvcf2/), version: 0.6.5
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2021-07-13T11:03:31,873   Found link https://files.pythonhosted.org/packages/cb/4c/18e0e6237cd4e8bf926c2a294db496ea32f0fff50fb6f06d8a817e985a64/cyvcf2-0.10.0.tar.gz#sha256=3b4e7294abd7efe91fbee993e078a1db2ebab4ce38bdd2e17e50d2b2dd8f902e (from https://pypi.org/simple/cyvcf2/), version: 0.10.0
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2021-07-13T11:03:31,876   Found link https://files.pythonhosted.org/packages/6c/c5/388bee52648892053ccc717062155cc6bcb1f0ea6ce7a1c5f45b1407c8e3/cyvcf2-0.11.0.tar.gz#sha256=780e6fc2b878a5a13471871b3425e8413d7f2f984ce1a8284ebbfb3926213ed0 (from https://pypi.org/simple/cyvcf2/), version: 0.11.0
2021-07-13T11:03:31,876   Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/58/37/febdfa18e4afbe2a52b54f35dac94591b65744a66620396f548995a5d056/cyvcf2-0.11.1-py3.7-linux-x86_64.egg#sha256=590aa6ba7635c18a0f028d5b24dffef648235faddd382df68a3d6b31036295fa (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,876   Found link https://files.pythonhosted.org/packages/93/6e/c17ebd3d332af5baa8e076b9de7115c8447d3453a4726a5c7e716a2946b2/cyvcf2-0.11.1.tar.gz#sha256=4c206b6a75e1ee91496b3f0a79d40c5bed86c6f33c71c16ac0fcb36c7d8606cd (from https://pypi.org/simple/cyvcf2/), version: 0.11.1
2021-07-13T11:03:31,876   Found link https://files.pythonhosted.org/packages/55/65/dfb085bb7082b4b23d15403cd0a6573088eeabcd24d06559c1d2e131c861/cyvcf2-0.11.2.tar.gz#sha256=2c50a9e9606d19b97123e003e08ef63ccb3cabbd2d0d560dc2908176b46e4b2e (from https://pypi.org/simple/cyvcf2/), version: 0.11.2
2021-07-13T11:03:31,877   Found link https://files.pythonhosted.org/packages/19/f6/4c7685dfc8734076ef708c62c8f7adbdaab3aa92547bb1c64e32e427845d/cyvcf2-0.11.3.tar.gz#sha256=ed64074324503fbd886d88a4820a7d5058382926aa963d9f4a8df51ddc8ae7a7 (from https://pypi.org/simple/cyvcf2/), version: 0.11.3
2021-07-13T11:03:31,877   Found link https://files.pythonhosted.org/packages/83/15/6095aba5dde78dddc5ed6eca6f820813d7cd0bd73766501083c897c5da2c/cyvcf2-0.11.4.tar.gz#sha256=17c61840f05ae1dffc88c07cb20191125576f696e58fd6d68bc5904ffa1baddb (from https://pypi.org/simple/cyvcf2/), version: 0.11.4
2021-07-13T11:03:31,877   Found link https://files.pythonhosted.org/packages/dd/2e/2c80e524e5f98837274bad981a0b5621717283462fc0aca91823b76ab759/cyvcf2-0.11.5.tar.gz#sha256=20924e5b30e8308756575ac3ae8c28a8c717ed3c53b2adb297201428f43fae6e (from https://pypi.org/simple/cyvcf2/), version: 0.11.5
2021-07-13T11:03:31,878   Found link https://files.pythonhosted.org/packages/9a/21/e35e64f3a19ca916caae59e368da8b3c2d939c0a18c98fd7a701d86fa93a/cyvcf2-0.11.6.tar.gz#sha256=59de422bf54f8439cdd039230bf40ebed3d1284727f88e1a71e1baba0ff56d48 (from https://pypi.org/simple/cyvcf2/), version: 0.11.6
2021-07-13T11:03:31,878   Found link https://files.pythonhosted.org/packages/69/7f/2f256704fdb1f00c78e45ee937a371a4ea16e7f883bd301f3337bdad10ee/cyvcf2-0.11.7.tar.gz#sha256=a4b6229b89a0a1043684c65cbdd702c366a8800dc3591fb44c4b5a08640cbeec (from https://pypi.org/simple/cyvcf2/), version: 0.11.7
2021-07-13T11:03:31,878   Found link https://files.pythonhosted.org/packages/d5/3d/b009123050b6e9bc32a2db4e75fdb192c630d18a5d32670d24c632927a86/cyvcf2-0.20.0.tar.gz#sha256=995364e4cbd97f172bd775249eee24ca61978af153f280c788e804a7d0196601 (from https://pypi.org/simple/cyvcf2/), version: 0.20.0
2021-07-13T11:03:31,878   Found link https://files.pythonhosted.org/packages/44/2d/7dd95bb914ae0614800b44b0f5abf5babb1c4e86c45742573f1a22ee76e9/cyvcf2-0.20.1.tar.gz#sha256=235135edc79f58015755aa493e4357acbde54a4f67fa5ab8cc24c1506404bbd9 (from https://pypi.org/simple/cyvcf2/), version: 0.20.1
2021-07-13T11:03:31,879   Found link https://files.pythonhosted.org/packages/e4/17/c87816887ebc08417befb96068627157c58fa044ed9cae483009ccffcb6b/cyvcf2-0.20.3.tar.gz#sha256=0747a862cdf930830c1add1cbc7da4f356c1a4cad4565aae4e385ede0499c645 (from https://pypi.org/simple/cyvcf2/), version: 0.20.3
2021-07-13T11:03:31,879   Found link https://files.pythonhosted.org/packages/25/a4/72475683568031ee8e7dde725c0de48d7d5bd6e4fce913540b1cc79ed6fc/cyvcf2-0.20.4.tar.gz#sha256=4e44a0aec80b31af91a4a45e879815bc251ec7e980633d492b672df3101d4d0d (from https://pypi.org/simple/cyvcf2/), version: 0.20.4
2021-07-13T11:03:31,879   Found link https://files.pythonhosted.org/packages/4d/84/d11e676f2e6b9dcceb148f2e3376940b58374d30b473b10472547c8ec5e6/cyvcf2-0.20.5.tar.gz#sha256=a831781f20f2fc35173eaa1d13363fe38ea5ac3d6c004144f0b4c71afb091737 (from https://pypi.org/simple/cyvcf2/), version: 0.20.5
2021-07-13T11:03:31,879   Found link https://files.pythonhosted.org/packages/d2/ee/68925242e464b3d22398d3a14d2cc98372f74eac9df443b0e7069d0c0390/cyvcf2-0.20.6.tar.gz#sha256=3b4c2924109750df9df853df8b754e39d201db18bc2974e6e95a87baf64da561 (from https://pypi.org/simple/cyvcf2/), version: 0.20.6
2021-07-13T11:03:31,880   Found link https://files.pythonhosted.org/packages/10/82/605f1cb01e5edb0625cd23e31c0feeec8e0d39db98a3aa85d8ba564f9e21/cyvcf2-0.20.7.tar.gz#sha256=13847815cc6700f3131b27e8b082101a804772bcafe7c4252c3c70fdb3e9f4f0 (from https://pypi.org/simple/cyvcf2/), version: 0.20.7
2021-07-13T11:03:31,880   Found link https://files.pythonhosted.org/packages/4e/0f/de77b049c61646e1b06e24dedb4e4b67acfcc8f0b8183e148d7e2709a13a/cyvcf2-0.20.8.tar.gz#sha256=4cabce94a50be2ad9baeef17222a9bae0d7a9e6788aff4c21e09d84c44564d74 (from https://pypi.org/simple/cyvcf2/), version: 0.20.8
2021-07-13T11:03:31,880   Found link https://files.pythonhosted.org/packages/1f/5d/9f9e93a87cd2d8246dccb3376e3b6fd39a44d0f84b33b86983b0de282bde/cyvcf2-0.20.9.tar.gz#sha256=e05d4e970d9048b1b779054c33970a908bd4c639e8b681e0a93ef443fdb95b28 (from https://pypi.org/simple/cyvcf2/), version: 0.20.9
2021-07-13T11:03:31,881   Found link https://files.pythonhosted.org/packages/df/23/733165d41604b6de0233fa56e7eb946432db42186359e0d82f584208931a/cyvcf2-0.30.1.tar.gz#sha256=c9e9ebfd425ebdda16c2f2004611fb80bf2cb2b7224f2505e6de8d212da073a1 (from https://pypi.org/simple/cyvcf2/), version: 0.30.1
2021-07-13T11:03:31,898   Skipping link: none of the wheel's tags (cp35-cp35m-macosx_10_9_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0a/77/255b67a45cc5be6b905abf0db25ff87a86dd306ec5b53603ac74cdc73a95/cyvcf2-0.30.4-cp35-cp35m-macosx_10_9_x86_64.whl#sha256=3188f4b0ae1ac8878541848d7700bcb4047db9dec803ad7bc4499a75753e2351 (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,898   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux2014_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d0/8a/14578d9e51d072100f04438c3d71017468e249ce2a9b669ff4c54505e8d7/cyvcf2-0.30.4-cp35-cp35m-manylinux2014_x86_64.whl#sha256=7abb92bfb46323136538496770bcf884a0c214e04f61cd474c1f0b99dfedfbcd (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,899   Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_9_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/37/88/de3a5253d673950fe38ceef11178bdceacf94ace4969e95419d6252b0d76/cyvcf2-0.30.4-cp36-cp36m-macosx_10_9_x86_64.whl#sha256=9a83ee065603430d6ef3761b97b646c18e65119d897741418c5ded2398d02cf8 (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,899   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux2014_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/e3/91/b0a2d168d7c4bee1e680c0052ff0bb80c106b5d7f85745c47e6967854b70/cyvcf2-0.30.4-cp36-cp36m-manylinux2014_x86_64.whl#sha256=36e0e2aa5374a6d68a63833eabd77d4d7a0ea6ec24dec7dbff63e7510241ab5f (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,900   Skipping link: none of the wheel's tags (cp37-cp37m-macosx_10_9_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/04/34/2606ae509e361929375ffff892353064ceccb4c10569a01f28a8985805b8/cyvcf2-0.30.4-cp37-cp37m-macosx_10_9_x86_64.whl#sha256=4185a38bcb02ef371995a8a30c0fe659a9a7cf713b958b483eae11831746dc69 (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,900   Skipping link: none of the wheel's tags (cp37-cp37m-manylinux2014_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/ab/5e/14576bfddc8d3ee5083d281f89f741f72975b35983eed8e4ddeac900f9ad/cyvcf2-0.30.4-cp37-cp37m-manylinux2014_x86_64.whl#sha256=b6b55965d9b2be707d41fb2a5f49dbd75b01712621a2f200bcdb5ac25d68a7c3 (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,901   Skipping link: none of the wheel's tags (cp38-cp38-macosx_10_9_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d0/36/1f0183af88e2cf1aa2a1744a30bd06eb12deed6da8c0c05e5322c2b3b4c5/cyvcf2-0.30.4-cp38-cp38-macosx_10_9_x86_64.whl#sha256=f6c4b7905f2f3c1d618122b94b8c2437e81106a2bf6f3677e5e211bb9fd122db (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,901   Skipping link: none of the wheel's tags (cp38-cp38-manylinux2014_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/61/aa/a51b16c716394180ac7b73980976e07444a107d039a1a666c01c4b16195a/cyvcf2-0.30.4-cp38-cp38-manylinux2014_x86_64.whl#sha256=3f8324b9aa78a5fac47e61b7670206d2df079a2f9dade54ccd2b8d8a4a0a59d4 (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,902   Skipping link: none of the wheel's tags (cp39-cp39-macosx_10_9_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/ee/37/499e48500bee6e96a2f9d67242d09e7e6a684defb011125548daf24558bc/cyvcf2-0.30.4-cp39-cp39-macosx_10_9_x86_64.whl#sha256=40c567096aa6393796df2aa7afa5d23cace5a718f26902563a5a28982125abce (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,902   Skipping link: none of the wheel's tags (cp39-cp39-manylinux2014_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0d/f1/ec51368cfb9898c8cd30a29dbabb9585f22957280545561bd1e4bdbc1613/cyvcf2-0.30.4-cp39-cp39-manylinux2014_x86_64.whl#sha256=2a9c950e4e8370b0d8914ebd508fff15fc1ca2ea1b21d2cd787ba967d91615c4 (from https://pypi.org/simple/cyvcf2/)
2021-07-13T11:03:31,903   Found link https://files.pythonhosted.org/packages/63/2b/4313b604598a32075a649a45c3cbaff3c0136f49eb1c4da8dc45cd5b957c/cyvcf2-0.30.4.tar.gz#sha256=5088c1df2f1569392395c2e4c93e749149cd18e8e914257077581ee2fdb226a8 (from https://pypi.org/simple/cyvcf2/), version: 0.30.4
2021-07-13T11:03:31,903 Skipping link: not a file: https://pypi.org/simple/cyvcf2/
2021-07-13T11:03:31,915 Given no hashes to check 1 links for project 'cyvcf2': discarding no candidates
2021-07-13T11:03:31,934 Collecting cyvcf2==0.9.0
2021-07-13T11:03:31,936   Created temporary directory: /tmp/pip-unpack-wekj8fxp
2021-07-13T11:03:32,741   Downloading cyvcf2-0.9.0.tar.gz (1.2 MB)
2021-07-13T11:03:33,491   Added cyvcf2==0.9.0 from https://files.pythonhosted.org/packages/3f/21/29c8dc12e91d55e953f230bf9e96af779b224f6d59f4eacc3dcb80753d34/cyvcf2-0.9.0.tar.gz#sha256=cd2aa6b825842cfdff4ecacb0532114487e6d185435fda1c5b90b1f610874e92 to build tracker '/tmp/pip-req-tracker-8wlln_k6'
2021-07-13T11:03:33,493     Running setup.py (path:/tmp/pip-wheel-79xzglx3/cyvcf2_8ea2952a9a5e4c149654d392512ca218/setup.py) egg_info for package cyvcf2
2021-07-13T11:03:33,494     Created temporary directory: /tmp/pip-pip-egg-info-ty2s56_p
2021-07-13T11:03:33,494     Running command python setup.py egg_info
2021-07-13T11:03:36,804     Collecting coloredlogs
2021-07-13T11:03:36,915       Downloading coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)
2021-07-13T11:03:37,188     Collecting humanfriendly>=9.1
2021-07-13T11:03:37,195       Downloading humanfriendly-9.2-py2.py3-none-any.whl (86 kB)
2021-07-13T11:03:42,337     Installing collected packages: humanfriendly, coloredlogs
2021-07-13T11:03:42,675     Successfully installed coloredlogs-15.0.1 humanfriendly-9.2
2021-07-13T11:03:43,520     running egg_info
2021-07-13T11:03:43,522     creating /tmp/pip-pip-egg-info-ty2s56_p/cyvcf2.egg-info
2021-07-13T11:03:43,523     writing /tmp/pip-pip-egg-info-ty2s56_p/cyvcf2.egg-info/PKG-INFO
2021-07-13T11:03:43,526     writing dependency_links to /tmp/pip-pip-egg-info-ty2s56_p/cyvcf2.egg-info/dependency_links.txt
2021-07-13T11:03:43,527     writing entry points to /tmp/pip-pip-egg-info-ty2s56_p/cyvcf2.egg-info/entry_points.txt
2021-07-13T11:03:43,529     writing requirements to /tmp/pip-pip-egg-info-ty2s56_p/cyvcf2.egg-info/requires.txt
2021-07-13T11:03:43,529     writing top-level names to /tmp/pip-pip-egg-info-ty2s56_p/cyvcf2.egg-info/top_level.txt
2021-07-13T11:03:43,531     writing manifest file '/tmp/pip-pip-egg-info-ty2s56_p/cyvcf2.egg-info/SOURCES.txt'
2021-07-13T11:03:43,681     reading manifest file '/tmp/pip-pip-egg-info-ty2s56_p/cyvcf2.egg-info/SOURCES.txt'
2021-07-13T11:03:43,682     reading manifest template 'MANIFEST.in'
2021-07-13T11:03:43,694     adding license file 'LICENSE'
2021-07-13T11:03:43,700     writing manifest file '/tmp/pip-pip-egg-info-ty2s56_p/cyvcf2.egg-info/SOURCES.txt'
2021-07-13T11:03:43,801   Source in /tmp/pip-wheel-79xzglx3/cyvcf2_8ea2952a9a5e4c149654d392512ca218 has version 0.9.0, which satisfies requirement cyvcf2==0.9.0 from https://files.pythonhosted.org/packages/3f/21/29c8dc12e91d55e953f230bf9e96af779b224f6d59f4eacc3dcb80753d34/cyvcf2-0.9.0.tar.gz#sha256=cd2aa6b825842cfdff4ecacb0532114487e6d185435fda1c5b90b1f610874e92
2021-07-13T11:03:43,802   Removed cyvcf2==0.9.0 from https://files.pythonhosted.org/packages/3f/21/29c8dc12e91d55e953f230bf9e96af779b224f6d59f4eacc3dcb80753d34/cyvcf2-0.9.0.tar.gz#sha256=cd2aa6b825842cfdff4ecacb0532114487e6d185435fda1c5b90b1f610874e92 from build tracker '/tmp/pip-req-tracker-8wlln_k6'
2021-07-13T11:03:43,806 Created temporary directory: /tmp/pip-unpack-5yq__bjk
2021-07-13T11:03:43,807 Building wheels for collected packages: cyvcf2
2021-07-13T11:03:43,811   Created temporary directory: /tmp/pip-wheel-zc_l4eed
2021-07-13T11:03:43,811   Building wheel for cyvcf2 (setup.py): started
2021-07-13T11:03:43,811   Destination directory: /tmp/pip-wheel-zc_l4eed
2021-07-13T11:03:43,812   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-79xzglx3/cyvcf2_8ea2952a9a5e4c149654d392512ca218/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-79xzglx3/cyvcf2_8ea2952a9a5e4c149654d392512ca218/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-zc_l4eed
2021-07-13T11:03:45,383   running bdist_wheel
2021-07-13T11:03:45,389   running build
2021-07-13T11:03:45,389   running build_py
2021-07-13T11:03:45,526   creating build
2021-07-13T11:03:45,526   creating build/lib.linux-armv7l-3.9
2021-07-13T11:03:45,527   creating build/lib.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:45,528   copying cyvcf2/cli.py -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:45,530   copying cyvcf2/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:45,532   copying cyvcf2/__main__.py -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:45,534   creating build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,535   copying cyvcf2/tests/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,537   copying cyvcf2/tests/test_hemi.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,539   copying cyvcf2/tests/test_reader.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,541   running egg_info
2021-07-13T11:03:45,555   writing cyvcf2.egg-info/PKG-INFO
2021-07-13T11:03:45,557   writing dependency_links to cyvcf2.egg-info/dependency_links.txt
2021-07-13T11:03:45,559   writing entry points to cyvcf2.egg-info/entry_points.txt
2021-07-13T11:03:45,560   writing requirements to cyvcf2.egg-info/requires.txt
2021-07-13T11:03:45,561   writing top-level names to cyvcf2.egg-info/top_level.txt
2021-07-13T11:03:45,569   reading manifest file 'cyvcf2.egg-info/SOURCES.txt'
2021-07-13T11:03:45,574   reading manifest template 'MANIFEST.in'
2021-07-13T11:03:45,586   adding license file 'LICENSE'
2021-07-13T11:03:45,595   writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
2021-07-13T11:03:45,602   copying cyvcf2/cyvcf2.c -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:45,663   copying cyvcf2/cyvcf2.pxd -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:45,665   copying cyvcf2/cyvcf2.pyx -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:45,669   copying cyvcf2/helpers.c -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:45,671   copying cyvcf2/helpers.h -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:45,674   copying cyvcf2/relatedness.h -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:45,676   copying cyvcf2/tests/__init__.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,679   copying cyvcf2/tests/bug.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,682   copying cyvcf2/tests/decomposed.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,684   copying cyvcf2/tests/empty.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,686   copying cyvcf2/tests/issue_44.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,688   copying cyvcf2/tests/o.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,693   copying cyvcf2/tests/seg.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,695   copying cyvcf2/tests/test-alt-repr-1.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,697   copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,699   copying cyvcf2/tests/test-format-string.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,702   copying cyvcf2/tests/test-haploidX.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,719   copying cyvcf2/tests/test-hemi.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,722   copying cyvcf2/tests/test-issue-48.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,724   copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,726   copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,728   copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,730   copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,733   copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,736   copying cyvcf2/tests/test.snpeff.bcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,739   copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,741   copying cyvcf2/tests/test.snpeff.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,744   copying cyvcf2/tests/test.t.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,773   copying cyvcf2/tests/test.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,779   copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,781   copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,784   copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,786   copying cyvcf2/tests/test_hemi.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,789   copying cyvcf2/tests/test_reader.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-13T11:03:45,794   running build_ext
2021-07-13T11:03:45,888   cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c
2021-07-13T11:03:46,486   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-79xzglx3/cyvcf2_8ea2952a9a5e4c149654d392512ca218/cyvcf2/cyvcf2.pxd
2021-07-13T11:03:46,486     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-13T11:03:47,914   warning: cyvcf2/cyvcf2.pxd:26:16: Declarations should not be declared inline.
2021-07-13T11:03:47,924   warning: cyvcf2/cyvcf2.pxd:188:14: 'BCF_HT_FLAG' redeclared
2021-07-13T11:03:47,934   warning: cyvcf2/cyvcf2.pxd:274:30: Declarations should not be declared inline.
2021-07-13T11:03:58,494   building 'cyvcf2.cyvcf2' extension
2021-07-13T11:03:58,495   creating build/temp.linux-armv7l-3.9
2021-07-13T11:03:58,496   creating build/temp.linux-armv7l-3.9/cyvcf2
2021-07-13T11:03:58,496   creating build/temp.linux-armv7l-3.9/htslib
2021-07-13T11:03:58,497   creating build/temp.linux-armv7l-3.9/htslib/cram
2021-07-13T11:03:58,499   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c cyvcf2/cyvcf2.c -o build/temp.linux-armv7l-3.9/cyvcf2/cyvcf2.o
2021-07-13T11:03:58,930   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-13T11:03:58,930                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-13T11:03:58,930                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-13T11:03:58,931                    from cyvcf2/cyvcf2.c:613:
2021-07-13T11:03:58,931   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-13T11:03:58,931      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-13T11:03:58,931         |  ^~~~~~~
2021-07-13T11:03:59,165   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’:
2021-07-13T11:03:59,170   cyvcf2/cyvcf2.c:8014:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:03:59,170    8014 |   __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2);
2021-07-13T11:03:59,170         |                                ~~~~~~~~~~~~^~~~~
2021-07-13T11:03:59,171   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:03:59,171                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:03:59,171   htslib/htslib/vcf.h:441:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:03:59,171     441 |     int bcf_hdr_append(bcf_hdr_t *h, const char *line);
2021-07-13T11:03:59,171         |                        ~~~~~~~~~~~^
2021-07-13T11:03:59,176   cyvcf2/cyvcf2.c:8056:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:03:59,176    8056 |   __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
2021-07-13T11:03:59,176         |                              ~~~~~~~~~~~~^~~~~
2021-07-13T11:03:59,176   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:03:59,177                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:03:59,177   htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:03:59,177     477 |     int bcf_hdr_sync(bcf_hdr_t *h);
2021-07-13T11:03:59,177         |                      ~~~~~~~~~~~^
2021-07-13T11:03:59,185   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’:
2021-07-13T11:03:59,191   cyvcf2/cyvcf2.c:8584:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:03:59,191    8584 |   __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0);
2021-07-13T11:03:59,191         |                                     ~~~~~~~~~~~~^~~~~
2021-07-13T11:03:59,191   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:03:59,191                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:03:59,192   htslib/htslib/vcf.h:313:40: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:03:59,192     313 |     int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file);
2021-07-13T11:03:59,192         |                             ~~~~~~~~~~~^~~
2021-07-13T11:03:59,200   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’:
2021-07-13T11:03:59,206   cyvcf2/cyvcf2.c:8885:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:03:59,206    8885 |   __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4);
2021-07-13T11:03:59,206         |                                ~~~~~~~~~~~~^~~~~
2021-07-13T11:03:59,207   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:03:59,207                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:03:59,207   htslib/htslib/vcf.h:441:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:03:59,207     441 |     int bcf_hdr_append(bcf_hdr_t *h, const char *line);
2021-07-13T11:03:59,207         |                        ~~~~~~~~~~~^
2021-07-13T11:03:59,213   cyvcf2/cyvcf2.c:8938:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:03:59,213    8938 |   __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
2021-07-13T11:03:59,213         |                              ~~~~~~~~~~~~^~~~~
2021-07-13T11:03:59,213   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:03:59,214                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:03:59,214   htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:03:59,214     477 |     int bcf_hdr_sync(bcf_hdr_t *h);
2021-07-13T11:03:59,214         |                      ~~~~~~~~~~~^
2021-07-13T11:03:59,217   cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_18generator’:
2021-07-13T11:03:59,219   cyvcf2/cyvcf2.c:9153:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:03:59,219    9153 |   __pyx_cur_scope->__pyx_v_itr = bcf_itr_querys(__pyx_cur_scope->__pyx_v_self->hidx, __pyx_cur_scope->__pyx_v_self->hdr, __pyx_t_2);
2021-07-13T11:03:59,220   htslib/htslib/vcf.h:762:103: note: in definition of macro ‘bcf_itr_querys’
2021-07-13T11:03:59,220     762 |     #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec)
2021-07-13T11:03:59,220         |                                                                                                       ^~~
2021-07-13T11:03:59,220   In file included from htslib/htslib/vcf.h:39,
2021-07-13T11:03:59,220                    from cyvcf2/helpers.h:1,
2021-07-13T11:03:59,220                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:03:59,220   htslib/htslib/hts.h:534:97: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:03:59,221     534 |     hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec);
2021-07-13T11:03:59,221         |                                                                                           ~~~~~~^~~
2021-07-13T11:03:59,242   cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_24generator2’:
2021-07-13T11:03:59,249   cyvcf2/cyvcf2.c:10427:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:03:59,250   10427 |     __pyx_t_4 = ((PyObject *)__pyx_f_6cyvcf2_6cyvcf2_newHREC((__pyx_cur_scope->__pyx_v_self->hdr->hrec[__pyx_cur_scope->__pyx_v_i]), __pyx_cur_scope->__pyx_v_self->hdr)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 411, __pyx_L1_error)
2021-07-13T11:03:59,250         |                                                                                                                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2021-07-13T11:03:59,251   cyvcf2/cyvcf2.c:2958:107: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:03:59,252    2958 | static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/
2021-07-13T11:03:59,252         |                                                                                                           ^~~~~~~~~~~
2021-07-13T11:03:59,329   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_35__dealloc__’:
2021-07-13T11:03:59,337   cyvcf2/cyvcf2.c:12110:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:03:59,337   12110 |     bcf_hdr_destroy(__pyx_v_self->hdr);
2021-07-13T11:03:59,337         |                     ~~~~~~~~~~~~^~~~~
2021-07-13T11:03:59,338   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:03:59,338                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:03:59,338   htslib/htslib/vcf.h:259:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:03:59,338     259 |     void bcf_hdr_destroy(bcf_hdr_t *h);
2021-07-13T11:03:59,338         |                          ~~~~~~~~~~~^
2021-07-13T11:03:59,341   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’:
2021-07-13T11:03:59,350   cyvcf2/cyvcf2.c:12600:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
2021-07-13T11:03:59,350   12600 |   __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen));
2021-07-13T11:03:59,350         |   ^~~~~~~~~
2021-07-13T11:03:59,350   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:03:59,351                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:03:59,351   htslib/htslib/vcf.h:437:11: note: declared here
2021-07-13T11:03:59,351     437 |     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
2021-07-13T11:03:59,351         |           ^~~~~~~~~~~~~~~~
2021-07-13T11:03:59,353   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’:
2021-07-13T11:03:59,362   cyvcf2/cyvcf2.c:12859:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
2021-07-13T11:03:59,362   12859 |   __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n));
2021-07-13T11:03:59,362         |                  ^
2021-07-13T11:03:59,368   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:03:59,368                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:03:59,368   cyvcf2/cyvcf2.c:12968:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:03:59,369   12968 |       __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
2021-07-13T11:03:59,369   htslib/htslib/vcf.h:765:112: note: in definition of macro ‘bcf_index_seqnames’
2021-07-13T11:03:59,369     765 |     #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr))
2021-07-13T11:03:59,369         |                                                                                                                ^~~
2021-07-13T11:03:59,369   In file included from htslib/htslib/vcf.h:39,
2021-07-13T11:03:59,369                    from cyvcf2/helpers.h:1,
2021-07-13T11:03:59,369                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:03:59,369   htslib/htslib/hts.h:536:92: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:03:59,370     536 |     const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values
2021-07-13T11:03:59,370         |                                                                                      ~~~~~~^~~
2021-07-13T11:03:59,379   cyvcf2/cyvcf2.c:12968:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
2021-07-13T11:03:59,379   12968 |       __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
2021-07-13T11:03:59,379         |                      ^
2021-07-13T11:03:59,392   cyvcf2/cyvcf2.c:13141:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
2021-07-13T11:03:59,392   13141 |       __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n));
2021-07-13T11:03:59,392         |                      ^
2021-07-13T11:04:00,116   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8gt_bases___get__’:
2021-07-13T11:04:00,132   cyvcf2/cyvcf2.c:22924:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:04:00,132   22924 |   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) {
2021-07-13T11:04:00,132         |                                 ^
2021-07-13T11:04:00,262   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’:
2021-07-13T11:04:00,279   cyvcf2/cyvcf2.c:25004:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:04:00,279   25004 |     __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id);
2021-07-13T11:04:00,279         |                 ^
2021-07-13T11:04:00,572   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_3ALT___get__’:
2021-07-13T11:04:00,594   cyvcf2/cyvcf2.c:32137:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:04:00,595   32137 |   for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
2021-07-13T11:04:00,595         |                                 ^
2021-07-13T11:04:00,596   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6is_snp___get__’:
2021-07-13T11:04:00,618   cyvcf2/cyvcf2.c:32232:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:04:00,618   32232 |   for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
2021-07-13T11:04:00,618         |                                 ^
2021-07-13T11:04:00,621   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8is_indel___get__’:
2021-07-13T11:04:00,644   cyvcf2/cyvcf2.c:32447:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:04:00,644   32447 |   for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
2021-07-13T11:04:00,645         |                                 ^
2021-07-13T11:04:00,668   cyvcf2/cyvcf2.c:32505:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:04:00,668   32505 |     __pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0);
2021-07-13T11:04:00,668         |                             ^~
2021-07-13T11:04:00,694   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’:
2021-07-13T11:04:00,718   cyvcf2/cyvcf2.c:34659:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:04:00,719   34659 |   __pyx_v_h = __pyx_t_6;
2021-07-13T11:04:00,719         |             ^
2021-07-13T11:04:00,814   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’:
2021-07-13T11:04:00,841   cyvcf2/cyvcf2.c:37668:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:04:00,841   37668 |   __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key);
2021-07-13T11:04:00,841         |                ^
2021-07-13T11:04:00,849   cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’:
2021-07-13T11:04:00,876   cyvcf2/cyvcf2.c:38663:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:04:00,876   38663 |   __pyx_v_i->hdr = __pyx_t_4;
2021-07-13T11:04:00,877         |                  ^
2021-07-13T11:04:00,895   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’:
2021-07-13T11:04:00,923   cyvcf2/cyvcf2.c:39196:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:04:00,923   39196 |   (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr));
2021-07-13T11:04:00,923         |                       ~~~~~~~~~~~~^~~~~
2021-07-13T11:04:00,924   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:04:00,924                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:04:00,924   htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:04:00,924     477 |     int bcf_hdr_sync(bcf_hdr_t *h);
2021-07-13T11:04:00,924         |                      ~~~~~~~~~~~^
2021-07-13T11:04:00,951   cyvcf2/cyvcf2.c:39224:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:04:00,951   39224 |   (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
2021-07-13T11:04:00,951         |                       ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
2021-07-13T11:04:00,951   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:04:00,951                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:04:00,951   htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:04:00,952     477 |     int bcf_hdr_sync(bcf_hdr_t *h);
2021-07-13T11:04:00,952         |                      ~~~~~~~~~~~^
2021-07-13T11:04:00,952   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2write_header’:
2021-07-13T11:04:00,979   cyvcf2/cyvcf2.c:39290:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:04:00,979   39290 |   (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr));
2021-07-13T11:04:00,979         |                                                      ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
2021-07-13T11:04:00,979   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:04:00,979                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:04:00,979   htslib/htslib/vcf.h:318:47: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:04:00,980     318 |     int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h);
2021-07-13T11:04:00,980         |                                    ~~~~~~~~~~~^
2021-07-13T11:04:00,981   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_4write_record’:
2021-07-13T11:04:01,009   cyvcf2/cyvcf2.c:39468:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:04:01,009   39468 |     __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0);
2021-07-13T11:04:01,009         |                                    ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
2021-07-13T11:04:01,009   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:04:01,010                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:04:01,010   htslib/htslib/vcf.h:480:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:04:01,010     480 |     int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec);
2021-07-13T11:04:01,010         |                          ~~~~~~~~~~~^~~
2021-07-13T11:04:01,037   cyvcf2/cyvcf2.c:39506:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:04:01,038   39506 |     (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
2021-07-13T11:04:01,038         |                         ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
2021-07-13T11:04:01,038   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:04:01,038                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:04:01,038   htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:04:01,038     477 |     int bcf_hdr_sync(bcf_hdr_t *h);
2021-07-13T11:04:01,038         |                      ~~~~~~~~~~~^
2021-07-13T11:04:01,066   cyvcf2/cyvcf2.c:39565:100: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-13T11:04:01,066   39565 |   __pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2072, __pyx_L1_error)
2021-07-13T11:04:01,066         |                                                                            ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
2021-07-13T11:04:01,066   In file included from cyvcf2/helpers.h:1,
2021-07-13T11:04:01,066                    from cyvcf2/cyvcf2.c:622:
2021-07-13T11:04:01,066   htslib/htslib/vcf.h:368:43: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-13T11:04:01,067     368 |     int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v);
2021-07-13T11:04:01,067         |                                ~~~~~~~~~~~^
2021-07-13T11:04:05,709   At top level:
2021-07-13T11:04:05,714   cyvcf2/cyvcf2.c:6614:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function]
2021-07-13T11:04:05,714    6614 | static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) {
2021-07-13T11:04:05,714         |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-13T11:04:59,716   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c cyvcf2/helpers.c -o build/temp.linux-armv7l-3.9/cyvcf2/helpers.o
2021-07-13T11:05:00,091   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/bgzf.c -o build/temp.linux-armv7l-3.9/htslib/bgzf.o
2021-07-13T11:05:00,381   htslib/bgzf.c: In function ‘bgzf_read’:
2021-07-13T11:05:00,382   htslib/bgzf.c:691:23: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:00,382     691 |     while (bytes_read < length) {
2021-07-13T11:05:00,382         |                       ^
2021-07-13T11:05:00,382   htslib/bgzf.c:706:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:00,382     706 |         copy_length = length - bytes_read < available? length - bytes_read : available;
2021-07-13T11:05:00,383         |                                           ^
2021-07-13T11:05:00,383   htslib/bgzf.c:706:78: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2021-07-13T11:05:00,383     706 |         copy_length = length - bytes_read < available? length - bytes_read : available;
2021-07-13T11:05:00,383         |                                                                              ^~~~~~~~~
2021-07-13T11:05:00,403   htslib/bgzf.c: In function ‘bgzf_useek’:
2021-07-13T11:05:00,404   htslib/bgzf.c:1301:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare]
2021-07-13T11:05:00,404    1301 |         if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1;
2021-07-13T11:05:00,404         |                      ^
2021-07-13T11:05:00,405   htslib/bgzf.c:1302:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare]
2021-07-13T11:05:00,405    1302 |         else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1;
2021-07-13T11:05:00,405         |                           ^~
2021-07-13T11:05:02,138   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_codecs.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_codecs.o
2021-07-13T11:05:02,337   In file included from htslib/cram/cram.h:52,
2021-07-13T11:05:02,338                    from htslib/cram/cram_codecs.c:43:
2021-07-13T11:05:02,338   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-13T11:05:02,339   htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:02,339     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-13T11:05:02,339         |             ^~
2021-07-13T11:05:02,339   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:02,339     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-13T11:05:02,340         |                                                     ^
2021-07-13T11:05:02,342   htslib/cram/cram_codecs.c: In function ‘get_one_bits_MSB’:
2021-07-13T11:05:02,343   htslib/cram/cram_codecs.c:77:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:02,344      77 |     if (block->byte >= block->uncomp_size)
2021-07-13T11:05:02,344         |                     ^~
2021-07-13T11:05:02,344   htslib/cram/cram_codecs.c:84:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:02,344      84 |      if (block->byte == block->uncomp_size && (b&1))
2021-07-13T11:05:02,345         |                      ^~
2021-07-13T11:05:02,345   htslib/cram/cram_codecs.c: In function ‘get_zero_bits_MSB’:
2021-07-13T11:05:02,345   htslib/cram/cram_codecs.c:95:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:02,346      95 |     if (block->byte >= block->uncomp_size)
2021-07-13T11:05:02,346         |                     ^~
2021-07-13T11:05:02,346   htslib/cram/cram_codecs.c:102:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:02,346     102 |      if (block->byte == block->uncomp_size && !(b&1))
2021-07-13T11:05:02,346         |                      ^~
2021-07-13T11:05:02,358   htslib/cram/cram_codecs.c: In function ‘cram_beta_decode_init’:
2021-07-13T11:05:02,358   htslib/cram/cram_codecs.c:544:47: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:02,358     544 |         || c->beta.nbits < 0 || c->beta.nbits > 8 * sizeof(int)) {
2021-07-13T11:05:02,359         |                                               ^
2021-07-13T11:05:02,391   htslib/cram/cram_codecs.c: In function ‘cram_byte_array_stop_decode_block’:
2021-07-13T11:05:02,392   htslib/cram/cram_codecs.c:1587:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:02,392    1587 |     if (cp_end - cp < out->alloc - out->byte) {
2021-07-13T11:05:02,392         |                     ^
2021-07-13T11:05:04,765   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_decode.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_decode.o
2021-07-13T11:05:05,026   In file included from htslib/cram/cram.h:52,
2021-07-13T11:05:05,026                    from htslib/cram/cram_decode.c:48:
2021-07-13T11:05:05,026   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-13T11:05:05,026   htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:05,027     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-13T11:05:05,027         |             ^~
2021-07-13T11:05:05,027   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:05,027     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-13T11:05:05,028         |                                                     ^
2021-07-13T11:05:05,031   htslib/cram/cram_decode.c: In function ‘cram_decode_TD’:
2021-07-13T11:05:05,032   htslib/cram/cram_decode.c:101:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:05,032     101 |     for (nTL = i = 0; i < BLOCK_SIZE(b); i++) {
2021-07-13T11:05:05,032         |                         ^
2021-07-13T11:05:05,032   htslib/cram/cram_decode.c:113:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:05,032     113 |     for (nTL = i = 0; i < BLOCK_SIZE(b); i++) {
2021-07-13T11:05:05,033         |                         ^
2021-07-13T11:05:05,052   htslib/cram/cram_decode.c: In function ‘cram_dependent_data_series’:
2021-07-13T11:05:05,052   htslib/cram/cram_decode.c:794:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:05,052     794 |  for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) {
2021-07-13T11:05:05,052         |                ^
2021-07-13T11:05:05,054   htslib/cram/cram_decode.c:886:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:05,054     886 |  for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) {
2021-07-13T11:05:05,054         |                ^
2021-07-13T11:05:05,058   htslib/cram/cram_decode.c: In function ‘cram_decode_slice_header’:
2021-07-13T11:05:05,059   htslib/cram/cram_decode.c:1102:23: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:05,059    1102 |  hdr->num_content_ids >= SIZE_MAX / sizeof(int32_t)) {
2021-07-13T11:05:05,059         |                       ^~
2021-07-13T11:05:05,064   htslib/cram/cram_decode.c: In function ‘cram_decode_seq’:
2021-07-13T11:05:05,064   htslib/cram/cram_decode.c:1275:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:05,064    1275 |   if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) {
2021-07-13T11:05:05,064         |                               ^
2021-07-13T11:05:05,068   htslib/cram/cram_decode.c:1425:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:05,069    1425 |   if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) {
2021-07-13T11:05:05,069         |               ^~
2021-07-13T11:05:05,072   htslib/cram/cram_decode.c:1469:25: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:05,072    1469 |       if (ref_pos + i32 <= bfd->ref[cr->ref_id].len) {
2021-07-13T11:05:05,072         |                         ^~
2021-07-13T11:05:05,073   htslib/cram/cram_decode.c:1480:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:05,073    1480 |    if (bfd->ref[cr->ref_id].len >= ref_pos) {
2021-07-13T11:05:05,074         |                                 ^~
2021-07-13T11:05:05,078   htslib/cram/cram_decode.c:1573:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:05,079    1573 |    if (ref_pos+x >= bfd->ref[cr->ref_id].len || !s->ref) {
2021-07-13T11:05:05,079         |                  ^~
2021-07-13T11:05:05,081   htslib/cram/cram_decode.c:1644:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:05,082    1644 |       if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) {
2021-07-13T11:05:05,082         |                   ^~
2021-07-13T11:05:05,087   htslib/cram/cram_decode.c:1748:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:05,087    1748 |      if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) {
2021-07-13T11:05:05,087         |                                          ^
2021-07-13T11:05:05,111   htslib/cram/cram_decode.c: In function ‘cram_decode_slice’:
2021-07-13T11:05:05,112   htslib/cram/cram_decode.c:2367:6: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:05,112    2367 |   bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap))
2021-07-13T11:05:05,112         |      ^~
2021-07-13T11:05:10,635   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_encode.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_encode.o
2021-07-13T11:05:10,897   In file included from htslib/cram/cram.h:52,
2021-07-13T11:05:10,898                    from htslib/cram/cram_encode.c:43:
2021-07-13T11:05:10,898   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-13T11:05:10,898   htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:10,898     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-13T11:05:10,898         |             ^~
2021-07-13T11:05:10,899   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:10,899     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-13T11:05:10,899         |                                                     ^
2021-07-13T11:05:10,947   htslib/cram/cram_encode.c: In function ‘lossy_read_names’:
2021-07-13T11:05:10,948   htslib/cram/cram_encode.c:1297:14: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare]
2021-07-13T11:05:10,948    1297 |      if (u.e != e) {
2021-07-13T11:05:10,948         |              ^~
2021-07-13T11:05:10,949   htslib/cram/cram_encode.c:1327:23: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:10,949    1327 |  if (kh_val(names, k) == -1)
2021-07-13T11:05:10,950         |                       ^~
2021-07-13T11:05:10,991   htslib/cram/cram_encode.c: In function ‘process_one_read’:
2021-07-13T11:05:10,993   htslib/cram/cram_encode.c:2650:10: warning: unused variable ‘brg’ [-Wunused-variable]
2021-07-13T11:05:10,993    2650 |  SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN");
2021-07-13T11:05:10,993         |          ^~~
2021-07-13T11:05:10,997   htslib/cram/cram_encode.c:2758:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:10,997    2758 |  while (cr->cigar + cr->ncigar >= s->cigar_alloc) {
2021-07-13T11:05:10,998         |                                ^~
2021-07-13T11:05:10,999   htslib/cram/cram_encode.c:2788:30: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:10,999    2788 |       int end = cig_len+apos < c->ref_end
2021-07-13T11:05:10,999         |                              ^
2021-07-13T11:05:11,000   htslib/cram/cram_encode.c:2789:16: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2021-07-13T11:05:11,000    2789 |    ? cig_len : c->ref_end - apos;
2021-07-13T11:05:11,001         |                ^~~~~~~~~~~~~~~~~
2021-07-13T11:05:11,004   htslib/cram/cram_encode.c:2831:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:11,004    2831 |   if (l < cig_len && cr->len) {
2021-07-13T11:05:11,004         |         ^
2021-07-13T11:05:11,006   htslib/cram/cram_encode.c:2839:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:11,006    2839 |        for (; l < cig_len && seq[spos]; l++, spos++) {
2021-07-13T11:05:11,006         |                 ^
2021-07-13T11:05:11,007   htslib/cram/cram_encode.c:2847:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:11,008    2847 |    for (; l < cig_len && seq[spos]; l++, spos++) {
2021-07-13T11:05:11,008         |             ^
2021-07-13T11:05:11,011   htslib/cram/cram_encode.c:2878:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:11,012    2878 |       for (l = 0; l < cig_len; l++, spos++) {
2021-07-13T11:05:11,012         |                     ^
2021-07-13T11:05:11,014   htslib/cram/cram_encode.c:2894:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:11,014    2894 |    for (l = 0; l < cig_len; l++, spos++) {
2021-07-13T11:05:11,014         |                  ^
2021-07-13T11:05:11,015   htslib/cram/cram_encode.c:2898:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:11,015    2898 |    for (l = 0; l < cig_len; l++, spos++) {
2021-07-13T11:05:11,015         |                  ^
2021-07-13T11:05:16,398   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_external.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_external.o
2021-07-13T11:05:16,599   In file included from htslib/cram/cram.h:52,
2021-07-13T11:05:16,600                    from htslib/cram/cram_external.c:44:
2021-07-13T11:05:16,600   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-13T11:05:16,601   htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:16,601     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-13T11:05:16,601         |             ^~
2021-07-13T11:05:16,601   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:16,602     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-13T11:05:16,602         |                                                     ^
2021-07-13T11:05:16,975   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_index.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_index.o
2021-07-13T11:05:17,236   In file included from htslib/cram/cram.h:52,
2021-07-13T11:05:17,237                    from htslib/cram/cram_index.c:65:
2021-07-13T11:05:17,237   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-13T11:05:17,237   htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:17,237     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-13T11:05:17,237         |             ^~
2021-07-13T11:05:17,238   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:17,238     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-13T11:05:17,238         |                                                     ^
2021-07-13T11:05:17,248   htslib/cram/cram_index.c: In function ‘cram_index_build’:
2021-07-13T11:05:17,248   htslib/cram/cram_index.c:502:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable]
2021-07-13T11:05:17,249     502 |     off_t cpos, spos, hpos;
2021-07-13T11:05:17,250         |                       ^~~~
2021-07-13T11:05:17,928   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_io.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_io.o
2021-07-13T11:05:18,182   In file included from htslib/cram/cram.h:52,
2021-07-13T11:05:18,182                    from htslib/cram/cram_io.c:67:
2021-07-13T11:05:18,183   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-13T11:05:18,183   htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:18,183     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-13T11:05:18,183         |             ^~
2021-07-13T11:05:18,183   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:18,184     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-13T11:05:18,184         |                                                     ^
2021-07-13T11:05:18,254   In file included from htslib/cram/cram_io.h:48,
2021-07-13T11:05:18,254                    from htslib/cram/cram.h:48,
2021-07-13T11:05:18,254                    from htslib/cram/cram_io.c:67:
2021-07-13T11:05:18,255   htslib/cram/cram_io.c: In function ‘expand_cache_path’:
2021-07-13T11:05:18,255   htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:18,255     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-13T11:05:18,255         |                          ^
2021-07-13T11:05:18,256   htslib/cram/cram_io.c:2081:10: note: in expansion of macro ‘MIN’
2021-07-13T11:05:18,256    2081 |      l = MIN(l, strlen(fn));
2021-07-13T11:05:18,256         |          ^~~
2021-07-13T11:05:18,256   htslib/cram/misc.h:103:36: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2021-07-13T11:05:18,256     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-13T11:05:18,257         |                                    ^~~
2021-07-13T11:05:18,257   htslib/cram/cram_io.c:2081:10: note: in expansion of macro ‘MIN’
2021-07-13T11:05:18,257    2081 |      l = MIN(l, strlen(fn));
2021-07-13T11:05:18,257         |          ^~~
2021-07-13T11:05:18,379   In file included from htslib/cram/cram.h:48,
2021-07-13T11:05:18,379                    from htslib/cram/cram_io.c:67:
2021-07-13T11:05:18,379   htslib/cram/cram_io.c: In function ‘cram_write_SAM_hdr’:
2021-07-13T11:05:18,380   htslib/cram/cram_io.h:269:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:18,381     269 |  while((b)->alloc <= (l)) {    \
2021-07-13T11:05:18,381         |                   ^~
2021-07-13T11:05:18,381   htslib/cram/cram_io.c:3983:6: note: in expansion of macro ‘BLOCK_RESIZE’
2021-07-13T11:05:18,381    3983 |      BLOCK_RESIZE(b, padded_length);
2021-07-13T11:05:18,381         |      ^~~~~~~~~~~~
2021-07-13T11:05:20,947   In file included from /usr/include/string.h:495,
2021-07-13T11:05:20,947                    from htslib/cram/cram_io.c:53:
2021-07-13T11:05:20,948   In function ‘strncpy’,
2021-07-13T11:05:20,948       inlined from ‘cram_populate_ref’ at htslib/cram/cram_io.c:2229:2:
2021-07-13T11:05:20,948   /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
2021-07-13T11:05:20,948     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-13T11:05:20,948         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-13T11:05:20,948   htslib/cram/cram_io.c: In function ‘cram_populate_ref’:
2021-07-13T11:05:20,949   htslib/cram/cram_io.c:2337:27: warning: ‘.tmp_’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
2021-07-13T11:05:20,949    2337 |      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
2021-07-13T11:05:20,950         |                           ^~~~~
2021-07-13T11:05:20,950   In file included from /usr/include/stdio.h:867,
2021-07-13T11:05:20,950                    from htslib/cram/cram_io.c:49:
2021-07-13T11:05:20,950   /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 11 and 4134 bytes into a destination of size 4096
2021-07-13T11:05:20,950      36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
2021-07-13T11:05:20,950         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-13T11:05:20,950      37 |       __bos (__s), __fmt, __va_arg_pack ());
2021-07-13T11:05:20,951         |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-13T11:05:22,311   In file included from /usr/include/string.h:495,
2021-07-13T11:05:22,311                    from htslib/cram/cram_io.c:53:
2021-07-13T11:05:22,311   In function ‘strncpy’,
2021-07-13T11:05:22,311       inlined from ‘full_path’ at htslib/cram/cram_io.c:3807:6,
2021-07-13T11:05:22,311       inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3882:3:
2021-07-13T11:05:22,311   /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
2021-07-13T11:05:22,312     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-13T11:05:22,312         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-13T11:05:22,312   In function ‘strncpy’,
2021-07-13T11:05:22,312       inlined from ‘full_path’ at htslib/cram/cram_io.c:3799:2,
2021-07-13T11:05:22,312       inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3882:3:
2021-07-13T11:05:22,312   /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
2021-07-13T11:05:22,312     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-13T11:05:22,313         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-13T11:05:22,559   In function ‘strncpy’,
2021-07-13T11:05:22,559       inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4182:2:
2021-07-13T11:05:22,559   /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation]
2021-07-13T11:05:22,560     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-13T11:05:22,560         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-13T11:05:23,220   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_samtools.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_samtools.o
2021-07-13T11:05:23,417   In file included from htslib/cram/cram.h:52,
2021-07-13T11:05:23,417                    from htslib/cram/cram_samtools.c:37:
2021-07-13T11:05:23,417   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-13T11:05:23,418   htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:23,418     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-13T11:05:23,418         |             ^~
2021-07-13T11:05:23,419   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:23,419     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-13T11:05:23,419         |                                                     ^
2021-07-13T11:05:23,581   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_stats.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_stats.o
2021-07-13T11:05:23,844   In file included from htslib/cram/cram.h:52,
2021-07-13T11:05:23,845                    from htslib/cram/cram_stats.c:43:
2021-07-13T11:05:23,845   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-13T11:05:23,846   htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:23,846     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-13T11:05:23,846         |             ^~
2021-07-13T11:05:23,846   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:23,847     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-13T11:05:23,847         |                                                     ^
2021-07-13T11:05:24,218   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/files.c -o build/temp.linux-armv7l-3.9/htslib/cram/files.o
2021-07-13T11:05:24,400   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/mFILE.c -o build/temp.linux-armv7l-3.9/htslib/cram/mFILE.o
2021-07-13T11:05:24,561   htslib/cram/mFILE.c: In function ‘mfload’:
2021-07-13T11:05:24,562   htslib/cram/mFILE.c:103:47: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘__off_t’ {aka ‘long int’} [-Wsign-compare]
2021-07-13T11:05:24,562     103 |     } while (!feof(fp) && (fn == NULL || used < sb.st_size));
2021-07-13T11:05:24,562         |                                               ^
2021-07-13T11:05:24,566   htslib/cram/mFILE.c: In function ‘mftruncate’:
2021-07-13T11:05:24,566   htslib/cram/mFILE.c:476:31: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2021-07-13T11:05:24,566     476 |     mf->size = offset != -1 ? offset : mf->offset;
2021-07-13T11:05:24,566         |                               ^~~~~~
2021-07-13T11:05:25,003   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/open_trace_file.c -o build/temp.linux-armv7l-3.9/htslib/cram/open_trace_file.o
2021-07-13T11:05:25,164   In file included from htslib/cram/open_trace_file.c:79:
2021-07-13T11:05:25,164   htslib/cram/open_trace_file.c: In function ‘expand_path’:
2021-07-13T11:05:25,164   htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare]
2021-07-13T11:05:25,164     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-13T11:05:25,164         |                          ^
2021-07-13T11:05:25,165   htslib/cram/open_trace_file.c:243:15: note: in expansion of macro ‘MIN’
2021-07-13T11:05:25,165     243 |   path_end += MIN(strlen(file), l);
2021-07-13T11:05:25,165         |               ^~~
2021-07-13T11:05:25,165   htslib/cram/misc.h:103:42: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2021-07-13T11:05:25,165     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-13T11:05:25,165         |                                          ^~~
2021-07-13T11:05:25,165   htslib/cram/open_trace_file.c:243:15: note: in expansion of macro ‘MIN’
2021-07-13T11:05:25,166     243 |   path_end += MIN(strlen(file), l);
2021-07-13T11:05:25,166         |               ^~~
2021-07-13T11:05:25,166   htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare]
2021-07-13T11:05:25,166     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-13T11:05:25,166         |                          ^
2021-07-13T11:05:25,166   htslib/cram/open_trace_file.c:244:15: note: in expansion of macro ‘MIN’
2021-07-13T11:05:25,166     244 |   file     += MIN(strlen(file), l);
2021-07-13T11:05:25,167         |               ^~~
2021-07-13T11:05:25,167   htslib/cram/misc.h:103:42: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2021-07-13T11:05:25,167     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-13T11:05:25,167         |                                          ^~~
2021-07-13T11:05:25,168   htslib/cram/open_trace_file.c:244:15: note: in expansion of macro ‘MIN’
2021-07-13T11:05:25,168     244 |   file     += MIN(strlen(file), l);
2021-07-13T11:05:25,168         |               ^~~
2021-07-13T11:05:25,509   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/pooled_alloc.c -o build/temp.linux-armv7l-3.9/htslib/cram/pooled_alloc.o
2021-07-13T11:05:25,731   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/rANS_static.c -o build/temp.linux-armv7l-3.9/htslib/cram/rANS_static.o
2021-07-13T11:05:25,877   htslib/cram/rANS_static.c: In function ‘rans_compress_O0’:
2021-07-13T11:05:25,877   htslib/cram/rANS_static.c:86:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:25,878      86 |     for (i = 0; i < in_size; i++) {
2021-07-13T11:05:25,878         |                   ^
2021-07-13T11:05:25,881   htslib/cram/rANS_static.c: In function ‘rans_uncompress_O0’:
2021-07-13T11:05:25,881   htslib/cram/rANS_static.c:222:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:25,881     222 |     if (in_sz != in_size-9)
2021-07-13T11:05:25,881         |               ^~
2021-07-13T11:05:25,885   htslib/cram/rANS_static.c: In function ‘rans_compress_O1’:
2021-07-13T11:05:25,885   htslib/cram/rANS_static.c:390:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:25,886     390 |     for (last_i=i=0; i<in_size; i++) {
2021-07-13T11:05:25,886         |                       ^
2021-07-13T11:05:25,890   htslib/cram/rANS_static.c: In function ‘rans_uncompress_O1’:
2021-07-13T11:05:25,891   htslib/cram/rANS_static.c:579:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:25,891     579 |     if (in_sz != in_size-9)
2021-07-13T11:05:25,891         |               ^~
2021-07-13T11:05:27,258   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/sam_header.c -o build/temp.linux-armv7l-3.9/htslib/cram/sam_header.o
2021-07-13T11:05:27,405   htslib/cram/sam_header.c: In function ‘sam_hdr_add_lines’:
2021-07-13T11:05:27,405   htslib/cram/sam_header.c:327:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:27,406     327 |  if (-1 == (k = kh_put(sam_hdr, sh->h, type, &new)))
2021-07-13T11:05:27,406         |         ^~
2021-07-13T11:05:27,408   htslib/cram/sam_header.c: In function ‘sam_hdr_vadd’:
2021-07-13T11:05:27,408   htslib/cram/sam_header.c:450:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:27,408     450 |     if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new)))
2021-07-13T11:05:27,409         |            ^~
2021-07-13T11:05:27,417   htslib/cram/sam_header.c: In function ‘sam_hdr_rebuild’:
2021-07-13T11:05:27,417   htslib/cram/sam_header.c:821:24: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:27,417     821 |  if (kh_key(hdr->h, k) == K("HD"))
2021-07-13T11:05:27,417         |                        ^~
2021-07-13T11:05:29,431   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/string_alloc.c -o build/temp.linux-armv7l-3.9/htslib/cram/string_alloc.o
2021-07-13T11:05:29,653   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/thread_pool.c -o build/temp.linux-armv7l-3.9/htslib/cram/thread_pool.o
2021-07-13T11:05:30,141   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/vlen.c -o build/temp.linux-armv7l-3.9/htslib/cram/vlen.o
2021-07-13T11:05:30,268   htslib/cram/vlen.c: In function ‘vflen’:
2021-07-13T11:05:30,268   htslib/cram/vlen.c:77:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:30,269      77 | #define MAX(a,b) ((a)>(b)?(a):(b))
2021-07-13T11:05:30,269         |                      ^
2021-07-13T11:05:30,269   htslib/cram/vlen.c:239:10: note: in expansion of macro ‘MAX’
2021-07-13T11:05:30,269     239 |   len += MAX(conv_len1, i>=0x80 ?MB_CUR_MAX :1);
2021-07-13T11:05:30,269         |          ^~~
2021-07-13T11:05:30,269   htslib/cram/vlen.c:77:27: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2021-07-13T11:05:30,270      77 | #define MAX(a,b) ((a)>(b)?(a):(b))
2021-07-13T11:05:30,270         |                           ^~~
2021-07-13T11:05:30,270   htslib/cram/vlen.c:239:10: note: in expansion of macro ‘MAX’
2021-07-13T11:05:30,271     239 |   len += MAX(conv_len1, i>=0x80 ?MB_CUR_MAX :1);
2021-07-13T11:05:30,271         |          ^~~
2021-07-13T11:05:30,423   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/zfio.c -o build/temp.linux-armv7l-3.9/htslib/cram/zfio.o
2021-07-13T11:05:30,715   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/errmod.c -o build/temp.linux-armv7l-3.9/htslib/errmod.o
2021-07-13T11:05:31,458   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/faidx.c -o build/temp.linux-armv7l-3.9/htslib/faidx.o
2021-07-13T11:05:32,775   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hfile.c -o build/temp.linux-armv7l-3.9/htslib/hfile.o
2021-07-13T11:05:32,993   htslib/hfile.c: In function ‘find_scheme_handler’:
2021-07-13T11:05:32,993   htslib/hfile.c:717:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:32,993     717 |     for (i = 0; i < sizeof scheme; i++)
2021-07-13T11:05:32,993         |                   ^
2021-07-13T11:05:32,994   htslib/hfile.c:723:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-13T11:05:32,994     723 |     if (i == 0 || i >= sizeof scheme) return NULL;
2021-07-13T11:05:32,994         |                     ^~
2021-07-13T11:05:33,769   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hfile_net.c -o build/temp.linux-armv7l-3.9/htslib/hfile_net.o
2021-07-13T11:05:33,962   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hts.c -o build/temp.linux-armv7l-3.9/htslib/hts.o
2021-07-13T11:05:34,206   In file included from htslib/cram/cram.h:52,
2021-07-13T11:05:34,206                    from htslib/hts.c:39:
2021-07-13T11:05:34,207   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-13T11:05:34,207   htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:34,207     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-13T11:05:34,207         |             ^~
2021-07-13T11:05:34,207   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:34,207     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-13T11:05:34,208         |                                                     ^
2021-07-13T11:05:34,262   htslib/hts.c: In function ‘hts_idx_init’:
2021-07-13T11:05:34,262   htslib/hts.c:1222:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow]
2021-07-13T11:05:34,263    1222 |     idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
2021-07-13T11:05:34,263         |                                                           ^~~
2021-07-13T11:05:34,265   htslib/hts.c: In function ‘update_loff’:
2021-07-13T11:05:34,265   htslib/hts.c:1256:34: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:34,265    1256 |             if ( kh_key(bidx, k) < idx->n_bins )
2021-07-13T11:05:34,266         |                                  ^
2021-07-13T11:05:34,266   htslib/hts.c: In function ‘compress_binning’:
2021-07-13T11:05:34,267   htslib/hts.c:1283:55: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:34,267    1283 |             if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue;
2021-07-13T11:05:34,267         |                                                       ^~
2021-07-13T11:05:34,269   htslib/hts.c:1308:51: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:34,269    1308 |         if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue;
2021-07-13T11:05:34,270         |                                                   ^~
2021-07-13T11:05:34,290   htslib/hts.c: In function ‘hts_idx_load_local’:
2021-07-13T11:05:34,290   htslib/hts.c:1618:43: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:34,291    1618 |             if (bgzf_read(fp, meta, x[2]) != x[2]) goto fail;
2021-07-13T11:05:34,291         |                                           ^~
2021-07-13T11:05:34,294   htslib/hts.c:1636:49: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:34,294    1636 |         if (bgzf_read(fp, idx->meta + 28, x[7]) != x[7]) goto fail;
2021-07-13T11:05:34,295         |                                                 ^~
2021-07-13T11:05:38,266   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/kfunc.c -o build/temp.linux-armv7l-3.9/htslib/kfunc.o
2021-07-13T11:05:38,699   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/knetfile.c -o build/temp.linux-armv7l-3.9/htslib/knetfile.o
2021-07-13T11:05:39,470   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/kstring.c -o build/temp.linux-armv7l-3.9/htslib/kstring.o
2021-07-13T11:05:39,598   htslib/kstring.c: In function ‘kvsprintf’:
2021-07-13T11:05:39,599   htslib/kstring.c:42:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:39,599      42 |  if (l + 1 > s->m - s->l) {
2021-07-13T11:05:39,599         |            ^
2021-07-13T11:05:39,983   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/md5.c -o build/temp.linux-armv7l-3.9/htslib/md5.o
2021-07-13T11:05:40,544   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/probaln.c -o build/temp.linux-armv7l-3.9/htslib/probaln.o
2021-07-13T11:05:41,254   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/realn.c -o build/temp.linux-armv7l-3.9/htslib/realn.o
2021-07-13T11:05:41,944   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/regidx.c -o build/temp.linux-armv7l-3.9/htslib/regidx.o
2021-07-13T11:05:42,097   htslib/regidx.c: In function ‘regidx_insert’:
2021-07-13T11:05:42,098   htslib/regidx.c:155:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:42,098     155 |         if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
2021-07-13T11:05:42,098         |                              ^
2021-07-13T11:05:42,098   htslib/regidx.c:155:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:42,098     155 |         if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
2021-07-13T11:05:42,098         |                                                             ^~
2021-07-13T11:05:42,099   htslib/regidx.c:155:89: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:42,099     155 |         if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
2021-07-13T11:05:42,099         |                                                                                         ^
2021-07-13T11:05:42,860   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/sam.c -o build/temp.linux-armv7l-3.9/htslib/sam.o
2021-07-13T11:05:43,088   In file included from htslib/cram/cram.h:52,
2021-07-13T11:05:43,089                    from htslib/sam.c:35:
2021-07-13T11:05:43,089   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-13T11:05:43,089   htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare]
2021-07-13T11:05:43,090     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-13T11:05:43,090         |             ^~
2021-07-13T11:05:43,090   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:43,090     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-13T11:05:43,090         |                                                     ^
2021-07-13T11:05:43,105   htslib/sam.c: In function ‘bam_hdr_read’:
2021-07-13T11:05:43,106   htslib/sam.c:147:15: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:43,106     147 |     if (bytes != h->l_text) goto read_err;
2021-07-13T11:05:43,106         |               ^~
2021-07-13T11:05:43,115   htslib/sam.c: In function ‘bam_write1’:
2021-07-13T11:05:43,115   htslib/sam.c:467:32: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2021-07-13T11:05:43,116     467 |     return ok? 4 + block_len : -1;
2021-07-13T11:05:43,116         |                                ^~
2021-07-13T11:05:43,127   htslib/sam.c: In function ‘sam_hdr_write’:
2021-07-13T11:05:43,128   htslib/sam.c:818:67: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:43,128     818 |                 if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
2021-07-13T11:05:43,128         |                                                                   ^~
2021-07-13T11:05:43,145   htslib/sam.c: In function ‘sam_format1’:
2021-07-13T11:05:43,146   htslib/sam.c:1181:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:43,147    1181 |             if ((b->data + b->l_data - s) / sub_type_size < n)
2021-07-13T11:05:43,147         |                                                           ^
2021-07-13T11:05:43,148   htslib/sam.c:1184:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:43,148    1184 |             for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if"
2021-07-13T11:05:43,148         |                           ^
2021-07-13T11:05:43,150   htslib/sam.c: In function ‘sam_write1’:
2021-07-13T11:05:43,151   htslib/sam.c:1220:59: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:43,151    1220 |         if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
2021-07-13T11:05:43,151         |                                                           ^~
2021-07-13T11:05:43,366   In file included from /usr/include/string.h:495,
2021-07-13T11:05:43,366                    from htslib/sam.c:30:
2021-07-13T11:05:43,366   In function ‘strncpy’,
2021-07-13T11:05:43,366       inlined from ‘bam_hdr_write’ at htslib/sam.c:229:5:
2021-07-13T11:05:43,366   /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
2021-07-13T11:05:43,367     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-13T11:05:43,367         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-13T11:05:48,710   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/synced_bcf_reader.c -o build/temp.linux-armv7l-3.9/htslib/synced_bcf_reader.o
2021-07-13T11:05:48,914   htslib/synced_bcf_reader.c: In function ‘_regions_add’:
2021-07-13T11:05:48,915   htslib/synced_bcf_reader.c:860:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:48,915     860 |         if ( start < creg->regs[i].start ) max = i - 1;
2021-07-13T11:05:48,915         |                    ^
2021-07-13T11:05:48,916   htslib/synced_bcf_reader.c:861:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:48,916     861 |         else if ( start > creg->regs[i].start ) min = i + 1;
2021-07-13T11:05:48,916         |                         ^
2021-07-13T11:05:48,917   htslib/synced_bcf_reader.c:864:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:48,917     864 |     if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end )
2021-07-13T11:05:48,917         |                                        ^~
2021-07-13T11:05:48,918   htslib/synced_bcf_reader.c:864:68: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:05:48,918     864 |     if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end )
2021-07-13T11:05:48,918         |                                                                    ^~
2021-07-13T11:05:50,909   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/tbx.c -o build/temp.linux-armv7l-3.9/htslib/tbx.o
2021-07-13T11:05:51,552   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/vcf.c -o build/temp.linux-armv7l-3.9/htslib/vcf.o
2021-07-13T11:05:51,748   htslib/vcf.c: In function ‘bcf_hdr_sync’:
2021-07-13T11:05:51,749   htslib/vcf.c:151:22: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:51,749     151 |         if ( h->n[i] < kh_size(d) )
2021-07-13T11:05:51,749         |                      ^
2021-07-13T11:05:51,772   htslib/vcf.c: In function ‘bcf_hdr_read’:
2021-07-13T11:05:51,772   htslib/vcf.c:861:35: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:51,773     861 |     if (bgzf_read(fp, htxt, hlen) != hlen) goto fail;
2021-07-13T11:05:51,773         |                                   ^~
2021-07-13T11:05:51,774   htslib/vcf.c: In function ‘bcf_hdr_write’:
2021-07-13T11:05:51,775   htslib/vcf.c:888:41: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:51,775     888 |     if ( bgzf_write(fp, htxt.s, htxt.l) != htxt.l ) return -1;
2021-07-13T11:05:51,775         |                                         ^~
2021-07-13T11:05:51,778   htslib/vcf.c: In function ‘bcf_read1_core’:
2021-07-13T11:05:51,779   htslib/vcf.c:972:49: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:51,779     972 |     if (bgzf_read(fp, v->shared.s, v->shared.l) != v->shared.l) return -1;
2021-07-13T11:05:51,779         |                                                 ^~
2021-07-13T11:05:51,780   htslib/vcf.c:973:47: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:51,780     973 |     if (bgzf_read(fp, v->indiv.s, v->indiv.l) != v->indiv.l) return -1;
2021-07-13T11:05:51,780         |                                               ^~
2021-07-13T11:05:51,792   htslib/vcf.c: In function ‘bcf_write’:
2021-07-13T11:05:51,793   htslib/vcf.c:1287:51: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:51,793    1287 |     if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1;
2021-07-13T11:05:51,793         |                                                   ^~
2021-07-13T11:05:51,794   htslib/vcf.c:1288:49: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:51,794    1288 |     if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1;
2021-07-13T11:05:51,795         |                                                 ^~
2021-07-13T11:05:51,809   htslib/vcf.c: In function ‘vcf_parse_format’:
2021-07-13T11:05:51,810   htslib/vcf.c:1680:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-13T11:05:51,811    1680 |                 if (fmt[j].max_l < l) fmt[j].max_l = l;
2021-07-13T11:05:51,811         |                                  ^
2021-07-13T11:05:51,815   htslib/vcf.c:1709:33: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-13T11:05:51,815    1709 |             f->size = f->is_gt? f->max_g << 2 : f->max_l;
2021-07-13T11:05:51,815         |                                 ^~~~~~~~~~~~~
2021-07-13T11:05:51,853   htslib/vcf.c: In function ‘vcf_write_line’:
2021-07-13T11:05:51,855   htslib/vcf.c:2274:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:51,855    2274 |     return ret==line->l ? 0 : -1;
2021-07-13T11:05:51,855         |               ^~
2021-07-13T11:05:51,856   htslib/vcf.c: In function ‘vcf_write’:
2021-07-13T11:05:51,857   htslib/vcf.c:2286:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:51,857    2286 |     return ret==fp->line.l ? 0 : -1;
2021-07-13T11:05:51,858         |               ^~
2021-07-13T11:05:51,883   htslib/vcf.c: In function ‘bcf_hdr_set_samples’:
2021-07-13T11:05:51,884   htslib/vcf.c:2755:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-13T11:05:51,885    2755 |         for (k = kh_begin(d); k != kh_end(d); ++k)
2021-07-13T11:05:51,885         |                                 ^~
2021-07-13T11:05:51,929   htslib/vcf.c: In function ‘_bcf1_sync_alleles’:
2021-07-13T11:05:51,930   htslib/vcf.c:3204:29: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2021-07-13T11:05:51,931    3204 |     line->rlen = end_info ? end_info->v1.i : strlen(line->d.allele[0]);
2021-07-13T11:05:51,931         |                             ^~~~~~~~~~~~~~
2021-07-13T11:05:51,941   htslib/vcf.c: In function ‘bcf_get_info_values’:
2021-07-13T11:05:51,943   htslib/vcf.c:3334:49: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-13T11:05:51,943    3334 |     if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2;     // expected different type
2021-07-13T11:05:51,943         |                                                 ^~
2021-07-13T11:05:51,957   htslib/vcf.c: In function ‘bcf_get_format_values’:
2021-07-13T11:05:51,959   htslib/vcf.c:3456:53: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-13T11:05:51,959    3456 |     else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2;     // expected different type
2021-07-13T11:05:51,959         |                                                     ^~
2021-07-13T11:06:00,262   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/vcf_sweep.c -o build/temp.linux-armv7l-3.9/htslib/vcf_sweep.o
2021-07-13T11:06:00,436   htslib/vcf_sweep.c: In function ‘bcf_sweep_fwd’:
2021-07-13T11:06:00,436   htslib/vcf_sweep.c:164:53: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-13T11:06:00,436     164 |         if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size )
2021-07-13T11:06:00,436         |                                                     ^
2021-07-13T11:06:00,634   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 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/vcfutils.c -o build/temp.linux-armv7l-3.9/htslib/vcfutils.o
2021-07-13T11:06:02,765   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/cyvcf2/cyvcf2.o build/temp.linux-armv7l-3.9/cyvcf2/helpers.o build/temp.linux-armv7l-3.9/htslib/bgzf.o build/temp.linux-armv7l-3.9/htslib/cram/cram_codecs.o build/temp.linux-armv7l-3.9/htslib/cram/cram_decode.o build/temp.linux-armv7l-3.9/htslib/cram/cram_encode.o build/temp.linux-armv7l-3.9/htslib/cram/cram_external.o build/temp.linux-armv7l-3.9/htslib/cram/cram_index.o build/temp.linux-armv7l-3.9/htslib/cram/cram_io.o build/temp.linux-armv7l-3.9/htslib/cram/cram_samtools.o build/temp.linux-armv7l-3.9/htslib/cram/cram_stats.o build/temp.linux-armv7l-3.9/htslib/cram/files.o build/temp.linux-armv7l-3.9/htslib/cram/mFILE.o build/temp.linux-armv7l-3.9/htslib/cram/open_trace_file.o build/temp.linux-armv7l-3.9/htslib/cram/pooled_alloc.o build/temp.linux-armv7l-3.9/htslib/cram/rANS_static.o build/temp.linux-armv7l-3.9/htslib/cram/sam_header.o build/temp.linux-armv7l-3.9/htslib/cram/string_alloc.o build/temp.linux-armv7l-3.9/htslib/cram/thread_pool.o build/temp.linux-armv7l-3.9/htslib/cram/vlen.o build/temp.linux-armv7l-3.9/htslib/cram/zfio.o build/temp.linux-armv7l-3.9/htslib/errmod.o build/temp.linux-armv7l-3.9/htslib/faidx.o build/temp.linux-armv7l-3.9/htslib/hfile.o build/temp.linux-armv7l-3.9/htslib/hfile_net.o build/temp.linux-armv7l-3.9/htslib/hts.o build/temp.linux-armv7l-3.9/htslib/kfunc.o build/temp.linux-armv7l-3.9/htslib/knetfile.o build/temp.linux-armv7l-3.9/htslib/kstring.o build/temp.linux-armv7l-3.9/htslib/md5.o build/temp.linux-armv7l-3.9/htslib/probaln.o build/temp.linux-armv7l-3.9/htslib/realn.o build/temp.linux-armv7l-3.9/htslib/regidx.o build/temp.linux-armv7l-3.9/htslib/sam.o build/temp.linux-armv7l-3.9/htslib/synced_bcf_reader.o build/temp.linux-armv7l-3.9/htslib/tbx.o build/temp.linux-armv7l-3.9/htslib/vcf.o build/temp.linux-armv7l-3.9/htslib/vcf_sweep.o build/temp.linux-armv7l-3.9/htslib/vcfutils.o -lz -o build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so
2021-07-13T11:06:03,401   installing to build/bdist.linux-armv7l/wheel
2021-07-13T11:06:03,401   running install
2021-07-13T11:06:03,403   running install_lib
2021-07-13T11:06:03,407   creating build/bdist.linux-armv7l
2021-07-13T11:06:03,407   creating build/bdist.linux-armv7l/wheel
2021-07-13T11:06:03,409   creating build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,410   copying build/lib.linux-armv7l-3.9/cyvcf2/cli.py -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,413   copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pxd -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,416   copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.c -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,418   copying build/lib.linux-armv7l-3.9/cyvcf2/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,419   copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pyx -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,426   creating build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,426   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,428   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,430   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.t.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,457   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/seg.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,458   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,460   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-alt-repr.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,462   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-haploidX.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,477   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_alt_freqs.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,480   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,483   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/bug.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,485   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.comp_het.3.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,487   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_bases.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,490   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,496   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-format-string.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,498   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,499   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,501   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,503   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf.csi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,505   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,507   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,509   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,512   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-issue-48.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,514   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/empty.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,515   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,517   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/o.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,521   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,524   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/decomposed.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,525   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/issue_44.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,527   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-hemi.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,530   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,531   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-alt-repr-1.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-13T11:06:03,533   copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.c -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,596   copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,737   copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.h -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,739   copying build/lib.linux-armv7l-3.9/cyvcf2/relatedness.h -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,741   copying build/lib.linux-armv7l-3.9/cyvcf2/__main__.py -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-13T11:06:03,742   running install_egg_info
2021-07-13T11:06:03,755   Copying cyvcf2.egg-info to build/bdist.linux-armv7l/wheel/cyvcf2-0.9.0-py3.9.egg-info
2021-07-13T11:06:03,772   running install_scripts
2021-07-13T11:06:03,812   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2021-07-13T11:06:03,817   creating build/bdist.linux-armv7l/wheel/cyvcf2-0.9.0.dist-info/WHEEL
2021-07-13T11:06:03,819   creating '/tmp/pip-wheel-zc_l4eed/cyvcf2-0.9.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-13T11:06:03,822   adding 'cyvcf2/__init__.py'
2021-07-13T11:06:03,823   adding 'cyvcf2/__main__.py'
2021-07-13T11:06:03,825   adding 'cyvcf2/cli.py'
2021-07-13T11:06:04,018   adding 'cyvcf2/cyvcf2.c'
2021-07-13T11:06:05,266   adding 'cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so'
2021-07-13T11:06:05,316   adding 'cyvcf2/cyvcf2.pxd'
2021-07-13T11:06:05,324   adding 'cyvcf2/cyvcf2.pyx'
2021-07-13T11:06:05,326   adding 'cyvcf2/helpers.c'
2021-07-13T11:06:05,327   adding 'cyvcf2/helpers.h'
2021-07-13T11:06:05,329   adding 'cyvcf2/relatedness.h'
2021-07-13T11:06:05,331   adding 'cyvcf2/tests/__init__.py'
2021-07-13T11:06:05,332   adding 'cyvcf2/tests/__init__.pyc'
2021-07-13T11:06:05,333   adding 'cyvcf2/tests/bug.vcf.gz'
2021-07-13T11:06:05,334   adding 'cyvcf2/tests/decomposed.vcf'
2021-07-13T11:06:05,335   adding 'cyvcf2/tests/empty.vcf'
2021-07-13T11:06:05,337   adding 'cyvcf2/tests/issue_44.vcf'
2021-07-13T11:06:05,342   adding 'cyvcf2/tests/o.vcf.gz'
2021-07-13T11:06:05,343   adding 'cyvcf2/tests/seg.vcf.gz'
2021-07-13T11:06:05,345   adding 'cyvcf2/tests/test-alt-repr-1.vcf'
2021-07-13T11:06:05,346   adding 'cyvcf2/tests/test-alt-repr.vcf'
2021-07-13T11:06:05,347   adding 'cyvcf2/tests/test-format-string.vcf'
2021-07-13T11:06:05,388   adding 'cyvcf2/tests/test-haploidX.vcf'
2021-07-13T11:06:05,395   adding 'cyvcf2/tests/test-hemi.vcf'
2021-07-13T11:06:05,397   adding 'cyvcf2/tests/test-issue-48.vcf.gz'
2021-07-13T11:06:05,398   adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz'
2021-07-13T11:06:05,399   adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi'
2021-07-13T11:06:05,400   adding 'cyvcf2/tests/test-strict-gt-option-flag.vcf.gz'
2021-07-13T11:06:05,401   adding 'cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi'
2021-07-13T11:06:05,403   adding 'cyvcf2/tests/test.comp_het.3.vcf'
2021-07-13T11:06:05,405   adding 'cyvcf2/tests/test.snpeff.bcf'
2021-07-13T11:06:05,406   adding 'cyvcf2/tests/test.snpeff.bcf.csi'
2021-07-13T11:06:05,408   adding 'cyvcf2/tests/test.snpeff.vcf'
2021-07-13T11:06:05,509   adding 'cyvcf2/tests/test.t.vcf'
2021-07-13T11:06:05,535   adding 'cyvcf2/tests/test.vcf.gz'
2021-07-13T11:06:05,537   adding 'cyvcf2/tests/test.vcf.gz.tbi'
2021-07-13T11:06:05,540   adding 'cyvcf2/tests/test_gt_alt_freqs.vcf'
2021-07-13T11:06:05,541   adding 'cyvcf2/tests/test_gt_bases.vcf.gz'
2021-07-13T11:06:05,543   adding 'cyvcf2/tests/test_hemi.py'
2021-07-13T11:06:05,544   adding 'cyvcf2/tests/test_hemi.pyc'
2021-07-13T11:06:05,547   adding 'cyvcf2/tests/test_reader.py'
2021-07-13T11:06:05,554   adding 'cyvcf2/tests/test_reader.pyc'
2021-07-13T11:06:05,556   adding 'cyvcf2-0.9.0.dist-info/LICENSE'
2021-07-13T11:06:05,558   adding 'cyvcf2-0.9.0.dist-info/METADATA'
2021-07-13T11:06:05,559   adding 'cyvcf2-0.9.0.dist-info/WHEEL'
2021-07-13T11:06:05,560   adding 'cyvcf2-0.9.0.dist-info/entry_points.txt'
2021-07-13T11:06:05,561   adding 'cyvcf2-0.9.0.dist-info/top_level.txt'
2021-07-13T11:06:05,562   adding 'cyvcf2-0.9.0.dist-info/RECORD'
2021-07-13T11:06:05,615   removing build/bdist.linux-armv7l/wheel
2021-07-13T11:06:06,174   Building wheel for cyvcf2 (setup.py): finished with status 'done'
2021-07-13T11:06:06,222   Created wheel for cyvcf2: filename=cyvcf2-0.9.0-cp39-cp39-linux_armv7l.whl size=3181906 sha256=f243d74f04aed85b9b0f07f1efc0694c7b2f772d8cb20e484330d12a47f2a160
2021-07-13T11:06:06,222   Stored in directory: /tmp/pip-ephem-wheel-cache-8qwq46g8/wheels/b1/79/6b/7131cd3e377dc5154f0dc92bbd76f68dab99251cfa68c33e5d
2021-07-13T11:06:06,235 Successfully built cyvcf2
2021-07-13T11:06:06,351 Removed build tracker: '/tmp/pip-req-tracker-8wlln_k6'