2021-07-16T07:36:11,500 Created temporary directory: /tmp/pip-ephem-wheel-cache-q_l_f_rf
2021-07-16T07:36:11,503 Created temporary directory: /tmp/pip-req-tracker-7ma6u161
2021-07-16T07:36:11,503 Initialized build tracking at /tmp/pip-req-tracker-7ma6u161
2021-07-16T07:36:11,503 Created build tracker: /tmp/pip-req-tracker-7ma6u161
2021-07-16T07:36:11,504 Entered build tracker: /tmp/pip-req-tracker-7ma6u161
2021-07-16T07:36:11,504 Created temporary directory: /tmp/pip-wheel-yq1k2inu
2021-07-16T07:36:11,534 1 location(s) to search for versions of pysam:
2021-07-16T07:36:11,534 * https://pypi.org/simple/pysam/
2021-07-16T07:36:11,535 Fetching project page and analyzing links: https://pypi.org/simple/pysam/
2021-07-16T07:36:11,535 Getting page https://pypi.org/simple/pysam/
2021-07-16T07:36:11,537 Found index url https://pypi.org/simple
2021-07-16T07:36:11,782   Found link https://files.pythonhosted.org/packages/7f/ce/e9405fcf72096f78dc7d75e8ce2a1cd907e1b4a9af0dbf1fc4dac5770f81/pysam-0.4.tar.gz#sha256=d8d437fadc283be6fc96f932a1417c43f5fb0a7cf267f8a750e819aa2babe1c5 (from https://pypi.org/simple/pysam/), version: 0.4
2021-07-16T07:36:11,783   Found link https://files.pythonhosted.org/packages/df/58/508dc40f603551d34b815560d52d9532dd243f1a8c35d9317ebff15d27e7/pysam-0.4.1.tar.gz#sha256=4a358266f93c103e4f003ae9a539fef1d91f572a6cbe7ace9a03ea220712d195 (from https://pypi.org/simple/pysam/), version: 0.4.1
2021-07-16T07:36:11,783   Found link https://files.pythonhosted.org/packages/64/7b/09ff2b61c7600a5aefd7ee0c37cec60140d31f8194d237e1d63c4d457931/pysam-0.7.6.tar.gz#sha256=d082ee3c8d7f105968719170956456d3660ef3a199bf53f9667f959ca4d11200 (from https://pypi.org/simple/pysam/), version: 0.7.6
2021-07-16T07:36:11,783   Found link https://files.pythonhosted.org/packages/46/b5/877f40fbb84f588b69b4afcb1409b8bdeed7ef980113d3e8ef69bab26e09/pysam-0.7.7.tar.gz#sha256=c9f3018482eec99ee199dda3fdef2aa7424dde6574672a4c0d209a10985755cc (from https://pypi.org/simple/pysam/), version: 0.7.7
2021-07-16T07:36:11,783   Found link https://files.pythonhosted.org/packages/b5/0f/436d15f08096dd9869a956e502fd119c15efbd84896aa53df50c7c6c0e13/pysam-0.7.8.tar.gz#sha256=d5deb64156ced1b95799854d8e9d5acdea1b2c9fdb7ffc3348e599a907bb810a (from https://pypi.org/simple/pysam/), version: 0.7.8
2021-07-16T07:36:11,784   Found link https://files.pythonhosted.org/packages/a4/ea/901d47d5621f15c05079dcf45e746a77bab21dbf0f9ce272993a3ca3a367/pysam-0.8.0.tar.gz#sha256=50cb6a68ce18eec604a6ef10fd6e85d4b836aa570758acbe02c54e0ff51bf282 (from https://pypi.org/simple/pysam/), version: 0.8.0
2021-07-16T07:36:11,784   Found link https://files.pythonhosted.org/packages/0e/4a/d1625792b2fd3a172d4bad096ab1559bcb7a81fa5fa6f9bc3937de23340d/pysam-0.8.1.tar.gz#sha256=a9105a1aa65f5a93e1e2cfb0e3009190b7a8a82ad7fb29cceaaaffbba08966b9 (from https://pypi.org/simple/pysam/), version: 0.8.1
2021-07-16T07:36:11,784   Found link https://files.pythonhosted.org/packages/10/42/7f51e1ad0c283e1d6bf826d3a193fa0644e675c9c6d42263b69fefc3b527/pysam-0.8.2.tar.gz#sha256=90cf4c05358b8e545f4f00c0637488d85b78d6170af093cd1e4762128b6427f2 (from https://pypi.org/simple/pysam/), version: 0.8.2
2021-07-16T07:36:11,785   Found link https://files.pythonhosted.org/packages/07/6b/3f48a2f05fbde46f2c52fc5f9adc15d928951cd54035109d553e14b774c7/pysam-0.8.2.1.tar.gz#sha256=8dc442b5b185bda37be8c3053b7f4fac438e3836dc2b190254d666d67ebb3a03 (from https://pypi.org/simple/pysam/), version: 0.8.2.1
2021-07-16T07:36:11,785   Found link https://files.pythonhosted.org/packages/f9/b9/8cfad46376335001f0cbbc46bf402fa107b0e8af8fe9e4192702b251f628/pysam-0.8.3.tar.gz#sha256=343e91a1882278455ef9a5f3c9fc4921c37964341785bf22432381d18e6d115e (from https://pypi.org/simple/pysam/), version: 0.8.3
2021-07-16T07:36:11,785   Found link https://files.pythonhosted.org/packages/27/89/bf8c44d0bfe9d0cadab062893806994c168c9f490f67370fc56d6e8ba224/pysam-0.8.4.tar.gz#sha256=30cf23931edf8a426678811f234bca4a83a53438028b323f2ef55792562d9dea (from https://pypi.org/simple/pysam/), version: 0.8.4
2021-07-16T07:36:11,785   Found link https://files.pythonhosted.org/packages/0f/37/fa514cb2163997551e95f63ec12f7bec7b640a601456f1d0ab3ab900c05f/pysam-0.9.0.tar.gz#sha256=90edf568835245e03eea176196cfafdfcb3af7e5fb40e48923a63f75c266c03c (from https://pypi.org/simple/pysam/), version: 0.9.0
2021-07-16T07:36:11,786   Found link https://files.pythonhosted.org/packages/40/15/20b22dc3d017ec123e533d062b982b111b0214168905de3221b5caf5f766/pysam-0.9.1.tar.gz#sha256=2969e080d435c62c4dd497294dfdb36eb92cd31f551c1030c0159481a5ef101e (from https://pypi.org/simple/pysam/), version: 0.9.1
2021-07-16T07:36:11,786   Found link https://files.pythonhosted.org/packages/f7/ae/59341d9fd2bed1cc32225115fc3f866a0e4e020f31073d698785c956360f/pysam-0.9.1.1.tar.gz#sha256=c3c106fc5e93f226d7830bbb4bb2c7238a993ef7de07c627f90944140a997d3d (from https://pypi.org/simple/pysam/), version: 0.9.1.1
2021-07-16T07:36:11,786   Found link https://files.pythonhosted.org/packages/76/62/908776209238850eca22e7139cc23ce2ba14b2941ceb438b1572f84e8d82/pysam-0.9.1.2.tar.gz#sha256=da49d15c3adca67c46d0aa418e8d2b27d1667890a444886dd95d6da55e6e5e2b (from https://pypi.org/simple/pysam/), version: 0.9.1.2
2021-07-16T07:36:11,786   Found link https://files.pythonhosted.org/packages/e7/e9/db49c8bd39673c1f48200f69ccc34784016d664136f36e03a090411a95fc/pysam-0.9.1.3.tar.gz#sha256=137fa5e288284e3708a7287ad9b4d08c0f069af8da5811e575e9aeabdcfa227b (from https://pypi.org/simple/pysam/), version: 0.9.1.3
2021-07-16T07:36:11,787   Found link https://files.pythonhosted.org/packages/de/03/02934438b204565bc5231f38a11da840a3c3e4b2beac8c8770d675770668/pysam-0.9.1.4.tar.gz#sha256=56ee7f8d07fa9d78b5c00dfbf335c95edbfed1518a2c14f8f108e58599922dc4 (from https://pypi.org/simple/pysam/), version: 0.9.1.4
2021-07-16T07:36:11,804   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/29/5a/0b25d6d734e1797c7ce06442ff6714af53cb1c8cd6c6cfd1a32df4587e33/pysam-0.10.0-cp27-cp27m-manylinux1_x86_64.whl#sha256=7fe3ee09e9eb70887f04900ce9444ab52ad16b78b85be6e3b1857a14b2ee36f9 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,804   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/72/d2/d106b2fc317e838f7eea7140c8d0ad4df4fde6a456a526649a58397f638c/pysam-0.10.0-cp27-cp27mu-manylinux1_x86_64.whl#sha256=01b3c10052c561f9dacf98478ef7195dc68a92706eb6d279c8fdc3c0ef14629a (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,805   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0c/55/d775726477bfe55e06c88701c8cf9a4b2596a877b09e562551c00cf4a931/pysam-0.10.0-cp34-cp34m-manylinux1_x86_64.whl#sha256=e2b86a6aac3df4fd5f658604af934c7fce61ba4ade188d1af1c17cce17d38094 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,805   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/89/ea/01735cceef15296bad16873979ae6848efebbbc9ab20eba244d532846dbf/pysam-0.10.0-cp35-cp35m-manylinux1_x86_64.whl#sha256=a2838dc68f6ec91957347c8e286bec9d2a8557ae44bc59232aefc6c5a7a25e81 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,806   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/8a/09/526378006226fb39eb54d9935c407c9b3c0302792c89e50d6b4f14d6f4b8/pysam-0.10.0-cp36-cp36m-manylinux1_x86_64.whl#sha256=81e3a70c6801b92714123d576f23aab792f5111a49282f7c050fd2620d38e465 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,806   Found link https://files.pythonhosted.org/packages/87/8e/d2d8238558970df37c7aa01ddec63057a98042334e939b4c1c69cb9a2504/pysam-0.10.0.tar.gz#sha256=1e925d2c9bf7b1753392da4fee3c0c184f8b062acd074905caa20569f87354e0 (from https://pypi.org/simple/pysam/), version: 0.10.0
2021-07-16T07:36:11,807   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/93/f5/bfca0394bb90cc5993b7595d7c6aeebfc43dce8bf97394df4bfba9141caf/pysam-0.11-cp27-cp27m-manylinux1_x86_64.whl#sha256=0196588bf9a2d499abf1882e3c04431dc81faaa4432feddd6eb03fe7a430a62e (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,807   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/4b/ff/7e0c6169883a26cee912ce25ef98893c13966cce1064fd6136b53e28d365/pysam-0.11-cp27-cp27mu-manylinux1_x86_64.whl#sha256=9de9d06f2de8949d062cd995bee982940283c309426d7ee287a2de22e3b2e92e (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,808   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/39/ba/91614d3e18818011decdb5cda8991cea11330d274399492822fb50b7478e/pysam-0.11-cp34-cp34m-manylinux1_x86_64.whl#sha256=f3280509966dbc44e1d5669ce9fe523e67eebe970f304e626f210df999b12731 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,808   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/3e/6f/2b166df4d7d55e2f69551b85ec2bba01048e5dc2307163ab8ad7d694bde1/pysam-0.11-cp35-cp35m-manylinux1_x86_64.whl#sha256=1943e27e8584dacbd1098fc17b55c6fc80765c1df6b9fb4844d3925232453afe (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,808   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0b/28/cd6fde9c19444f779130e27195b4c1d9d896266e4e0b0bc8d515c031854f/pysam-0.11-cp36-cp36m-manylinux1_x86_64.whl#sha256=4f598c325cefba2b09adc53e4e7fd669f6855ab6db52f27ff4d73da48bc2b2a9 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,809   Found link https://files.pythonhosted.org/packages/f4/bb/c5fcaace8857bdf8a430de41b5298c602fdce4917494f7a941c038e5861a/pysam-0.11.tar.gz#sha256=815c8a6150c5fe21df227e730dd57e4212984ae568854fcc5873e243072dcbad (from https://pypi.org/simple/pysam/), version: 0.11
2021-07-16T07:36:11,809   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/81/01/2304e5367c566f538cf64bad1bd41ec41e47d8aeefd197a209c8c1cf14fa/pysam-0.11.1-cp27-cp27m-manylinux1_x86_64.whl#sha256=4ade89003f13c6eb6b243c76eb782b2bcf3f8320a7675758b553d7c2e7214743 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,810   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/ef/b3/b7ea200fc6e16af0cd2397659a2a2dd383f4ea71d2e0948f7215e73fb6a6/pysam-0.11.1-cp27-cp27mu-manylinux1_x86_64.whl#sha256=5a4ac394b644c7cb9782351aff7e782c7f4c670df54c0bb170fa36c10e1a5c86 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,810   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/e5/00/0d55946c0b1c781caee096ef9c4e9e54047ecf897874bf791c5ea8351df3/pysam-0.11.1-cp34-cp34m-manylinux1_x86_64.whl#sha256=19f37b28ec1f5125a47080ea2b87cd801a8cf3c67dd4f2a872cfd0ecb6673ecb (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,811   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/45/2a/b5e9e88b0d5097fa45f0832a05acfb39879679a087e55145198d47bb6099/pysam-0.11.1-cp35-cp35m-manylinux1_x86_64.whl#sha256=ec38dddadc0c6cbcbfc38f481ffbb33f888a91665a29bca10077a4380eeb4aae (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,811   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/6e/0e/967ed910f8ce74ed5ea6b7a4775a86d05205963bf927a8452604ad277913/pysam-0.11.1-cp36-cp36m-manylinux1_x86_64.whl#sha256=1663730a69bfe7e84e7dcd9bcc3a35d8d2ad2c023746f1806b678e294fe21b8a (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,811   Found link https://files.pythonhosted.org/packages/be/70/16cdd6c5ef799b2db2af4fd5f9720df0f3206b0a06ed40e03692aa80ae25/pysam-0.11.1.tar.gz#sha256=fbc710f82cb4334b3b88be9b7a9781547456fdcb2135755b68e041e96fc28de1 (from https://pypi.org/simple/pysam/), version: 0.11.1
2021-07-16T07:36:11,812   Found link https://files.pythonhosted.org/packages/89/d9/52995323a3a15e14f2cd579a49f953c804b36a1a7d7dc09a08b7de3591d2/pysam-0.11.2.tar.gz#sha256=d64e1b5b6b0aeac2effa7f9f6117f5413ccf6a0028935d45491a1553154a17b1 (from https://pypi.org/simple/pysam/), version: 0.11.2
2021-07-16T07:36:11,812   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/8f/23/12b4829036ce49ec068c61a28057029dd19a6a1a29855dff0efb785e0d12/pysam-0.11.2.1-cp27-cp27m-manylinux1_x86_64.whl#sha256=da2dc02fc9d92ed72bdcf22e03e06ba06c6119c858b1de5cec992e2e98977ea5 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,813   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0a/d8/daa0986a5049b66b4ab2fc8093a17a961cedc75d1a39e1a4821d19f4f13f/pysam-0.11.2.1-cp27-cp27mu-manylinux1_x86_64.whl#sha256=713e897ab7e3a82cb92a0a5fda1fd7e968c75a4d990c778e2433cf6f10d12b2f (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,813   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/34/5f/254cec485fedd72269c061262eb2bc36f8a438a5badb78c8582e46905623/pysam-0.11.2.1-cp34-cp34m-manylinux1_x86_64.whl#sha256=89d1715f90e65ffce7dfca7fa5040b8965b6324f1b343ebd540500eed9c1862b (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,814   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c3/cc/47ae71c341bd822dfeec2148f6521c1bba690e4581814114519b3cc611d4/pysam-0.11.2.1-cp35-cp35m-manylinux1_x86_64.whl#sha256=acbfdffa8dae9dd3569af65569639694f128a598691ec471de3c54e3831baee4 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,814   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c7/b0/4acf13c3b125db232e8ed93fec3e5b3a90abe47fd27aaacc15c9e03caf6f/pysam-0.11.2.1-cp36-cp36m-manylinux1_x86_64.whl#sha256=71f2c4ef61ac64954bf1fdfcf6ea1912350145ede753db10e04fb3d87ffec2e2 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,814   Found link https://files.pythonhosted.org/packages/4b/d2/152284e08c551471c7a7b9b23b4d0916637705ee4f979314ca1750b37c83/pysam-0.11.2.1.tar.gz#sha256=5de4744e451652db70bfd5494606fde8d4c58d3ae55b9816329dc905c80a7c60 (from https://pypi.org/simple/pysam/), version: 0.11.2.1
2021-07-16T07:36:11,815   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/24/dd/2a9226b90d8c98482209617c2376434e1c19da4981de49c78af0e763988f/pysam-0.11.2.2-cp27-cp27m-manylinux1_x86_64.whl#sha256=e7826460c3178ff35e91b511a8fb3e978fc916c3e1d9b388eb9f62bb51410b58 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,815   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0d/9d/d30859cf5a7555719e9b28d34f61bbd4ef0e811fb8a857a986ee9913b79a/pysam-0.11.2.2-cp27-cp27mu-manylinux1_x86_64.whl#sha256=7af66c50f7766419ad458f55b0349597361a38eb45b7d98e3730863f60d7d4ae (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,816   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d8/34/b0a7ece94bf7af7d482282ccd8430fe291147960d900b514b7aa606c9170/pysam-0.11.2.2-cp34-cp34m-manylinux1_x86_64.whl#sha256=6a86f8ed81ceae1122edfcff65329b260a359ed601a657f47f33f7009d8c2516 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,816   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/9d/a0/2bc18552108cf9605e0ffa7c31673bc56653c0cd7521730a2d5eeb06939f/pysam-0.11.2.2-cp35-cp35m-manylinux1_x86_64.whl#sha256=8362ef266063047d156770ae2bff875aa7ec0d906b8b298479705e6117370f6f (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,816   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/23/c0/18436ad1db0ed38c997b7fda42db8b6489c50abcb321320015de12bdd164/pysam-0.11.2.2-cp36-cp36m-manylinux1_x86_64.whl#sha256=ee5126b00628fd959cb99d4ff196493c0bc952f51dcb558f4154407c3d31a10b (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,817   Found link https://files.pythonhosted.org/packages/a4/1b/b6dfd92aea876647d20d9a8bd8618e4f2af6300539426be83c8bb0912d6f/pysam-0.11.2.2.tar.gz#sha256=9cd66406eaff40986302e9e1edc5872538f0fed9623aa8ceb15f9b80bbabfe03 (from https://pypi.org/simple/pysam/), version: 0.11.2.2
2021-07-16T07:36:11,817   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/be/3c/9c0d31f4baa506057e781641325f52f709ca4fe777065e39be08e690752b/pysam-0.12-cp27-cp27m-manylinux1_x86_64.whl#sha256=dcd17f2dbe7b9e0742856cd23fd4ae7d6ecc9c48e3baa91bf019b63d935fa1e9 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,818   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/5e/f1/28f7e3df4941ac01c2c1794b1009000fad81cf026da6c04e223e5e86e6ad/pysam-0.12-cp27-cp27mu-manylinux1_x86_64.whl#sha256=e8205678d96c33f122caa1e12dcb41a2db20d9147ef02c4f4f9c76b98a6362d8 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,818   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/e7/a7/9225250a464b91caba6c88e82b59755e07a30aa803085febbb923655d2d5/pysam-0.12-cp34-cp34m-manylinux1_x86_64.whl#sha256=b50500a772b9e3b13daea2ca43bfc0c7251369bf361b6579ad579d4f8887b9d2 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,819   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c6/ce/08728c6f395b46cdb75b79d4c554184b624fbe344a6a99b62b1a7f58a5df/pysam-0.12-cp35-cp35m-manylinux1_x86_64.whl#sha256=454e083cb80cf14fd73b5230c9f58836215b0bc961ec3d88a25897d05d24cd5f (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,819   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/ef/bd/a741af36309bfbd8d40e5c5c9fc9f2ca3c7a86c2d1ff7c2563a81d851a44/pysam-0.12-cp36-cp36m-manylinux1_x86_64.whl#sha256=692afc5ae93ca6dbd6aaf12d79e9c376d7df42e600ceb73dcf1c1d3c238d6a67 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,819   Found link https://files.pythonhosted.org/packages/0f/e0/19046ae89307ddeadfa8dabc305a9cfce67865de06b762057edd84bc0fd6/pysam-0.12.tar.gz#sha256=33922cb3277ed9a63457c1b6a9dcad2774a217ababcc97a854435be87ba80488 (from https://pypi.org/simple/pysam/), version: 0.12
2021-07-16T07:36:11,820   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/15/bc/9d27138acddecbeca3a010691e71e89ad02e5c6dc3a38ca9d8cc94c92295/pysam-0.12.0.1-cp27-cp27m-manylinux1_x86_64.whl#sha256=ecde3b5e8051c04ab455a5822e4b5dd58b48344ca2f256d6f0f899426e823b05 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,820   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/29/d9/7a508464feb23b750ba0d56e10e014f0d1a8cd6a4e8fe3887c75affa5fa9/pysam-0.12.0.1-cp27-cp27mu-manylinux1_x86_64.whl#sha256=035238322ad06d853173ad4203f393e1c2fff9e6bb560b90a37890a77e4d9f1d (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,821   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/eb/d5/4b67f2767fc352d8246c3eed4ce0f5d61fdbf6cef6e5b57d433ed63f7ed8/pysam-0.12.0.1-cp34-cp34m-manylinux1_x86_64.whl#sha256=02d818752e93a4263a6d41a4fc6e46ad6180e1bdc6906da0f88d7ef0a986ff14 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,821   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0e/d9/91db21a596a3a896365a90c5b44c6722b4e0acfd5e90c52071175e77aad4/pysam-0.12.0.1-cp35-cp35m-manylinux1_x86_64.whl#sha256=a99cd626ff0fdc09b68a1cc9cc9551f4dc3c4cd49872583de1a2f39e69520923 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,822   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/50/28/f3a3989a9a34fa6c84fdba3d80b4b1624b2c253d7906a13638152b20555b/pysam-0.12.0.1-cp36-cp36m-manylinux1_x86_64.whl#sha256=f1cd051d474a72079dbeaa3d6cb1b26dac005af8e4cf71b4dddad7c66b08ce26 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,822   Found link https://files.pythonhosted.org/packages/b9/98/d98b250f98a6b91df71a03083219bec786cdda5408f77997f8ad81d06058/pysam-0.12.0.1.tar.gz#sha256=04837bf0b1313e57d50076f228463262b9982c410b973eb184c033528f83d523 (from https://pypi.org/simple/pysam/), version: 0.12.0.1
2021-07-16T07:36:11,822   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/14/cd/676a08a4bd77fd21716add76f946235780a5673c75c7408b2449db2dde5a/pysam-0.13-cp27-cp27m-manylinux1_x86_64.whl#sha256=a87d86c69c4007b898e1c0256da1eef6f9c67d8bfaa2208591e7e43b02c8ee92 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,823   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/59/7e/55048651e80ca7ebbed41489ec53da863a500d536fbff5884175e81b40c1/pysam-0.13-cp27-cp27mu-manylinux1_x86_64.whl#sha256=d977b0cfed87ae9fc0fcac1b03a676f95ce9b6f574105311d7f1e106826d8256 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,823   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/fc/63/4a758298dafa37a719540fd55c4e76de15e3ad6be0201c9e0e6ed59b3d8c/pysam-0.13-cp34-cp34m-manylinux1_x86_64.whl#sha256=539203173afb0f8672284969077f32e487690dd1a3e7458d3cd1e2f69dfe7637 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,824   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/8b/08/8f6ea307458945f9e5db70e460b7902f210f08646af35800372907095f06/pysam-0.13-cp35-cp35m-manylinux1_x86_64.whl#sha256=c0b11efe9ffc66e4ccbbadb992a0ca39ba736ca985cb02423ec1a7ed95b3f6d8 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,824   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f1/dd/5f41722f95749537e2f5a84414a4b08fc4e14d39552df8171e375129edf5/pysam-0.13-cp36-cp36m-manylinux1_x86_64.whl#sha256=cd86023f429ef7eeb8dd19f85553c2f4544e2927e0d23d99cbc907f4c74dce8d (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,824   Found link https://files.pythonhosted.org/packages/31/17/31d317006a74941d2caddac97c5106601fe4da467653d0f061702e9ead95/pysam-0.13.tar.gz#sha256=1829035f58bddf26b0cb6867968178701c2a243518ea697dcedeebff487979af (from https://pypi.org/simple/pysam/), version: 0.13
2021-07-16T07:36:11,825   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c9/0b/ca7620a778a1ac5a6669b750ab82cd8e2ca29f671cf2ab929cf907338bf5/pysam-0.14-cp27-cp27m-manylinux1_x86_64.whl#sha256=f08e3ee089a1691be837473a40eea097be7de3c066ce3ebc1e2d486d0ebda29c (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,825   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/2b/ff/a7cdcde7f79ca59cd6a6921f55f0cce8fb3d4ff273257e313efc3e52853a/pysam-0.14-cp27-cp27mu-manylinux1_x86_64.whl#sha256=f0973c10a3377d5d8291aeebd03ce9a79192581903407b475223428b0843e063 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,826   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/51/c1/474c632acbbd7c06921a4ad31b237c3f41fe662101ec775be6a9c3c8cf20/pysam-0.14-cp34-cp34m-manylinux1_x86_64.whl#sha256=6da96be7861ca95a7c4378ac15c2e9372b45d99a3f5360d88e21a9d45fe6718c (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,826   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f7/53/6e677a66b02755d9d631a7ffa37b23b8eca7b2463faf14dcf3bcbbcbec24/pysam-0.14-cp35-cp35m-manylinux1_x86_64.whl#sha256=02cb2d210be93782179e94565ee7531a7e4ff2ddff05967ed9c502445a7544ed (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,827   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/96/7b/845e49997825cf2aaef3719853e8d2d07b43d3a5e096cb9863208b7d0af8/pysam-0.14-cp36-cp36m-manylinux1_x86_64.whl#sha256=2aec5aebb90c1c1fe0f596984663773af7cc98ef1de0db047d93c99aac52177f (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,827   Found link https://files.pythonhosted.org/packages/d8/78/8b3fad13d3bd8787c0d922056061727c2a0cf91c45a836c98342594dd293/pysam-0.14.tar.gz#sha256=c9c8ea82b4deee7607d5885fc7cc92311f06e765ff30e0b2b2d3d85b28cf5687 (from https://pypi.org/simple/pysam/), version: 0.14
2021-07-16T07:36:11,827   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/cd/9b/2627df910452b49bef57dd5ce720832d49faadea3e3d86f940f168b807b4/pysam-0.14.1-cp27-cp27m-manylinux1_x86_64.whl#sha256=d571e8536b3bc9807577e0e2744247d1887b90a6ad005c0dedea7639bb04d5fd (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,828   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/b3/96/a9b21863c30c00bde76ab9bd3b538ed9f4d872f6767217c930cd0246fd21/pysam-0.14.1-cp27-cp27mu-manylinux1_x86_64.whl#sha256=dadf1c6c7c3be79d526c38fcf6ff577062efed814b17341a4b8fbde7226a9555 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,828   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/a0/ba/95ee9ea7921ae153c51880ffe047269a7ccf396442214f4fc965cc66ea68/pysam-0.14.1-cp34-cp34m-manylinux1_x86_64.whl#sha256=3d064977832536287d95e657d9ed184a0cc6e331b877637b203d50d4762bec5e (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,829   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/09/a9/d74aa164efb28ce328cd4890b0182ccdf2e781c192910072717c965765c6/pysam-0.14.1-cp35-cp35m-manylinux1_x86_64.whl#sha256=4279edd397a32e665e20d53d878a5604b98cc57067a0fc3d58f6933a5b6f82fb (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,829   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/97/bb/65b3a258ffca71251ae1d07c1d3eb54448da31ee74106e49e2f251f066d4/pysam-0.14.1-cp36-cp36m-manylinux1_x86_64.whl#sha256=37fba70c6273329eb60383154189c6a72a960186d5e9d8cf0f757f2ba9f08b32 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,829   Found link https://files.pythonhosted.org/packages/fc/9b/4bb8d016406dcff47e2866e14d3dcb10741ec3920649e8c521996830944f/pysam-0.14.1.tar.gz#sha256=2e86f5228429d08975c8adb9030296699012a8deba8ba26cbfc09b374f792c97 (from https://pypi.org/simple/pysam/), version: 0.14.1
2021-07-16T07:36:11,830   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/2f/d8/57e6c36c4069e3b240115b3cb98bf1d5a2989d76815aff14fb0149d27781/pysam-0.15.0-cp27-cp27m-manylinux1_x86_64.whl#sha256=3cb1cda2a501751231fc7358d4b8d981ca13d9fe5e9a5a04ccd728a56a28bb96 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,830   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/dc/af/c14708a4d43effb82bd14302e41e9fa818b724ada9b9d89283319a22a585/pysam-0.15.0-cp27-cp27mu-manylinux1_x86_64.whl#sha256=43165efe8f1d8b7e2dd254dae93e88b5ed3de4fb6e9c54f32274c1e2c6124a68 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,831   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/15/77/2e258a5ff090226516c4338d682c6f8ed13e5be2ac7a67e6b452b04b0237/pysam-0.15.0-cp34-cp34m-manylinux1_x86_64.whl#sha256=c66d08f45dd2b3404d65429f792c9b79fac8ab29b09941aff0cb47cd29a7d16f (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,831   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0d/5d/d96d3662647a3cf33b1e3fe6d21eaecd00f47d39edbe4cd85486639cb603/pysam-0.15.0-cp35-cp35m-manylinux1_x86_64.whl#sha256=044541e8310c64993ba201cd9c32659acd2f1400a5094c52353030e082f2a831 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,832   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/47/da/6a0cc06c65acaea0b8830e632712d53fa8bc88ea19096038b3bef22b25da/pysam-0.15.0-cp36-cp36m-manylinux1_x86_64.whl#sha256=dbb2de0144fb16adaa49bfd67ca919e27404996bdd060a06bbcd82eb60ff09de (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,832   Found link https://files.pythonhosted.org/packages/f9/c4/f1b6963a05f415aa69c8efd64ebe460d56d03ecc75db70b0e8606b589ade/pysam-0.15.0.tar.gz#sha256=51e7030bebff68502a69fabc601727f827cd6e7c08c5899b11ad8c6084ba4ba5 (from https://pypi.org/simple/pysam/), version: 0.15.0
2021-07-16T07:36:11,832   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/b4/d8/9afa92bd4b48ebd6896d22bb7cdaeb5aa4577983333df5e99160c62fb6ff/pysam-0.15.1-cp27-cp27m-manylinux1_x86_64.whl#sha256=cc6b5bcc464bebe5c932cb1ba0ff9d3a6193d9b72d05aba9f16e8d115c06149c (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,833   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/66/6b/f1a4f142d884b6e1cda6542bf4b89ce88ad8465197511d83994f2cf6484d/pysam-0.15.1-cp27-cp27mu-manylinux1_x86_64.whl#sha256=e1271bfb05a87cff378c88c956c96f6ae040a2d996104a31effa817929578e8f (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,833   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/69/5f/030c774b44932d2e23d773558679d553fb31dd5ecdb094b8e26b316de784/pysam-0.15.1-cp34-cp34m-manylinux1_x86_64.whl#sha256=d164917496b6569d727505fef0b6623dc3485d6f45ebd8394b124b155a3c0419 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,834   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/37/27/7d7ce83c0acac59b95849f2fb678484147f1e1393162ee0975cb7f84e53c/pysam-0.15.1-cp35-cp35m-manylinux1_x86_64.whl#sha256=c54403c26490afdfc5db68a0ca1e846b94daa8ee0f571e278efda428257016af (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,834   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/6f/f4/e12faf1618e977a868fe66d40288fc3dd989a10cc4c77603da33a7634a18/pysam-0.15.1-cp36-cp36m-manylinux1_x86_64.whl#sha256=8616649ad4e3538236636d068361bc9716ad45700f65bd46b7508cbc69ca49d7 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,835   Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/1e/04/3e22a04ade5291e968b3f3e9195929574221d86fd8982a4976a40b045060/pysam-0.15.1-cp37-cp37m-manylinux1_x86_64.whl#sha256=1173a05c88752f2b871cc902fa33769a85c052f28bf0a94946f4a1576e300bce (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,835   Found link https://files.pythonhosted.org/packages/73/59/c319f1bde3019bbce4583cecb12b9e3e52ffcfbe2c96d8b1fb131c0d4fb7/pysam-0.15.1.tar.gz#sha256=658421124c2f3de1b7445e03ca8413df0077f67ea9980abdaab0d1b5f7a8936f (from https://pypi.org/simple/pysam/), version: 0.15.1
2021-07-16T07:36:11,835   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/1b/7d/68b6555c7bb414b655495305d2add784c251fc83d4e698878e6d1d35fc9a/pysam-0.15.2-cp27-cp27m-manylinux1_x86_64.whl#sha256=34dd4cf08cbdea1329a140f5446c319992460d400b9851c0cb5607f3c58ad256 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,836   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0f/bd/f5ab828a9ff45a6ca14d5ea2a3580f720134052db258cd7ef929a4ed1d7a/pysam-0.15.2-cp27-cp27mu-manylinux1_x86_64.whl#sha256=236ae950c0194037ac3e8a11fa7bda6b46db17ee3f86e1111775ed4b9cdaf95b (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,836   Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/4b/04/d5a6386b6d124bcdf27d81ab952e5d24e37ff98b97f992aa5b83c647e9c9/pysam-0.15.2-cp34-cp34m-manylinux1_x86_64.whl#sha256=975fbd395b5c4d360be5fde2e34d418c64718ba732ae5b2bfb712e6cefa750d5 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,837   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/aa/e6/0b18d30c30e3690c5774446c1d7246c5e37c4710e38d93a20bb56cad4bc0/pysam-0.15.2-cp35-cp35m-manylinux1_x86_64.whl#sha256=1e0a6abf4fe0d3934fee8d662f6fda28e466b60209b5b1fd41070e1ccfbe87f2 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,837   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f1/fc/d2be1a093bd8494ab63e3168aca36c2494753bbff190f3201ce2e7da9cda/pysam-0.15.2-cp36-cp36m-manylinux1_x86_64.whl#sha256=0f063380ebd727f58483b256fe21d90358527fbdf48b925ae2680cc1f2c553ae (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,837   Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/20/1a/4fd27da2d19f7d914f757097605709a6509776b4cb63f42bca63f3531058/pysam-0.15.2-cp37-cp37m-manylinux1_x86_64.whl#sha256=e8166058e01d5b7fd2d82c5fee29f9c22e6016091b8c397cc029f7cc2f2f61ff (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,838   Found link https://files.pythonhosted.org/packages/15/f6/ce0611aaa1865a616f7dc164fbf046eaf38f2b17c6d404403c56250beb93/pysam-0.15.2.tar.gz#sha256=d049efd91ed5b1af515aa30280bc9cb46a92ddd15d546c9b21ee68a6ed4055d9 (from https://pypi.org/simple/pysam/), version: 0.15.2
2021-07-16T07:36:11,838   Found link https://files.pythonhosted.org/packages/15/e7/2dab8bb0ac739555e69586f1492f0ff6bc4a1f8312992a83001d3deb77ac/pysam-0.15.3.tar.gz#sha256=a98dd0a164aa664b1ab30a36f653752f00e93c13deeb66868597f4b2a30f7265 (from https://pypi.org/simple/pysam/), version: 0.15.3
2021-07-16T07:36:11,838   Skipping link: none of the wheel's tags (cp27-cp27m-macosx_10_6_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/bc/99/5b711afad53f7ebdafc182bae1642fd764e569a8c0de9408ea6138c668b0/pysam-0.15.4-cp27-cp27m-macosx_10_6_intel.whl#sha256=0b0f407ad96b3bd492017ee82a317ac0fc68dc858ecba9119e4ae69b1cda9910 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,839   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux2010_i686) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/1b/28/60742ebf8afa6efdf7d2cc3552cbef24da33bf0f76b26b5afef2406683fd/pysam-0.15.4-cp27-cp27m-manylinux2010_i686.whl#sha256=5b6a2258e326204ee94bf4d482d9a137ce8cbb3f3cefada42c7f26802d15b95d (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,839   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f2/c1/8f1562c2b89bc5606a3e8c57add0078af4cee3050507eac4b67b37309b16/pysam-0.15.4-cp27-cp27m-manylinux2010_x86_64.whl#sha256=495815ef466aefa80d949ac449cd364f21cb20ee56b1a0bd623352ad3f73bf14 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,840   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux2010_i686) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/0e/f3/2b9802c61089f6c94c73f902f17046c416793da9242dfe73462e79ec4635/pysam-0.15.4-cp27-cp27mu-manylinux2010_i686.whl#sha256=00a1f62e704410343ef6a6232f5bdd29f67f88326a89757e665dee035ef36112 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,840   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/68/7b/a54f66a8b126c0d6eefa3f71ebdd46bf967c0452759b553432e845e927f3/pysam-0.15.4-cp27-cp27mu-manylinux2010_x86_64.whl#sha256=3d5158231cab88cb8a931b78f34fb6eb939a093cb8d5273452cc12d3206e445e (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,841   Skipping link: none of the wheel's tags (cp35-cp35m-macosx_10_6_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/a9/c6/a337077e2cbae228a7f1b0ee1d97b240609c9377b6d46df9dc0a477eff73/pysam-0.15.4-cp35-cp35m-macosx_10_6_intel.whl#sha256=7c358f69620e7b9af7548a62ca2a1fb6b51c03fcdc79a0ca8d1839ad92a532ce (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,841   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux2010_i686) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/55/9c/b064140318b64910f0a7938b385f10b88428aaa50f720038b2927a7db908/pysam-0.15.4-cp35-cp35m-manylinux2010_i686.whl#sha256=2581ab403fdba02e2261cf2f9df783f24de5530e1f77c84236707f8d8706cd91 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,842   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/3f/b4/075c25bf8e1aaa11d178fdfe267d73f1ea14f9e90ecb0fe58cb98911bdc5/pysam-0.15.4-cp35-cp35m-manylinux2010_x86_64.whl#sha256=00c7f094be02ba8daf2feb51467b70142f9cca22fb5336b504bc58568a2500de (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,842   Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_6_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/b2/78/df321a985e93be0d2dbf2249e9d79a33131381e8d9ef5c965db643183561/pysam-0.15.4-cp36-cp36m-macosx_10_6_intel.whl#sha256=4ddcb84e471aff2f55beb5ed2d368dc6e773947c628a1a7b6d5ceec9c141ce51 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,842   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux2010_i686) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/47/cc/a9546377a762a84bd17ca313f182e8eba833e579a568c3d62571edd8c2f7/pysam-0.15.4-cp36-cp36m-manylinux2010_i686.whl#sha256=0f3e42cbc9bac07cf6a880c2ae318c24aea20f43a3f3562e53068266627cb7a7 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,843   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/2b/01/2be4def91aeb50ccb963879b8193ca667087308696f2fe6aa86c6da9db72/pysam-0.15.4-cp36-cp36m-manylinux2010_x86_64.whl#sha256=d9f116b2e32b678bbd95ba0c83a449d0a59f2deb04a6fc02f42b5cd9e406bde5 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,843   Skipping link: none of the wheel's tags (cp37-cp37m-macosx_10_6_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c1/b9/4a37921da49d89c855b0fae747843b7d07187edd4f35d0069a7b02ce89cc/pysam-0.15.4-cp37-cp37m-macosx_10_6_intel.whl#sha256=5bcf5d49922aeaccd0dbf0b3e4327b03be2883814bf2476e83f20fc24d7be02b (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,844   Skipping link: none of the wheel's tags (cp37-cp37m-manylinux2010_i686) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/7e/46/d3abc41217b9cdd97109ab648094915ea55038bfa1d7d880012652704b37/pysam-0.15.4-cp37-cp37m-manylinux2010_i686.whl#sha256=179e68c5acb8cc6a79a79441ba6cffb88d7c3afb74c7b170395c248cb7b9f138 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,844   Skipping link: none of the wheel's tags (cp37-cp37m-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/63/ee/2c5dacd21d02d3bb7c7baf03dba8f42bc4af8b02370b7e52b6e5425d2366/pysam-0.15.4-cp37-cp37m-manylinux2010_x86_64.whl#sha256=333e9e73addb0579aa8af08c6618b359bd038a3710428b7ce1caef0075392b3c (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,845   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/ae/1d/8569d5bb7592afa48796e2fc743372eb690c776fe21dce0ccb9607a202cd/pysam-0.15.4-cp38-cp38-macosx_10_9_x86_64.whl#sha256=62b72de5af5b8550f376a580fecb23b81d989140cf95f8465fef2c3d96006424 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,845   Skipping link: none of the wheel's tags (cp38-cp38-manylinux2010_i686) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d3/77/b885532e487e15db1b78fa2ecf00ef6edf5f4743025080941f60924da6ea/pysam-0.15.4-cp38-cp38-manylinux2010_i686.whl#sha256=28fd770354ecf621ee47425bfdcf012097fa7a8ff590b49ec953d059221886c2 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,845   Skipping link: none of the wheel's tags (cp38-cp38-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/78/63/0e143ae469f418cfab28fb165936d4101e1b813e3ce657762d51723ab38a/pysam-0.15.4-cp38-cp38-manylinux2010_x86_64.whl#sha256=5a9730d9775dc30a8cc197ca3e5340b7c3cb63b66c387ecfd8e665426f083f65 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,846   Found link https://files.pythonhosted.org/packages/25/7e/098753acbdac54ace0c6dc1f8a74b54c8028ab73fb027f6a4215487d1fea/pysam-0.15.4.tar.gz#sha256=a535e15cbd6e27f4ab74cabca30ca1df7eea283cb91d3b536d47fe113fee066f (from https://pypi.org/simple/pysam/), version: 0.15.4
2021-07-16T07:36:11,846   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f7/55/6f5ce9cfe9631c32b58d50be54b2d1ef7e53937d6e9208ac98ea41cc264b/pysam-0.16.0-cp27-cp27m-manylinux1_x86_64.whl#sha256=688ac7f4d7f134a8c7193963c7cccbb3f3f630c51909bb76d809b4db35aaf8f0 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,847   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/1d/c6/49045eba4ae325d15e9de03802a633fe0d8e9ac2d02ad6de723ca99a9772/pysam-0.16.0-cp27-cp27mu-manylinux1_x86_64.whl#sha256=1cb17ff9562a5b075a609f070ab4b3290e8a8021eaf2016f4248ee4202e47957 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,847   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/9c/24/537e86533e773c3dcb6bd05de60bf118cf8ccf60dcf24386a5c3807120bd/pysam-0.16.0-cp35-cp35m-manylinux1_x86_64.whl#sha256=d01e72eafea1867c714f0754339b3c549c44dc535e5c497601789ba1dc1f3fca (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,848   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/87/92/44f62c9b75b8f01f4671e7d4ac0951d3379126c7e2d280ebdcba3d7cb0df/pysam-0.16.0-cp36-cp36m-manylinux1_x86_64.whl#sha256=f4e31ffd685d333431ac7e7dd74f83f4e14eff1905a4ef1188b2b03da8854f01 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,848   Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/f9/21/dc7ec647d83a21a3b805a20f0039f466d5cfd4acc40f411aaf78da83ebb4/pysam-0.16.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=9c532f33b5379744941d8fcdf00e6d75aef48319372789836ff1c3f717b84563 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,848   Skipping link: none of the wheel's tags (cp38-cp38-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/b6/ad/442c56d798a3e8c762f71af8c8c7f75c16599f6e51e1f6dd4df1688ad6d7/pysam-0.16.0-cp38-cp38-manylinux1_x86_64.whl#sha256=e1aa22051efa4305ca045209bb184731f8f8e20afc833716ed91e89f1533ff53 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,849   Found link https://files.pythonhosted.org/packages/18/74/69018650a6ec9dae2eb2f710e158fa395134ce579c605f152e41890e7f3c/pysam-0.16.0.tar.gz#sha256=07c9d3a772f90e9907a68bc3f495e2c608018a92888b9cf9f1197cb3a35aa9c3 (from https://pypi.org/simple/pysam/), version: 0.16.0
2021-07-16T07:36:11,849   Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/9b/57/65c688a9f5757c82fc3954e5562725dbeaf3866f13d71d92d715263cd707/pysam-0.16.0.1-cp27-cp27m-manylinux1_x86_64.whl#sha256=9e3597a49e4bc72c31199d6231018ad3034e08a8243b9f8086953afb2ab5a3af (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,850   Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/9b/ab/a7f2637b5bc8fb278aa9b5a5d4eab70856625c09b1d95328e3b78132847c/pysam-0.16.0.1-cp27-cp27mu-manylinux1_x86_64.whl#sha256=a5a0fc1f0d724d0b7789341add26ba181ac009430021f0998f6083fb62432193 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,850   Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/ca/09/ad780f4430777a7bfca63ee2d4d4584436d2f31f010d6bab743cfc97da48/pysam-0.16.0.1-cp35-cp35m-manylinux1_x86_64.whl#sha256=9da29490c666a963e5a7f6f5114e86c9b36a8a6adc2227f5772bdc38c09d2d37 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,851   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/87/a1/73e80a7a873f3fb0e52d368a4343eb9882b737c932b95020d82251f1087e/pysam-0.16.0.1-cp36-cp36m-manylinux1_x86_64.whl#sha256=107eca9050d8140910b5ea5c5a9e66313e1155eb44cc180e10f48f9cb71e8095 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,851   Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/20/85/335857b9888f6d9a13b03a8f21b0a6228b180c361631d9d70e7be3e22163/pysam-0.16.0.1-cp37-cp37m-manylinux1_x86_64.whl#sha256=f65659deadc4904984de24cb6f3878b6052cf504a2a85a50b80f2ff7939f96db (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,851   Skipping link: none of the wheel's tags (cp38-cp38-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/8c/e6/a26fac418a7481b5ce1ffc162fe033edc9a935536f893a0838842c011371/pysam-0.16.0.1-cp38-cp38-manylinux1_x86_64.whl#sha256=3eb70111a5ed86cc7a048c9b2205087b1184093e6135f02ad7f144b206951452 (from https://pypi.org/simple/pysam/)
2021-07-16T07:36:11,852   Found link https://files.pythonhosted.org/packages/99/5a/fc440eb5fffb5346e61a38b49991aa552e4b8b31e8493a101d2833ed1e19/pysam-0.16.0.1.tar.gz#sha256=d428a9768691d5ea3c28cc52a949c920ae691aa4c110a8b7328dc4d165ef1ad6 (from https://pypi.org/simple/pysam/), version: 0.16.0.1
2021-07-16T07:36:11,852 Skipping link: not a file: https://pypi.org/simple/pysam/
2021-07-16T07:36:11,858 Given no hashes to check 1 links for project 'pysam': discarding no candidates
2021-07-16T07:36:11,879 Collecting pysam==0.16.0
2021-07-16T07:36:11,881   Created temporary directory: /tmp/pip-unpack-jveis_vk
2021-07-16T07:36:12,338   Downloading pysam-0.16.0.tar.gz (3.4 MB)
2021-07-16T07:36:14,591   Added pysam==0.16.0 from https://files.pythonhosted.org/packages/18/74/69018650a6ec9dae2eb2f710e158fa395134ce579c605f152e41890e7f3c/pysam-0.16.0.tar.gz#sha256=07c9d3a772f90e9907a68bc3f495e2c608018a92888b9cf9f1197cb3a35aa9c3 to build tracker '/tmp/pip-req-tracker-7ma6u161'
2021-07-16T07:36:14,592     Running setup.py (path:/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/setup.py) egg_info for package pysam
2021-07-16T07:36:14,593     Created temporary directory: /tmp/pip-pip-egg-info-fvsia10i
2021-07-16T07:36:14,593     Running command python setup.py egg_info
2021-07-16T07:36:15,628     # pysam: cython is available - using cythonize if necessary
2021-07-16T07:36:15,628     # pysam: htslib mode is shared
2021-07-16T07:36:15,628     # pysam: HTSLIB_CONFIGURE_OPTIONS=None
2021-07-16T07:36:15,628     # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc -pthread
2021-07-16T07:36:15,629     # pysam: (sysconfig) CFLAGS=-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
2021-07-16T07:36:15,629     # pysam: (sysconfig) LDFLAGS= -Wl,-z,relro -g -fwrapv -O2
2021-07-16T07:36:16,116     checking for gcc... arm-linux-gnueabihf-gcc -pthread
2021-07-16T07:36:16,465     checking whether the C compiler works... yes
2021-07-16T07:36:16,467     checking for C compiler default output file name... a.out
2021-07-16T07:36:16,653     checking for suffix of executables...
2021-07-16T07:36:16,885     checking whether we are cross compiling... no
2021-07-16T07:36:17,004     checking for suffix of object files... o
2021-07-16T07:36:17,108     checking whether we are using the GNU C compiler... yes
2021-07-16T07:36:17,211     checking whether arm-linux-gnueabihf-gcc -pthread accepts -g... yes
2021-07-16T07:36:17,380     checking for arm-linux-gnueabihf-gcc -pthread option to accept ISO C89... none needed
2021-07-16T07:36:17,383     checking for ranlib... ranlib
2021-07-16T07:36:17,395     checking for grep that handles long lines and -e... /usr/bin/grep
2021-07-16T07:36:17,478     checking for C compiler warning flags... unknown
2021-07-16T07:36:17,481     checking for pkg-config... /usr/bin/pkg-config
2021-07-16T07:36:17,489     checking pkg-config is at least version 0.9.0... yes
2021-07-16T07:36:17,492     checking for special C compiler options needed for large files... no
2021-07-16T07:36:17,724     checking for _FILE_OFFSET_BITS value needed for large files... 64
2021-07-16T07:36:17,742     checking shared library type for unknown-Linux... plain .so
2021-07-16T07:36:17,966     checking whether the compiler accepts -fvisibility=hidden... yes
2021-07-16T07:36:18,111     checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -pthread -E
2021-07-16T07:36:18,260     checking for egrep... /usr/bin/grep -E
2021-07-16T07:36:18,864     checking for ANSI C header files... yes
2021-07-16T07:36:19,016     checking for sys/types.h... yes
2021-07-16T07:36:19,189     checking for sys/stat.h... yes
2021-07-16T07:36:19,366     checking for stdlib.h... yes
2021-07-16T07:36:19,546     checking for string.h... yes
2021-07-16T07:36:19,729     checking for memory.h... yes
2021-07-16T07:36:19,912     checking for strings.h... yes
2021-07-16T07:36:20,104     checking for inttypes.h... yes
2021-07-16T07:36:20,290     checking for stdint.h... yes
2021-07-16T07:36:20,491     checking for unistd.h... yes
2021-07-16T07:36:20,529     checking for stdlib.h... (cached) yes
2021-07-16T07:36:20,567     checking for unistd.h... (cached) yes
2021-07-16T07:36:20,888     checking for sys/param.h... yes
2021-07-16T07:36:21,124     checking for getpagesize... yes
2021-07-16T07:36:21,490     checking for working mmap... yes
2021-07-16T07:36:21,729     checking for gmtime_r... yes
2021-07-16T07:36:21,983     checking for fsync... yes
2021-07-16T07:36:22,228     checking for drand48... yes
2021-07-16T07:36:22,459     checking whether fdatasync is declared... yes
2021-07-16T07:36:22,669     checking for fdatasync... yes
2021-07-16T07:36:23,150     checking for library containing log... -lm
2021-07-16T07:36:23,286     checking for zlib.h... yes
2021-07-16T07:36:23,505     checking for inflate in -lz... yes
2021-07-16T07:36:23,727     checking for library containing recv... none required
2021-07-16T07:36:23,843     checking for bzlib.h... yes
2021-07-16T07:36:24,055     checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
2021-07-16T07:36:24,248     checking for lzma.h... yes
2021-07-16T07:36:24,477     checking for lzma_easy_buffer_encode in -llzma... yes
2021-07-16T07:36:24,608     checking for libdeflate.h... yes
2021-07-16T07:36:24,834     checking for libdeflate_deflate_compress in -ldeflate... yes
2021-07-16T07:36:25,277     checking for curl_easy_pause in -lcurl... yes
2021-07-16T07:36:25,538     checking for CCHmac... no
2021-07-16T07:36:26,180     checking for library containing HMAC... -lcrypto
2021-07-16T07:36:26,338     checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
2021-07-16T07:36:26,423     configure: creating ./config.status
2021-07-16T07:36:26,927     config.status: creating config.mk
2021-07-16T07:36:26,990     config.status: creating htslib.pc.tmp
2021-07-16T07:36:27,059     config.status: creating config.h
2021-07-16T07:36:27,213     make: ./version.sh: No such file or directory
2021-07-16T07:36:27,214     make: ./version.sh: No such file or directory
2021-07-16T07:36:27,470     # pysam: htslib configure options: --enable-libcurl
2021-07-16T07:36:27,471     # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o
2021-07-16T07:36:27,471     # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
2021-07-16T07:36:27,471     # pysam: htslib_config PLATFORM=default
2021-07-16T07:36:27,471     # pysam: config_option: ENABLE_GCS=1
2021-07-16T07:36:27,471     # pysam: config_option: ENABLE_PLUGINS=0
2021-07-16T07:36:27,471     # pysam: config_option: ENABLE_S3=1
2021-07-16T07:36:27,472     # pysam: config_option: HAVE_COMMONCRYPTO=0
2021-07-16T07:36:27,472     # pysam: config_option: HAVE_HMAC=1
2021-07-16T07:36:27,472     # pysam: config_option: HAVE_LIBBZ2=1
2021-07-16T07:36:27,472     # pysam: config_option: HAVE_LIBCURL=1
2021-07-16T07:36:27,472     # pysam: config_option: HAVE_LIBDEFLATE=1
2021-07-16T07:36:27,472     # pysam: config_option: HAVE_LIBLZMA=1
2021-07-16T07:36:27,472     # pysam: config_option: HAVE_MMAP=1
2021-07-16T07:36:27,473     running egg_info
2021-07-16T07:36:27,473     creating /tmp/pip-pip-egg-info-fvsia10i/pysam.egg-info
2021-07-16T07:36:27,474     writing /tmp/pip-pip-egg-info-fvsia10i/pysam.egg-info/PKG-INFO
2021-07-16T07:36:27,477     writing dependency_links to /tmp/pip-pip-egg-info-fvsia10i/pysam.egg-info/dependency_links.txt
2021-07-16T07:36:27,479     writing top-level names to /tmp/pip-pip-egg-info-fvsia10i/pysam.egg-info/top_level.txt
2021-07-16T07:36:27,480     writing manifest file '/tmp/pip-pip-egg-info-fvsia10i/pysam.egg-info/SOURCES.txt'
2021-07-16T07:36:27,629     package init file 'samtools/__init__.py' not found (or not a regular file)
2021-07-16T07:36:27,630     package init file 'bcftools/__init__.py' not found (or not a regular file)
2021-07-16T07:36:27,632     package init file 'htslib/__init__.py' not found (or not a regular file)
2021-07-16T07:36:27,632     package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
2021-07-16T07:36:27,684     reading manifest file '/tmp/pip-pip-egg-info-fvsia10i/pysam.egg-info/SOURCES.txt'
2021-07-16T07:36:27,686     reading manifest template 'MANIFEST.in'
2021-07-16T07:36:27,689     warning: no files found matching 'KNOWN_BUGS'
2021-07-16T07:36:27,689     warning: no files found matching 'THANKS'
2021-07-16T07:36:27,697     no previously-included directories found matching 'tests/'
2021-07-16T07:36:27,698     warning: no files found matching 'samtools/configure'
2021-07-16T07:36:27,698     warning: no files found matching 'samtools/config.mk.in'
2021-07-16T07:36:27,699     warning: no files found matching 'samtools/config.h.in'
2021-07-16T07:36:27,734     warning: no files found matching 'htslib/INSTALL'
2021-07-16T07:36:27,734     warning: no files found matching 'htslib/NEWS'
2021-07-16T07:36:27,743     adding license file 'COPYING'
2021-07-16T07:36:27,763     writing manifest file '/tmp/pip-pip-egg-info-fvsia10i/pysam.egg-info/SOURCES.txt'
2021-07-16T07:36:27,840   Source in /tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 has version 0.16.0, which satisfies requirement pysam==0.16.0 from https://files.pythonhosted.org/packages/18/74/69018650a6ec9dae2eb2f710e158fa395134ce579c605f152e41890e7f3c/pysam-0.16.0.tar.gz#sha256=07c9d3a772f90e9907a68bc3f495e2c608018a92888b9cf9f1197cb3a35aa9c3
2021-07-16T07:36:27,841   Removed pysam==0.16.0 from https://files.pythonhosted.org/packages/18/74/69018650a6ec9dae2eb2f710e158fa395134ce579c605f152e41890e7f3c/pysam-0.16.0.tar.gz#sha256=07c9d3a772f90e9907a68bc3f495e2c608018a92888b9cf9f1197cb3a35aa9c3 from build tracker '/tmp/pip-req-tracker-7ma6u161'
2021-07-16T07:36:27,845 Created temporary directory: /tmp/pip-unpack-a6udxf55
2021-07-16T07:36:27,846 Building wheels for collected packages: pysam
2021-07-16T07:36:27,850   Created temporary directory: /tmp/pip-wheel-fclmz1qd
2021-07-16T07:36:27,850   Building wheel for pysam (setup.py): started
2021-07-16T07:36:27,851   Destination directory: /tmp/pip-wheel-fclmz1qd
2021-07-16T07:36:27,851   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/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-fclmz1qd
2021-07-16T07:36:28,862   # pysam: cython is available - using cythonize if necessary
2021-07-16T07:36:28,862   # pysam: htslib mode is shared
2021-07-16T07:36:28,862   # pysam: HTSLIB_CONFIGURE_OPTIONS=None
2021-07-16T07:36:28,863   # pysam: (sysconfig) CC=arm-linux-gnueabihf-gcc -pthread
2021-07-16T07:36:28,863   # pysam: (sysconfig) CFLAGS=-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
2021-07-16T07:36:28,863   # pysam: (sysconfig) LDFLAGS= -Wl,-z,relro -g -fwrapv -O2
2021-07-16T07:36:29,335   checking for gcc... arm-linux-gnueabihf-gcc -pthread
2021-07-16T07:36:29,667   checking whether the C compiler works... yes
2021-07-16T07:36:29,668   checking for C compiler default output file name... a.out
2021-07-16T07:36:29,858   checking for suffix of executables...
2021-07-16T07:36:30,080   checking whether we are cross compiling... no
2021-07-16T07:36:30,196   checking for suffix of object files... o
2021-07-16T07:36:30,301   checking whether we are using the GNU C compiler... yes
2021-07-16T07:36:30,400   checking whether arm-linux-gnueabihf-gcc -pthread accepts -g... yes
2021-07-16T07:36:30,569   checking for arm-linux-gnueabihf-gcc -pthread option to accept ISO C89... none needed
2021-07-16T07:36:30,572   checking for ranlib... ranlib
2021-07-16T07:36:30,584   checking for grep that handles long lines and -e... /usr/bin/grep
2021-07-16T07:36:30,670   checking for C compiler warning flags... unknown
2021-07-16T07:36:30,674   checking for pkg-config... /usr/bin/pkg-config
2021-07-16T07:36:30,684   checking pkg-config is at least version 0.9.0... yes
2021-07-16T07:36:30,687   checking for special C compiler options needed for large files... no
2021-07-16T07:36:30,921   checking for _FILE_OFFSET_BITS value needed for large files... 64
2021-07-16T07:36:30,938   checking shared library type for unknown-Linux... plain .so
2021-07-16T07:36:31,152   checking whether the compiler accepts -fvisibility=hidden... yes
2021-07-16T07:36:31,292   checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -pthread -E
2021-07-16T07:36:31,442   checking for egrep... /usr/bin/grep -E
2021-07-16T07:36:31,980   checking for ANSI C header files... yes
2021-07-16T07:36:32,137   checking for sys/types.h... yes
2021-07-16T07:36:32,310   checking for sys/stat.h... yes
2021-07-16T07:36:32,511   checking for stdlib.h... yes
2021-07-16T07:36:32,695   checking for string.h... yes
2021-07-16T07:36:32,877   checking for memory.h... yes
2021-07-16T07:36:33,052   checking for strings.h... yes
2021-07-16T07:36:33,238   checking for inttypes.h... yes
2021-07-16T07:36:33,427   checking for stdint.h... yes
2021-07-16T07:36:33,621   checking for unistd.h... yes
2021-07-16T07:36:33,658   checking for stdlib.h... (cached) yes
2021-07-16T07:36:33,693   checking for unistd.h... (cached) yes
2021-07-16T07:36:33,906   checking for sys/param.h... yes
2021-07-16T07:36:34,136   checking for getpagesize... yes
2021-07-16T07:36:34,500   checking for working mmap... yes
2021-07-16T07:36:34,737   checking for gmtime_r... yes
2021-07-16T07:36:34,996   checking for fsync... yes
2021-07-16T07:36:35,247   checking for drand48... yes
2021-07-16T07:36:35,481   checking whether fdatasync is declared... yes
2021-07-16T07:36:35,690   checking for fdatasync... yes
2021-07-16T07:36:36,172   checking for library containing log... -lm
2021-07-16T07:36:36,311   checking for zlib.h... yes
2021-07-16T07:36:36,518   checking for inflate in -lz... yes
2021-07-16T07:36:36,746   checking for library containing recv... none required
2021-07-16T07:36:36,856   checking for bzlib.h... yes
2021-07-16T07:36:37,072   checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
2021-07-16T07:36:37,208   checking for lzma.h... yes
2021-07-16T07:36:37,436   checking for lzma_easy_buffer_encode in -llzma... yes
2021-07-16T07:36:37,548   checking for libdeflate.h... yes
2021-07-16T07:36:37,763   checking for libdeflate_deflate_compress in -ldeflate... yes
2021-07-16T07:36:38,171   checking for curl_easy_pause in -lcurl... yes
2021-07-16T07:36:38,457   checking for CCHmac... no
2021-07-16T07:36:39,227   checking for library containing HMAC... -lcrypto
2021-07-16T07:36:39,440   checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
2021-07-16T07:36:39,532   configure: creating ./config.status
2021-07-16T07:36:40,017   config.status: creating config.mk
2021-07-16T07:36:40,078   config.status: creating htslib.pc.tmp
2021-07-16T07:36:40,149   config.status: creating config.h
2021-07-16T07:36:40,178   config.status: config.h is unchanged
2021-07-16T07:36:40,293   # pysam: htslib configure options: --enable-libcurl
2021-07-16T07:36:40,309   make: ./version.sh: No such file or directory
2021-07-16T07:36:40,310   make: ./version.sh: No such file or directory
2021-07-16T07:36:40,346   # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o
2021-07-16T07:36:40,347   # pysam: htslib_config LIBS=-ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto
2021-07-16T07:36:40,347   # pysam: htslib_config PLATFORM=default
2021-07-16T07:36:40,351   # pysam: config_option: ENABLE_GCS=1
2021-07-16T07:36:40,352   # pysam: config_option: ENABLE_PLUGINS=0
2021-07-16T07:36:40,352   # pysam: config_option: ENABLE_S3=1
2021-07-16T07:36:40,352   # pysam: config_option: HAVE_COMMONCRYPTO=0
2021-07-16T07:36:40,352   # pysam: config_option: HAVE_HMAC=1
2021-07-16T07:36:40,353   # pysam: config_option: HAVE_LIBBZ2=1
2021-07-16T07:36:40,353   # pysam: config_option: HAVE_LIBCURL=1
2021-07-16T07:36:40,353   # pysam: config_option: HAVE_LIBDEFLATE=1
2021-07-16T07:36:40,353   # pysam: config_option: HAVE_LIBLZMA=1
2021-07-16T07:36:40,353   # pysam: config_option: HAVE_MMAP=1
2021-07-16T07:36:40,568   running bdist_wheel
2021-07-16T07:36:40,574   running build
2021-07-16T07:36:40,574   running build_py
2021-07-16T07:36:40,718   creating build
2021-07-16T07:36:40,718   creating build/lib.linux-armv7l-3.9
2021-07-16T07:36:40,719   creating build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,720   copying pysam/config.py -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,722   copying pysam/__init__.py -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,724   copying pysam/samtools.py -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,726   copying pysam/bcftools.py -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,727   copying pysam/Pileup.py -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,730   copying pysam/utils.py -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,732   copying pysam/version.py -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,734   creating build/lib.linux-armv7l-3.9/pysam/include
2021-07-16T07:36:40,735   copying pysam/include/__init__.py -> build/lib.linux-armv7l-3.9/pysam/include
2021-07-16T07:36:40,736   package init file 'samtools/__init__.py' not found (or not a regular file)
2021-07-16T07:36:40,737   package init file 'bcftools/__init__.py' not found (or not a regular file)
2021-07-16T07:36:40,738   package init file 'htslib/__init__.py' not found (or not a regular file)
2021-07-16T07:36:40,739   package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
2021-07-16T07:36:40,769   copying pysam/libcalignedsegment.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,772   copying pysam/libcutils.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,774   copying pysam/libcalignmentfile.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,776   copying pysam/libctabixproxies.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,778   copying pysam/libcvcf.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,781   copying pysam/libctabix.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,783   copying pysam/libcbcftools.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,785   copying pysam/libcsamtools.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,787   copying pysam/libcbcf.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,790   copying pysam/libcsamfile.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,792   copying pysam/libchtslib.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,798   copying pysam/libcfaidx.pxd -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,801   copying pysam/htslib_util.h -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,803   copying pysam/csamtools_util.h -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,805   copying pysam/version.h -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,808   copying pysam/cbcftools_util.h -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,810   copying pysam/pysam_util.h -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,812   copying pysam/pysam_stream.h -> build/lib.linux-armv7l-3.9/pysam
2021-07-16T07:36:40,814   creating build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,815   copying samtools/tmp_file.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,818   copying samtools/samtools.pysam.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,820   copying samtools/config.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,822   copying samtools/sam.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,825   copying samtools/sample.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,827   copying samtools/bam_endian.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,830   copying samtools/bam_lpileup.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,832   copying samtools/bedidx.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,835   copying samtools/bam2bcf.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,837   copying samtools/sam_opts.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,840   copying samtools/bam_plbuf.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,842   copying samtools/samtools.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,845   copying samtools/stats_isize.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,847   copying samtools/bam.h -> build/lib.linux-armv7l-3.9/pysam/include/samtools
2021-07-16T07:36:40,850   creating build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,851   copying bcftools/khash_str2str.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,854   copying bcftools/prob1.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,856   copying bcftools/gvcf.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,859   copying bcftools/convert.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,861   copying bcftools/bcftools.pysam.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,863   copying bcftools/tsv2vcf.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,866   copying bcftools/config.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,868   copying bcftools/hclust.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,871   copying bcftools/kmin.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,873   copying bcftools/HMM.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,876   copying bcftools/vcmp.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,878   copying bcftools/regidx.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,881   copying bcftools/mw.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,886   copying bcftools/call.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,889   copying bcftools/hex.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,891   copying bcftools/smpl_ilist.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,894   copying bcftools/kheap.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,897   copying bcftools/vcfbuf.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,899   copying bcftools/ploidy.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,902   copying bcftools/rbuf.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,905   copying bcftools/cols.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,908   copying bcftools/bam_sample.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,911   copying bcftools/bam2bcf.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,913   copying bcftools/variantkey.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,917   copying bcftools/filter.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,919   copying bcftools/bin.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,921   copying bcftools/bcftools.h -> build/lib.linux-armv7l-3.9/pysam/include/bcftools
2021-07-16T07:36:40,924   creating build/lib.linux-armv7l-3.9/pysam/include/htslib
2021-07-16T07:36:40,925   copying htslib/thread_pool_internal.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib
2021-07-16T07:36:40,928   copying htslib/header.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib
2021-07-16T07:36:40,931   copying htslib/hts_internal.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib
2021-07-16T07:36:40,933   copying htslib/sam_internal.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib
2021-07-16T07:36:40,935   copying htslib/config.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib
2021-07-16T07:36:40,938   copying htslib/textutils_internal.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib
2021-07-16T07:36:40,941   copying htslib/hfile_internal.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib
2021-07-16T07:36:40,944   copying htslib/bcf_sr_sort.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib
2021-07-16T07:36:40,946   creating build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,947   copying htslib/htslib/hts_endian.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,950   copying htslib/htslib/hfile.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,953   copying htslib/htslib/kseq.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,956   copying htslib/htslib/faidx.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,959   copying htslib/htslib/ksort.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,962   copying htslib/htslib/vcf_sweep.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,965   copying htslib/htslib/khash_str2int.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,967   copying htslib/htslib/kbitset.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,970   copying htslib/htslib/hts_os.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,972   copying htslib/htslib/kstring.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,976   copying htslib/htslib/tbx.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,979   copying htslib/htslib/cram.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,982   copying htslib/htslib/khash.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,986   copying htslib/htslib/bgzf.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,990   copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,993   copying htslib/htslib/hts.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:40,998   copying htslib/htslib/regidx.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:41,001   copying htslib/htslib/hts_defs.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:41,003   copying htslib/htslib/klist.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:41,006   copying htslib/htslib/sam.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:41,011   copying htslib/htslib/kfunc.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:41,013   copying htslib/htslib/knetfile.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:41,016   copying htslib/htslib/thread_pool.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:41,019   copying htslib/htslib/hts_log.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:41,021   copying htslib/htslib/vcfutils.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:41,025   copying htslib/htslib/vcf.h -> build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib
2021-07-16T07:36:41,030   /usr/local/lib/python3.9/dist-packages/setuptools/lib2to3_ex.py:36: SetuptoolsDeprecationWarning: 2to3 support is deprecated. If the project still requires Python 2 support, please migrate to a single-codebase solution or employ an independent conversion process.
2021-07-16T07:36:41,031     warnings.warn(
2021-07-16T07:36:41,031   Fixing build/lib.linux-armv7l-3.9/pysam/config.py build/lib.linux-armv7l-3.9/pysam/__init__.py build/lib.linux-armv7l-3.9/pysam/samtools.py build/lib.linux-armv7l-3.9/pysam/bcftools.py build/lib.linux-armv7l-3.9/pysam/Pileup.py build/lib.linux-armv7l-3.9/pysam/utils.py build/lib.linux-armv7l-3.9/pysam/version.py build/lib.linux-armv7l-3.9/pysam/include/__init__.py
2021-07-16T07:36:41,275   Skipping optional fixer: buffer
2021-07-16T07:36:41,339   Skipping optional fixer: idioms
2021-07-16T07:36:41,510   Skipping optional fixer: set_literal
2021-07-16T07:36:41,637   Skipping optional fixer: ws_comma
2021-07-16T07:36:42,312   Fixing build/lib.linux-armv7l-3.9/pysam/config.py build/lib.linux-armv7l-3.9/pysam/__init__.py build/lib.linux-armv7l-3.9/pysam/samtools.py build/lib.linux-armv7l-3.9/pysam/bcftools.py build/lib.linux-armv7l-3.9/pysam/Pileup.py build/lib.linux-armv7l-3.9/pysam/utils.py build/lib.linux-armv7l-3.9/pysam/version.py build/lib.linux-armv7l-3.9/pysam/include/__init__.py
2021-07-16T07:36:42,321   Skipping optional fixer: buffer
2021-07-16T07:36:42,372   Skipping optional fixer: idioms
2021-07-16T07:36:42,504   Skipping optional fixer: set_literal
2021-07-16T07:36:42,597   Skipping optional fixer: ws_comma
2021-07-16T07:36:42,749   running build_ext
2021-07-16T07:36:42,812   skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
2021-07-16T07:36:42,813   skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
2021-07-16T07:36:42,814   skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
2021-07-16T07:36:42,814   skipping 'pysam/libcutils.c' Cython extension (up-to-date)
2021-07-16T07:36:42,815   skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
2021-07-16T07:36:42,815   skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
2021-07-16T07:36:42,816   skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
2021-07-16T07:36:42,816   skipping 'pysam/libctabix.c' Cython extension (up-to-date)
2021-07-16T07:36:42,817   skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
2021-07-16T07:36:42,818   skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
2021-07-16T07:36:42,818   skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
2021-07-16T07:36:42,819   skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
2021-07-16T07:36:42,820   skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
2021-07-16T07:36:42,820   building 'pysam.libchtslib' extension
2021-07-16T07:36:42,821   creating build/temp.linux-armv7l-3.9
2021-07-16T07:36:42,822   creating build/temp.linux-armv7l-3.9/htslib
2021-07-16T07:36:42,823   creating build/temp.linux-armv7l-3.9/htslib/cram
2021-07-16T07:36:42,825   creating build/temp.linux-armv7l-3.9/pysam
2021-07-16T07:36:42,826   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/bcf_sr_sort.c -o build/temp.linux-armv7l-3.9/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:36:45,042   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/bgzf.c -o build/temp.linux-armv7l-3.9/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:36:47,736   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/cram_codecs.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:36:51,072   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/cram_decode.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:36:57,024   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/cram_encode.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:03,341   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/cram_external.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:03,950   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/cram_index.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:05,081   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/cram_io.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:10,029   In file included from /usr/include/string.h:495,
2021-07-16T07:37:10,029                    from htslib/cram/cram_io.c:49:
2021-07-16T07:37:10,029   In function ‘strncpy’,
2021-07-16T07:37:10,030       inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4304:9:
2021-07-16T07:37:10,030   /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation]
2021-07-16T07:37:10,030     106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
2021-07-16T07:37:10,030         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T07:37:10,836   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/cram_samtools.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:11,218   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/cram_stats.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:11,868   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/mFILE.c -o build/temp.linux-armv7l-3.9/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:12,480   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -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 -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:13,071   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/pooled_alloc.c -o build/temp.linux-armv7l-3.9/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:13,285   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/rANS_static.c -o build/temp.linux-armv7l-3.9/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:14,774   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/cram/string_alloc.c -o build/temp.linux-armv7l-3.9/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:14,994   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/errmod.c -o build/temp.linux-armv7l-3.9/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:15,605   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/faidx.c -o build/temp.linux-armv7l-3.9/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:17,246   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/header.c -o build/temp.linux-armv7l-3.9/htslib/header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:21,006   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/hfile.c -o build/temp.linux-armv7l-3.9/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:22,359   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/hfile_gcs.c -o build/temp.linux-armv7l-3.9/htslib/hfile_gcs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:22,842   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/hfile_libcurl.c -o build/temp.linux-armv7l-3.9/htslib/hfile_libcurl.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:25,070   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/hfile_net.c -o build/temp.linux-armv7l-3.9/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:25,294   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/hfile_s3.c -o build/temp.linux-armv7l-3.9/htslib/hfile_s3.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:27,685   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/hfile_s3_write.c -o build/temp.linux-armv7l-3.9/htslib/hfile_s3_write.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:28,959   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/hts.c -o build/temp.linux-armv7l-3.9/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:29,323   htslib/hts.c: In function ‘hts_idx_init’:
2021-07-16T07:37:29,324   htslib/hts.c:1631:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow]
2021-07-16T07:37:29,324    1631 |     idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
2021-07-16T07:37:29,324         |                                                           ^~~
2021-07-16T07:37:35,359   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/hts_os.c -o build/temp.linux-armv7l-3.9/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:35,516   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/kfunc.c -o build/temp.linux-armv7l-3.9/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:35,984   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/knetfile.c -o build/temp.linux-armv7l-3.9/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:36,790   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/kstring.c -o build/temp.linux-armv7l-3.9/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:37,579   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/md5.c -o build/temp.linux-armv7l-3.9/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:38,168   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/multipart.c -o build/temp.linux-armv7l-3.9/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:38,706   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/probaln.c -o build/temp.linux-armv7l-3.9/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:39,399   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/realn.c -o build/temp.linux-armv7l-3.9/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:40,239   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/regidx.c -o build/temp.linux-armv7l-3.9/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:41,561   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/region.c -o build/temp.linux-armv7l-3.9/htslib/region.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:42,145   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/sam.c -o build/temp.linux-armv7l-3.9/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:51,339   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/synced_bcf_reader.c -o build/temp.linux-armv7l-3.9/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:53,451   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/tbx.c -o build/temp.linux-armv7l-3.9/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:54,225   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/textutils.c -o build/temp.linux-armv7l-3.9/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:55,048   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/thread_pool.c -o build/temp.linux-armv7l-3.9/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:37:55,823   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/vcf.c -o build/temp.linux-armv7l-3.9/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:06,060   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/vcf_sweep.c -o build/temp.linux-armv7l-3.9/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:06,424   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c htslib/vcfutils.c -o build/temp.linux-armv7l-3.9/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:08,950   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.9/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:09,245   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libchtslib.c -o build/temp.linux-armv7l-3.9/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:22,282   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/htslib/bcf_sr_sort.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/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/string_alloc.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/header.o build/temp.linux-armv7l-3.9/htslib/hfile.o build/temp.linux-armv7l-3.9/htslib/hfile_gcs.o build/temp.linux-armv7l-3.9/htslib/hfile_libcurl.o build/temp.linux-armv7l-3.9/htslib/hfile_net.o build/temp.linux-armv7l-3.9/htslib/hfile_s3.o build/temp.linux-armv7l-3.9/htslib/hfile_s3_write.o build/temp.linux-armv7l-3.9/htslib/hts.o build/temp.linux-armv7l-3.9/htslib/hts_os.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/multipart.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/region.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/textutils.o build/temp.linux-armv7l-3.9/htslib/thread_pool.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 build/temp.linux-armv7l-3.9/pysam/htslib_util.o build/temp.linux-armv7l-3.9/pysam/libchtslib.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -o build/lib.linux-armv7l-3.9/pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:38:23,010   building 'pysam.libcsamtools' extension
2021-07-16T07:38:23,012   creating build/temp.linux-armv7l-3.9/samtools
2021-07-16T07:38:23,014   creating build/temp.linux-armv7l-3.9/samtools/lz4
2021-07-16T07:38:23,015   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libcsamtools.c -o build/temp.linux-armv7l-3.9/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:23,848   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:24,338   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:25,937   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:28,433   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:29,195   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:29,870   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:30,127   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:30,882   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:31,163   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:33,392   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:33,639   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:34,044   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:34,937   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:38,099   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:39,147   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:39,971   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:40,176   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:43,122   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:43,476   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:44,229   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:45,507   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:46,585   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:53,804   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:54,995   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:55,706   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:57,713   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:58,070   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:38:58,817   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:00,363   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/coverage.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:01,401   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:02,014   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/dict.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:02,619   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:03,220   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/lz4/lz4.c -o build/temp.linux-armv7l-3.9/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:08,544   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:09,757   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:12,442   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:12,797   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:13,121   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:13,394   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:15,159   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:15,884   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/samtools.pysam.c -o build/temp.linux-armv7l-3.9/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:16,106   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:20,287   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:20,868   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armv7l-3.9/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:21,326   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/pysam/libcsamtools.o build/temp.linux-armv7l-3.9/samtools/bam.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_addrprg.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_fastq.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_markdup.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bamtk.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-3.9/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-3.9/samtools/coverage.c.pysam.o build/temp.linux-armv7l-3.9/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-3.9/samtools/dict.c.pysam.o build/temp.linux-armv7l-3.9/samtools/faidx.c.pysam.o build/temp.linux-armv7l-3.9/samtools/lz4/lz4.o build/temp.linux-armv7l-3.9/samtools/padding.c.pysam.o build/temp.linux-armv7l-3.9/samtools/phase.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sam.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sam_opts.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sam_utils.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-3.9/samtools/sample.c.pysam.o build/temp.linux-armv7l-3.9/samtools/samtools.pysam.o build/temp.linux-armv7l-3.9/samtools/stats.c.pysam.o build/temp.linux-armv7l-3.9/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-3.9/samtools/tmp_file.c.pysam.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:39:21,767   building 'pysam.libcbcftools' extension
2021-07-16T07:39:21,769   creating build/temp.linux-armv7l-3.9/bcftools
2021-07-16T07:39:21,771   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:22,676   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:24,375   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:26,361   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:28,061   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/bcftools.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:28,287   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/bin.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:28,610   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:29,287   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/cols.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:29,542   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:30,989   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/convert.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:36,134   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/csq.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:43,888   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/em.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:44,428   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/filter.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:54,010   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:54,557   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:55,136   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:55,580   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/main.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:55,937   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:39:59,611   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:01,305   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:02,237   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:03,686   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:04,929   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:07,726   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:08,161   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:08,554   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:08,913   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:15,398   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:16,354   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:18,678   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:20,525   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:22,477   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:25,616   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:26,885   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:28,205   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:28,717   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:30,300   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:31,886   bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’:
2021-07-16T07:40:31,886   bcftools/vcfmerge.c.pysam.c:694:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
2021-07-16T07:40:31,886     694 |         ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t));
2021-07-16T07:40:31,886         |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T07:40:31,886   In file included from /tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib/htslib/kstring.h:30,
2021-07-16T07:40:31,887                    from /tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib/htslib/vcf.h:41,
2021-07-16T07:40:31,887                    from bcftools/vcfmerge.c.pysam.c:34:
2021-07-16T07:40:31,887   /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here
2021-07-16T07:40:31,887     542 | extern void *calloc (size_t __nmemb, size_t __size)
2021-07-16T07:40:31,887         |              ^~~~~~
2021-07-16T07:40:37,700   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:44,672   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:44,961   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:46,054   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:48,284   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:49,540   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:50,250   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:53,807   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:55,568   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:55,983   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c bcftools/version.c.pysam.c -o build/temp.linux-armv7l-3.9/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:56,248   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libcbcftools.c -o build/temp.linux-armv7l-3.9/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:57,085   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/bcftools/HMM.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/bam2bcf.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/bam_sample.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/bcftools.pysam.o build/temp.linux-armv7l-3.9/bcftools/bin.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/ccall.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/cols.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/consensus.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/convert.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/csq.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/em.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/filter.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/gvcf.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/hclust.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/kmin.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/main.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/mcall.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/mpileup.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/ploidy.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/prob1.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/regidx.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/reheader.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/tabix.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfannotate.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfbuf.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfcall.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfcnv.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfconcat.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfconvert.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcffilter.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfindex.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfisec.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfmerge.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfnorm.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfplugin.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfquery.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfroh.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfsom.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfsort.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfstats.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcfview.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/vcmp.c.pysam.o build/temp.linux-armv7l-3.9/bcftools/version.c.pysam.o build/temp.linux-armv7l-3.9/pysam/libcbcftools.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcbcftools.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:40:57,615   building 'pysam.libcutils' extension
2021-07-16T07:40:57,615   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libcutils.c -o build/temp.linux-armv7l-3.9/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:40:58,203   pysam/libcutils.c: In function ‘__Pyx_decode_c_string’:
2021-07-16T07:40:58,208   pysam/libcutils.c:9984:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-16T07:40:58,208    9984 |         return PyUnicode_FromUnicode(NULL, 0);
2021-07-16T07:40:58,208         |         ^~~~~~
2021-07-16T07:40:58,209   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-16T07:40:58,209                    from /usr/include/python3.9/Python.h:97,
2021-07-16T07:40:58,210                    from pysam/libcutils.c:4:
2021-07-16T07:40:58,210   /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here
2021-07-16T07:40:58,210     551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
2021-07-16T07:40:58,210         |                                          ^~~~~~~~~~~~~~~~~~~~~
2021-07-16T07:41:04,950   pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
2021-07-16T07:41:04,950   pysam/libcutils.c:513:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T07:41:04,950     513 |   #define PyInt_FromLong               PyLong_FromLong
2021-07-16T07:41:04,950         |                                        ^~~~~~~~~~~~~~~
2021-07-16T07:41:04,954   pysam/libcutils.c:5960:7: note: ‘__pyx_v_retval’ was declared here
2021-07-16T07:41:04,954    5960 |   int __pyx_v_retval;
2021-07-16T07:41:04,954         |       ^~~~~~~~~~~~~~
2021-07-16T07:41:07,526   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/pysam_util.c -o build/temp.linux-armv7l-3.9/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:41:07,720   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/pysam/libcutils.o build/temp.linux-armv7l-3.9/pysam/pysam_util.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcsamtools.cpython-39-arm-linux-gnueabihf -lcbcftools.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcutils.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:41:07,922   building 'pysam.libcalignmentfile' extension
2021-07-16T07:41:07,922   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libcalignmentfile.c -o build/temp.linux-armv7l-3.9/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:41:09,060   pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
2021-07-16T07:41:09,075   pysam/libcalignmentfile.c:30101:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
2021-07-16T07:41:09,075   30101 |   __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
2021-07-16T07:41:09,076         |                                                                                                                              ~^~~~~~~~~~~~~~~~~~~
2021-07-16T07:41:09,076         |                                                                                                                               |
2021-07-16T07:41:09,076         |                                                                                                                               bam_pileup1_t **
2021-07-16T07:41:09,076   In file included from pysam/htslib_util.h:4,
2021-07-16T07:41:09,076                    from pysam/libcalignmentfile.c:605:
2021-07-16T07:41:09,077   /tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib/htslib/sam.h:1709:96: note: expected ‘const bam_pileup1_t **’ but argument is of type ‘bam_pileup1_t **’
2021-07-16T07:41:09,077    1709 |     int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
2021-07-16T07:41:09,077         |                                                                          ~~~~~~~~~~~~~~~~~~~~~~^~~
2021-07-16T07:41:48,118   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/pysam/libcalignmentfile.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:41:48,437   building 'pysam.libcsamfile' extension
2021-07-16T07:41:48,438   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libcsamfile.c -o build/temp.linux-armv7l-3.9/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:41:50,542   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/pysam/libcsamfile.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:41:50,707   building 'pysam.libcalignedsegment' extension
2021-07-16T07:41:50,707   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libcalignedsegment.c -o build/temp.linux-armv7l-3.9/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:41:53,494   pysam/libcalignedsegment.c: In function ‘__Pyx_decode_c_string’:
2021-07-16T07:41:53,526   pysam/libcalignedsegment.c:63092:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-16T07:41:53,526   63092 |         return PyUnicode_FromUnicode(NULL, 0);
2021-07-16T07:41:53,526         |         ^~~~~~
2021-07-16T07:41:53,526   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-16T07:41:53,526                    from /usr/include/python3.9/Python.h:97,
2021-07-16T07:41:53,526                    from pysam/libcalignedsegment.c:4:
2021-07-16T07:41:53,527   /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here
2021-07-16T07:41:53,527     551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
2021-07-16T07:41:53,527         |                                          ^~~~~~~~~~~~~~~~~~~~~
2021-07-16T07:42:42,198   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/pysam/libcalignedsegment.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcalignedsegment.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:42:42,566   building 'pysam.libctabix' extension
2021-07-16T07:42:42,566   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libctabix.c -o build/temp.linux-armv7l-3.9/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:42:43,140   pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
2021-07-16T07:42:43,145   pysam/libctabix.c:8752:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
2021-07-16T07:42:43,145    8752 |         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
2021-07-16T07:42:43,145         |                           ^
2021-07-16T07:42:43,245   In file included from pysam/libctabix.c:612:
2021-07-16T07:42:43,245   pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
2021-07-16T07:42:43,253   /tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
2021-07-16T07:42:43,253      41 | #define TBX_UCSC    0x10000
2021-07-16T07:42:43,253         |                     ^~~~~~~
2021-07-16T07:42:43,253   pysam/libctabix.c:13947:39: note: in expansion of macro ‘TBX_UCSC’
2021-07-16T07:42:43,254   13947 |   __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
2021-07-16T07:42:43,254         |                                       ^~~~~~~~
2021-07-16T07:42:43,262   /tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
2021-07-16T07:42:43,262      41 | #define TBX_UCSC    0x10000
2021-07-16T07:42:43,262         |                     ^~~~~~~
2021-07-16T07:42:43,262   pysam/libctabix.c:13979:39: note: in expansion of macro ‘TBX_UCSC’
2021-07-16T07:42:43,262   13979 |   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error)
2021-07-16T07:42:43,262         |                                       ^~~~~~~~
2021-07-16T07:42:43,277   /tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
2021-07-16T07:42:43,277      41 | #define TBX_UCSC    0x10000
2021-07-16T07:42:43,278         |                     ^~~~~~~
2021-07-16T07:42:43,278   pysam/libctabix.c:14349:43: note: in expansion of macro ‘TBX_UCSC’
2021-07-16T07:42:43,278   14349 |       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error)
2021-07-16T07:42:43,278         |                                           ^~~~~~~~
2021-07-16T07:43:02,964   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/pysam/libctabix.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libctabix.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:43:03,215   building 'pysam.libcfaidx' extension
2021-07-16T07:43:03,216   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libcfaidx.c -o build/temp.linux-armv7l-3.9/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:43:14,805   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/pysam/libcfaidx.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcfaidx.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:43:15,010   building 'pysam.libcbcf' extension
2021-07-16T07:43:15,010   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libcbcf.c -o build/temp.linux-armv7l-3.9/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:44:27,550   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/pysam/libcbcf.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:44:28,002   building 'pysam.libcbgzf' extension
2021-07-16T07:44:28,003   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libcbgzf.c -o build/temp.linux-armv7l-3.9/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:44:33,149   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/pysam/libcbgzf.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcbgzf.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:44:33,335   building 'pysam.libctabixproxies' extension
2021-07-16T07:44:33,335   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libctabixproxies.c -o build/temp.linux-armv7l-3.9/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:44:50,260   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/pysam/libctabixproxies.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libctabixproxies.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:44:50,507   building 'pysam.libcvcf' extension
2021-07-16T07:44:50,507   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 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/htslib -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/samtools/lz4 -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/bcftools -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -I/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -I/usr/include/python3.9 -c pysam/libcvcf.c -o build/temp.linux-armv7l-3.9/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
2021-07-16T07:45:33,928   pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’:
2021-07-16T07:45:33,944   pysam/libcvcf.c:25030:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T07:45:33,944   25030 |   __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error)
2021-07-16T07:45:33,945         |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T07:45:52,632   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/pysam/libcvcf.o -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/pysam -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5 -L/tmp/pip-wheel-yq1k2inu/pysam_1e380816146b4a438913c387d102abb5/build/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -Lbuild/lib.linux-armv7l-3.9/pysam -lz -ldeflate -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o build/lib.linux-armv7l-3.9/pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
2021-07-16T07:45:52,968   installing to build/bdist.linux-armv7l/wheel
2021-07-16T07:45:52,969   running install
2021-07-16T07:45:52,970   running install_lib
2021-07-16T07:45:52,974   creating build/bdist.linux-armv7l
2021-07-16T07:45:52,974   creating build/bdist.linux-armv7l/wheel
2021-07-16T07:45:52,977   creating build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:52,978   copying build/lib.linux-armv7l-3.9/pysam/libcalignedsegment.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:52,980   copying build/lib.linux-armv7l-3.9/pysam/htslib_util.h -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:52,981   copying build/lib.linux-armv7l-3.9/pysam/libctabix.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,012   copying build/lib.linux-armv7l-3.9/pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,079   copying build/lib.linux-armv7l-3.9/pysam/libcutils.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,081   copying build/lib.linux-armv7l-3.9/pysam/config.py -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,083   copying build/lib.linux-armv7l-3.9/pysam/__init__.py -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,085   copying build/lib.linux-armv7l-3.9/pysam/csamtools_util.h -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,088   copying build/lib.linux-armv7l-3.9/pysam/version.h -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,090   copying build/lib.linux-armv7l-3.9/pysam/libcbgzf.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,102   copying build/lib.linux-armv7l-3.9/pysam/libcalignmentfile.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,105   copying build/lib.linux-armv7l-3.9/pysam/libctabixproxies.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,107   copying build/lib.linux-armv7l-3.9/pysam/libcvcf.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,109   copying build/lib.linux-armv7l-3.9/pysam/libctabix.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,112   copying build/lib.linux-armv7l-3.9/pysam/cbcftools_util.h -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,114   copying build/lib.linux-armv7l-3.9/pysam/libcbcftools.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,116   copying build/lib.linux-armv7l-3.9/pysam/samtools.py -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,119   copying build/lib.linux-armv7l-3.9/pysam/libcbcftools.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,207   copying build/lib.linux-armv7l-3.9/pysam/libcsamtools.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,209   copying build/lib.linux-armv7l-3.9/pysam/libcutils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,232   copying build/lib.linux-armv7l-3.9/pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,342   copying build/lib.linux-armv7l-3.9/pysam/libcbcf.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,343   copying build/lib.linux-armv7l-3.9/pysam/bcftools.py -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,345   copying build/lib.linux-armv7l-3.9/pysam/libcalignedsegment.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,419   copying build/lib.linux-armv7l-3.9/pysam/libctabixproxies.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,445   copying build/lib.linux-armv7l-3.9/pysam/Pileup.py -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,447   copying build/lib.linux-armv7l-3.9/pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,496   copying build/lib.linux-armv7l-3.9/pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,552   copying build/lib.linux-armv7l-3.9/pysam/pysam_util.h -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,554   copying build/lib.linux-armv7l-3.9/pysam/libcsamfile.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,556   copying build/lib.linux-armv7l-3.9/pysam/libcfaidx.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,575   copying build/lib.linux-armv7l-3.9/pysam/utils.py -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,577   copying build/lib.linux-armv7l-3.9/pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,663   copying build/lib.linux-armv7l-3.9/pysam/libchtslib.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,668   copying build/lib.linux-armv7l-3.9/pysam/version.py -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,671   creating build/bdist.linux-armv7l/wheel/pysam/include
2021-07-16T07:45:53,672   creating build/bdist.linux-armv7l/wheel/pysam/include/htslib
2021-07-16T07:45:53,673   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/thread_pool_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2021-07-16T07:45:53,676   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/header.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2021-07-16T07:45:53,680   creating build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,681   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hts_endian.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,683   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,686   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/kseq.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,689   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/faidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,692   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/ksort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,695   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/vcf_sweep.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,697   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/khash_str2int.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,700   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/kbitset.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,702   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hts_os.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,705   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/kstring.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,708   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/tbx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,710   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/cram.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,713   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/khash.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,716   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/bgzf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,719   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/synced_bcf_reader.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,722   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hts.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,726   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,729   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hts_defs.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,732   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/klist.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,734   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/sam.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,740   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/kfunc.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,742   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/knetfile.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,744   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/thread_pool.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,747   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/hts_log.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,750   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/vcfutils.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,752   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/htslib/vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib/htslib
2021-07-16T07:45:53,756   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/hts_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2021-07-16T07:45:53,758   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/sam_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2021-07-16T07:45:53,761   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2021-07-16T07:45:53,763   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/textutils_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2021-07-16T07:45:53,766   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/hfile_internal.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2021-07-16T07:45:53,768   copying build/lib.linux-armv7l-3.9/pysam/include/htslib/bcf_sr_sort.h -> build/bdist.linux-armv7l/wheel/pysam/include/htslib
2021-07-16T07:45:53,771   copying build/lib.linux-armv7l-3.9/pysam/include/__init__.py -> build/bdist.linux-armv7l/wheel/pysam/include
2021-07-16T07:45:53,774   creating build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,775   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/tmp_file.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,778   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/samtools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,780   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,782   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/sam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,785   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,787   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bam_endian.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,789   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bam_lpileup.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,791   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bedidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,794   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bam2bcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,796   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/sam_opts.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,799   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bam_plbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,801   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/samtools.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,804   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/stats_isize.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,806   copying build/lib.linux-armv7l-3.9/pysam/include/samtools/bam.h -> build/bdist.linux-armv7l/wheel/pysam/include/samtools
2021-07-16T07:45:53,810   creating build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,811   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/khash_str2str.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,814   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/prob1.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,816   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/gvcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,818   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/convert.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,820   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/bcftools.pysam.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,823   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/tsv2vcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,825   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/config.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,827   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/hclust.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,829   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/kmin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,832   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/HMM.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,834   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/vcmp.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,836   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/regidx.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,840   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/mw.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,843   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/call.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,845   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/hex.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,847   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/smpl_ilist.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,849   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/kheap.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,852   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/vcfbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,854   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/ploidy.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,856   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/rbuf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,859   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/cols.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,861   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/bam_sample.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,863   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/bam2bcf.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,865   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/variantkey.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,868   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/filter.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,870   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/bin.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,872   copying build/lib.linux-armv7l-3.9/pysam/include/bcftools/bcftools.h -> build/bdist.linux-armv7l/wheel/pysam/include/bcftools
2021-07-16T07:45:53,874   copying build/lib.linux-armv7l-3.9/pysam/libcfaidx.pxd -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,876   copying build/lib.linux-armv7l-3.9/pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,882   copying build/lib.linux-armv7l-3.9/pysam/pysam_stream.h -> build/bdist.linux-armv7l/wheel/pysam
2021-07-16T07:45:53,884   running install_egg_info
2021-07-16T07:45:53,914   running egg_info
2021-07-16T07:45:53,915   writing pysam.egg-info/PKG-INFO
2021-07-16T07:45:53,918   writing dependency_links to pysam.egg-info/dependency_links.txt
2021-07-16T07:45:53,919   writing top-level names to pysam.egg-info/top_level.txt
2021-07-16T07:45:54,005   reading manifest file 'pysam.egg-info/SOURCES.txt'
2021-07-16T07:45:54,043   reading manifest template 'MANIFEST.in'
2021-07-16T07:45:54,045   warning: no files found matching 'KNOWN_BUGS'
2021-07-16T07:45:54,045   warning: no files found matching 'THANKS'
2021-07-16T07:45:54,053   no previously-included directories found matching 'tests/'
2021-07-16T07:45:54,054   warning: no files found matching 'samtools/configure'
2021-07-16T07:45:54,054   warning: no files found matching 'samtools/config.mk.in'
2021-07-16T07:45:54,054   warning: no files found matching 'samtools/config.h.in'
2021-07-16T07:45:54,087   warning: no files found matching 'htslib/INSTALL'
2021-07-16T07:45:54,087   warning: no files found matching 'htslib/NEWS'
2021-07-16T07:45:54,094   adding license file 'COPYING'
2021-07-16T07:45:54,120   writing manifest file 'pysam.egg-info/SOURCES.txt'
2021-07-16T07:45:54,122   Copying pysam.egg-info to build/bdist.linux-armv7l/wheel/pysam-0.16.0-py3.9.egg-info
2021-07-16T07:45:54,133   running install_scripts
2021-07-16T07:45:54,212   adding license file "COPYING" (matched pattern "COPYING*")
2021-07-16T07:45:54,216   creating build/bdist.linux-armv7l/wheel/pysam-0.16.0.dist-info/WHEEL
2021-07-16T07:45:54,219   creating '/tmp/pip-wheel-fclmz1qd/pysam-0.16.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-16T07:45:54,223   adding 'pysam/Pileup.py'
2021-07-16T07:45:54,224   adding 'pysam/__init__.py'
2021-07-16T07:45:54,226   adding 'pysam/bcftools.py'
2021-07-16T07:45:54,227   adding 'pysam/cbcftools_util.h'
2021-07-16T07:45:54,228   adding 'pysam/config.py'
2021-07-16T07:45:54,229   adding 'pysam/csamtools_util.h'
2021-07-16T07:45:54,230   adding 'pysam/htslib_util.h'
2021-07-16T07:45:54,840   adding 'pysam/libcalignedsegment.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:54,868   adding 'pysam/libcalignedsegment.pxd'
2021-07-16T07:45:55,341   adding 'pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:55,362   adding 'pysam/libcalignmentfile.pxd'
2021-07-16T07:45:56,159   adding 'pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:56,198   adding 'pysam/libcbcf.pxd'
2021-07-16T07:45:57,025   adding 'pysam/libcbcftools.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:57,055   adding 'pysam/libcbcftools.pxd'
2021-07-16T07:45:57,128   adding 'pysam/libcbgzf.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:57,294   adding 'pysam/libcfaidx.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:57,302   adding 'pysam/libcfaidx.pxd'
2021-07-16T07:45:58,298   adding 'pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:58,347   adding 'pysam/libchtslib.pxd'
2021-07-16T07:45:58,375   adding 'pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:58,377   adding 'pysam/libcsamfile.pxd'
2021-07-16T07:45:58,925   adding 'pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:58,946   adding 'pysam/libcsamtools.pxd'
2021-07-16T07:45:59,198   adding 'pysam/libctabix.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:59,210   adding 'pysam/libctabix.pxd'
2021-07-16T07:45:59,448   adding 'pysam/libctabixproxies.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:59,459   adding 'pysam/libctabixproxies.pxd'
2021-07-16T07:45:59,588   adding 'pysam/libcutils.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:45:59,594   adding 'pysam/libcutils.pxd'
2021-07-16T07:46:00,149   adding 'pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T07:46:00,173   adding 'pysam/libcvcf.pxd'
2021-07-16T07:46:00,175   adding 'pysam/pysam_stream.h'
2021-07-16T07:46:00,176   adding 'pysam/pysam_util.h'
2021-07-16T07:46:00,177   adding 'pysam/samtools.py'
2021-07-16T07:46:00,178   adding 'pysam/utils.py'
2021-07-16T07:46:00,180   adding 'pysam/version.h'
2021-07-16T07:46:00,181   adding 'pysam/version.py'
2021-07-16T07:46:00,183   adding 'pysam/include/__init__.py'
2021-07-16T07:46:00,185   adding 'pysam/include/bcftools/HMM.h'
2021-07-16T07:46:00,187   adding 'pysam/include/bcftools/bam2bcf.h'
2021-07-16T07:46:00,188   adding 'pysam/include/bcftools/bam_sample.h'
2021-07-16T07:46:00,189   adding 'pysam/include/bcftools/bcftools.h'
2021-07-16T07:46:00,190   adding 'pysam/include/bcftools/bcftools.pysam.h'
2021-07-16T07:46:00,192   adding 'pysam/include/bcftools/bin.h'
2021-07-16T07:46:00,193   adding 'pysam/include/bcftools/call.h'
2021-07-16T07:46:00,194   adding 'pysam/include/bcftools/cols.h'
2021-07-16T07:46:00,196   adding 'pysam/include/bcftools/config.h'
2021-07-16T07:46:00,197   adding 'pysam/include/bcftools/convert.h'
2021-07-16T07:46:00,198   adding 'pysam/include/bcftools/filter.h'
2021-07-16T07:46:00,199   adding 'pysam/include/bcftools/gvcf.h'
2021-07-16T07:46:00,200   adding 'pysam/include/bcftools/hclust.h'
2021-07-16T07:46:00,202   adding 'pysam/include/bcftools/hex.h'
2021-07-16T07:46:00,203   adding 'pysam/include/bcftools/khash_str2str.h'
2021-07-16T07:46:00,205   adding 'pysam/include/bcftools/kheap.h'
2021-07-16T07:46:00,206   adding 'pysam/include/bcftools/kmin.h'
2021-07-16T07:46:00,210   adding 'pysam/include/bcftools/mw.h'
2021-07-16T07:46:00,212   adding 'pysam/include/bcftools/ploidy.h'
2021-07-16T07:46:00,213   adding 'pysam/include/bcftools/prob1.h'
2021-07-16T07:46:00,215   adding 'pysam/include/bcftools/rbuf.h'
2021-07-16T07:46:00,217   adding 'pysam/include/bcftools/regidx.h'
2021-07-16T07:46:00,218   adding 'pysam/include/bcftools/smpl_ilist.h'
2021-07-16T07:46:00,220   adding 'pysam/include/bcftools/tsv2vcf.h'
2021-07-16T07:46:00,222   adding 'pysam/include/bcftools/variantkey.h'
2021-07-16T07:46:00,224   adding 'pysam/include/bcftools/vcfbuf.h'
2021-07-16T07:46:00,225   adding 'pysam/include/bcftools/vcmp.h'
2021-07-16T07:46:00,227   adding 'pysam/include/htslib/bcf_sr_sort.h'
2021-07-16T07:46:00,229   adding 'pysam/include/htslib/config.h'
2021-07-16T07:46:00,231   adding 'pysam/include/htslib/header.h'
2021-07-16T07:46:00,233   adding 'pysam/include/htslib/hfile_internal.h'
2021-07-16T07:46:00,234   adding 'pysam/include/htslib/hts_internal.h'
2021-07-16T07:46:00,235   adding 'pysam/include/htslib/sam_internal.h'
2021-07-16T07:46:00,237   adding 'pysam/include/htslib/textutils_internal.h'
2021-07-16T07:46:00,239   adding 'pysam/include/htslib/thread_pool_internal.h'
2021-07-16T07:46:00,242   adding 'pysam/include/htslib/htslib/bgzf.h'
2021-07-16T07:46:00,245   adding 'pysam/include/htslib/htslib/cram.h'
2021-07-16T07:46:00,247   adding 'pysam/include/htslib/htslib/faidx.h'
2021-07-16T07:46:00,250   adding 'pysam/include/htslib/htslib/hfile.h'
2021-07-16T07:46:00,257   adding 'pysam/include/htslib/htslib/hts.h'
2021-07-16T07:46:00,258   adding 'pysam/include/htslib/htslib/hts_defs.h'
2021-07-16T07:46:00,260   adding 'pysam/include/htslib/htslib/hts_endian.h'
2021-07-16T07:46:00,262   adding 'pysam/include/htslib/htslib/hts_log.h'
2021-07-16T07:46:00,263   adding 'pysam/include/htslib/htslib/hts_os.h'
2021-07-16T07:46:00,264   adding 'pysam/include/htslib/htslib/kbitset.h'
2021-07-16T07:46:00,266   adding 'pysam/include/htslib/htslib/kfunc.h'
2021-07-16T07:46:00,269   adding 'pysam/include/htslib/htslib/khash.h'
2021-07-16T07:46:00,270   adding 'pysam/include/htslib/htslib/khash_str2int.h'
2021-07-16T07:46:00,272   adding 'pysam/include/htslib/htslib/klist.h'
2021-07-16T07:46:00,273   adding 'pysam/include/htslib/htslib/knetfile.h'
2021-07-16T07:46:00,275   adding 'pysam/include/htslib/htslib/kseq.h'
2021-07-16T07:46:00,277   adding 'pysam/include/htslib/htslib/ksort.h'
2021-07-16T07:46:00,279   adding 'pysam/include/htslib/htslib/kstring.h'
2021-07-16T07:46:00,281   adding 'pysam/include/htslib/htslib/regidx.h'
2021-07-16T07:46:00,291   adding 'pysam/include/htslib/htslib/sam.h'
2021-07-16T07:46:00,294   adding 'pysam/include/htslib/htslib/synced_bcf_reader.h'
2021-07-16T07:46:00,296   adding 'pysam/include/htslib/htslib/tbx.h'
2021-07-16T07:46:00,298   adding 'pysam/include/htslib/htslib/thread_pool.h'
2021-07-16T07:46:00,306   adding 'pysam/include/htslib/htslib/vcf.h'
2021-07-16T07:46:00,307   adding 'pysam/include/htslib/htslib/vcf_sweep.h'
2021-07-16T07:46:00,309   adding 'pysam/include/htslib/htslib/vcfutils.h'
2021-07-16T07:46:00,313   adding 'pysam/include/samtools/bam.h'
2021-07-16T07:46:00,314   adding 'pysam/include/samtools/bam2bcf.h'
2021-07-16T07:46:00,315   adding 'pysam/include/samtools/bam_endian.h'
2021-07-16T07:46:00,317   adding 'pysam/include/samtools/bam_lpileup.h'
2021-07-16T07:46:00,318   adding 'pysam/include/samtools/bam_plbuf.h'
2021-07-16T07:46:00,319   adding 'pysam/include/samtools/bedidx.h'
2021-07-16T07:46:00,320   adding 'pysam/include/samtools/config.h'
2021-07-16T07:46:00,322   adding 'pysam/include/samtools/sam.h'
2021-07-16T07:46:00,323   adding 'pysam/include/samtools/sam_opts.h'
2021-07-16T07:46:00,324   adding 'pysam/include/samtools/sample.h'
2021-07-16T07:46:00,325   adding 'pysam/include/samtools/samtools.h'
2021-07-16T07:46:00,326   adding 'pysam/include/samtools/samtools.pysam.h'
2021-07-16T07:46:00,328   adding 'pysam/include/samtools/stats_isize.h'
2021-07-16T07:46:00,329   adding 'pysam/include/samtools/tmp_file.h'
2021-07-16T07:46:00,332   adding 'pysam-0.16.0.dist-info/COPYING'
2021-07-16T07:46:00,333   adding 'pysam-0.16.0.dist-info/METADATA'
2021-07-16T07:46:00,333   adding 'pysam-0.16.0.dist-info/WHEEL'
2021-07-16T07:46:00,334   adding 'pysam-0.16.0.dist-info/top_level.txt'
2021-07-16T07:46:00,336   adding 'pysam-0.16.0.dist-info/RECORD'
2021-07-16T07:46:00,470   removing build/bdist.linux-armv7l/wheel
2021-07-16T07:46:00,673   Building wheel for pysam (setup.py): finished with status 'done'
2021-07-16T07:46:00,807   Created wheel for pysam: filename=pysam-0.16.0-cp39-cp39-linux_armv7l.whl size=10762232 sha256=f362a21d3d76e12110a57f6a4318e7c6ce8d4428993de45100ee729c34870663
2021-07-16T07:46:00,807   Stored in directory: /tmp/pip-ephem-wheel-cache-q_l_f_rf/wheels/d7/b2/2e/f012bd4b5b7584f63860ec01ba1fe47ceae2104766d0c9e97c
2021-07-16T07:46:00,824 Successfully built pysam
2021-07-16T07:46:01,148 Removed build tracker: '/tmp/pip-req-tracker-7ma6u161'