2021-07-12T03:08:00,077 Created temporary directory: /tmp/pip-ephem-wheel-cache-473y8h7f
2021-07-12T03:08:00,080 Created temporary directory: /tmp/pip-req-tracker-vap6cr58
2021-07-12T03:08:00,080 Initialized build tracking at /tmp/pip-req-tracker-vap6cr58
2021-07-12T03:08:00,081 Created build tracker: /tmp/pip-req-tracker-vap6cr58
2021-07-12T03:08:00,081 Entered build tracker: /tmp/pip-req-tracker-vap6cr58
2021-07-12T03:08:00,081 Created temporary directory: /tmp/pip-wheel-qazep9h7
2021-07-12T03:08:00,112 1 location(s) to search for versions of cyvcf2:
2021-07-12T03:08:00,112 * https://pypi.org/simple/cyvcf2/
2021-07-12T03:08:00,113 Fetching project page and analyzing links: https://pypi.org/simple/cyvcf2/
2021-07-12T03:08:00,113 Getting page https://pypi.org/simple/cyvcf2/
2021-07-12T03:08:00,114 Found index url https://pypi.org/simple
2021-07-12T03:08:00,335   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
2021-07-12T03:08:00,335   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
2021-07-12T03:08:00,335   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
2021-07-12T03:08:00,336   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
2021-07-12T03:08:00,336   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
2021-07-12T03:08:00,336   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
2021-07-12T03:08:00,337   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
2021-07-12T03:08:00,337   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
2021-07-12T03:08:00,337   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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2021-07-12T03:08:00,338   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
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2021-07-12T03:08:00,339   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
2021-07-12T03:08:00,340   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
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2021-07-12T03:08:00,341   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
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2021-07-12T03:08:00,341   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
2021-07-12T03:08:00,342   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
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2021-07-12T03:08:00,348   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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2021-07-12T03:08:00,351   Found link https://files.pythonhosted.org/packages/10/69/888f23e07de1364533ac666941b0e1229c7e60c1a5080b1234b849bd8b97/cyvcf2-0.10.10.tar.gz#sha256=14a469567992c218d1f1b8ab76b93ec5c1bf56c9f071cf93a3affdaabc9268e0 (from https://pypi.org/simple/cyvcf2/), version: 0.10.10
2021-07-12T03:08:00,351   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
2021-07-12T03:08:00,354   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/)
2021-07-12T03:08:00,354   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
2021-07-12T03:08:00,354   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
2021-07-12T03:08:00,355   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
2021-07-12T03:08:00,355   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
2021-07-12T03:08:00,355   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
2021-07-12T03:08:00,356   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
2021-07-12T03:08:00,356   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
2021-07-12T03:08:00,356   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
2021-07-12T03:08:00,356   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
2021-07-12T03:08:00,357   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
2021-07-12T03:08:00,357   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
2021-07-12T03:08:00,357   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
2021-07-12T03:08:00,357   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
2021-07-12T03:08:00,358   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
2021-07-12T03:08:00,358   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
2021-07-12T03:08:00,358   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
2021-07-12T03:08:00,359   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
2021-07-12T03:08:00,376   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/)
2021-07-12T03:08:00,376   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/)
2021-07-12T03:08:00,377   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/)
2021-07-12T03:08:00,377   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/)
2021-07-12T03:08:00,378   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/)
2021-07-12T03:08:00,378   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/)
2021-07-12T03:08:00,379   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/)
2021-07-12T03:08:00,379   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/)
2021-07-12T03:08:00,379   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/)
2021-07-12T03:08:00,380   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/)
2021-07-12T03:08:00,380   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
2021-07-12T03:08:00,381 Skipping link: not a file: https://pypi.org/simple/cyvcf2/
2021-07-12T03:08:00,393 Given no hashes to check 1 links for project 'cyvcf2': discarding no candidates
2021-07-12T03:08:00,412 Collecting cyvcf2==0.7.2
2021-07-12T03:08:00,414   Created temporary directory: /tmp/pip-unpack-xhi2uaa9
2021-07-12T03:08:00,938   Downloading cyvcf2-0.7.2.tar.gz (1.0 MB)
2021-07-12T03:08:01,553   Added cyvcf2==0.7.2 from https://files.pythonhosted.org/packages/66/f5/cb923cec9bb0fd761bde06cc1890fa280f1ff198156db92df69b8d152fd8/cyvcf2-0.7.2.tar.gz#sha256=8864f49491de89d2b117d4aa7e985491f5b5ef411615d303c62e4b97b810d755 to build tracker '/tmp/pip-req-tracker-vap6cr58'
2021-07-12T03:08:01,554     Running setup.py (path:/tmp/pip-wheel-qazep9h7/cyvcf2_96ac09ff0474485795f66bd2dd514bcc/setup.py) egg_info for package cyvcf2
2021-07-12T03:08:01,555     Created temporary directory: /tmp/pip-pip-egg-info-9s204jyk
2021-07-12T03:08:01,555     Running command python setup.py egg_info
2021-07-12T03:08:03,109     running egg_info
2021-07-12T03:08:03,111     creating /tmp/pip-pip-egg-info-9s204jyk/cyvcf2.egg-info
2021-07-12T03:08:03,112     writing /tmp/pip-pip-egg-info-9s204jyk/cyvcf2.egg-info/PKG-INFO
2021-07-12T03:08:03,115     writing dependency_links to /tmp/pip-pip-egg-info-9s204jyk/cyvcf2.egg-info/dependency_links.txt
2021-07-12T03:08:03,117     writing requirements to /tmp/pip-pip-egg-info-9s204jyk/cyvcf2.egg-info/requires.txt
2021-07-12T03:08:03,118     writing top-level names to /tmp/pip-pip-egg-info-9s204jyk/cyvcf2.egg-info/top_level.txt
2021-07-12T03:08:03,119     writing manifest file '/tmp/pip-pip-egg-info-9s204jyk/cyvcf2.egg-info/SOURCES.txt'
2021-07-12T03:08:03,297     reading manifest file '/tmp/pip-pip-egg-info-9s204jyk/cyvcf2.egg-info/SOURCES.txt'
2021-07-12T03:08:03,299     reading manifest template 'MANIFEST.in'
2021-07-12T03:08:03,314     adding license file 'LICENSE'
2021-07-12T03:08:03,321     writing manifest file '/tmp/pip-pip-egg-info-9s204jyk/cyvcf2.egg-info/SOURCES.txt'
2021-07-12T03:08:03,432   Source in /tmp/pip-wheel-qazep9h7/cyvcf2_96ac09ff0474485795f66bd2dd514bcc has version 0.7.2, which satisfies requirement cyvcf2==0.7.2 from https://files.pythonhosted.org/packages/66/f5/cb923cec9bb0fd761bde06cc1890fa280f1ff198156db92df69b8d152fd8/cyvcf2-0.7.2.tar.gz#sha256=8864f49491de89d2b117d4aa7e985491f5b5ef411615d303c62e4b97b810d755
2021-07-12T03:08:03,433   Removed cyvcf2==0.7.2 from https://files.pythonhosted.org/packages/66/f5/cb923cec9bb0fd761bde06cc1890fa280f1ff198156db92df69b8d152fd8/cyvcf2-0.7.2.tar.gz#sha256=8864f49491de89d2b117d4aa7e985491f5b5ef411615d303c62e4b97b810d755 from build tracker '/tmp/pip-req-tracker-vap6cr58'
2021-07-12T03:08:03,437 Created temporary directory: /tmp/pip-unpack-hy6vqhvu
2021-07-12T03:08:03,438 Building wheels for collected packages: cyvcf2
2021-07-12T03:08:03,441   Created temporary directory: /tmp/pip-wheel-hzvyqkvf
2021-07-12T03:08:03,442   Building wheel for cyvcf2 (setup.py): started
2021-07-12T03:08:03,442   Destination directory: /tmp/pip-wheel-hzvyqkvf
2021-07-12T03:08:03,443   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-qazep9h7/cyvcf2_96ac09ff0474485795f66bd2dd514bcc/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-qazep9h7/cyvcf2_96ac09ff0474485795f66bd2dd514bcc/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-hzvyqkvf
2021-07-12T03:08:04,916   running bdist_wheel
2021-07-12T03:08:04,921   running build
2021-07-12T03:08:04,921   running build_py
2021-07-12T03:08:05,058   creating build
2021-07-12T03:08:05,058   creating build/lib.linux-armv7l-3.9
2021-07-12T03:08:05,059   creating build/lib.linux-armv7l-3.9/cyvcf2
2021-07-12T03:08:05,060   copying cyvcf2/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-12T03:08:05,062   creating build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,063   copying cyvcf2/tests/test_reader.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,066   copying cyvcf2/tests/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,067   copying cyvcf2/tests/test_hemi.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,069   running egg_info
2021-07-12T03:08:05,082   writing cyvcf2.egg-info/PKG-INFO
2021-07-12T03:08:05,084   writing dependency_links to cyvcf2.egg-info/dependency_links.txt
2021-07-12T03:08:05,086   writing requirements to cyvcf2.egg-info/requires.txt
2021-07-12T03:08:05,087   writing top-level names to cyvcf2.egg-info/top_level.txt
2021-07-12T03:08:05,125   reading manifest file 'cyvcf2.egg-info/SOURCES.txt'
2021-07-12T03:08:05,131   reading manifest template 'MANIFEST.in'
2021-07-12T03:08:05,145   adding license file 'LICENSE'
2021-07-12T03:08:05,155   writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
2021-07-12T03:08:05,161   copying cyvcf2/cyvcf2.c -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-12T03:08:05,221   copying cyvcf2/cyvcf2.pxd -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-12T03:08:05,224   copying cyvcf2/cyvcf2.pyx -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-12T03:08:05,228   copying cyvcf2/helpers.c -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-12T03:08:05,230   copying cyvcf2/helpers.h -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-12T03:08:05,232   copying cyvcf2/relatedness.h -> build/lib.linux-armv7l-3.9/cyvcf2
2021-07-12T03:08:05,235   copying cyvcf2/tests/__init__.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,238   copying cyvcf2/tests/bug.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,241   copying cyvcf2/tests/empty.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,243   copying cyvcf2/tests/o.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,247   copying cyvcf2/tests/test-format-string.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,250   copying cyvcf2/tests/test-haploidX.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,280   copying cyvcf2/tests/test-hemi.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,283   copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,286   copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,288   copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,291   copying cyvcf2/tests/test.snpeff.bcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,294   copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,296   copying cyvcf2/tests/test.snpeff.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,300   copying cyvcf2/tests/test.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,309   copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,312   copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,317   copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,319   copying cyvcf2/tests/test_hemi.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,322   copying cyvcf2/tests/test_reader.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests
2021-07-12T03:08:05,327   running build_ext
2021-07-12T03:08:05,391   cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c
2021-07-12T03:08:06,019   /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-qazep9h7/cyvcf2_96ac09ff0474485795f66bd2dd514bcc/cyvcf2/cyvcf2.pxd
2021-07-12T03:08:06,020     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-12T03:08:07,440   warning: cyvcf2/cyvcf2.pxd:24:16: Declarations should not be declared inline.
2021-07-12T03:08:07,451   warning: cyvcf2/cyvcf2.pxd:177:14: 'BCF_HT_FLAG' redeclared
2021-07-12T03:08:07,462   warning: cyvcf2/cyvcf2.pxd:261:30: Declarations should not be declared inline.
2021-07-12T03:08:17,884   building 'cyvcf2.cyvcf2' extension
2021-07-12T03:08:17,886   creating build/temp.linux-armv7l-3.9
2021-07-12T03:08:17,886   creating build/temp.linux-armv7l-3.9/cyvcf2
2021-07-12T03:08:17,887   creating build/temp.linux-armv7l-3.9/htslib
2021-07-12T03:08:17,888   creating build/temp.linux-armv7l-3.9/htslib/cram
2021-07-12T03:08:17,890   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
2021-07-12T03:08:18,295   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-12T03:08:18,295                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-12T03:08:18,295                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-12T03:08:18,296                    from cyvcf2/cyvcf2.c:613:
2021-07-12T03:08:18,296   /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]
2021-07-12T03:08:18,296      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-12T03:08:18,296         |  ^~~~~~~
2021-07-12T03:08:18,519   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’:
2021-07-12T03:08:18,524   cyvcf2/cyvcf2.c:7814:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:18,524    7814 |   __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2);
2021-07-12T03:08:18,524         |                                ~~~~~~~~~~~~^~~~~
2021-07-12T03:08:18,524   In file included from cyvcf2/cyvcf2.c:626:
2021-07-12T03:08:18,524   htslib/htslib/vcf.h:441:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-12T03:08:18,525     441 |     int bcf_hdr_append(bcf_hdr_t *h, const char *line);
2021-07-12T03:08:18,525         |                        ~~~~~~~~~~~^
2021-07-12T03:08:18,529   cyvcf2/cyvcf2.c:7856:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:18,530    7856 |   __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
2021-07-12T03:08:18,530         |                              ~~~~~~~~~~~~^~~~~
2021-07-12T03:08:18,530   In file included from cyvcf2/cyvcf2.c:626:
2021-07-12T03:08:18,530   htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-12T03:08:18,530     477 |     int bcf_hdr_sync(bcf_hdr_t *h);
2021-07-12T03:08:18,531         |                      ~~~~~~~~~~~^
2021-07-12T03:08:18,540   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’:
2021-07-12T03:08:18,544   cyvcf2/cyvcf2.c:8384:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:18,545    8384 |   __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0);
2021-07-12T03:08:18,545         |                                     ~~~~~~~~~~~~^~~~~
2021-07-12T03:08:18,545   In file included from cyvcf2/cyvcf2.c:626:
2021-07-12T03:08:18,545   htslib/htslib/vcf.h:313:40: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-12T03:08:18,545     313 |     int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file);
2021-07-12T03:08:18,545         |                             ~~~~~~~~~~~^~~
2021-07-12T03:08:18,555   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’:
2021-07-12T03:08:18,559   cyvcf2/cyvcf2.c:8676:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:18,559    8676 |   __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4);
2021-07-12T03:08:18,559         |                                ~~~~~~~~~~~~^~~~~
2021-07-12T03:08:18,560   In file included from cyvcf2/cyvcf2.c:626:
2021-07-12T03:08:18,560   htslib/htslib/vcf.h:441:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-12T03:08:18,560     441 |     int bcf_hdr_append(bcf_hdr_t *h, const char *line);
2021-07-12T03:08:18,560         |                        ~~~~~~~~~~~^
2021-07-12T03:08:18,566   cyvcf2/cyvcf2.c:8729:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:18,566    8729 |   __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
2021-07-12T03:08:18,566         |                              ~~~~~~~~~~~~^~~~~
2021-07-12T03:08:18,566   In file included from cyvcf2/cyvcf2.c:626:
2021-07-12T03:08:18,566   htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-12T03:08:18,566     477 |     int bcf_hdr_sync(bcf_hdr_t *h);
2021-07-12T03:08:18,567         |                      ~~~~~~~~~~~^
2021-07-12T03:08:18,570   cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_18generator’:
2021-07-12T03:08:18,572   cyvcf2/cyvcf2.c:8944:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:18,573    8944 |   __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);
2021-07-12T03:08:18,573   htslib/htslib/vcf.h:762:103: note: in definition of macro ‘bcf_itr_querys’
2021-07-12T03:08:18,573     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)
2021-07-12T03:08:18,573         |                                                                                                       ^~~
2021-07-12T03:08:18,573   In file included from cyvcf2/cyvcf2.c:624:
2021-07-12T03:08:18,573   htslib/htslib/hts.h:534:97: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-12T03:08:18,574     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);
2021-07-12T03:08:18,574         |                                                                                           ~~~~~~^~~
2021-07-12T03:08:18,596   cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_24generator2’:
2021-07-12T03:08:18,602   cyvcf2/cyvcf2.c:10136:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:18,602   10136 |     __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, 388, __pyx_L1_error)
2021-07-12T03:08:18,602         |                                                                                                                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2021-07-12T03:08:18,603   cyvcf2/cyvcf2.c:2922:107: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-12T03:08:18,604    2922 | static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/
2021-07-12T03:08:18,604         |                                                                                                           ^~~~~~~~~~~
2021-07-12T03:08:18,659   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_31__dealloc__’:
2021-07-12T03:08:18,664   cyvcf2/cyvcf2.c:11402:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:18,665   11402 |     bcf_hdr_destroy(__pyx_v_self->hdr);
2021-07-12T03:08:18,665         |                     ~~~~~~~~~~~~^~~~~
2021-07-12T03:08:18,665   In file included from cyvcf2/cyvcf2.c:626:
2021-07-12T03:08:18,665   htslib/htslib/vcf.h:259:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-12T03:08:18,665     259 |     void bcf_hdr_destroy(bcf_hdr_t *h);
2021-07-12T03:08:18,665         |                          ~~~~~~~~~~~^
2021-07-12T03:08:18,668   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’:
2021-07-12T03:08:18,674   cyvcf2/cyvcf2.c:11864:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
2021-07-12T03:08:18,674   11864 |   __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen));
2021-07-12T03:08:18,674         |   ^~~~~~~~~
2021-07-12T03:08:18,674   In file included from cyvcf2/cyvcf2.c:626:
2021-07-12T03:08:18,674   htslib/htslib/vcf.h:437:11: note: declared here
2021-07-12T03:08:18,674     437 |     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
2021-07-12T03:08:18,674         |           ^~~~~~~~~~~~~~~~
2021-07-12T03:08:18,678   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’:
2021-07-12T03:08:18,680   cyvcf2/cyvcf2.c:12079:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:18,680   12079 |       __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
2021-07-12T03:08:18,681   htslib/htslib/vcf.h:765:112: note: in definition of macro ‘bcf_index_seqnames’
2021-07-12T03:08:18,681     765 |     #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr))
2021-07-12T03:08:18,681         |                                                                                                                ^~~
2021-07-12T03:08:18,681   In file included from cyvcf2/cyvcf2.c:624:
2021-07-12T03:08:18,681   htslib/htslib/hts.h:536:92: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’
2021-07-12T03:08:18,681     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
2021-07-12T03:08:18,681         |                                                                                      ~~~~~~^~~
2021-07-12T03:08:18,687   cyvcf2/cyvcf2.c:12079:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
2021-07-12T03:08:18,688   12079 |       __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
2021-07-12T03:08:18,688         |                      ^
2021-07-12T03:08:18,697   cyvcf2/cyvcf2.c:12243:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
2021-07-12T03:08:18,698   12243 |       __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n));
2021-07-12T03:08:18,698         |                      ^
2021-07-12T03:08:18,704   cyvcf2/cyvcf2.c:12273:20: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
2021-07-12T03:08:18,704   12273 |     __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n));
2021-07-12T03:08:18,704         |                    ^
2021-07-12T03:08:19,232   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8gt_bases___get__’:
2021-07-12T03:08:19,243   cyvcf2/cyvcf2.c:21666:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:08:19,243   21666 |   for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) {
2021-07-12T03:08:19,243         |                                 ^
2021-07-12T03:08:19,332   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’:
2021-07-12T03:08:19,344   cyvcf2/cyvcf2.c:23692:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:19,344   23692 |     __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id);
2021-07-12T03:08:19,345         |                 ^
2021-07-12T03:08:19,588   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_3ALT___get__’:
2021-07-12T03:08:19,604   cyvcf2/cyvcf2.c:30581:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:08:19,604   30581 |   for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
2021-07-12T03:08:19,604         |                                 ^
2021-07-12T03:08:19,605   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6is_snp___get__’:
2021-07-12T03:08:19,621   cyvcf2/cyvcf2.c:30676:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:08:19,621   30676 |   for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
2021-07-12T03:08:19,621         |                                 ^
2021-07-12T03:08:19,624   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8is_indel___get__’:
2021-07-12T03:08:19,640   cyvcf2/cyvcf2.c:30891:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:08:19,640   30891 |   for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
2021-07-12T03:08:19,641         |                                 ^
2021-07-12T03:08:19,657   cyvcf2/cyvcf2.c:30949:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare]
2021-07-12T03:08:19,657   30949 |     __pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0);
2021-07-12T03:08:19,657         |                             ^~
2021-07-12T03:08:19,681   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’:
2021-07-12T03:08:19,698   cyvcf2/cyvcf2.c:32937:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:19,698   32937 |   __pyx_v_h = __pyx_t_6;
2021-07-12T03:08:19,698         |             ^
2021-07-12T03:08:19,774   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’:
2021-07-12T03:08:19,793   cyvcf2/cyvcf2.c:35792:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:19,793   35792 |   __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key);
2021-07-12T03:08:19,793         |                ^
2021-07-12T03:08:19,801   cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’:
2021-07-12T03:08:19,820   cyvcf2/cyvcf2.c:36787:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:19,820   36787 |   __pyx_v_i->hdr = __pyx_t_4;
2021-07-12T03:08:19,820         |                  ^
2021-07-12T03:08:19,835   cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’:
2021-07-12T03:08:19,854   cyvcf2/cyvcf2.c:37297:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-12T03:08:19,855   37297 |   __pyx_v_h = __pyx_t_3;
2021-07-12T03:08:19,855         |             ^
2021-07-12T03:08:23,370   At top level:
2021-07-12T03:08:23,374   cyvcf2/cyvcf2.c:6527:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function]
2021-07-12T03:08:23,374    6527 | static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) {
2021-07-12T03:08:23,374         |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-12T03:08:58,027   cyvcf2/cyvcf2.c: In function ‘__pyx_getprop_6cyvcf2_6cyvcf2_3VCF_seqnames’:
2021-07-12T03:08:58,033   cyvcf2/cyvcf2.c:11925:10: warning: ‘__pyx_v_cnames’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-12T03:08:58,033   11925 |   char **__pyx_v_cnames;
2021-07-12T03:08:58,034         |          ^~~~~~~~~~~~~~
2021-07-12T03:09:15,617   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
2021-07-12T03:09:15,908   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
2021-07-12T03:09:16,110   htslib/bgzf.c: In function ‘bgzf_read’:
2021-07-12T03:09:16,110   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]
2021-07-12T03:09:16,110     691 |     while (bytes_read < length) {
2021-07-12T03:09:16,111         |                       ^
2021-07-12T03:09:16,111   htslib/bgzf.c:706:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:16,111     706 |         copy_length = length - bytes_read < available? length - bytes_read : available;
2021-07-12T03:09:16,111         |                                           ^
2021-07-12T03:09:16,111   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]
2021-07-12T03:09:16,111     706 |         copy_length = length - bytes_read < available? length - bytes_read : available;
2021-07-12T03:09:16,112         |                                                                              ^~~~~~~~~
2021-07-12T03:09:16,132   htslib/bgzf.c: In function ‘bgzf_useek’:
2021-07-12T03:09:16,132   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]
2021-07-12T03:09:16,133    1301 |         if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1;
2021-07-12T03:09:16,133         |                      ^
2021-07-12T03:09:16,133   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]
2021-07-12T03:09:16,133    1302 |         else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1;
2021-07-12T03:09:16,133         |                           ^~
2021-07-12T03:09:17,846   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
2021-07-12T03:09:18,050   In file included from htslib/cram/cram.h:52,
2021-07-12T03:09:18,051                    from htslib/cram/cram_codecs.c:43:
2021-07-12T03:09:18,051   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-12T03:09:18,051   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]
2021-07-12T03:09:18,051     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-12T03:09:18,051         |             ^~
2021-07-12T03:09:18,052   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:18,052     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-12T03:09:18,052         |                                                     ^
2021-07-12T03:09:18,054   htslib/cram/cram_codecs.c: In function ‘get_one_bits_MSB’:
2021-07-12T03:09:18,054   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]
2021-07-12T03:09:18,055      77 |     if (block->byte >= block->uncomp_size)
2021-07-12T03:09:18,055         |                     ^~
2021-07-12T03:09:18,055   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]
2021-07-12T03:09:18,055      84 |      if (block->byte == block->uncomp_size && (b&1))
2021-07-12T03:09:18,055         |                      ^~
2021-07-12T03:09:18,055   htslib/cram/cram_codecs.c: In function ‘get_zero_bits_MSB’:
2021-07-12T03:09:18,056   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]
2021-07-12T03:09:18,056      95 |     if (block->byte >= block->uncomp_size)
2021-07-12T03:09:18,056         |                     ^~
2021-07-12T03:09:18,056   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]
2021-07-12T03:09:18,056     102 |      if (block->byte == block->uncomp_size && !(b&1))
2021-07-12T03:09:18,056         |                      ^~
2021-07-12T03:09:18,067   htslib/cram/cram_codecs.c: In function ‘cram_beta_decode_init’:
2021-07-12T03:09:18,067   htslib/cram/cram_codecs.c:544:47: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:18,067     544 |         || c->beta.nbits < 0 || c->beta.nbits > 8 * sizeof(int)) {
2021-07-12T03:09:18,067         |                                               ^
2021-07-12T03:09:18,099   htslib/cram/cram_codecs.c: In function ‘cram_byte_array_stop_decode_block’:
2021-07-12T03:09:18,099   htslib/cram/cram_codecs.c:1587:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:18,099    1587 |     if (cp_end - cp < out->alloc - out->byte) {
2021-07-12T03:09:18,099         |                     ^
2021-07-12T03:09:20,475   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
2021-07-12T03:09:20,735   In file included from htslib/cram/cram.h:52,
2021-07-12T03:09:20,736                    from htslib/cram/cram_decode.c:48:
2021-07-12T03:09:20,736   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-12T03:09:20,736   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]
2021-07-12T03:09:20,736     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-12T03:09:20,736         |             ^~
2021-07-12T03:09:20,736   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:20,737     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-12T03:09:20,737         |                                                     ^
2021-07-12T03:09:20,741   htslib/cram/cram_decode.c: In function ‘cram_decode_TD’:
2021-07-12T03:09:20,741   htslib/cram/cram_decode.c:101:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:20,741     101 |     for (nTL = i = 0; i < BLOCK_SIZE(b); i++) {
2021-07-12T03:09:20,741         |                         ^
2021-07-12T03:09:20,742   htslib/cram/cram_decode.c:113:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:20,742     113 |     for (nTL = i = 0; i < BLOCK_SIZE(b); i++) {
2021-07-12T03:09:20,742         |                         ^
2021-07-12T03:09:20,763   htslib/cram/cram_decode.c: In function ‘cram_dependent_data_series’:
2021-07-12T03:09:20,763   htslib/cram/cram_decode.c:794:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:20,763     794 |  for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) {
2021-07-12T03:09:20,763         |                ^
2021-07-12T03:09:20,766   htslib/cram/cram_decode.c:886:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:20,766     886 |  for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) {
2021-07-12T03:09:20,766         |                ^
2021-07-12T03:09:20,770   htslib/cram/cram_decode.c: In function ‘cram_decode_slice_header’:
2021-07-12T03:09:20,771   htslib/cram/cram_decode.c:1102:23: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:20,771    1102 |  hdr->num_content_ids >= SIZE_MAX / sizeof(int32_t)) {
2021-07-12T03:09:20,771         |                       ^~
2021-07-12T03:09:20,777   htslib/cram/cram_decode.c: In function ‘cram_decode_seq’:
2021-07-12T03:09:20,777   htslib/cram/cram_decode.c:1275:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:20,777    1275 |   if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) {
2021-07-12T03:09:20,778         |                               ^
2021-07-12T03:09:20,782   htslib/cram/cram_decode.c:1425:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:20,783    1425 |   if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) {
2021-07-12T03:09:20,783         |               ^~
2021-07-12T03:09:20,786   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]
2021-07-12T03:09:20,786    1469 |       if (ref_pos + i32 <= bfd->ref[cr->ref_id].len) {
2021-07-12T03:09:20,787         |                         ^~
2021-07-12T03:09:20,788   htslib/cram/cram_decode.c:1480:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:20,788    1480 |    if (bfd->ref[cr->ref_id].len >= ref_pos) {
2021-07-12T03:09:20,788         |                                 ^~
2021-07-12T03:09:20,794   htslib/cram/cram_decode.c:1573:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:20,794    1573 |    if (ref_pos+x >= bfd->ref[cr->ref_id].len || !s->ref) {
2021-07-12T03:09:20,794         |                  ^~
2021-07-12T03:09:20,797   htslib/cram/cram_decode.c:1644:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:20,797    1644 |       if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) {
2021-07-12T03:09:20,798         |                   ^~
2021-07-12T03:09:20,804   htslib/cram/cram_decode.c:1748:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:20,804    1748 |      if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) {
2021-07-12T03:09:20,804         |                                          ^
2021-07-12T03:09:20,832   htslib/cram/cram_decode.c: In function ‘cram_decode_slice’:
2021-07-12T03:09:20,834   htslib/cram/cram_decode.c:2367:6: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:20,834    2367 |   bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap))
2021-07-12T03:09:20,834         |      ^~
2021-07-12T03:09:26,362   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
2021-07-12T03:09:26,617   In file included from htslib/cram/cram.h:52,
2021-07-12T03:09:26,617                    from htslib/cram/cram_encode.c:43:
2021-07-12T03:09:26,618   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-12T03:09:26,618   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]
2021-07-12T03:09:26,618     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-12T03:09:26,618         |             ^~
2021-07-12T03:09:26,618   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:26,618     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-12T03:09:26,619         |                                                     ^
2021-07-12T03:09:26,666   htslib/cram/cram_encode.c: In function ‘lossy_read_names’:
2021-07-12T03:09:26,666   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]
2021-07-12T03:09:26,667    1297 |      if (u.e != e) {
2021-07-12T03:09:26,667         |              ^~
2021-07-12T03:09:26,668   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]
2021-07-12T03:09:26,668    1327 |  if (kh_val(names, k) == -1)
2021-07-12T03:09:26,668         |                       ^~
2021-07-12T03:09:26,711   htslib/cram/cram_encode.c: In function ‘process_one_read’:
2021-07-12T03:09:26,712   htslib/cram/cram_encode.c:2650:10: warning: unused variable ‘brg’ [-Wunused-variable]
2021-07-12T03:09:26,712    2650 |  SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN");
2021-07-12T03:09:26,712         |          ^~~
2021-07-12T03:09:26,716   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]
2021-07-12T03:09:26,716    2758 |  while (cr->cigar + cr->ncigar >= s->cigar_alloc) {
2021-07-12T03:09:26,717         |                                ^~
2021-07-12T03:09:26,718   htslib/cram/cram_encode.c:2788:30: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:26,718    2788 |       int end = cig_len+apos < c->ref_end
2021-07-12T03:09:26,718         |                              ^
2021-07-12T03:09:26,719   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]
2021-07-12T03:09:26,719    2789 |    ? cig_len : c->ref_end - apos;
2021-07-12T03:09:26,720         |                ^~~~~~~~~~~~~~~~~
2021-07-12T03:09:26,723   htslib/cram/cram_encode.c:2831:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:26,723    2831 |   if (l < cig_len && cr->len) {
2021-07-12T03:09:26,723         |         ^
2021-07-12T03:09:26,725   htslib/cram/cram_encode.c:2839:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:26,725    2839 |        for (; l < cig_len && seq[spos]; l++, spos++) {
2021-07-12T03:09:26,725         |                 ^
2021-07-12T03:09:26,726   htslib/cram/cram_encode.c:2847:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:26,727    2847 |    for (; l < cig_len && seq[spos]; l++, spos++) {
2021-07-12T03:09:26,727         |             ^
2021-07-12T03:09:26,730   htslib/cram/cram_encode.c:2878:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:26,731    2878 |       for (l = 0; l < cig_len; l++, spos++) {
2021-07-12T03:09:26,731         |                     ^
2021-07-12T03:09:26,733   htslib/cram/cram_encode.c:2894:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:26,733    2894 |    for (l = 0; l < cig_len; l++, spos++) {
2021-07-12T03:09:26,733         |                  ^
2021-07-12T03:09:26,734   htslib/cram/cram_encode.c:2898:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:26,734    2898 |    for (l = 0; l < cig_len; l++, spos++) {
2021-07-12T03:09:26,734         |                  ^
2021-07-12T03:09:32,130   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
2021-07-12T03:09:32,337   In file included from htslib/cram/cram.h:52,
2021-07-12T03:09:32,338                    from htslib/cram/cram_external.c:44:
2021-07-12T03:09:32,338   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-12T03:09:32,338   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]
2021-07-12T03:09:32,339     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-12T03:09:32,339         |             ^~
2021-07-12T03:09:32,339   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:32,339     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-12T03:09:32,339         |                                                     ^
2021-07-12T03:09:32,717   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
2021-07-12T03:09:32,991   In file included from htslib/cram/cram.h:52,
2021-07-12T03:09:32,991                    from htslib/cram/cram_index.c:65:
2021-07-12T03:09:32,991   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-12T03:09:32,992   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]
2021-07-12T03:09:32,992     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-12T03:09:32,992         |             ^~
2021-07-12T03:09:32,992   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:32,992     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-12T03:09:32,992         |                                                     ^
2021-07-12T03:09:33,004   htslib/cram/cram_index.c: In function ‘cram_index_build’:
2021-07-12T03:09:33,005   htslib/cram/cram_index.c:502:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable]
2021-07-12T03:09:33,005     502 |     off_t cpos, spos, hpos;
2021-07-12T03:09:33,006         |                       ^~~~
2021-07-12T03:09:33,686   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
2021-07-12T03:09:33,944   In file included from htslib/cram/cram.h:52,
2021-07-12T03:09:33,944                    from htslib/cram/cram_io.c:67:
2021-07-12T03:09:33,944   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-12T03:09:33,944   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]
2021-07-12T03:09:33,945     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-12T03:09:33,945         |             ^~
2021-07-12T03:09:33,945   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:33,945     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-12T03:09:33,945         |                                                     ^
2021-07-12T03:09:34,016   In file included from htslib/cram/cram_io.h:48,
2021-07-12T03:09:34,016                    from htslib/cram/cram.h:48,
2021-07-12T03:09:34,016                    from htslib/cram/cram_io.c:67:
2021-07-12T03:09:34,016   htslib/cram/cram_io.c: In function ‘expand_cache_path’:
2021-07-12T03:09:34,017   htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:34,017     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-12T03:09:34,017         |                          ^
2021-07-12T03:09:34,017   htslib/cram/cram_io.c:2081:10: note: in expansion of macro ‘MIN’
2021-07-12T03:09:34,017    2081 |      l = MIN(l, strlen(fn));
2021-07-12T03:09:34,017         |          ^~~
2021-07-12T03:09:34,018   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]
2021-07-12T03:09:34,018     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-12T03:09:34,018         |                                    ^~~
2021-07-12T03:09:34,018   htslib/cram/cram_io.c:2081:10: note: in expansion of macro ‘MIN’
2021-07-12T03:09:34,018    2081 |      l = MIN(l, strlen(fn));
2021-07-12T03:09:34,019         |          ^~~
2021-07-12T03:09:34,140   In file included from htslib/cram/cram.h:48,
2021-07-12T03:09:34,140                    from htslib/cram/cram_io.c:67:
2021-07-12T03:09:34,140   htslib/cram/cram_io.c: In function ‘cram_write_SAM_hdr’:
2021-07-12T03:09:34,141   htslib/cram/cram_io.h:269:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:34,142     269 |  while((b)->alloc <= (l)) {    \
2021-07-12T03:09:34,142         |                   ^~
2021-07-12T03:09:34,142   htslib/cram/cram_io.c:3983:6: note: in expansion of macro ‘BLOCK_RESIZE’
2021-07-12T03:09:34,142    3983 |      BLOCK_RESIZE(b, padded_length);
2021-07-12T03:09:34,142         |      ^~~~~~~~~~~~
2021-07-12T03:09:36,683   In file included from /usr/include/string.h:495,
2021-07-12T03:09:36,683                    from htslib/cram/cram_io.c:53:
2021-07-12T03:09:36,683   In function ‘strncpy’,
2021-07-12T03:09:36,683       inlined from ‘cram_populate_ref’ at htslib/cram/cram_io.c:2229:2:
2021-07-12T03:09:36,683   /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
2021-07-12T03:09:36,683     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-12T03:09:36,684         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-12T03:09:36,684   htslib/cram/cram_io.c: In function ‘cram_populate_ref’:
2021-07-12T03:09:36,685   htslib/cram/cram_io.c:2337:27: warning: ‘.tmp_’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
2021-07-12T03:09:36,685    2337 |      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
2021-07-12T03:09:36,685         |                           ^~~~~
2021-07-12T03:09:36,685   In file included from /usr/include/stdio.h:867,
2021-07-12T03:09:36,685                    from htslib/cram/cram_io.c:49:
2021-07-12T03:09:36,685   /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
2021-07-12T03:09:36,685      36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
2021-07-12T03:09:36,686         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-12T03:09:36,686      37 |       __bos (__s), __fmt, __va_arg_pack ());
2021-07-12T03:09:36,686         |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-12T03:09:38,047   In file included from /usr/include/string.h:495,
2021-07-12T03:09:38,047                    from htslib/cram/cram_io.c:53:
2021-07-12T03:09:38,047   In function ‘strncpy’,
2021-07-12T03:09:38,047       inlined from ‘full_path’ at htslib/cram/cram_io.c:3807:6,
2021-07-12T03:09:38,047       inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3882:3:
2021-07-12T03:09:38,048   /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
2021-07-12T03:09:38,048     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-12T03:09:38,048         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-12T03:09:38,048   In function ‘strncpy’,
2021-07-12T03:09:38,048       inlined from ‘full_path’ at htslib/cram/cram_io.c:3799:2,
2021-07-12T03:09:38,048       inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3882:3:
2021-07-12T03:09:38,048   /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
2021-07-12T03:09:38,049     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-12T03:09:38,049         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-12T03:09:38,294   In function ‘strncpy’,
2021-07-12T03:09:38,294       inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4182:2:
2021-07-12T03:09:38,294   /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation]
2021-07-12T03:09:38,294     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-12T03:09:38,295         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-12T03:09:39,002   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
2021-07-12T03:09:39,208   In file included from htslib/cram/cram.h:52,
2021-07-12T03:09:39,208                    from htslib/cram/cram_samtools.c:37:
2021-07-12T03:09:39,208   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-12T03:09:39,208   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]
2021-07-12T03:09:39,208     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-12T03:09:39,208         |             ^~
2021-07-12T03:09:39,209   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:39,209     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-12T03:09:39,209         |                                                     ^
2021-07-12T03:09:39,376   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
2021-07-12T03:09:39,642   In file included from htslib/cram/cram.h:52,
2021-07-12T03:09:39,642                    from htslib/cram/cram_stats.c:43:
2021-07-12T03:09:39,642   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-12T03:09:39,643   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]
2021-07-12T03:09:39,643     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-12T03:09:39,643         |             ^~
2021-07-12T03:09:39,644   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:39,644     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-12T03:09:39,644         |                                                     ^
2021-07-12T03:09:40,017   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
2021-07-12T03:09:40,206   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
2021-07-12T03:09:40,371   htslib/cram/mFILE.c: In function ‘mfload’:
2021-07-12T03:09:40,372   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]
2021-07-12T03:09:40,372     103 |     } while (!feof(fp) && (fn == NULL || used < sb.st_size));
2021-07-12T03:09:40,372         |                                               ^
2021-07-12T03:09:40,376   htslib/cram/mFILE.c: In function ‘mftruncate’:
2021-07-12T03:09:40,376   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]
2021-07-12T03:09:40,376     476 |     mf->size = offset != -1 ? offset : mf->offset;
2021-07-12T03:09:40,376         |                               ^~~~~~
2021-07-12T03:09:40,813   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
2021-07-12T03:09:40,972   In file included from htslib/cram/open_trace_file.c:79:
2021-07-12T03:09:40,973   htslib/cram/open_trace_file.c: In function ‘expand_path’:
2021-07-12T03:09:40,973   htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare]
2021-07-12T03:09:40,973     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-12T03:09:40,973         |                          ^
2021-07-12T03:09:40,973   htslib/cram/open_trace_file.c:243:15: note: in expansion of macro ‘MIN’
2021-07-12T03:09:40,974     243 |   path_end += MIN(strlen(file), l);
2021-07-12T03:09:40,974         |               ^~~
2021-07-12T03:09:40,974   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]
2021-07-12T03:09:40,974     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-12T03:09:40,974         |                                          ^~~
2021-07-12T03:09:40,974   htslib/cram/open_trace_file.c:243:15: note: in expansion of macro ‘MIN’
2021-07-12T03:09:40,974     243 |   path_end += MIN(strlen(file), l);
2021-07-12T03:09:40,975         |               ^~~
2021-07-12T03:09:40,975   htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare]
2021-07-12T03:09:40,975     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-12T03:09:40,975         |                          ^
2021-07-12T03:09:40,975   htslib/cram/open_trace_file.c:244:15: note: in expansion of macro ‘MIN’
2021-07-12T03:09:40,975     244 |   file     += MIN(strlen(file), l);
2021-07-12T03:09:40,975         |               ^~~
2021-07-12T03:09:40,976   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]
2021-07-12T03:09:40,976     103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
2021-07-12T03:09:40,976         |                                          ^~~
2021-07-12T03:09:40,976   htslib/cram/open_trace_file.c:244:15: note: in expansion of macro ‘MIN’
2021-07-12T03:09:40,977     244 |   file     += MIN(strlen(file), l);
2021-07-12T03:09:40,977         |               ^~~
2021-07-12T03:09:41,323   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
2021-07-12T03:09:41,542   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
2021-07-12T03:09:41,688   htslib/cram/rANS_static.c: In function ‘rans_compress_O0’:
2021-07-12T03:09:41,689   htslib/cram/rANS_static.c:86:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:41,689      86 |     for (i = 0; i < in_size; i++) {
2021-07-12T03:09:41,689         |                   ^
2021-07-12T03:09:41,692   htslib/cram/rANS_static.c: In function ‘rans_uncompress_O0’:
2021-07-12T03:09:41,693   htslib/cram/rANS_static.c:222:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:41,693     222 |     if (in_sz != in_size-9)
2021-07-12T03:09:41,693         |               ^~
2021-07-12T03:09:41,697   htslib/cram/rANS_static.c: In function ‘rans_compress_O1’:
2021-07-12T03:09:41,697   htslib/cram/rANS_static.c:390:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:41,697     390 |     for (last_i=i=0; i<in_size; i++) {
2021-07-12T03:09:41,697         |                       ^
2021-07-12T03:09:41,702   htslib/cram/rANS_static.c: In function ‘rans_uncompress_O1’:
2021-07-12T03:09:41,702   htslib/cram/rANS_static.c:579:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:41,703     579 |     if (in_sz != in_size-9)
2021-07-12T03:09:41,703         |               ^~
2021-07-12T03:09:43,074   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
2021-07-12T03:09:43,232   htslib/cram/sam_header.c: In function ‘sam_hdr_add_lines’:
2021-07-12T03:09:43,232   htslib/cram/sam_header.c:327:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:43,232     327 |  if (-1 == (k = kh_put(sam_hdr, sh->h, type, &new)))
2021-07-12T03:09:43,233         |         ^~
2021-07-12T03:09:43,235   htslib/cram/sam_header.c: In function ‘sam_hdr_vadd’:
2021-07-12T03:09:43,235   htslib/cram/sam_header.c:450:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:43,235     450 |     if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new)))
2021-07-12T03:09:43,236         |            ^~
2021-07-12T03:09:43,245   htslib/cram/sam_header.c: In function ‘sam_hdr_rebuild’:
2021-07-12T03:09:43,245   htslib/cram/sam_header.c:821:24: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:43,245     821 |  if (kh_key(hdr->h, k) == K("HD"))
2021-07-12T03:09:43,245         |                        ^~
2021-07-12T03:09:45,271   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
2021-07-12T03:09:45,500   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
2021-07-12T03:09:45,997   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
2021-07-12T03:09:46,130   htslib/cram/vlen.c: In function ‘vflen’:
2021-07-12T03:09:46,130   htslib/cram/vlen.c:77:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:46,131      77 | #define MAX(a,b) ((a)>(b)?(a):(b))
2021-07-12T03:09:46,131         |                      ^
2021-07-12T03:09:46,131   htslib/cram/vlen.c:239:10: note: in expansion of macro ‘MAX’
2021-07-12T03:09:46,131     239 |   len += MAX(conv_len1, i>=0x80 ?MB_CUR_MAX :1);
2021-07-12T03:09:46,131         |          ^~~
2021-07-12T03:09:46,132   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]
2021-07-12T03:09:46,132      77 | #define MAX(a,b) ((a)>(b)?(a):(b))
2021-07-12T03:09:46,132         |                           ^~~
2021-07-12T03:09:46,132   htslib/cram/vlen.c:239:10: note: in expansion of macro ‘MAX’
2021-07-12T03:09:46,132     239 |   len += MAX(conv_len1, i>=0x80 ?MB_CUR_MAX :1);
2021-07-12T03:09:46,132         |          ^~~
2021-07-12T03:09:46,287   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
2021-07-12T03:09:46,582   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
2021-07-12T03:09:47,327   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
2021-07-12T03:09:48,651   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
2021-07-12T03:09:48,871   htslib/hfile.c: In function ‘find_scheme_handler’:
2021-07-12T03:09:48,871   htslib/hfile.c:717:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:48,871     717 |     for (i = 0; i < sizeof scheme; i++)
2021-07-12T03:09:48,871         |                   ^
2021-07-12T03:09:48,872   htslib/hfile.c:723:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-12T03:09:48,872     723 |     if (i == 0 || i >= sizeof scheme) return NULL;
2021-07-12T03:09:48,872         |                     ^~
2021-07-12T03:09:49,641   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
2021-07-12T03:09:49,836   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
2021-07-12T03:09:50,080   In file included from htslib/cram/cram.h:52,
2021-07-12T03:09:50,080                    from htslib/hts.c:39:
2021-07-12T03:09:50,080   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-12T03:09:50,080   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]
2021-07-12T03:09:50,081     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-12T03:09:50,081         |             ^~
2021-07-12T03:09:50,081   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:50,081     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-12T03:09:50,081         |                                                     ^
2021-07-12T03:09:50,135   htslib/hts.c: In function ‘hts_idx_init’:
2021-07-12T03:09:50,136   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]
2021-07-12T03:09:50,136    1222 |     idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
2021-07-12T03:09:50,136         |                                                           ^~~
2021-07-12T03:09:50,138   htslib/hts.c: In function ‘update_loff’:
2021-07-12T03:09:50,139   htslib/hts.c:1256:34: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:50,139    1256 |             if ( kh_key(bidx, k) < idx->n_bins )
2021-07-12T03:09:50,139         |                                  ^
2021-07-12T03:09:50,140   htslib/hts.c: In function ‘compress_binning’:
2021-07-12T03:09:50,140   htslib/hts.c:1283:55: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:50,141    1283 |             if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue;
2021-07-12T03:09:50,141         |                                                       ^~
2021-07-12T03:09:50,143   htslib/hts.c:1308:51: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:50,143    1308 |         if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue;
2021-07-12T03:09:50,143         |                                                   ^~
2021-07-12T03:09:50,164   htslib/hts.c: In function ‘hts_idx_load_local’:
2021-07-12T03:09:50,164   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]
2021-07-12T03:09:50,164    1618 |             if (bgzf_read(fp, meta, x[2]) != x[2]) goto fail;
2021-07-12T03:09:50,165         |                                           ^~
2021-07-12T03:09:50,168   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]
2021-07-12T03:09:50,168    1636 |         if (bgzf_read(fp, idx->meta + 28, x[7]) != x[7]) goto fail;
2021-07-12T03:09:50,168         |                                                 ^~
2021-07-12T03:09:54,148   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
2021-07-12T03:09:54,577   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
2021-07-12T03:09:55,586   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
2021-07-12T03:09:55,717   htslib/kstring.c: In function ‘kvsprintf’:
2021-07-12T03:09:55,717   htslib/kstring.c:42:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:55,718      42 |  if (l + 1 > s->m - s->l) {
2021-07-12T03:09:55,718         |            ^
2021-07-12T03:09:56,104   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
2021-07-12T03:09:56,669   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
2021-07-12T03:09:57,380   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
2021-07-12T03:09:58,075   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
2021-07-12T03:09:58,230   htslib/regidx.c: In function ‘regidx_insert’:
2021-07-12T03:09:58,230   htslib/regidx.c:155:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:58,230     155 |         if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
2021-07-12T03:09:58,231         |                              ^
2021-07-12T03:09:58,231   htslib/regidx.c:155:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:58,231     155 |         if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
2021-07-12T03:09:58,231         |                                                             ^~
2021-07-12T03:09:58,231   htslib/regidx.c:155:89: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:58,231     155 |         if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
2021-07-12T03:09:58,231         |                                                                                         ^
2021-07-12T03:09:58,993   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
2021-07-12T03:09:59,220   In file included from htslib/cram/cram.h:52,
2021-07-12T03:09:59,220                    from htslib/sam.c:35:
2021-07-12T03:09:59,220   htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’:
2021-07-12T03:09:59,221   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]
2021-07-12T03:09:59,221     162 |  (blk->byte >= blk->uncomp_size && nbits > 0) ||
2021-07-12T03:09:59,221         |             ^~
2021-07-12T03:09:59,221   htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:09:59,221     164 |   (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
2021-07-12T03:09:59,221         |                                                     ^
2021-07-12T03:09:59,235   htslib/sam.c: In function ‘bam_hdr_read’:
2021-07-12T03:09:59,235   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]
2021-07-12T03:09:59,235     147 |     if (bytes != h->l_text) goto read_err;
2021-07-12T03:09:59,236         |               ^~
2021-07-12T03:09:59,244   htslib/sam.c: In function ‘bam_write1’:
2021-07-12T03:09:59,244   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]
2021-07-12T03:09:59,244     467 |     return ok? 4 + block_len : -1;
2021-07-12T03:09:59,244         |                                ^~
2021-07-12T03:09:59,255   htslib/sam.c: In function ‘sam_hdr_write’:
2021-07-12T03:09:59,255   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]
2021-07-12T03:09:59,255     818 |                 if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
2021-07-12T03:09:59,256         |                                                                   ^~
2021-07-12T03:09:59,272   htslib/sam.c: In function ‘sam_format1’:
2021-07-12T03:09:59,273   htslib/sam.c:1181:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:59,273    1181 |             if ((b->data + b->l_data - s) / sub_type_size < n)
2021-07-12T03:09:59,273         |                                                           ^
2021-07-12T03:09:59,274   htslib/sam.c:1184:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:09:59,274    1184 |             for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if"
2021-07-12T03:09:59,274         |                           ^
2021-07-12T03:09:59,275   htslib/sam.c: In function ‘sam_write1’:
2021-07-12T03:09:59,275   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]
2021-07-12T03:09:59,276    1220 |         if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
2021-07-12T03:09:59,276         |                                                           ^~
2021-07-12T03:09:59,482   In file included from /usr/include/string.h:495,
2021-07-12T03:09:59,483                    from htslib/sam.c:30:
2021-07-12T03:09:59,483   In function ‘strncpy’,
2021-07-12T03:09:59,483       inlined from ‘bam_hdr_write’ at htslib/sam.c:229:5:
2021-07-12T03:09:59,483   /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]
2021-07-12T03:09:59,483     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-12T03:09:59,483         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-12T03:10:04,874   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
2021-07-12T03:10:05,098   htslib/synced_bcf_reader.c: In function ‘_regions_add’:
2021-07-12T03:10:05,098   htslib/synced_bcf_reader.c:860:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:10:05,099     860 |         if ( start < creg->regs[i].start ) max = i - 1;
2021-07-12T03:10:05,099         |                    ^
2021-07-12T03:10:05,099   htslib/synced_bcf_reader.c:861:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:10:05,099     861 |         else if ( start > creg->regs[i].start ) min = i + 1;
2021-07-12T03:10:05,099         |                         ^
2021-07-12T03:10:05,099   htslib/synced_bcf_reader.c:864:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:10:05,100     864 |     if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end )
2021-07-12T03:10:05,100         |                                        ^~
2021-07-12T03:10:05,100   htslib/synced_bcf_reader.c:864:68: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-12T03:10:05,100     864 |     if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end )
2021-07-12T03:10:05,100         |                                                                    ^~
2021-07-12T03:10:07,098   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
2021-07-12T03:10:07,739   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
2021-07-12T03:10:07,943   htslib/vcf.c: In function ‘bcf_hdr_sync’:
2021-07-12T03:10:07,943   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]
2021-07-12T03:10:07,944     151 |         if ( h->n[i] < kh_size(d) )
2021-07-12T03:10:07,944         |                      ^
2021-07-12T03:10:07,965   htslib/vcf.c: In function ‘bcf_hdr_read’:
2021-07-12T03:10:07,965   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]
2021-07-12T03:10:07,966     861 |     if (bgzf_read(fp, htxt, hlen) != hlen) goto fail;
2021-07-12T03:10:07,966         |                                   ^~
2021-07-12T03:10:07,967   htslib/vcf.c: In function ‘bcf_hdr_write’:
2021-07-12T03:10:07,967   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]
2021-07-12T03:10:07,967     888 |     if ( bgzf_write(fp, htxt.s, htxt.l) != htxt.l ) return -1;
2021-07-12T03:10:07,968         |                                         ^~
2021-07-12T03:10:07,970   htslib/vcf.c: In function ‘bcf_read1_core’:
2021-07-12T03:10:07,970   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]
2021-07-12T03:10:07,971     972 |     if (bgzf_read(fp, v->shared.s, v->shared.l) != v->shared.l) return -1;
2021-07-12T03:10:07,971         |                                                 ^~
2021-07-12T03:10:07,971   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]
2021-07-12T03:10:07,971     973 |     if (bgzf_read(fp, v->indiv.s, v->indiv.l) != v->indiv.l) return -1;
2021-07-12T03:10:07,971         |                                               ^~
2021-07-12T03:10:07,982   htslib/vcf.c: In function ‘bcf_write’:
2021-07-12T03:10:07,983   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]
2021-07-12T03:10:07,983    1287 |     if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1;
2021-07-12T03:10:07,983         |                                                   ^~
2021-07-12T03:10:07,984   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]
2021-07-12T03:10:07,984    1288 |     if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1;
2021-07-12T03:10:07,984         |                                                 ^~
2021-07-12T03:10:07,998   htslib/vcf.c: In function ‘vcf_parse_format’:
2021-07-12T03:10:07,999   htslib/vcf.c:1680:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-12T03:10:07,999    1680 |                 if (fmt[j].max_l < l) fmt[j].max_l = l;
2021-07-12T03:10:07,999         |                                  ^
2021-07-12T03:10:08,003   htslib/vcf.c:1709:33: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-12T03:10:08,003    1709 |             f->size = f->is_gt? f->max_g << 2 : f->max_l;
2021-07-12T03:10:08,004         |                                 ^~~~~~~~~~~~~
2021-07-12T03:10:08,041   htslib/vcf.c: In function ‘vcf_write_line’:
2021-07-12T03:10:08,042   htslib/vcf.c:2274:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:10:08,042    2274 |     return ret==line->l ? 0 : -1;
2021-07-12T03:10:08,042         |               ^~
2021-07-12T03:10:08,043   htslib/vcf.c: In function ‘vcf_write’:
2021-07-12T03:10:08,044   htslib/vcf.c:2286:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:10:08,044    2286 |     return ret==fp->line.l ? 0 : -1;
2021-07-12T03:10:08,044         |               ^~
2021-07-12T03:10:08,069   htslib/vcf.c: In function ‘bcf_hdr_set_samples’:
2021-07-12T03:10:08,070   htslib/vcf.c:2755:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-12T03:10:08,070    2755 |         for (k = kh_begin(d); k != kh_end(d); ++k)
2021-07-12T03:10:08,071         |                                 ^~
2021-07-12T03:10:08,114   htslib/vcf.c: In function ‘_bcf1_sync_alleles’:
2021-07-12T03:10:08,115   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]
2021-07-12T03:10:08,115    3204 |     line->rlen = end_info ? end_info->v1.i : strlen(line->d.allele[0]);
2021-07-12T03:10:08,116         |                             ^~~~~~~~~~~~~~
2021-07-12T03:10:08,126   htslib/vcf.c: In function ‘bcf_get_info_values’:
2021-07-12T03:10:08,127   htslib/vcf.c:3334:49: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-12T03:10:08,127    3334 |     if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2;     // expected different type
2021-07-12T03:10:08,127         |                                                 ^~
2021-07-12T03:10:08,142   htslib/vcf.c: In function ‘bcf_get_format_values’:
2021-07-12T03:10:08,143   htslib/vcf.c:3456:53: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-12T03:10:08,144    3456 |     else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2;     // expected different type
2021-07-12T03:10:08,144         |                                                     ^~
2021-07-12T03:10:16,510   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
2021-07-12T03:10:16,702   htslib/vcf_sweep.c: In function ‘bcf_sweep_fwd’:
2021-07-12T03:10:16,702   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]
2021-07-12T03:10:16,703     164 |         if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size )
2021-07-12T03:10:16,703         |                                                     ^
2021-07-12T03:10:16,900   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
2021-07-12T03:10:18,994   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
2021-07-12T03:10:19,612   installing to build/bdist.linux-armv7l/wheel
2021-07-12T03:10:19,612   running install
2021-07-12T03:10:19,614   running install_lib
2021-07-12T03:10:19,619   creating build/bdist.linux-armv7l
2021-07-12T03:10:19,619   creating build/bdist.linux-armv7l/wheel
2021-07-12T03:10:19,621   creating build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-12T03:10:19,622   copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.c -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-12T03:10:19,624   copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pxd -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-12T03:10:19,627   copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.h -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-12T03:10:19,629   copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pyx -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-12T03:10:19,633   copying build/lib.linux-armv7l-3.9/cyvcf2/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-12T03:10:19,635   copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-12T03:10:19,759   copying build/lib.linux-armv7l-3.9/cyvcf2/relatedness.h -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-12T03:10:19,762   creating build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,762   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,764   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-haploidX.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,783   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,786   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,787   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-hemi.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,790   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,794   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/o.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,797   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.comp_het.3.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,800   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,802   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_alt_freqs.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,805   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_bases.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,807   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,810   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf.csi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,812   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,814   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,817   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,819   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,826   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-format-string.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,828   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,830   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,832   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/bug.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,834   copying build/lib.linux-armv7l-3.9/cyvcf2/tests/empty.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests
2021-07-12T03:10:19,836   copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.c -> build/bdist.linux-armv7l/wheel/cyvcf2
2021-07-12T03:10:19,898   running install_egg_info
2021-07-12T03:10:19,903   Copying cyvcf2.egg-info to build/bdist.linux-armv7l/wheel/cyvcf2-0.7.2-py3.9.egg-info
2021-07-12T03:10:19,916   running install_scripts
2021-07-12T03:10:19,955   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2021-07-12T03:10:19,959   creating build/bdist.linux-armv7l/wheel/cyvcf2-0.7.2.dist-info/WHEEL
2021-07-12T03:10:19,962   creating '/tmp/pip-wheel-hzvyqkvf/cyvcf2-0.7.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-12T03:10:19,965   adding 'cyvcf2/__init__.py'
2021-07-12T03:10:20,155   adding 'cyvcf2/cyvcf2.c'
2021-07-12T03:10:21,383   adding 'cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so'
2021-07-12T03:10:21,431   adding 'cyvcf2/cyvcf2.pxd'
2021-07-12T03:10:21,439   adding 'cyvcf2/cyvcf2.pyx'
2021-07-12T03:10:21,441   adding 'cyvcf2/helpers.c'
2021-07-12T03:10:21,442   adding 'cyvcf2/helpers.h'
2021-07-12T03:10:21,443   adding 'cyvcf2/relatedness.h'
2021-07-12T03:10:21,445   adding 'cyvcf2/tests/__init__.py'
2021-07-12T03:10:21,446   adding 'cyvcf2/tests/__init__.pyc'
2021-07-12T03:10:21,448   adding 'cyvcf2/tests/bug.vcf.gz'
2021-07-12T03:10:21,449   adding 'cyvcf2/tests/empty.vcf'
2021-07-12T03:10:21,454   adding 'cyvcf2/tests/o.vcf.gz'
2021-07-12T03:10:21,455   adding 'cyvcf2/tests/test-format-string.vcf'
2021-07-12T03:10:21,497   adding 'cyvcf2/tests/test-haploidX.vcf'
2021-07-12T03:10:21,504   adding 'cyvcf2/tests/test-hemi.vcf'
2021-07-12T03:10:21,505   adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz'
2021-07-12T03:10:21,506   adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi'
2021-07-12T03:10:21,508   adding 'cyvcf2/tests/test.comp_het.3.vcf'
2021-07-12T03:10:21,510   adding 'cyvcf2/tests/test.snpeff.bcf'
2021-07-12T03:10:21,511   adding 'cyvcf2/tests/test.snpeff.bcf.csi'
2021-07-12T03:10:21,513   adding 'cyvcf2/tests/test.snpeff.vcf'
2021-07-12T03:10:21,533   adding 'cyvcf2/tests/test.vcf.gz'
2021-07-12T03:10:21,535   adding 'cyvcf2/tests/test.vcf.gz.tbi'
2021-07-12T03:10:21,538   adding 'cyvcf2/tests/test_gt_alt_freqs.vcf'
2021-07-12T03:10:21,540   adding 'cyvcf2/tests/test_gt_bases.vcf.gz'
2021-07-12T03:10:21,541   adding 'cyvcf2/tests/test_hemi.py'
2021-07-12T03:10:21,542   adding 'cyvcf2/tests/test_hemi.pyc'
2021-07-12T03:10:21,545   adding 'cyvcf2/tests/test_reader.py'
2021-07-12T03:10:21,549   adding 'cyvcf2/tests/test_reader.pyc'
2021-07-12T03:10:21,552   adding 'cyvcf2-0.7.2.dist-info/LICENSE'
2021-07-12T03:10:21,553   adding 'cyvcf2-0.7.2.dist-info/METADATA'
2021-07-12T03:10:21,554   adding 'cyvcf2-0.7.2.dist-info/WHEEL'
2021-07-12T03:10:21,555   adding 'cyvcf2-0.7.2.dist-info/top_level.txt'
2021-07-12T03:10:21,556   adding 'cyvcf2-0.7.2.dist-info/RECORD'
2021-07-12T03:10:21,593   removing build/bdist.linux-armv7l/wheel
2021-07-12T03:10:22,095   Building wheel for cyvcf2 (setup.py): finished with status 'done'
2021-07-12T03:10:22,138   Created wheel for cyvcf2: filename=cyvcf2-0.7.2-cp39-cp39-linux_armv7l.whl size=2950123 sha256=cb02f6846d9666cc50dda5d0c406f8015b575bab4f24cd731a9e57b95ccafb63
2021-07-12T03:10:22,138   Stored in directory: /tmp/pip-ephem-wheel-cache-473y8h7f/wheels/c0/23/37/ac9dbd9251f342e96be7b55d9a6ff641cca3358e9fc4a7be22
2021-07-12T03:10:22,150 Successfully built cyvcf2
2021-07-12T03:10:22,245 Removed build tracker: '/tmp/pip-req-tracker-vap6cr58'